U.S. patent application number 16/679927 was filed with the patent office on 2020-09-10 for systems, apparatus, and methods for generating and analyzing resistome profiles.
This patent application is currently assigned to OpGen, Inc.. The applicant listed for this patent is OpGen, Inc.. Invention is credited to Evan Jones, Alex Saeed, Vadim Sapiro, George Terrance Walker.
Application Number | 20200286590 16/679927 |
Document ID | / |
Family ID | 1000004845343 |
Filed Date | 2020-09-10 |
![](/patent/app/20200286590/US20200286590A1-20200910-D00000.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00001.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00002.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00003.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00004.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00005.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00006.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00007.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00008.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00009.png)
![](/patent/app/20200286590/US20200286590A1-20200910-D00010.png)
United States Patent
Application |
20200286590 |
Kind Code |
A1 |
Jones; Evan ; et
al. |
September 10, 2020 |
SYSTEMS, APPARATUS, AND METHODS FOR GENERATING AND ANALYZING
RESISTOME PROFILES
Abstract
Systems, apparatus, and methods are disclosed for generating a
resistome profile for a subject, monitoring an infection state of
one or more subjects, and/or identifying a potential infection
outbreak at a facility, for example, by obtaining first data
representative of at least one measure of antibiotic resistance of
an organism from a first sample, identifying the organism,
determining at least one of an antibiotic susceptibility phenotype,
an identity of an antibiotic resistance gene, and an antibiotic to
which the organism is non-susceptible, generating and comparing a
first pattern to at least one known pattern to determine and
generate a profile uniqueness identifier indicating a degree of
similarity above a threshold between the first pattern and the at
least one known pattern.
Inventors: |
Jones; Evan; (Potomac,
MD) ; Sapiro; Vadim; (North Potomac, MD) ;
Walker; George Terrance; (Chevy Chase, MD) ; Saeed;
Alex; (Germantown, MD) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
OpGen, Inc. |
Gaithersburg |
MD |
US |
|
|
Assignee: |
OpGen, Inc.
Gaithersburg
MD
|
Family ID: |
1000004845343 |
Appl. No.: |
16/679927 |
Filed: |
November 11, 2019 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
14723424 |
May 27, 2015 |
10475526 |
|
|
16679927 |
|
|
|
|
62003351 |
May 27, 2014 |
|
|
|
62004026 |
May 28, 2014 |
|
|
|
62024322 |
Jul 14, 2014 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
G16B 40/00 20190201;
G16B 20/00 20190201; G16B 45/00 20190201; G16H 50/80 20180101; G16B
20/40 20190201 |
International
Class: |
G16B 40/00 20060101
G16B040/00; G16B 20/00 20060101 G16B020/00; G16B 45/00 20060101
G16B045/00; G16H 50/80 20060101 G16H050/80; G16B 20/40 20060101
G16B020/40 |
Claims
1. A system, comprising: at least one communication interface; at
least one memory for storing processor executable instructions; and
at least one processor, communicatively coupled to the at least one
communication interface and the at least one memory, wherein upon
execution of the processor-executable instructions, the at least
one processor: generates a first resistome profile for a first
subject based on first data representative of at least one measure
of antibiotic resistance of an organism from a first sample;
generates a second resistome profile for the first subject based on
second data representative of at least one measure of antibiotic
resistance of an organism from a second sample; compares the first
resistome profile to the second resistome profile; determines a
degree of difference between the first resistome profile and the
second resistome profile; and automatically generates, via the
communication interface, a real-time alert when the degree of
difference is above the threshold, indicating a change in the
infection state of the first subject.
2. The system of claim 1, wherein upon execution of the
processor-executable instructions, the at least one processor
further at least one of determines or modifies a course of
treatment for the first subject based on at least the change in the
infection state of the first subject.
3. A system, comprising: at least one communication interface; at
least one memory for storing processor executable instructions; and
at least one processor, communicatively coupled to the at least one
communication interface and the at least one memory, wherein upon
execution of the processor-executable instructions, the at least
one processor: generates a first resistome profile for a first
subject based on first data representative of at least one measure
of antibiotic resistance of an organism from a first sample; assign
a first infection state to the first subject based on the first
resistome profile; generates a second resistome profile for a
second subject based on second data representative of at least one
measure of antibiotic resistance of an organism from a second
sample; compares the first resistome profile to the second
resistome profile; assigns a second infection state to the second
subject based at least in part on the comparison of the first
resistome profile to the second resistome profile; and
automatically sends an alert via the communication system based on
the second infection state.
4. A system, comprising: at least one communication interface; at
least one memory for storing processor executable instructions; and
at least one processor, communicatively coupled to the at least one
communication interface and the at least one memory, wherein upon
execution of the processor-executable instructions, the at least
one processor: generates a first resistome profile for a first
subject based on first data representative of at least one measure
of antibiotic resistance of an organism from a first sample;
compares the first resistome profile to a plurality of candidate
resistome profiles, each candidate resistome profile from the
plurality of candidate resistome profiles being associated with an
infection outbreak potential; and if a degree of similarity between
the first resistome profile and a candidate resistome profile from
the plurality of candidate resistome profiles is above a first
threshold and an infection outbreak potential associated with that
candidate resistome profile is above a second threshold,
automatically generate an alert that a facility associated with the
first resistome profile is at risk of an infection outbreak.
5. The system of claim 4, wherein the plurality of candidate
resistome profiles is stored in a computer database.
6. The system of claim 4, wherein a candidate resistome profile
comprising a phenotype code indicating a carbapenem-resistant
Enterobacteriaceae is ranked above the second threshold according
to a high potential basis for indicating an infection outbreak.
7. The system of claim 4, further comprising a graphical display
communicatively coupled to the at least one processor, wherein upon
execution of the processor-executable instructions, the at least
one processor further displays an indication of the classification
using a graphical representation, the graphical representation
comprising at least one of: a quick response (QR) code; a tube
graph; or an epidemiology star chart.
8. The system of claim 4, wherein the first resistome profile
includes: an organism identification code associated with the
organism; a phenotype code indicating an antibiotic susceptibility
phenotype of the organism; a genotype code indicating an identity
of the antibiotic resistance gene associated with the antibiotic
susceptibility phenotype; and a susceptibility code indicating an
antibiotic to which the organism is non-susceptible.
9. The system of claim 8, wherein the genotype code is from a
plurality of genotype codes, each genotype code from the plurality
of genotype codes indicating an identity of a different antibiotic
resistant gene.
10. The system of claim 4, wherein at least one candidate resistome
profile from the plurality of candidate resistome profiles is
associated with a second subject at the facility associated with
the first resistome profile.
11. The system of claim 4, wherein at least one candidate resistome
profile from the plurality of candidate resistome profiles is
associated with an infected patient who has at least one of a
central line blood infection, ventilator associated pneumonia, a
urinary tract infection, or a surgical site infection.
12. The system of claim 4, wherein at least one candidate resistome
profile from the plurality of candidate resistome profiles is
derived from in silico data from a reference organism involved in
an outbreak.
13. The system of claim 4, wherein the first resistome profile and
at least one candidate resistome profile from the plurality of
candidate resistome profiles includes metadata associated with a
location, the alert being associated with a spread of an infection
to and/or from a location associated with the first subject.
14. The system of claim 4, wherein the first resistome profile and
at least one candidate resistome profile from the plurality of
candidate resistome profiles includes metadata associated with a
location, the alert being associated a quantity of samples
associated with the location associated with the first subject and
that have resistome profiles with a degree of similarity to the
first resistome profile that is above the first threshold.
15. The system of claim 1, wherein the first resistome profile
includes: an organism identification code associated with an
organism; a phenotype code indicating an antibiotic susceptibility
phenotype of the organism; a genotype code indicating an identity
of the antibiotic resistance gene associated with the antibiotic
susceptibility phenotype; and a susceptibility code indicating an
antibiotic to which the organism is non-susceptible.
16. The system of claim 3, wherein the first resistome profile
includes: an organism identification code associated with the
organism; a phenotype code indicating an antibiotic susceptibility
phenotype of the organism; a genotype code indicating an identity
of the antibiotic resistance gene associated with the antibiotic
susceptibility phenotype; and a susceptibility code indicating an
antibiotic to which the organism is non-susceptible.
17. The system of claim 3, wherein the second infection state is
assigned to the second subject based at least in part on a degree
of similarity between the first resistome profile and the second
resistome profile being above a threshold.
18. The system of claim 3, wherein: the second infection state is
the same as the first infection state; and the alert indicates a
transmission between the first patient and the second patient.
19. The system of claim 3, wherein the first sample is associated
with a first geographic location; the second sample is associated
with a second geographic location; and the alert indicates a
transmission between the first geographic location and the second
geographic location.
20. The system of claim 3, wherein the first resistome profile is
from a plurality of candidate resistome profiles, upon execution of
the processor-executable instructions, the at least one processor
further: compares the first resistome profile to each resistome
profile from the plurality of candidate resistome profiles; and
calculates a repetition index indicating a number of resistome
profiles from the plurality of candidate resistome profiles which
the second resistome profile matches with a degree of similarity
above a threshold, the alert indicating an increase in a number of
patients infected with the organism and indicating an outbreak
potential.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. patent application
Ser. No. 14/723,424, entitled "Systems, Apparatus, and Methods for
Generating and Analyzing Resistome profiles," filed on May 27,
2015, which is incorporated herein by reference in its
entirety.
[0002] U.S. patent application Ser. No. 14/723,424 claims a
priority benefit to U.S. provisional patent application Ser. No.
62/024,322, entitled "Analysis Platform Based on Resistome
Profiles," filed on Jul. 14, 2014, which is incorporated herein by
reference in its entirety.
[0003] U.S. patent application Ser. No. 14/723,424 also claims a
priority benefit to U.S. provisional patent application Ser. No.
62/004,026, entitled "Systems and Methods for Infection Control and
Patient Management," filed on May 28, 2014, which is incorporated
herein by reference in its entirety.
[0004] U.S. patent application Ser. No. 14/723,424 also claims a
priority benefit to U.S. provisional patent application Ser. No.
62/003,351, entitled "Systems and Methods for Infection Control and
Patient Management," filed on May 27, 2014, which is incorporated
herein by reference in its entirety.
TECHNICAL FIELD
[0005] The present disclosure relates generally to monitoring
multi-gene resistant colonization and infection in subjects and
potential for outbreaks at facilities. More specifically, the
present disclosure relates to generating and using resistome
profiles based on measurements of biological samples.
BACKGROUND
[0006] Antibiotic-resistant bacterial infections are associated
with poor clinical outcomes including increased morbidity,
mortality, and healthcare costs among infected patients. Colonized
patients are an important reservoir of beta-lactamases leading to
the transmission and spread of these organisms within hospitals and
long term care facilities. The prevalence of these organisms in
such facilities in the United States has steadily increased over
the last 30 years. Treatment options for patients with multi-drug
resistant organisms (MDROs) are extremely limited; therefore,
identification of infection and containment of any potential
outbreak within facilities is crucial.
SUMMARY
[0007] The inventors have recognized and appreciated that an
ultra-sensitive method for generating a resistome profile for a
subject based on measurements of biological samples and monitoring
the multi-gene resistant colonization and infection in subjects
could be beneficial, for example, for identification of potentially
dangerous infections. The inventors have also recognized that
methods for identifying a potential for an infection outbreak at a
facility could be beneficial for containment of any such potential
outbreak. In view of the foregoing, various embodiments herein are
directed generally to systems, apparatus, and methods for
generating a resistome profile for a subject, monitoring the
infection state of one or more subjects, and/or identifying a
potential for an infection outbreak at a facility.
[0008] According to some embodiments, systems, apparatus, and
methods of the instant disclosure provide a dynamic way to
identify, categorize, consolidate, compare, manage, and make
predictions from different classes of diagnostic information
relevant to infections and outbreaks, particularly by drug
resistant organisms. The systems, apparatus, and methods may rely
on diagnostically useful information based on phenotype
information, genotype information, or some combination thereof. For
example, genetic analysis of DNA or RNA sequence information or
matches thereof may be used to identify organisms such as E. coli
b0507, which is known to be a pathogenic strain of bacteria. Beyond
looking at single types of organisms, in some embodiments, systems,
methods and apparatus provide for subject classification, infection
state classification, facility classification, and outbreak
monitoring based on analysis of the multi-drug resistance of
organisms.
[0009] The present disclosure provides systems, methods and
apparatus for generating a resistome profile for a subject
according to some embodiments. In one embodiment, a system for
generating a resistome profile includes at least one communication
interface, at least one memory for storing processor executable
instructions, and at least one processor, communicatively coupled
to the at least one communication interface and the at least one
memory. Upon execution of the processor-executable instructions,
the at least one processor obtains first data representative of at
least one measure of antibiotic resistance of an organism from a
first sample, identifies the organism based on at least the first
data, determines at least one of an antibiotic susceptibility
phenotype, an identity of an antibiotic resistance gene, and an
antibiotic to which the organism is non-susceptible based on at
least the first data, and generates a first pattern associated with
the first sample. The first pattern includes an organism
identification code indicating the organism identified based on the
first data and at least one of a phenotype code indicating the
antibiotic susceptibility phenotype determined from the first data,
a genotype code indicating the identity of the antibiotic
resistance gene determined from the first data, and a
susceptibility code indicating the antibiotic to which the organism
is non-susceptible determined from the first data. The at least one
processor also compares the first pattern to at least one known
pattern, determines a degree of similarity above a threshold
between the first pattern and the at least one known pattern,
generates a profile uniqueness identifier indicating the degree of
similarity above the threshold between the first pattern and the at
least one known pattern, and generates a first resistome profile
based on at least the first pattern and the profile uniqueness
identifier.
[0010] In an embodiment, the first pattern includes a plurality of
genotype codes, each genotype code indicating the identity of a
different antibiotic resistance gene. The profile uniqueness
identifier may include a uniqueness code determined based on the
degree of similarity above the threshold between the first pattern
and the at least one known pattern and a repetition index
indicating an increase in a number of known patterns having the
degree of similarity above the threshold with the first pattern.
The at least one processor may compare the first pattern to the at
least one known pattern by applying a similarity metric to the
first pattern and the at least one known pattern to determine the
degree of similarity above the threshold between the first pattern
and the at least one known pattern.
[0011] In an embodiment, the first sample is obtained from at least
one of an anal swab, a rectal swab, a skin swab, nasal swab, wound
swab, stool, blood, plasma, serum, urine, sputum, respiratory
lavage, and cerebrospinal fluid. The first data representative of
the at least one measure of antibiotic resistance of the organism
from the first sample may include data representative of at least
one of a type of gene, a gene sequence, a gene family, a DNA
sequence, a single-nucleotide polymorphism, a type of nucleic acid,
a type of protein, and a protein expression. The first resistome
profile further may include metadata associated with at least one
of the first sample and a first subject from which the first sample
was obtained. The first data representative of the at least one
measure of antibiotic resistance of the organism from the first
sample may include data representative of at least one measure of a
susceptibility test performed on a first bacterial isolate from the
first sample.
[0012] In an embodiment, the system further includes a graphical
display communicatively coupled to the at least one processor. Upon
execution of the processor-executable instructions, the at least
one processor may display the first resistome profile using a
graphical representation. The graphical representation may include
a quick response (QR) code, a tube graph, and/or an epidemiology
star chart.
[0013] In an embodiment, the first data representative of the at
least one measure of antibiotic resistance of the organism from the
first sample is collected from at least one measurement of a first
bacterial isolate from the first sample and indicates at least one
of an antibiotic resistance of the first bacterial isolate and an
antibiotic susceptibility of the first bacterial isolate. The at
least one known pattern may be derived from measurement data
associated with a second bacterial isolate from a second sample
obtained from at least one of a colonized subject and an infected
subject, the colonized patient having tested positive for at least
one drug-resistant organism, and the infected patient having at
least one of a central line blood infection, ventilator associated
pneumonia, a urinary tract infection, and a surgical site
infection, the measurement data indicating at least one of an
antibiotic resistance of the first bacterial isolate and an
antibiotic susceptibility of the first bacterial isolate. The first
data representative of the at least one measure of antibiotic
resistance of the organism from the first sample may indicate at
least one of a genome sequence, a minimum inhibitory concentration
for an antibiotic, and MALDI-TOF data. The first data
representative of the at least one measure of antibiotic resistance
of the organism from the first sample may include in silico data
from a reference organism involved in an outbreak.
[0014] In one embodiment, a method includes providing a first data
representative of at least one measure of antibiotic resistance of
an organism, from a sample obtained from a first subject, and
generating a first pattern associated with the first subject. The
first pattern includes an organism identification code indicating
the identity of the organism identified based on the first data.
The first pattern also includes at least one of: a phenotype code
based on an antibiotic susceptibility phenotype determined from the
first data, a genotype code based on an identity of an antibiotic
resistance gene determined from the first data, and a
susceptibility code indicating an antibiotic to which the organism
is non-susceptible. The method includes assigning a profile
uniqueness identifier to the first subject, where the profile
uniqueness identifier indicates a degree of similarity above a
predetermined threshold between the first pattern and a known
pattern associated with a classified subject. A first resistome
profile is generated for the first subject based on the first
pattern and the profile uniqueness identifier.
[0015] The present disclosure provides systems, apparatus, and
methods for monitoring an infection state of a subject according to
some embodiments. In one embodiment, a system for monitoring an
infection state of a first subject includes at least one
communication interface, at least one memory for storing processor
executable instructions, and at least one processor,
communicatively coupled to the at least one communication interface
and the at least one memory. Upon execution of the
processor-executable instructions, the at least one processor
generates a first resistome profile for the first subject based on
first data representative of at least one measure of antibiotic
resistance of an organism from a first sample, generates a second
resistome profile for the first subject based on second data
representative of at least one measure of antibiotic resistance of
an organism from a second sample, compares the first resistome
profile to the second resistome profile, and determines a degree of
difference above a threshold between the first resistome profile
and the second resistome profile, wherein the degree of difference
above the threshold between the first resistome profile and the
second resistome profile indicates a change in the infection state
of the first subject. In an embodiment, the at least one processor
further determines and/or modifies a course of treatment for the
first subject based on at least the change in the infection state
of the first subject.
[0016] In one embodiment, a method includes generating a first
resistome profile for the subject based on first data
representative of a first sample derived from the subject, and
generating a second resistome profile for the subject based on
second data representative of a second sample derived from the
subject. The resistome profiles may be generated using any method
described herein. The first resistome profile is compared to the
second resistome profile, and a difference between the first
resistome profile and the second resistome profile is indicating a
change in the infection state.
[0017] The present disclosure also provides systems, apparatus, and
methods for determining an infection state of two or more subjects
according to some embodiments. In one embodiment, a system for
determining an infection state of at least one subject includes at
least one communication interface, at least one memory for storing
processor executable instructions, and at least one processor,
communicatively coupled to the at least one communication interface
and the at least one memory. Upon execution of the
processor-executable instructions, the at least one processor
generates a first resistome profile for a first subject based on
first data representative of at least one measure of antibiotic
resistance of an organism from a first sample, generates a second
resistome profile for a second subject based on second data
representative of at least one measure of antibiotic resistance of
an organism from a second sample, compares the first resistome
profile to the second resistome profile, and assigns at least one
infection category to at least one of the first subject and the
second subject based at least in part on the comparison of the
first resistome profile to the second resistome profile, the at
least one infection category indicating at least one infection
state. In an embodiment, the at least one processor further
determines and/or modifies a course of treatment for at least one
of the first subject and the second subject based on the at least
one infection category assigned to at least one of the first
subject and the second subject.
[0018] In one embodiment, a method includes determining a first
resistome profile for a first subject based on first data
representative of at least one first measure of antibiotic
resistance of a first organism, from a first biological sample
obtained from the first subject, and determining a second resistome
profile for a second subject based on second data representative of
at least one second measure of antibiotic resistance of a second
organism, from a second biological sample derived from the second
subject. The resistome profiles may be generated using any method
described herein. The first resistome profile is compared to the
second resistome profile, at least one of the first subject and the
second subject is assigned to an infection category based on the
comparing. The infection category provides an indication of the
infection state.
[0019] The present disclosure also provides systems, apparatus, and
methods for identifying an infection outbreak at a facility
according to some embodiments. In one embodiment, a system for
monitoring risk of an infection outbreak at a facility includes at
least one communication interface, at least one memory for storing
processor executable instructions, and at least one processor,
communicatively coupled to the at least one communication interface
and the at least one memory. Upon execution of the
processor-executable instructions, the at least one processor
generates a first resistome profile for a first subject based on
first data representative of at least one measure of antibiotic
resistance of an organism from a first sample, compares the first
resistome profile to a plurality of candidate resistome profiles,
each candidate resistome profile of the plurality of candidate
resistome profiles being associated with the facility and ranked
according to a potential basis for indicating an infection
outbreak, and determines a degree of similarity above a first
threshold between the first resistome profile and each candidate
resistome profile. If at least one candidate resistome profile has
at least one degree of similarity above the first threshold with
the first resistome profile, the at least one processor determines
a degree of rank above a second threshold according to the
potential basis for indicating an infection outbreak. If the at
least one candidate resistome profile has at least one degree of
rank above the second threshold, the at least one processor assigns
to the facility a classification indicating risk of an infection
outbreak.
[0020] In an embodiment, the plurality of candidate resistome
profiles is stored in a computer database. A candidate resistome
profile may include a phenotype code indicating a
carbapenem-resistant Enterobacteriaceae is ranked above the second
threshold according to a high potential basis for indicating an
infection outbreak. The system may include a graphical display
communicatively coupled to the at least one processor. Upon
execution of the processor-executable instructions, the at least
one processor may display an indication of the classification using
a graphical representation. The graphical representation may
include a quick response (QR) code, a tube graph, and/or an
epidemiology star chart.
[0021] In one embodiment, a method includes determining a first
resistome profile for a first subject based on first data
representative of at least one measure of antibiotic resistance of
a first organism, from a first biological sample obtained from the
first subject. The resistome profile may be generated using any
method described herein. The first resistome profile is compared to
a plurality of candidate resistome profiles, each candidate
resistome profile of the plurality of candidate resistome profiles
being determined for a known subject associated with the facility.
Each candidate resistome profile is ranked according to a potential
basis for indicating an infection outbreak. The method includes
identifying each candidate resistome profile of the plurality of
candidate resistome profiles that has a degree of similarity above
a predetermined threshold with the first resistome profile, and
classifying the facility as being at risk of an infection outbreak
if at least one of the candidate resistome profiles is ranked as
potentially indicating an infection outbreak.
[0022] In one embodiment, a system includes at least one memory for
storing processor executable instructions, and at least one
processor, communicatively coupled to the at least one memory. Upon
execution of the processor-executable instructions, the at least
one processor performs any of the methods described herein.
[0023] It should be appreciated that all combinations of the
foregoing concepts and additional concepts discussed in greater
detail below (provided such concepts are not mutually inconsistent)
are contemplated as being part of the inventive subject matter
disclosed herein. In particular, all combinations of claimed
subject matter appearing at the end of this disclosure are
contemplated as being part of the inventive subject matter
disclosed herein. It should also be appreciated that terminology
explicitly employed herein that also may appear in any disclosure
incorporated by reference should be accorded a meaning most
consistent with the particular concepts disclosed herein.
[0024] Other systems, processes, and features will become apparent
to those skilled in the art upon examination of the following
drawings and detailed description. It is intended that all such
additional systems, processes, and features be included within this
description, be within the scope of the present invention, and be
protected by the accompanying claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0025] The skilled artisan will understand that the drawings
primarily are for illustrative purposes and are not intended to
limit the scope of the inventive subject matter described herein.
The drawings are not necessarily to scale; in some instances,
various aspects of the inventive subject matter disclosed herein
may be shown exaggerated or enlarged in the drawings to facilitate
an understanding of different features. In the drawings, like
reference characters generally refer to like features (e.g.,
functionally similar and/or structurally similar elements).
[0026] FIG. 1 illustrates an apparatus in accordance with some
embodiments.
[0027] FIG. 2 is a flowchart illustrating a method of generating a
resistome profile in accordance with some embodiments.
[0028] FIG. 3 is a flowchart illustrating a method for monitoring
an infection state of a subject in accordance with some
embodiments.
[0029] FIG. 4 is a flowchart illustrating a method of determining
an infection state in accordance with some embodiments.
[0030] FIG. 5 is a flowchart illustrating a method for identifying
a potential infection outbreak in accordance with some
embodiments.
[0031] FIG. 6 is a block diagram illustrating a gene detection
system and analysis platform in accordance with some
embodiments.
[0032] FIGS. 7 and 8 are plots illustrating a resistome test to
associate genotypic resistome results and antibiotic susceptibility
test results in accordance with some embodiments.
[0033] FIG. 9 is a flowchart illustrating methods of using a varied
data classes in accordance with some embodiments.
[0034] FIGS. 10A and 10B illustrate graphical representations of
resistome profiles in accordance with some embodiments.
DETAILED DESCRIPTION
[0035] According to some embodiments, systems, apparatus, and
methods disclosed herein provide a bioinformatics solution for
diagnosing infected and colonized patients in a manner far
exceeding conventional approaches to improve patient treatment,
control pathogen transmission, manage health care infections, and
track public health. These systems, methods, and/or apparatus may
constitute a fully integrated set of analytical and reporting tools
to facilitate infection control and infection state management for
a single patient, a plurality of patients, or up to and including
an entire patient population. These systems, apparatus, and methods
may encompass or contribute to a comprehensive molecular diagnostic
and bioinformatics platform to, for example, generate a resistome
profile for a subject, monitor an infection state of one or more
subjects, and/or identify a potential infection outbreak at a
facility.
[0036] The systems, methods, and/or apparatus may facilitate
identification of, for example, antibiotic resistant Gram-negative
bacilli with superior throughput, sensitivity, and genotype
resolution. Infected and/or colonized patients may be diagnosed in
a manner that reduces pathogen transmission in healthcare settings.
Meanwhile, the epidemiological progression of emerging antibiotic
resistance patterns may be mapped on a global and local healthcare
institute level. For example, pathogen information may be used to
help guide antibiotic therapy and stewardship programs in acute
care settings. The overall approach described herein also may be
used in areas of infectious disease--including but not limited to
tuberculosis, malaria, gonorrhea, Gram-positive organisms, fungi,
and viruses--where multi-drug resistance is an issue. The systems,
apparatus, and methods described herein may provide classification
of infectious organisms that encompasses multiple variant organism
types.
[0037] In some embodiments, antibiotic resistance genetic profiles
may be combined with organism identification data and other
diagnostic test results to provide unique organism/isolate profiles
("resistome profiles") that may be used to compare with, match,
and/or differentiate from other resistome profiles from a plurality
of subjects and environmental swabs for real-time outbreak and
organism/isolate likeness information to help guide infection
control activities. For example, useful information on antibiotic
resistance and susceptibility information may be gained by testing
isolates from infected patients who have had central line blood
infections, ventilator associated pneumonia, urinary tract
infections, or surgical site infections. In some embodiments,
resistome profiles are generated using data from direct DNA tests,
including, but not limited to, a multi-drug resistant organism gene
detection system or any other DNA sequencing test on samples or
culture isolates. Thus, antibiotic resistance information may be
applied and developed further through sample testing and analysis
processes to facilitate early and ready access to valuable
information regarding organism species and antibiotic resistance
that may be used to guide subject treatment and infection
management according to some embodiments. In some embodiments, DNA
sequence-based genomic data may be used for providing community
profiling, pathogenicity prediction, strain attribution, or
surveillance. In some embodiments, systems, apparatus, and methods
facilitate combining the interpretation of sequence information,
and phenotype information (as appropriate), with a similarity
matching and numbering system.
[0038] Facility administrators, private industries, and public
health agencies (including the U.S. Centers for Disease Control and
Prevention (CDC) or the equivalent) may utilize systems, apparatus,
and methods according to some embodiments for infectious disease
management. Resistome profiles derived from colonized and/or
infected subjects may be used to populate databases, and to guide
infection management based on, for example, recommendations for
isolation and modifications to disinfection procedures. An analysis
engine (e.g., operating as a database engine) may be used to create
and manage resistome profiles. The analysis engine also may be used
to automatically check either individual facility databases or
large hosted databases for matching patterns or profiles.
[0039] Unique, new matches to a particular database may be numbered
on an ordered basis using a profile uniqueness identifier at the
end of the resistome profile. The first number in the profile
uniqueness identifier is the ordered individual match, and the
second number in the profile uniqueness identifier is the ordered
number of times there is a subject match in the database.
Individual facilities may use this information to provide detailed
diagnostic information, identify and track patients and individual
isolates. Alternatively, a centralized lab may host a database and
provide diagnostic results, for providing identification, matching,
and value-add reporting services to clients. Results may also be
generated in silico from third party data in computerized
databases.
[0040] If there is a matching resistome profile for two or more
subjects, a common infection may be occurring. Whether an
individual subject being colonized with a matching resistome
profile is important information for, among other things, infection
management. If a subject becomes infected, rather than just
colonized, the proper antibiotic for treating the individual
subject, based on the information from the matching resistome
profile, may be used until other antibiotic resistance and organism
identification data is available. Using the analysis engine,
clusters of subjects with common infections and prevalent resistome
profiles may be identified and tracked over time and over
geographic locations.
[0041] In some embodiments, common resistome profiles prevalent in
an intensive care unit (ICU) or a long term care facility may be
identified as a potential indicator of an outbreak among patients.
In other embodiments, common resistome profiles prevalent in an
livestock facility may be identified as a potential indicator of an
outbreak among animals. In any context, systems, apparatus, and
methods provided herein may be implemented to classify a
population, such as a population associated with a facility. Based
on a classification, agents of a facility, including, but not
limited to, doctors or veterinarians, may be alerted to emerging
infections (e.g., hospital acquired infections (HAIs)) and
infection outbreaks as soon as common resistome profiles are
associated with multiple subjects (e.g., S1:VIM:DPN_MPN:27-2, as
described further herein).
[0042] It should be appreciated that all combinations of these
concepts discussed in greater detail below (provided such concepts
are not mutually inconsistent) are contemplated as being part of
the inventive subject matter disclosed herein. It also should be
appreciated that terminology explicitly employed herein that also
may appear in any disclosure incorporated by reference should be
accorded a meaning most consistent with the particular concepts
disclosed herein.
Definitions
[0043] All definitions, as defined and used herein, should be
understood to control over dictionary definitions, definitions in
documents incorporated by reference, and/or ordinary meanings of
the defined terms.
[0044] The indefinite articles "a" and "an," as used herein in the
specification and in the claims, unless clearly indicated to the
contrary, should be understood to mean "at least one."
[0045] The phrase "and/or," as used herein in the specification and
in the claims, should be understood to mean "either or both" of the
elements so conjoined, i.e., elements that are conjunctively
present in some cases and disjunctively present in other cases.
Multiple elements listed with "and/or" should be construed in the
same fashion, i.e., "one or more" of the elements so conjoined.
Other elements may optionally be present other than the elements
specifically identified by the "and/or" clause, whether related or
unrelated to those elements specifically identified. Thus, as a
non-limiting example, a reference to "A and/or B", when used in
conjunction with open-ended language such as "comprising" may
refer, In some embodiments, to a only (optionally including
elements other than B); in another embodiment, to B only
(optionally including elements other than a); in yet another
embodiment, to both a and B (optionally including other elements);
etc.
[0046] As used herein in the specification and in the claims, "or"
should be understood to have the same meaning as "and/or" as
defined above. For example, when separating items in a list, "or"
or "and/or" shall be interpreted as being inclusive, i.e., the
inclusion of at least one, but also including more than one, of a
number or list of elements, and, optionally, additional unlisted
items. Only terms clearly indicated to the contrary, such as "only
one of" or "exactly one of," or, when used in the claims,
"consisting of," will refer to the inclusion of exactly one element
of a number or list of elements. In general, the term "or" as used
herein shall only be interpreted as indicating exclusive
alternatives (i.e., "one or the other but not both") when preceded
by terms of exclusivity, such as "either," "one of" "only one of"
or "exactly one of." "Consisting essentially of," when used in the
claims, shall have its ordinary meaning as used in the field of
patent law.
[0047] As used herein in the specification and in the claims, the
phrase "at least one," in reference to a list of one or more
elements, should be understood to mean at least one element
selected from any one or more of the elements in the list of
elements, but not necessarily including at least one of each and
every element specifically listed within the list of elements and
not excluding any combinations of elements in the list of elements.
This definition also allows that elements may optionally be present
other than the elements specifically identified within the list of
elements to which the phrase "at least one" refers, whether related
or unrelated to those elements specifically identified. Thus, as a
non-limiting example, "at least one of a and B" (or, equivalently,
"at least one of a or B," or, equivalently "at least one of a
and/or B") may refer, In some embodiments, to at least one,
optionally including more than one, a, with no B present (and
optionally including elements other than B); in another embodiment,
to at least one, optionally including more than one, B, with no a
present (and optionally including elements other than a); in yet
another embodiment, to at least one, optionally including more than
one, a, and at least one, optionally including more than one, B
(and optionally including other elements); etc.
[0048] In the claims, as well as in the specification above, all
transitional phrases such as "comprising," "including," "carrying,"
"having," "containing," "involving," "holding," "composed of," and
the like are to be understood to be open-ended, i.e., to mean
including but not limited to. Only the transitional phrases
"consisting of" and "consisting essentially of" shall be closed or
semi-closed transitional phrases, respectively, as set forth in the
United States Patent Office Manual of Patent Examining Procedures,
Section 2111.03.
[0049] As used herein, the terms "about" and "approximately" are
interchangeable, and should generally be understood to refer to a
range of numbers around a given number, as well as to all numbers
in a recited range of numbers (e.g., "about 5 to 15" means "about 5
to about 15" unless otherwise stated). Moreover, all numerical
ranges herein should be understood to include each whole integer
within the range.
[0050] As used herein, the term "e.g." is used merely by way of
example, without limitation intended, and should not be construed
as referring only those items explicitly enumerated in the
specification.
[0051] As used herein, the term "infection" is meant to include any
infectious agent of bacterial origin. The bacterial infection may
be the result of Gram-positive, Gram-negative bacteria or atypical
bacteria.
[0052] As used herein, "Gram-positive bacteria" are bacteria that
are stained dark blue by Gram staining. Gram-positive organisms are
able to retain the crystal violet stain because of the high amount
of peptidoglycan in the cell wall.
[0053] As used herein, "Gram-negative bacteria" are bacteria that
do not retain the crystal violet dye in the Gram staining
protocol.
[0054] As used herein, a "multi-drug resistant organism" is a
microorganism (bacteria, viruses, fungi or parasites) that is
resistant to distinct antimicrobial agents, first and foremost
antibiotics, but also antifungal drugs, antiviral medications, and
antiparasitic drugs.
[0055] Multi-drug resistant organisms may include, but are not
limited to, organisms belonging to the genus Acinetobacter,
Citrobacter, Enterobacter, Enteroccus, Escherichia, Kiebsiella,
Serratia or Staphylococcus. Exemplary multi-drug resistant
organisms include Acinetobacter baumannii such as ATCC isolate
#2894233-696-101-1, ATCC isolate #2894257-696-101-1 ATCC isolate
#2894255-696-101-1, ATCC isolate #2894253-696-101-1, or ATCC
#2894254-696-101-1; Citrobacter freundii such as ATCC isolate
#33128, ATCC isolate #2894218-696-101-1, ATCC isolate
#2894219-696-101-1, ATCC isolate #2894224-696-101-1, ATCC isolate
#2894218-632-101-1, or ATCC isolate #2894218-659-101-1;
Enterobacter cloacae such as ATCC isolate #22894251-659-101-1, ATCC
isolate #22894264-659-101-1, ATCC isolate #22894246-659-101-1, ATCC
isolate #22894243-659-101-1, or ATCC isolate #22894245-659-101-1;
Enteroccus facalis such as ATCC isolate #22894228-659-101-1 ATCC
isolate #22894222-659-101-1, ATCC isolate #22894221-659-101-1, ATCC
isolate #22894225-659-101-1, or ATCC isolate #22894245-659-101-1;
Enteroccus faecium such as ATCC isolate #51858, ATCC isolate
#35667, ATCC isolate #2954833_2694008 ATCC isolate
#2954833_2692765, or ATCC isolate #2954836_2694361; Escherichia
coli such as ATCC isolate CGUC 11332, CGUC 11350, CGUC 11371, CGUC
11378, or CGUC 11393; Kiebsiella pneumonia such as ATTC isolate
#27736, ATTC isolate #29011, ATTC isolate #20013, ATTC isolate
#33495, or ATTC isolate #35657; Serratia marcescens such as ATCC
isolate #43862, ATCC isolate #2338870, ATCC isolate #2426026, ATCC
isolate # SIID 2895511, or ATCC isolate # SIID 2895538; or
Staphylococcus aureus such as ATCC isolate # JHH 02, ATCC isolate #
JHH 02, ATCC isolate # JHH 03, ATCC isolate # JHH 04, ATCC isolate
# JHH 05, or ATCC isolate # JHH 06.
[0056] As used herein, "CRE" refers to carbapenem-resistant
Enterobacteriaceae.
[0057] As used herein, "ESBL" refers to extended spectrum beta
lactamase.
[0058] As used herein, a "method of treating" includes a method of
managing, and when used in connection with the biological organism
or infection, may include the amelioration, elimination, reduction,
prevention, and/or other relief from a detrimental effect of a
biological organism. Detrimental effects may include a
mycobacterial infection, symptoms characterizing and/or effects
associated with tuberculosis in the subject, or a combination
thereof.
[0059] As used herein, "nucleic acid" includes one or more types
of: polydeoxyribonucleotides (containing 2-deoxy-D-ribose),
polyribonucleotides (containing D-ribose), and any other type of
polynucleotide that is an N-glycoside of a purine or pyrimidine
base, or modified purine or pyrimidine bases (including abasic
sites). The term "nucleic acid," as used herein, also includes
polymers of ribonucleosides or deoxyribonucleosides that are
covalently bonded, typically by phosphodiester linkages between
subunits, but in some cases by phosphorothioates,
methylphosphonates, and the like. "Nucleic acids" include single-
and double-stranded DNA, as well as single- and double-stranded
RNA. Exemplary nucleic acids include, without limitation, gDNA;
hnRNA; mRNA; rRNA, tRNA, micro RNA (miRNA), small interfering RNA
(siRNA), small nucleolar RNA (snORNA), small nuclear RNA (snRNA),
and small temporal RNA (stRNA), and the like, and any combination
thereof.
[0060] As used herein, "DNA segment" refers to a DNA molecule that
has been isolated free of total genomic DNA of a particular
species. Therefore, a DNA segment obtained from a biological sample
using one of the compositions described herein refers to one or
more DNA segments that have been isolated away from, or purified
free from, total genomic DNA of the particular species from which
they are obtained, and also in the case of pathogens, optionally
isolated away from, or purified free from total mammalian
(preferably human) genomic DNA of the infected individual. Included
within the term "DNA segment," are DNA segments and smaller
fragments of such segments, as well as recombinant vectors,
including, for example, plasmids, cosmids, phage, viruses, and the
like.
[0061] As used herein, "RNA segment" refers to an RNA molecule that
has been isolated free of total cellular RNA of a particular
species. Therefore, RNA segments obtained from a biological sample
using one of the compositions disclosed herein, refers to one or
more RNA segments (either of native or synthetic origin) that have
been isolated away from, or purified free from, other RNAs.
Included within the term "RNA segment," are RNA segments and
smaller fragments of such segments.
[0062] As used herein, the terms "identical" or percent "identity,"
in the context of two or more nucleic acid or polypeptide
sequences, refer to two or more sequences or subsequences that are
the same or have a specified percentage of amino acid residues or
nucleotides that are the same, when compared and aligned for
maximum correspondence, as measured using one of the sequence
comparison algorithms described below (or other algorithms
available to persons of ordinary skill) or by visual
inspection.
[0063] As used herein, the phrase "substantially identical," in the
context of two nucleic acids refers to two or more sequences or
subsequences that have at least about 90%, preferably 91%, most
preferably about 92%, 93%, 94%, 95%, 96%, 97%, 98%, 98.5%, 99%,
99.1%, 99.2%, 99.3%, 99.4%, 99.5%, 99.6%, 99.7%, 99.8%, 99.9% or
more nucleotide residue identity, when compared and aligned for
maximum correspondence, as measured using a sequence comparison
algorithm or by visual inspection. Such "substantially identical"
sequences are typically considered "homologous," without reference
to actual ancestry.
[0064] As used herein, "sample" includes anything containing or
presumed to contain a substance of interest. It thus may be a
composition of matter containing nucleic acid, protein, or another
biomolecule of interest. The term "sample" may thus encompass a
solution, cell, tissue, or population of one of more of the same
that includes a population of nucleic acids (genomic DNA, cDNA,
RNA, protein, other cellular molecules, etc.). The terms "nucleic
acid source," "sample," and "specimen" are used interchangeably
herein in a broad sense, and are intended to encompass a variety of
biological sources that contain nucleic acids, protein, one or more
other biomolecules of interest, or any combination thereof.
Exemplary biological samples include, but are not limited to, whole
blood, plasma, serum, sputum, urine, stool, white blood cells, red
blood cells, buffy coat, swabs (including, without limitation,
buccal swabs, throat swabs, vaginal swabs, urethral swabs, cervical
swabs, rectal swabs, lesion swabs, abscess swabs, nasopharyngeal
swabs, and the like), urine, stool, sputum, tears, mucus, saliva,
semen, vaginal fluids, lymphatic fluid, amniotic fluid, spinal or
cerebrospinal fluid, peritoneal effusions, pleural effusions,
exudates, punctates, epithelial smears, biopsies, bone marrow
samples, fluids from cysts or abscesses, synovial fluid, vitreous
or aqueous humor, eye washes or aspirates, bronchial or pulmonary
lavage, lung aspirates, and organs and tissues, including but not
limited to, liver, spleen, kidney, lung, intestine, brain, heart,
muscle, pancreas, and the like, and any combination thereof. Tissue
culture cells, including explanted material, primary cells,
secondary cell lines, and the like, as well as lysates,
homogenates, extracts, or materials obtained from any cells, are
also within the meaning of the term "biological sample," as used
herein. The ordinary-skilled artisan will also appreciate that
lysates, extracts, or materials obtained from any of the above
exemplary biological samples are also within the scope of the
invention.
[0065] As used herein, "buffer" includes one or more compositions,
or aqueous solutions thereof, that resist fluctuation in the pH
when an acid or an alkali is added to the solution or composition
that includes the buffer. This resistance to pH change is due to
the buffering properties of such solutions, and may be a function
of one or more specific compounds included in the composition.
Thus, solutions or other compositions exhibiting buffering activity
are referred to as buffers or buffer solutions. Buffers generally
do not have an unlimited ability to maintain the pH of a solution
or composition; rather, they are typically able to maintain the pH
within certain ranges, for example from a pH of about 5 to 7.
[0066] As used herein, "patient" (also interchangeably referred to
as "host" or "subject") refers to any host that may serve as a
source of one or more of the biological samples or specimens as
discussed herein. In certain aspects, the donor will be a
vertebrate animal, which is intended to denote any animal species
(and preferably, a mammalian species such as a human being). In
certain embodiments, a "patient" refers to any animal host,
including but not limited to, human and non-human primates, avians,
reptiles, amphibians, bovines, canines, caprines, cavities,
corvines, epines, equines, felines, hircines, lapines, leporines,
lupines, ovines, porcines, racines, vulpines, and the like,
including, without limitation, domesticated livestock, herding or
migratory animals or birds, exotics or zoological specimens, as
well as companion animals, pets, and any animal under the care of a
veterinary practitioner.
[0067] As used herein, the term "substantially free" or
"essentially free," as used herein, typically means that a
composition contains less than about 10 weight percent, preferably
less than about 5 weight percent, and more preferably less than
about 1 weight percent of a compound. In a preferred embodiment,
these terms refer to less than about 0.5 weight percent, more
preferably less than about 0.1 weight percent or even less than
about 0.01 weight percent. The terms encompass a composition being
entirely free of a compound or other stated property, as well. With
respect to degradation or deterioration, the term "substantial" may
also refer to the above-noted weight percentages, such that
preventing substantial degradation would refer to less than about
15 weight percent, less than about 10 weight percent, preferably
less than about 5 weight percent, etc., being lost to degradation.
In other embodiments, these terms refer to mere percentages rather
than weight percentages, such as with respect to the term
"substantially non-pathogenic" where the term "substantially"
refers to leaving less than about 10 percent, less than about 5
percent, etc., of the pathogenic activity.
[0068] As used herein, "heterologous" is defined in relation to a
predetermined referenced nucleic acid sequence. For example, with
respect to a structural gene sequence, a heterologous promoter is
defined as a promoter that does not naturally occur adjacent to the
referenced structural gene, but which is positioned by the hand of
man in one or more laboratory manipulations that are routinely
employed by those of ordinary skill in the molecular biological
arts. Likewise, a heterologous gene or nucleic acid segment is
defined as a gene or nucleic acid segment that does not naturally
occur adjacent to the referenced sequence, promoter and/or enhancer
element(s), etc.
[0069] As used herein, the term "healthy" refers to a state of an
individual who is not at high risk of being infected with a
multi-drug resistant organism.
[0070] As used herein, "homology" refers to a degree of
complementarity between two or more polynucleotide or polypeptide
sequences. The word "identity" may substitute for the word
"homology" when a first nucleic acid or amino acid sequence has the
exact same primary sequence as a second nucleic acid or amino acid
sequence. Sequence homology and sequence identity may be determined
by analyzing two or more sequences using algorithms and computer
programs known in the art. Such methods may be used to assess
whether a given sequence is identical or homologous to another
selected sequence.
[0071] As used herein, "homologous" means, when referring to
polynucleotides, sequences that have the same essential nucleotide
sequence, despite arising from different origins. Typically,
homologous nucleic acid sequences are derived from closely related
genes or organisms possessing one or more substantially similar
genomic sequences. By contrast, an "analogous" polynucleotide is
one that shares the same function with a polynucleotide from a
different species or organism, but may have a significantly
different primary nucleotide sequence that encodes one or more
proteins or polypeptides that accomplish similar functions or
possess similar biological activity. Analogous polynucleotides may
often be derived from two or more organisms that are not closely
related (e.g., either genetically or phylogenetically).
[0072] As used herein, the terms "identical" or percent "identity",
in the context of two or more nucleic acid or polynucleotide
sequences, refer to two or more sequences or subsequences that are
the same or have a specified percentage of nucleotides that are the
same, when compared and aligned for maximum correspondence over a
comparison window, as measured using a sequence comparison
algorithm or by manual alignment and visual inspection.
[0073] As used herein, a "primer" or "primer sequence" may include
any nucleic acid sequence or segment that selectively hybridizes to
a complementary template nucleic acid strand ("target sequence")
and functions as an initiation point for the addition of
nucleotides to replicate the template strand. Primer sequences of
the present disclosure may be labeled or contain other
modifications which allow the detection and/or analysis of
amplification products. In addition to serving as initiators for
polymerase-mediated duplication of target DNA sequences, primer
sequences may also be used for the reverse transcription of
template RNAs into corresponding DNAs.
[0074] As used herein, a "target sequence" or "target nucleotide
sequence" as used herein includes any nucleotide sequence to which
one of the disclosed primer sequences hybridizes under conditions
that allow an enzyme having polymerase activity to elongate the
primer sequence, and thereby replicate the complementary
strand.
[0075] As used herein, the term "polypeptide" is intended to
encompass a singular "polypeptide" as well as plural
"polypeptides," and includes any chain or chains of two or more
amino acids. Thus, as used herein, terms including, but not limited
to "peptide," "dipeptide," "tripeptide," "protein," "enzyme,"
"amino acid chain," and "contiguous amino acid sequence" are all
encompassed within the definition of a "polypeptide," and the term
"polypeptide" may be used instead of, or interchangeably with, any
of these terms. The term further includes polypeptides that have
undergone one or more post-translational modification(s), including
for example, but not limited to, glycosylation, acetylation,
phosphorylation, amidation, derivatization, proteolytic cleavage,
post-translation processing, or modification by inclusion of one or
more non-naturally occurring amino acids. Conventional nomenclature
exists in the art for polynucleotide and polypeptide structures.
For example, one-letter and three-letter abbreviations are widely
employed to describe amino acids: Alanine (A; Ala), Arginine (R;
Arg), Asparagine (N; Asn), Aspartic Acid (D; Asp), Cysteine (C;
Cys), Glutamine (Q; Gln), Glutamic Acid (E; Glu), Glycine (G; Gly),
Histidine (H; His), Isoleucine (I; Ile), Leucine (L; Leu),
Methionine (M; Met), Phenylalanine (F; Phe), Proline (P; Pro),
Serine (S; Ser), Threonine (T; Thr), Tryptophan (W; Trp), Tyrosine
(Y; Tyr), Valine (V; Val), and Lysine (K; Lys). Amino acid residues
described herein are preferred to be in the "L" isomeric form.
However, residues in the "D" isomeric form may be substituted for
any L-amino acid residue provided the desired properties of the
polypeptide are retained.
[0076] As used herein, "protein" is used herein interchangeably
with "peptide" and "polypeptide," and includes both peptides and
polypeptides produced synthetically, recombinantly, or in vitro and
peptides and polypeptides expressed in vivo after nucleic acid
sequences are administered into a host animal or human subject. The
term "polypeptide" is preferably intended to refer to all amino
acid chain lengths, including those of short peptides of about 2 to
about 20 amino acid residues in length, oligopeptides of about 10
to about 100 amino acid residues in length, and polypeptides of
about 100 to about 5,000 or more amino acid residues in length. The
term "sequence," when referring to amino acids, relates to all or a
portion of the linear N-terminal to C-terminal order of amino acids
within a given amino acid chain, e.g., polypeptide or protein;
"subsequence" means any consecutive stretch of amino acids within a
sequence, e.g., at least 3 consecutive amino acids within a given
protein or polypeptide sequence. With reference to nucleotide and
polynucleotide chains, "sequence" and "subsequence" have similar
meanings relating to the 5' to 3' order of nucleotides.
[0077] As used herein, the term "substantially homologous"
encompasses two or more biomolecular sequences that are
significantly similar to each other at the primary nucleotide
sequence level. For example, in the context of two or more nucleic
acid sequences, "substantially homologous" may refer to at least
about 75%, preferably at least about 80%, and more preferably at
least about 85%, or at least about 90% identity, and even more
preferably at least about 95%, more preferably at least about 97%
identical, more preferably at least about 98% identical, more
preferably at least about 99% identical, and even more preferably
still, entirely identical (i.e., 100% or "invariant").
[0078] Likewise, as used herein, the term "substantially identical"
encompasses two or more biomolecular sequences (and in particular
polynucleotide sequences) that exhibit a high degree of identity to
each other at the nucleotide level. For example, in the context of
two or more nucleic acid sequences, "substantially identical" may
refer to sequences that at least about 80%, and more preferably at
least about 85% or at least about 90% identical to each other, and
even more preferably at least about 95%, more preferably at least
about 97% identical, more preferably at least about 98% identical,
more preferably at least about 99% identical, and even more
preferably still, entirely identical (i.e., 100% identical or
"non-degenerate").
[0079] As used herein, the term "recombinant" indicates that the
material (e.g., a polynucleotide or a polypeptide) has been
artificially or synthetically (non-naturally) altered by human
intervention. The alteration may be performed on the material
within or removed from, its natural environment or state.
Specifically, e.g., a promoter sequence is "recombinant" when it is
produced by the expression of a nucleic acid segment engineered by
the hand of man. For example, a "recombinant nucleic acid" is one
that is made by recombining nucleic acids, e.g., during cloning,
DNA shuffling or other procedures, or by chemical or other
mutagenesis; a "recombinant polypeptide" or "recombinant protein"
is a polypeptide or protein which is produced by expression of a
recombinant nucleic acid; and a "recombinant virus," e.g., a
recombinant influenza virus, is produced by the expression of a
recombinant nucleic acid.
[0080] As used herein, the term "operably linked" refers to a
linkage of two or more polynucleotides or two or more nucleic acid
sequences in a functional relationship. A nucleic acid is "operably
linked" when it is placed into a functional relationship with
another nucleic acid sequence. For instance, a promoter or enhancer
is operably linked to a coding sequence if it affects the
transcription of the coding sequence. "Operably linked" means that
the nucleic acid sequences being linked are typically contiguous,
or substantially contiguous, and, where necessary to join two
protein coding regions, contiguous and in reading frame. Since
enhancers generally function when separated from the promoter by
several kilobases and intronic sequences may be of variable
lengths; however, some polynucleotide elements may be operably
linked but not contiguous.
[0081] As used herein, the phrases "isolated" or "biologically
pure" refer to material that is substantially, or essentially, free
from components that normally accompany the material as it is found
in its native state. Thus, isolated polynucleotides in accordance
with the invention preferably do not contain materials normally
associated with those polynucleotides in their natural, or in situ,
environment.
[0082] As used herein, "link" or "join" refers to any method known
in the art for functionally connecting one or more proteins,
peptides, nucleic acids, or polynucleotides, including, without
limitation, recombinant fusion, covalent bonding, disulfide
bonding, ionic bonding, hydrogen bonding, electrostatic bonding,
and the like.
[0083] As used herein, "plasmid" refers to a genetic construct that
is composed of genetic material (i.e., nucleic acids). Typically, a
plasmid contains an origin of replication that is functional in
bacterial host cells, e.g., Escherichia coli, and selectable
markers for detecting bacterial host cells including the plasmid.
Plasmids of the present invention may include one or more genetic
elements as described herein arranged such that an inserted coding
sequence may be transcribed and translated in a suitable expression
cells. In addition, the plasmid may include one or more nucleic
acid segments, genes, promoters, enhancers, activators, multiple
cloning regions, or any combination thereof, including segments
that are obtained from or derived from one or more natural and/or
artificial sources.
[0084] As used herein, "resistome" refers to a collection of
antibiotic resistance genes and/or their precursors in both
pathogenic and non-pathogenic bacteria, which may be comprised of
antibiotic resistance genes found on antibiotic producers, such as
microorganisms in soil-dwelling bacteria and fungi that naturally
produce antibiotics which have their own protection mechanisms to
avoid the adverse effects of the antibiotics on themselves, and
cryptic resistance genes embedded in the bacterial chromosome, and
precursor genes which may not confer antibiotic resistance but may
encode proteins that confer to some kind of basal level activity
against the antibiotic molecule or have affinity to the molecule,
and antibiotic resistance genes associated with bacterial
biochemical, enzyme, and molecular regulatory pathways which may
confer antibiotic resistance including, for example, genes
affiliated with efflux pumps and cell wall porins.
Multi-Drug Resistant Organisms (MDROs)
[0085] According to some embodiments, the systems, apparatus, and
methods disclosed herein provide a bioinformatics solution for
rapidly detecting, tracking, and controlling multi-drug resistant
organisms (MDROs) in a single subject or a population of subjects
at risk for infection by or colonized or infected with MDROs.
Detection of MDRO-colonized or infected subjects may aid in
individual infection state management (e.g., the selection of
appropriate antibiotic therapy) and larger scale infection control
(e.g., containment).
[0086] For example, the systems, apparatus, and methods disclosed
herein may be used to detect beta-lactamase genes found in
beta-lactam antibiotic resistant Gram-negative bacteria and
vancomycin-resistant genes found in vancomycin-resistant
Gram-positive bacteria. More specifically, the systems, apparatus,
and methods disclosed herein may be used to detect genes,
including, but not limited to, Klebsiella pneumoniae carbapenemase
(KPC), New Delhi Metallo-beta-lactamase (NDM), Verona
integron-encoded metallo-beta-lactamase (VIM), IMP-type
carbapenemase (IMP), and OXA beta-lactamase (OXA) genes found in
carbapenem-resistant Gram-negative bacteria; CTX-M beta-lactamase
(CTX-M) genes found in extended spectrum resistant Gram-negative
bacteria; and Van-A found in vancomycin-resistant enterococci
(VRE).
[0087] Genes that confer multi-drug resistance to organisms are
referred to herein as MDRO-associated genes and may encompass one
or more of KPC, NDM, VIM, IMP, OXA, CTX-M, and Van-A, including all
family members. For example, reference to KPC includes KPC-2 and
KPC-16. Further description of these MDRO-associated genes is
provided herein.
KPC (K. pneumoniae Carbapenemase) (Class A)
[0088] A few class A enzymes, most noted the plasmid-mediated KPC
enzymes, are effective carbapenemases as well. Ten variants, KPC-2
through KPC-11 are known, and they are distinguished by one or two
amino acid substitutions (KPC-1 was re-sequenced in 2008 and found
to be 100% homologous to published sequences of KPC-2). KPC-1 was
found in North Carolina, KPC-2 in Maryland, and KPC-3 in New York.
They have only 45% homology with SME and NMC/IMI enzymes and,
unlike them, may be encoded by self-transmissible plasmids.
[0089] The class A Klebsiella pneumoniae carbapenemase (KPC) is
currently the most common carbapenemase, which was first detected
in North Carolina, US, in 1996 and has since spread worldwide. A
later publication indicated that Enterobacteriaceae that produce
KPC were becoming common in the United States.
NDM (New Delhi Metallo-Beta-Lactamase) (Class B)
[0090] Originally described from New Delhi in 2009, this gene is
now widespread in Escherichia coli and Klebsiella pneumoniae from
India and Pakistan. As of mid-2010, NDM carrying bacteria have been
introduced to other countries (including the United States and the
United Kingdom of Great Britain), most probably due to the large
number of tourists traveling the globe, who may have picked up the
strain from the environment, as strains containing the NDM gene
have been found in environmental samples in India Ten gene subtypes
have been reported for NDM: NDM-1 to NDM-10.
VIM (Verona Integron-Encoded Metallo-Beta-Lactamase) (Class B)
[0091] A second growing family of carbapenemases, the VIM family
now includes forty members, which have a wide geographic
distribution in Europe, South America, and East Asia and have been
found in the United States. VIM-1 was discovered in P. aeruginosa
in Italy in 1996; since then, VIM-2, which is now the predominant
variant has been found repeatedly in Europe and East Asia; VIM-3
and VIM-4 are minor variants of VIM-2 and VIM-1, respectively.
Forty gene subtypes have been reported for VIM: VIM-1 to VIM-40.
VIM enzymes occur mostly in P. aeruginosa, and also in P. putida
and, very rarely, in Enterobacteriaceae.
[0092] Amino acid sequence diversity is up to 10% in the VIM
family, 15% in the IMP family, and 70% between VIM and IMP. Enzymes
of both the families, nevertheless, are similar. Both are
integron-associated, sometimes within plasmids. Both hydrolyse all
beta-lactams except monobactams, and evade all beta-lactam
inhibitors.
IMP-Type Carbapenemases (Metallo-Beta-Lactamases) (Class B)
[0093] Plasmid-mediated IMP-type carbapenemases, 48 varieties (IMP
1-IMP48) of which are currently known, became established in Japan
in the 1990s both in enteric Gram-negative organisms and in
Pseudomonas and Acinetobacter species. IMP enzymes spread slowly to
other countries in East Asia, were reported from Europe in 1997,
and have been found in Canada and Brazil.
OXA Beta-Lactamases (Class D)
[0094] OXA beta-lactamases were long recognized as a less common
but also plasmid-mediated beta-lactamase variety that could
hydrolyze oxacillin and related anti-staphylococcal penicillins.
These beta-lactamases differ from the TEM and SHV enzymes in that
they belong to molecular class D and functional group 2d. The
OXA-type beta-lactamases confer resistance to ampicillin and
cephalothin and are characterized by their high hydrolytic activity
against oxacillin and cloxacillin and the fact that they are poorly
inhibited by clavulanic acid. Amino acid substitutions in OXA
enzymes may also give the ESBL phenotype. While most ESBLs have
been found in E. coli, K. pneumoniae, and other Enterobacteriaceae,
the OXA-type ESBLs have been found in P. aeruginosa and
Acinetobacter baumannii. OXA-type ESBLs have been found mainly in
Pseudomonas aeruginosa isolates from Turkey and France.
[0095] The OXA beta-lactamase family was originally created as a
phenotypic rather than a genotypic group for a few beta-lactamases
that had a specific hydrolysis profile. Therefore, there is as
little as 20% sequence homology among some of the members of this
family. However, recent additions to this family show some degree
of homology to one or more of the existing members of the OXA
beta-lactamase family. Some confer resistance predominantly to
ceftazidime, but OXA-17 confers greater resistance to cefotaxime
and cefepime than it does resistance to ceftazidime.
CTX-M Beta-Lactamases (Class A)
[0096] These enzymes were named for their greater activity against
cefotaxime than other oxyimino-beta-lactam substrates (e.g.,
ceftazidime, ceftriaxone, or cefepime). Rather than arising by
mutation, they represent examples of plasmid acquisition of
beta-lactamase genes normally found on the chromosome of Kluyvera
species, a group of rarely pathogenic commensal organisms. These
enzymes are not very closely related to TEM or SHV beta-lactamases
in that they show only approximately 40% identity with these two
commonly isolated beta-lactamases. More than eighty CTX-M enzymes
are currently known.
Van-A
[0097] Six different types of vancomycin resistance are shown by
Enterococcus: Van-A, Van-B, Van-C, Van-D, Van-E and Van-F. Of
these, only Van-A, Van-B, and Van-C have been seen in general
clinical practice, so far. The significance is that Van-A is
resistant to both vancomycin and teicoplanin. The mechanism of
resistance to vancomycin found in Enterococcus involves the
alteration to the terminal amino acid residues of the
NAM/NAG-peptide subunits, under normal conditions,
D-alanyl-D-alanine, to which vancomycin binds. The
D-alanyl-D-lactate variation results in the loss of one
hydrogen-bonding interaction (four, as opposed to five for
D-alanyl-D-alanine) being possible between vancomycin and the
peptide. This loss of just one point of interaction results in a
1000-fold decrease in affinity. The D-alanyl-D-serine variation
causes a six-fold loss of affinity between vancomycin and the
peptide, likely due to steric hindrance.
Resistome Profiles
[0098] According to some embodiments, dynamic naming and diagnostic
systems, apparatus, and methods are implemented to identifying,
diagnose, and manage subjects with complex drug resistant
infections. FIG. 1 illustrates an apparatus 100 for generating
resistome profiles in accordance with some embodiments. For
example, apparatus 100 may be used to implement the methods
described herein. The apparatus 100 includes at least one
communication interface 102, at least one memory 104, and at least
one processor 106, which is communicatively coupled to the at least
one communication interface 102 and the at least one memory
104.
[0099] The at least one memory 104 may be configured to store
processor-executable instructions 108 and/or data 110. For example,
data 110 may include raw sample data and/or processed data, such as
data representative of at least one measure of antibiotic
resistance of an organism. Data also may be stored on and/or
accessed from an external computing device over at least one
network 112 via the at least one communication interface 102. The
external computing device, such as a user device 114 and/or a
server 116 (e.g., cloud storage). Non-limiting examples of an
external computing device include a smartphone, a Personal Digital
assistant (PDA), a tablet computer, a laptop, a slate computer, an
electronic reader (e-reader), or any other suitable portable or
fixed electronic device.
[0100] According to some embodiments, the at least one processor
106 executes processor-executable instructions 108 to control the
at least one communication interface 102 to communicate over at
least one network with an external computing device 114, 116 and/or
control the at least one memory 104 to store and/or retrieve data.
In some embodiments, the at least one processor 106 includes a
profile generator 118, by which the at least one processor 106
executes processor-executable instructions 108 stored in the at
least one memory 104 to receive and analyze data representative of
a measure of antibiotic resistance of an organism in a sample
obtained from a subject, identify the organism, determine at least
one of an antibiotic susceptibility phenotype, an antibiotic
resistance gene, and an antibiotic to which the organism is
non-susceptible, and thereby generate at least one actionable
resistome profile for the subject. A resistome profile may be
assigned to one or more bacterial isolates from a sample. In some
embodiments, the at least one processor 106 may be configured to
execute processor-executable instructions 108 stored in the at
least one memory 104 to monitor an infection state of one or more
subjects and classify a population (e.g., facility) as to potential
outbreak risk, as described further herein.
[0101] FIG. 2 is a flowchart illustrating a method for generating a
resistome profile for a subject, based on a sample obtained from a
subject according to some embodiments. In step 200, data
representative of at least one measure of antibiotic resistance of
an organism in a sample from a subject is obtained. The sample may
be any biological sample obtained from the subject, including, but
not limited to, at least one of an anal swab, a rectal swab, a skin
swab, nasal swab, wound swab, stool, blood, plasma, serum, urine,
sputum, respiratory lavage, and a cerebrospinal fluid.
[0102] Data collected from analysis of the sample may be any type
of biological or diagnostic data, including, but not limited to,
data indicating at least one of a type or types of genes, a gene
sequence or sequences, a gene family or families, a DNA sequence or
sequences, one or more single-nucleotide polymorphisms (SNPs), a
type or types of nucleic acids, a type or types of proteins, and
protein expression. Data collected from analysis of a sample may
include data representative of at least one of a DNA probe assay, a
microbial identification test, and an antibiotic susceptibility
test performed on a bacterial isolate from the sample.
Alternatively or in addition, data collected from analysis of the
sample may include data representative of at least one antibiotic
resistance test performed on a bacterial isolate from the
sample.
[0103] In some embodiments, DNA sequencing is used to identify
organisms, indicate their genotype, genetically predict their
antimicrobial resistance, or match organisms infecting or
colonizing patients, using whole genome or targeted genome
analysis. Where this detailed DNA sequence information is available
on a timely or cost effective basis, phenotype information
describing actual antibiotic susceptibility may be used as
described herein.
[0104] In some embodiments, data from an MDRO gene detection system
(e.g., but not limited to, the ACUITAS.TM. MDRO Gene Test System
(available from OpGen, Inc., Gaithersburg, Md.)) is combined with
phenotypically derived isolate identification and antibiotic
resistance information. For example, the ACUITAS.TM. MDRO Gene Test
is a first generation multiplex assay that provides information
such as ESBL CTX type in groups (A, B, C). High resolution naming
at the type level, for instance C9, C15, etc., or even higher
resolution genotyping information also may be used.
[0105] In some embodiments, data representative of at least one
measure of antibiotic resistance of an organism in a sample
obtained from the subject may also include sample information,
including, but not limited to, high resolution mass spectra for
mass spectrometry data analysis to potentially identify the species
or otherwise differentiate individual isolates. For example, a
sample may be measured using matrix-assisted laser desorption
ionization (MALDI) mass spectrometry, a soft ionization technique
that allows analysis of biomolecules, which would otherwise tend to
be fragile and fragment when ionized by more conventional
ionization methods. In particular, the sample may be measured using
a time-of-flight (TOF) mass spectrometer, such as the 4800 MALDI
TOF/TOF.TM. Analyzer (available from Applied Biosystems.RTM./MDS
SCIEX, Grand Island, N.Y.) that doubles the ion flight path and
increases the resolution. Mass spectrometry measurements may be
used to identify isolate organisms from culture specimens using
molecular weight profiles or to determine SNPs.
[0106] Data collected from analysis of a sample also may include
data associated with an organism identified in the sample,
including, but not limited to, at least one of a genome sequence of
the identified organism, a minimum inhibitory concentration for an
antibiotic, and in silico data from a reference organism involved
in an outbreak.
[0107] In some embodiments, metadata associated with at least one
of the subject and the sample is collected (with necessary consent
of the subject as applicable), including, but not limited to, at
least one of identification information (e.g., a patient
identifier), demographic information, historical data (e.g.,
patient medical history), organization information (e.g., an agency
or a diagnosis and/or treatment facility), phenotype, collection
parameters (e.g., time, kit, media, etc.), and any other pertinent
information associated with the subject and/or the sample. A
diagnosis and/or treatment facility may be, but is not limited to,
at least one of a hospital, a clinic, a health center, a dental
office, a medical office, another private medical practitioner, a
non-governmental agency facility, and a gerontology agency. An
agency may include, but is not limited to, at least one of an
insurance agency, a government agency, a non-government agency, and
a gerontology agency.
[0108] In step 202 of FIG. 2, at least one organism in the sample
is identified from the data representative of at least one measure
of antibiotic resistance of an organism in the sample. An isolate
organism may be identified in a sample using molecular weight
profiles and mass spectrometry measurements (e.g., MALDI TOF).
[0109] In step 204 of FIG. 2, an antibiotic susceptibility
phenotype may be determined from the data representative of at
least one measure of antibiotic resistance of an organism in the
sample.
[0110] In step 206 of FIG. 2, an antibiotic resistance gene may be
determined from the data representative of at least one measure of
antibiotic resistance of an organism in the sample.
[0111] In step 208 of FIG. 2, an antibiotic to which the organism
is non-susceptible may be determined from the data representative
of at least one measure of antibiotic resistance of an organism in
the sample.
[0112] In step 210 of FIG. 2, a first pattern associated with the
first subject is generated based on the identified organism and at
least one of the determined antibiotic susceptibility phenotype,
the determined antibiotic resistance gene, and the determined
antibiotic to which the organism is non-susceptible. The first
pattern may include: [0113] an organism identification code to
indicate the identified organism; and at least one of: [0114] a
phenotype code, to indicate any antibiotic susceptibility phenotype
as determined from the data representative of at least one measure
of antibiotic resistance of an organism in the sample; [0115] a
genotype code, to indicate any antibiotic resistance gene as
determined from the data representative of at least one measure of
antibiotic resistance of an organism in the sample; and [0116] a
susceptibility code, to indicate any antibiotic to which the
organism is non-susceptible as determined from the data
representative of at least one measure of antibiotic resistance of
an organism in the sample.
[0117] According to some embodiments, the first pattern may include
a plurality of genotype codes, where each genotype code indicates
the identity of a different antibiotic resistance gene associated
with the identified organism.
[0118] According to some embodiments, a plurality of known patterns
are stored in one or more databases, for example, in memory 104 of
an apparatus for generating resistome profiles. Alternatively or in
addition, patterns may be stored on an external computing device
(e.g., in the cloud). Each known pattern may be associated with a
classified subject. The classified subject may be a colonized or
infected patient. According to some embodiments, colonized patients
test positive for at least one drug-resistant organism, and
infected patients have at least one of a central line blood
infection, ventilator associated pneumonia, a urinary tract
infection, and a surgical site infection. In some embodiments, the
known patterns have been determined based on measurement data of at
least one of antibiotic resistance and susceptibility performed on
isolates from samples from the classified subjects.
[0119] Known patterns associated with classified subjects may be
stored, for example, in a database of known patterns 212. In step
214 of FIG. 2, the first pattern is compared with the database of
known patterns 212 to identify a degree of similarity, if any,
between the first pattern and one or more of the known patterns. A
similarity metric may be applied to compare the first pattern to a
plurality of known patterns from previously classified
subjects.
[0120] In some embodiments, a threshold of similarity between the
first pattern and a known pattern is predetermined or determined.
If a degree of similarity between the first pattern and any of the
known patterns exceeds that threshold, as in step 216 of FIG. 2, a
profile uniqueness identifier is assigned to the subject. The
profile uniqueness identifier indicates the degree of similarity
above the threshold between the first pattern and at least one
known pattern associated with a classified subject.
[0121] A profile uniqueness identifier may be expressed using two
or more identifier codes. One identifier code may be used to
indicate a uniqueness of the first pattern compared to known
patterns in the database 212, and another identifier code may be
used to indicate how many profiles in the database share a
sufficiently similar pattern (i.e., have a degree of similarity
above the threshold). For example, a profile uniqueness identifier
may include a sequential uniqueness code determined based on the
degree of similarity above a threshold between the first pattern
and at least one of the known patterns and a repetition index to
indicate an increase in a number of known patterns that are
sufficiently similar to the first pattern.
[0122] A profile uniqueness identifier may be determined based on
additional information beyond that included in the known patterns
or in resistome profiles generated based at least in part on the
known patterns. Additional information may include nearest neighbor
information. For example, when genome sequence data is available, a
resistome profile may include information indicating a number of
nucleotide differences from nearest neighbors, including, but not
limited to, one or more locations of these differences in the
nucleotide sequences. In fact, a nearest neighbor indicator may be
included as a component of a profile uniqueness identifier and/or
as a separate classification parameter of a resistome profile.
[0123] In step 218 of FIG. 2, a first resistome profile is
generated for the subject based on the first pattern and the
associated profile uniqueness identifier according to some
embodiments. A resistome profile may be stored or output via a
network or displayed to a user as a code notation. For example, a
resistome profile may be stored, transmitted, and/or displayed as a
character string representation (e.g., K1:CRE:KPC_O1 . . . ) or a
user-specified notation (e.g., using a lookup table), as described
further herein. In some embodiments, a resistome profile is
displayed using a graphical representation, including, but not
limited to, various shapes, colors, and symbols, a two-dimensional
code (e.g., a QR code), a tube graph, and an epidemiology star
chart.
[0124] A resistome profile may be generated with a pattern
generator and analyzer, implemented, for example, as a database
engine. The pattern generator and analyzer may determine pattern
components from analysis of subject samples, generate patterns,
apply similarity metrics, determine resistome profile components
from analysis of patterns and subject sample metadata, and/or
generate resistome profiles using rules based on the methods
described herein. A resistome profiles may be constructed using a
set of rules according to the principles described herein. The
algorithms described herein, and associated systems, apparatus, and
methods for implementing the rules are not limited to the examples
herein, and may be altered or user-defined for greater flexibility
and to support future expansion and changes in antibiotic
resistomes and available antibiotic treatments.
Pattern Coding
[0125] According to some embodiments, a pattern associated with a
subject sample is generated based on the identified organism and at
least one of the determined antibiotic susceptibility phenotype,
the determined antibiotic resistance gene, and the determined
antibiotic to which the organism is non-susceptible. The pattern
components may be defined by an organism identification code,
phenotype code, genotype code, and/or susceptibility code, as
described herein, or any other appropriate abbreviations or other
representations beyond those described herein.
[0126] In some embodiments, the pattern includes an organism
identification code to indicate an organism (i.e., organism
species) identified in the subject sample. For example, the
following may be used as the organism identification code for the
organism indicated based on testing results for the measurement
data: E for Escherichia, K for Klebsiella, A for Acinetobacter, P
for Pseudomonas, etc. Other non-limiting examples of organism
identification codes are shown below in TABLE 1:
TABLE-US-00001 TABLE 1 Organism Organism Organism Full Name ID Code
A. baumannii Acinetobacter baumannii A1 C. amalonaticus Citrobacter
amalonaticus C4 C. freundii Citrobacter freundii C1 C. koseri
Citrobacter koseri C3 C. difficile Clostridium difficile C2 E.
aerogenes Enterobacter aerogenes E8 E. cloacae Enterobacter cloacae
E2 E. cloacae Enterobacter cloacae E10 complex complex E. gergoviae
Enterobacter gergoviae E9 E. avium Enterococcus avium E4 E.
canintestini Enterococcus canintestini E6 E. faecalis Enterococcus
faecalis E7 E. faecium Enterococcus faecium E3 E. raffinosus
Enterococcus raffinosus E5 E. coli Escherichia coli E1 K. oxytoca
Klebsiella oxytoca K3 K. pneumoniae Klebsiella pneumoniae K2 K.
pneumoniae Klebsiella pneumoniae K4 ssp ozaenae ssp ozaenae K.
pneumoniae Klebsiella pneumoniae K1 ssp pneumoniae ssp pneumoniae
P. mirabilis Proteus mirabilis P3 P. rettgeri Providencia rettgeri
P4 P. stuartii Providencia stuartii P2 P. aeruginosa Pseudomonas
aeruginosa P1 S. enterica Salmonella enterica S3 ser. Typhimurium
ser. Typhimurium S. marcescens Serratia marcescens S1 S. aureus
Staphylococcus aureus S2 S. maltophilia Stenotrophomonas
maltophilia S4
[0127] In some embodiments, the pattern includes a phenotype code
to indicate any corresponding antibiotic susceptibility phenotype
of the identified organism, as determined from the subject sample.
Some non-limiting examples of phenotype codes are shown below in
TABLE 2:
TABLE-US-00002 TABLE 2 Antibiotic Bacterial Phenotype Phenotype
Code Cephalosporin-resistant (3rd or 4th generation) CephR-GNB
Gram-negative bacillus Carbapenem-resistant Enterobacteriaceae CRE
Carbapenem-resistant Gram-negative bacillus CR-GNB
Extended-spectrum beta-lactamase ESBL Susceptible Gram-negative
bacillus S-GNB Vancomycin-resistant enterococcus VRE
Vancomycin-susceptible enterococcus VSE
[0128] In some embodiments, the pattern includes a genotype code to
indicate any antibiotic resistance gene or corresponding family of
genes as determined from the subject sample. The first pattern may
include a plurality of genotype codes, where each genotype code
indicates the identity of a different antibiotic resistance gene or
corresponding gene family associated with the identified organism
as determined from the subject sample. Some non-limiting examples
of genotype codes are shown below in TABLE 3:
TABLE-US-00003 TABLE 3 Antibiotic Resistance Gene Family Genotype
Code C. difficile binary BIN CTX-M-1 CTX1 or C1 CTX-M-2 CTX2 or C2
CTX-M-25 CTX25 or C25 CTX-M-8 CTX8 or C8 CTX-M-9 CTX9 or C9 IMP IMP
KPC KPC C. difficile NAP1 NAP1 NDM NDM OXA-23 O23 OXA-24 O24 OXA-48
O48 OXA-51 O51 OXA-58 O58 SHV(aa238) S238 SHV(aa240) S240
TEM(aa104) T104 TEM(aa164) T164 TEM(aa238) T238 TEM(aa240) T240 C.
difficile tcdB TXB C. difficile tcdC TXC Van A VANA VIM(A/B) VIM
VIM(C) VIMC
[0129] In some embodiments, the pattern includes a susceptibility
code to indicate any antibiotic to which the identified organism is
non-susceptible (i.e., has antibiotic resistance) as determined
from the subject sample. Some non-limiting examples of
susceptibility codes are shown below in TABLE 4:
TABLE-US-00004 TABLE 4 Antibiotic (Resistance) Susceptibility Code
Cefepime CFP Ceftazidime CTD Doripenem DPN Ertapenem EPN Imipenem
IPN Meropenem MPN
[0130] A pattern for a resistome profile may be generated to
include any combination of the codes described herein as well as
additional information. The pattern may be stored, transmitted,
and/or displayed in any permutation, including, but not limited to,
a list of codes. The codes may be stored, transmitted, and/or
displayed in a designated order, separated by a first type of
character or symbol, and/or identified by unique code-specific
characters or symbols. Where a pattern includes more than one code
of the same type (e.g., a plurality of genotype codes), the
plurality of codes of that type may be stored, transmitted, and/or
displayed in a designated order, separated by a second type of
character or symbol, and/or also identified by unique code-specific
characters or symbols.
[0131] In some embodiments, a pattern is stored, transmitted,
and/or displayed such that the codes are separated by a first
character or symbol (e.g., a colon) and multiple codes of a type
are separated by a second character or symbol (e.g., an
underscore). Some non-limiting examples of resistome profiles
generated for subjects based on the rules described herein are
shown below in TABLE 5:
TABLE-US-00005 TABLE 5 Antibiotic Antibiotic Profile Uniqueness
Bacterial Resistance Unique Profile Organism Organism Species
Phenotype Gene Family No. No. Resistome Profile E. coli
Carbapenem-resistant KPC and 64 3 E1:CRE:KPC_O48:64-3
Enterobacteriaceae OXA-48 K. pneumoniae Carbapenem-resistant VIM
and 4 1 K1:CRE:VIM_C1:4-1 Enterobacteriaceae CTX-M-1
[0132] In the examples in TABLE 5, the patterns (E1:CRE:KPC_O48 and
K1:CRE:VIM_C1, respectively) are generated based on organism
identification codes (E1 and K1, respectively) indicating organism
species identified from subject samples, a phenotype code (CRE)
indicating an organism antibiotic susceptibility phenotype
determined from subject samples, and genotype codes (KPC and O48,
and VIM and C1, respectively) indicating the presence of antibiotic
resistance genes as determined from subject samples. For the first
subject, the pattern derived is E1:CRE:KPC_O48, reflecting an
organism identification code of E1 (indicating E. coli), a
phenotype code of CRE (indicating Carbapenem-resistant
Enterobacteriaceae), and a genotype codes of KPC and O48
(indicating KPC and OXA-48 gene families), each pattern component
derived based on measurement data from a sample from the first
subject. For the second subject, the pattern derived is
K1:CRE:VIM_C1, reflecting an organism identification code of K1
(indicating K. pneumoniae), a phenotype code of CRE (indicating
Carbapenem-resistant Enterobacteriaceae), and a genotype codes of
VIM and C1 (indicating VIM and CTX-M-1 gene families), each pattern
component derived based on measurement data from a sample from the
second subject.
[0133] Based on an application of a similarity metric, as described
further herein, in comparing each pattern to known patterns from
previously classified subjects, profile uniqueness identifiers may
be assigned to indicate the uniqueness of each pattern (i.e., the
Unique Profile No.) and the number of known patterns (No. of
Organisms) that share the pattern or a sufficiently similar
pattern. A common infectious source or pathogen transmission route
may be identified if organisms from multiple subjects are
identified that share a similar resistome profile, such as
E1:CRE:KPC_O48:64-34, where profile uniqueness identifier component
i (the number of known patterns) differs for each resistome
profile. Where genome sequence data is available, the profile
uniqueness identifier component i further may include a nearest
neighbor indicator representative of the number nucleotides
difference from nearest neighbors (including an indication of the
location of these differences in the sequences).
[0134] According to some embodiments, the resistome profiles in
TABLE 5 include the patterns (E1:CRE:KPC_O48 and K1:CRE:VIM_C1,
respectively) and the associated profile uniqueness identifiers
(64-3 and 4-1, respectively). For the first subject, the pattern
(E1:CRE:KPC_O48) is compared to known patterns, for example, in a
database and according to a similarity metric, assigned a profile
uniqueness identifier of 64-3, indicating that the pattern has
already been assigned Unique Profile No. 64 and has been observed
three times in total (i.e., two of the known patterns in the
database share this pattern or a sufficiently similar pattern). For
the second subject, the pattern (K1:CRE:VIM_C1) is compared to
known patterns, for example, in the same database and according to
the same similarity metric, assigned a profile uniqueness
identifier of 4-1, indicating that the pattern is being assigned
Unique Profile No. 4 and is being observed for the first time
(i.e., none of the known patterns in the database share this
pattern or a sufficiently similar pattern).
[0135] TABLE 6 below provides other non-limiting examples of
resistome profiles generated for subjects based on the rules
described herein.
TABLE-US-00006 TABLE 6 Antibiotic Profile Uniqueness Resistance
Antibiotic Unique Profile Organism Organism Species Gene Family
(Resistance) No. No. Resistome Profile S. marcescens VIM Doripenem
27 2 S1:VIM:DPN_MPN:27-2 and Meropenem A. baumannii OXA-51 and
Doripenem, Ertapenem, 88 12 A1:O51_O23:DPN_EPN_MPN:88-12 OXA-23 and
Meropenem
[0136] In the examples in TABLE 6, the patterns (S1:VIM:DPN_MPN and
A1:O51_O23:DPN_EPN_MPN, respectively) are generated based on
organism identification codes (S1 and A1, respectively) indicating
organism species identified from subject samples, a genotype code
(VIM, and O51 and O23, respectively) indicating an antibiotic
resistance gene family determined from subject samples, and
susceptibility codes (DPN and MPN, and DPN, EPN, and MPN,
respectively) indicating antibiotics to which the subject samples
show resistance. For the first subject, the pattern derived is
S1:VIM:DPN_MPN, reflecting an organism identification code of S1
(indicating S. marcescens), a genotype code of VIM (indicating the
presence of the VIM gene family), and the susceptibility codes of
DPN and MPN (indicating resistance to Doripenem and Meropenem),
each pattern component derived based on measurement data from a
sample from the first subject. For the second subject, the pattern
derived is A1:O51_O23:DPN_EPN_MPN, reflecting an organism
identification code of A1 (indicating A. baumannii), genotype codes
of O51 and O23 (indicating the OXA-51 and OXA-23 gene families),
and the susceptibility codes of DPN and MPN (indicating resistance
to Doripenem, Ertapenem, and Meropenem), each pattern component
derived based on measurement data from a sample from the second
subject.
[0137] Based on an application of a similarity metric, as described
further herein, in comparing each pattern to known patterns from
previously classified subjects, profile uniqueness identifiers may
be assigned to indicate the uniqueness of each pattern and the
number of known patterns that share the pattern or a sufficiently
similar pattern. According to some embodiments, the resistome
profiles in TABLE 6 include the patterns (S1:VIM:DPN_MPN and
A1:O51_O23:DPN_EPN_MPN, respectively) and the associated profile
uniqueness identifiers (27-2 and 88-12, respectively). For the
first subject, the pattern (S1:VIM:DPN_MPN) is compared to known
patterns, for example, in a database and according to a similarity
metric, assigned a profile uniqueness identifier of 27-2,
indicating that the pattern has already been assigned Unique
Profile No. 27 and has been observed once before (i.e., one of the
known patterns in the database shares this pattern or a
sufficiently similar pattern). For the second subject, the pattern
(A1:O51_O23:DPN_EPN_MPN) is compared to known patterns, for
example, in the same database and according to the same similarity
metric, assigned a profile uniqueness identifier of 88-12,
indicating that the pattern is being assigned Unique Profile No. 88
and has been observed twelve times now (i.e., eleven of the known
patterns in the database share this pattern or a sufficiently
similar pattern).
[0138] The resistome profiles also may be generated based on
additional database information, including, but not limited to,
metadata, that is not included in TABLES 5 and 6. For example, a
nearest neighbor indicator representative of the number of
nucleotides differences from nearest neighbors (including locations
of those differences in the nucleotide sequences) may be obtained
from genome sequence data. The nearest neighbor indicator may be
included as a component of the profile uniqueness identifier (e.g.,
as a third number), or may be included in the resistome profile as
a separate classification parameter.
[0139] Other metadata that may be available and/or used includes,
but is not limited to, at least one of a facility indication (e.g.,
a descriptive name, such as "Pasteur"), a known gene (e.g.,
"NAP07"); a geographic location or region (e.g., where an organism
was first identified, such as "Europe," "Philippines,"
"California," or "Toronto"), one or more gene polymorphisms (e.g.,
spa typing nomenclature, such as "ClaI-MecA
polymorphisms::ClaI-Tm554 patterns::SmaI-PFGE restriction
profiles"), and a series of symbols to describe spa types (e.g.,
numbers or letters, such as "WGKAKBAOKAOMQ," where each letter
corresponds to a different polymorphism of a 24-base pair
repeat).
Similarity Metrics
[0140] In some embodiments, as described above with respect to step
214 of FIG. 2, a first pattern obtained from a subject is compared
with a plurality of known patterns from previously classified
subjects to identify a degree of similarity, if any, between the
first pattern and one or more of the known patterns. A similarity
metric may be applied to compare the first pattern to each of the
known patterns such that a profile uniqueness identifier may be
assigned to the pattern and a resistome profile may be generated
based on at least the first pattern and the profile uniqueness
identifier. For example, a profile uniqueness identifier may
reflect whether the degree of similarity is determined to be above
a predetermined threshold between the first pattern and one or more
known patterns.
[0141] In other embodiments, a first resistome profile is compared
with a plurality of candidate resistome profiles from previously
classified subjects to identify a degree of similarity, if any,
between the first resistome profile and one or more of the
candidate resistome profiles. A similarity metric may be applied to
compare the first resistome profile to each of the candidate
resistome profiles such that an outbreak of infection (e.g., at a
facility) may be identified.
[0142] In some embodiments, the similarity metric is configured to
compare patterns and/or resistome profiles to detect similarity on
an exact match basis and classify detected similarity using binary
rules. For example, if two patterns have coded notations indicating
the same species (e.g., based on data from an identification test),
the same resistance genes (e.g., based on data from a MDRO test),
and/or the same antibiotic susceptibility (e.g., based on data from
an AST), then the isolate samples may be designated as having
matching patterns according to a similarity metric.
[0143] In some embodiments, the profile uniqueness code reflects
pattern matching. A first part of a profile uniqueness code may
indicate a uniqueness of a first pattern compared to one or more
known patterns (i.e., the absence of a degree of similarity above a
threshold). A second part of a profile uniqueness code may indicate
how many known profiles share a sufficiently similar pattern (i.e.,
have a degree of similarity above a threshold). For example, if two
patterns are sufficiently similar (comparing, e.g., the character
string codes or additional information), the first part of each
profile uniqueness code will be the same. If the samples came from
different subjects, then the second part of the respective profile
uniqueness codes (i.e., the patient count or "number of organisms"
with a sufficiently similar patterns) will be different (e.g.,
incremented by one).
[0144] On the other hand, if one or more components of a pattern
and/or resistome profile differ from a known pattern and/or
resistome profile, the pattern and/or resistome profile may be
designated/classified as different depending on a threshold
determined or predetermined for the applied similarity metric. The
threshold may depend on, for example, a ranking of clinical
importance associated with different pattern and/or profile
components.
[0145] In the non-limiting sample examples Ex. 7A, Ex. 7B, Ex. 8A,
and Ex. 8B shown below in TABLES 7 and 8, all of the samples
include the organism Serratia marcescens (organism identification
code S1) and have a common antibiotic bacterial phenotype of
Carbapenem-resistant Enterobacteriaceae (phenotype code CRE);
however, Ex. 7A and Ex. 7B, and Ex. 8A and Ex. 8B, respectively,
differ in genotype. That is, although the genotypes of all the
samples include gene families NDM and OXA(C), the genotypes of Ex.
7B and Ex. 8B also includes gene families of the genotype
CTX-M(A).
TABLE-US-00007 TABLE 7 Ex. Species Phenotype Genotype Resistome
Profile 7A S1 CRE NDM, S1:CRE:NDM_O48:1-1 OXA(C) 7B S1 CRE NDM,
S1:CRE:NDM_O48:2-1 OXA(C), CTX-M(A)
[0146] Thus, the pattern notations assigned to the resistome
profiles of all the samples are the same (S1:CRE:NDM O48), but
differences recognized during application of the similarity metric
still may cause the two resistome profiles to be classified
differently (e.g., with profile uniqueness identifiers). In TABLE
7, Ex. 7A is designated/classified with profile uniqueness
identifier 1-1, while Ex. 7B is designated/classified with profile
uniqueness identifier 2-1. The first digit of the profile
uniqueness identifier indicates the uniqueness of the samples in
spite of a matching pattern notation, thereby
designating/classifying the resistome profiles as different from
each other. The second digit of the profile uniqueness identifier
indicates that both resistome profiles are being observed for the
first time.
TABLE-US-00008 TABLE 8 Ex. Species Phenotype Genotype Resistome
Profile 8A S1 CRE NDM, S1:CRE:NDM_O48:1-1 OXA(C) 8B S1 CRE NDM,
S1:CRE:NDM_O48:1-2 OXA(C), CTX-M(A)
[0147] In another example, the patterns of the two samples Ex. 8A
and Ex. 8B may be designated as a match based on a classification
rule of a similarity metric that sets rankings for profile
components based on clinical importance. That is, according to some
embodiments, two patterns that differ by a pattern or profile
component (e.g., drug resistance genotype) ranked as having a low
clinical importance score still may be designated/classified as a
match. Therefore, if the inclusion of CTX-M(A) in the genotype of
Ex. 8B is determined to have relatively less clinical importance
according to the similarity metric, then the pattern notations may
be designated/classified as a match. As shown in TABLE 8, Ex. 8A
may be designated with profile uniqueness identifier 1-1, while Ex.
8B is designated with profile uniqueness identifier 1-2. The first
digit of each profile uniqueness identifier indicates that the
samples are designated/classified as a match. Assuming that Ex. 8A
and Ex. 8B are from different samples/subjects, the second digit of
the profile uniqueness identifier for Ex. 8A indicates that the
pattern is being observed for the first time, and the second digit
of the profile uniqueness identifier for Ex. 8B indicates that this
is the second observation of this pattern.
[0148] While variations in similarity metrics may result in the
same or similar treatments for an individual subject, the
classification of a facility or subject population as to a
potential outbreak may change based on different similarity metrics
according to some embodiments. For example, a facility or
population may be classified as at risk or not at risk for a
potential outbreak precisely because of these types of differences
in genotypes reflected in Ex. 7A, Ex. 7B, Ex. 8A, and Ex. 8B.
[0149] Higher resolution data, including, but not limited to,
sequencing data, may be available and be incorporated into the
pattern generation engine used to assign the resistome profile. For
example, a similarity metric may be configured to search for one or
more nucleotide differences. The similarity metric also may be
configured to search for the locations of those differences in the
sequence, as described herein in connection with the nearest
neighbor determination. Any existing technique or tool used for
sequence comparison/alignment may be applied to the sample data to
determine similarity. For example, similarity information may be
extracted from similarity diagrams. The sequence alignment
stringency of the similarity metric may be adjustable or set
differently based on the type of organism or the sample conditions.
In some embodiments, a similarity metric may be configured to
generate an alignment score based, for example, on the degree of
alignment and/or the sequence difference locations.
Infection States
[0150] FIG. 3 is a flowchart illustrating a method for monitoring
an infection state of a subject according to some embodiments. In
step 300, first data representative of at least one measure of
antibiotic resistance of an organism in a first sample from a
subject is obtained. At least one organism in the sample may be
identified from the data using, for example, molecular weight
profiles and/or mass spectrometry measurements (e.g., MALDI TOF).
An antibiotic susceptibility phenotype, an antibiotic resistance
gene, and/or an antibiotic to which the organism is non-susceptible
also may be determined from the data. A first pattern associated
with the first sample may be generated based on the identified
organism and at least one of the determined antibiotic
susceptibility phenotype, the determined antibiotic resistance
gene, and the determined antibiotic to which the organism is
non-susceptible. The first pattern may include an organism
identification code and at least one of a phenotype code, a
genotype code, and a susceptibility code. A similarity metric may
be applied to compare the first pattern to a plurality of known
patterns from previously classified subjects. If a degree of
similarity between the first pattern and any of the known patterns
exceeds a threshold, a first profile uniqueness identifier may be
assigned to the first sample from the subject.
[0151] In step 302, a first resistome profile is generated for the
subject based on the first data representative of the first sample
derived from the subject. The first resistome profile may include
the first pattern and the first profile uniqueness identifier.
[0152] In step 304, second data representative of at least one
measure of antibiotic resistance of an organism in a second sample
from the subject is obtained. A second pattern associated with the
second sample may be generated, a similarity metric may be applied
to compare the second pattern to a plurality of known patterns from
previously classified subjects. If a degree of similarity between
the second pattern and any of the known patterns exceeds a
threshold, a second profile uniqueness identifier may be assigned
to the second sample from the subject.
[0153] In step 306, a second resistome profile is generated for the
subject based on the second data representative of the second
sample derived from the subject. The second resistome profile may
include the second pattern and the second profile uniqueness
identifier.
[0154] In step 308, the second resistome profile is compared to the
first resistome profile to identify any differences. A similarity
metric may be applied to compare the second profile to the first
profile and determine any differences, depending on a threshold
determined or predetermined for the applied similarity metric. The
threshold may depend on, for example, a ranking of clinical
importance associated with different profile components.
Differences between the first resistome profile and the second
resistome profile may indicate a change in the infection state of
the subject.
[0155] According to some embodiments, a facility may implement the
method of FIG. 3 to monitor a subject's infection state over time.
For example, in a diagnosis or treatment facility, a plurality of
samples may be obtained from a patient over the course of a single
visit or stay with the facility or over separate visits to the
facility and compared for indications of changes in the patient's
infection state. In some embodiments, a course of treatment for a
subject may be determined, or modified, based on the subject's
determined infection state and changes thereof.
[0156] FIG. 4 is a flowchart illustrating a method for determining
an infection state according to some embodiments. In step 400,
first data representative of at least one measure of antibiotic
resistance of an organism in a first sample from a first subject is
obtained. At least one organism in the sample may be identified
from the data using, for example, molecular weight profiles and/or
mass spectrometry measurements (e.g., MALDI TOF). An antibiotic
susceptibility phenotype, an antibiotic resistance gene, and/or an
antibiotic to which the organism is non-susceptible also may be
determined from the data. A first pattern associated with the first
sample may be generated based on the identified organism and at
least one of the determined antibiotic susceptibility phenotype,
the determined antibiotic resistance gene, and the determined
antibiotic to which the organism is non-susceptible. The first
pattern may include an organism identification code and at least
one of a phenotype code, a genotype code, and a susceptibility
code. A similarity metric may be applied to compare the first
pattern to a plurality of known patterns from previously classified
subjects. If a degree of similarity between the first pattern and
any of the known patterns exceeds a threshold, a first profile
uniqueness identifier may be assigned to the first sample from the
subject.
[0157] In step 402, a first resistome profile is generated for the
first subject based on the first data representative of the first
sample derived from the subject. The first resistome profile may
include the first pattern and the first profile uniqueness
identifier.
[0158] In step 404, second data representative of at least one
measure of antibiotic resistance of an organism in a first sample
from a second subject is obtained. A second pattern associated with
the first sample from the second subject may be generated, a
similarity metric may be applied to compare the second pattern to a
plurality of known patterns from previously classified subjects. If
a degree of similarity between the second pattern and any of the
known patterns exceeds a threshold, a second profile uniqueness
identifier may be assigned to the second sample from the
subject.
[0159] In step 406, a second resistome profile is generated for the
second subject based on the second data representative of the first
sample derived from the second subject. The second resistome
profile may include the second pattern and the second profile
uniqueness identifier.
[0160] In step 408, the second resistome profile is compared to the
first resistome profile to identify any differences indicating an
infection state of at least one of the subjects. A similarity
metric may be applied to compare the second profile to the first
profile and determine any differences, depending on a threshold
determined or predetermined for the applied similarity metric. The
threshold may depend on, for example, a ranking of clinical
importance associated with different profile components. If the
infection state of one subject is known (i.e., one subject is
assigned to an infection category, wherein the infection category
provides an indication of the infection state), differences or
similarities between the first resistome profile and the second
resistome profile may indicate an infection state of the other
subject (i.e., the other subject may be assigned to the same or a
different infection category based on the comparison).
[0161] In some embodiments, a diagnosis, course of treatment, or
assessment of treatment is informed by a determined infection
category or infection state. The apparatus 100 of FIG. 1 may be
used for monitoring infection states of one or more subjects and/or
assigning one or more subjects to an infection category in
accordance with some embodiments. For example, apparatus 100 may be
used to generate, store, transmit, and/or display resistome
profiles for a plurality of samples from the subject. In some
embodiments, the at least one processor 106 includes an infection
state classifier, by which the at least one processor 106 executes
processor-executable instructions 108 stored in the at least one
memory 104 to determine an infection state of one or more subjects
based on one or more resistome profiles generated according to any
of the principles described herein. The indication of the infection
state of the one or more subjects may be stored as data 110 on the
at least one memory 104 or may be stored externally to the
apparatus, e.g., at an external device 114, 116 (which may include
cloud data storage). The at least one processor 106 also may
execute processor-executable instructions 108 to control the
communication interface 102 to communicate to the external device
114, 116 and/or control the memory 104 to store resistome profiles
and/or infection state classifications.
[0162] Systems, apparatus, and methods also may be used to create
and maintain at least one database and informatics interface
according to the principles herein. A database and informatics
interface may have pro-active alert capabilities to identify and/or
monitor emerging trends of transmission with high resolution for
antibiotic resistance patterns.
Potential Infection Outbreaks
[0163] FIG. 5 is a flowchart illustrating a method for identifying
a potential infection outbreak in a subject population according to
some embodiments. In step 500, first data representative of at
least one measure of antibiotic resistance of an organism in a
first sample from a first subject is obtained.
[0164] In step 502, a first resistome profile is generated for the
first subject based on the first data representative of the first
sample derived from the subject. The first resistome profile may
include the first pattern and the first profile uniqueness
identifier.
[0165] A plurality of known patterns from previously classified
subjects 504 may be accessed in step 506 to identify a plurality of
candidate resistome profiles for subjects of the population or
associated with the population (e.g., a facility). The plurality of
candidate resistome profiles may be stored in one or more databases
across one or more devices. Each candidate resistome profile of the
plurality of candidate resistome profiles corresponds to a
previously classified subject (e.g., a subject that is known to
have been associated with the facility). For example, a previously
classified subject may be considered to be or have been associated
with the facility if the subject is currently being treated at the
facility, was previously treated at the facility, visited the
facility within a certain period of time (e.g., a time interval
equal to the incubation period of an infection), or came into
physical contact or was within a certain proximity of another
individual who is currently being treated at the facility, was
previously treated at the facility, or visited the facility within
a certain specified period of time. This certain specified period
of time may be set based on an average incubation period of an
infection or on another clinical measure specified by a user.
[0166] In step 508, each candidate resistome profile corresponding
to a previously classified subject is ranked according to a
potential basis for indicating an infection outbreak. In some
embodiments, the candidate resistome profiles may be already
associated with a rank that indicates a basis (i.e., likelihood)
for indicating an infection outbreak. Some bacterial organisms may
be ranked as potentially dangerous or deadly bacteria. Non-limiting
examples of these bacteria include carbapenem-resistant
Enterobacteriaceae (CRE) containing KPC, NDM-1, and OXA-48 genes.
These bacteria are resistant to nearly all antibiotics, including
carbapenems (a broad spectrum class of antibiotics used to treat
Gram-negative bacterial infections).
[0167] For example, a candidate resistome profile that includes the
phenotype code CRE (for carbapenem-resistant Enterobacteriaceae)
may be ranked as having a potentially high basis for indicating an
infection outbreak. In a further example, a candidate resistome
profile that includes the phenotype code CRE and a genotype code
for at least one of a KPC, an NDM-1, and an OXA-48 gene, may be
ranked as having a relatively higher basis for indicating an
infection outbreak, and a candidate resistome profile that includes
the phenotype code CRE, and a genotype code for a KPC gene may be
ranked as having an even higher basis for indicating an infection
outbreak.
[0168] In step 510, the first resistome profile is compared to each
candidate resistome profile. In step 512, it is determined whether
a degree of similarity above a threshold exists between the first
resistome profile and each candidate resistome profile. If there is
no degree of similarity or at least not a sufficient degree of
similarity (above the threshold), the process ends. However, if
there is a degree of similarity above the threshold, in step 514,
it is determined whether an infection outbreak is indicated, for
example, based on whether any candidate resistome profiles with
sufficient similarity is ranked as potentially indicating an
infection outbreak. If no candidate resistome profile with
sufficient similarity is ranked as potentially indicating an
infection outbreak, the process ends. However, if at least one
candidate resistome profile with sufficient similarity is ranked as
potentially indicating an infection outbreak, then in step 516, the
population (e.g., the facility) is classified as being at risk of
an infection outbreak.
[0169] The apparatus 100 of FIG. 1 may be used for identifying a
potential infection outbreak in a subject population according to
some embodiments. For example, apparatus 100 may be used to
generate, store, transmit, and/or display resistome profiles for a
plurality of samples from the subject. In some embodiments, the at
least one processor 106 includes an outbreak classifier, by which
the at least one processor 106 executes processor-executable
instructions 108 stored in the at least one memory 104 to determine
a potential for an infection outbreak based on a plurality of
resistome profiles generated for a plurality of subjects according
to any of the principles described herein. Information indicating
an outbreak classification may be stored as data 110 on the at
least one memory 104 or may be stored externally to the apparatus,
e.g., at an external device 114, 116 (which may include cloud data
storage). The at least one processor 106 also may execute
processor-executable instructions 108 to control the communication
interface 102 to communicate to the external device 114, 116 and/or
control the memory 104 to store resistome profiles and/or
information indicating an outbreak classification, such as for a
population or facility.
[0170] Information indicating an outbreak classification may be
stored or output via a network or displayed to a user as a code
notation. For example, information indicating an outbreak
classification may be stored, transmitted, and/or displayed as a
character string representation of the resistome profile(s) that
contributed to the classification or as a user-specified notation
(e.g., using a lookup table), as described further herein. In some
embodiments, information indicating an outbreak classification is
displayed to a user as a graphical representation, including, but
not limited to, a two-dimensional code (e.g., a QR code), a tube
graph, and an epidemiology star chart.
Gene Detection
[0171] In some embodiments, apparatus 100 includes, is a component
of, or is connected to a at least one gene detection system and
analysis platform. The at least one gene detection system may be a
multi-drug resistant organism (MDRO) gene detection system. Based
on data collected from analysis of a sample from a subject using
the at least one gene detection system and information associated
with the subject from whom the sample was obtained, a resistome
profile associated with the subject may be generated according to
the principles described herein. The data representative of a
measure of antibiotic resistance of an organism in the sample
obtained from the subject includes at least a portion of the data
collected from the analysis of the sample using the gene detection
system. A non-limiting example of an MDRO gene detection system is
disclosed in U.S. Provisional Application No. 61/952,795, filed on
Mar. 13, 2014, titled "Methods of Detecting Multi-Drug Resistant
Organisms," the disclosure of which is incorporated herein by
reference in its entirety.
[0172] FIG. 6 is a block diagram illustrating a gene detection
system and method for generating a resistome profile of a subject
in accordance with some embodiments. For example, a subject may be
suspected of or at high risk for having a MDRO colonization or
infection. High risk human subjects include, but are not limited
to, patients residing in or being admitted from a long-term care
facility, patients admitted to Intensive Care Units (ICUs),
immuno-compromised patients, patients being treated for cancer or
undergoing chemotherapy, organ and bone marrow transplant patients,
patients with ventilators or catheters, patients in preparation for
surgical procedures, postsurgical patients, patients previously
diagnosed or treated for a Healthcare-Associated Infection (HAI),
and others. Particularly high risk patients are neutropenic, have
cancer, or have received a transplant. In some aspects a patient
may be asymptomatic (not exhibiting the traditional signs and
symptoms) but still be at high risk, colonized, or infected.
[0173] In particular, FIG. 6 includes a multiplex MDRO gene
detection system (e.g., the ACUITAS.TM. MDRO Gene Test System),
which may be used to contribute to the sample data utilized by the
systems, apparatus, and methods described herein. For example, an
MDRO gene detection system may apply DNA amplification and
detection technology to detect genes associated with an identified
organism (e.g., bacteria).
[0174] According to some embodiments, a Gram-negative or
Gram-positive bacteria DNA sample is extracted from a biological
sample from a patient. The sample may be any biological sample,
including, but not limited to, an anal swab, a rectal swab, a skin
swab, nasal swab, wound swab, stool, blood, plasma, serum, urine,
sputum, respiratory lavage, cerebrospinal fluid, or an
environmental swab. Extraction may be accomplished by any known
method or system in the art, including, but not limited to, MagNA
Pure.TM. Systems (available from Roche, Basel, Switzerland).
Preferably, extraction both isolates and purifies the DNA sample,
such that the DNA sample is substantially free of protein, cellular
debris, and PCR inhibitors.
[0175] In some embodiments, the systems, apparatus, and methods
described herein have format flexibility to discriminate individual
gene subtypes, or to screen for all MDRO gene families and subtypes
in a combined probe "cocktail" assay format. The systems,
apparatus, and methods described herein may provide for an optimal
assay system whereby new MDRO genes or subtypes or infectious
disease organism molecular biomarkers or identification genes may
be incorporated into the assay format, to expand the scope of MDRO
screening and identification potential based on the emergence of
new MDROs over time.
[0176] This ultra-high sensitivity and resolution may be
accomplished by combining a pre-amplification step followed by a
detection step utilizing primers and probes based upon sequence
homology of the MRDO-associated gene families in accordance with
some embodiments. The primers and probes may include degenerate
primers sequence capable of amplifying and detecting
MDRO-associated gene sub-families and subtypes. Based on the level
of detection, the primers and probes may provide a
semi-quantitative assessment on the level of MDRO genes in the
sample. Thus, the methods are not only capable of detecting the
presence of a MRDO-associated gene in a sample, the method also
provide for the identification and semi-quantitative level of the
subtype of the MDRO-associated gene. This ability to provide a
genotype allows for the presumptive identification of bacterial
species. Thus, an unexpected advantage of the methods is that they
provides the clinician with some guidance as to which bacteria
species the subject is infected/or colonized with, and provides
guidance on the risk profile of the subject for potential
conversion from colonization to infection, or potential risk of
transmitting a MDRO to another individual. This ability to stratify
genotype is also very specific and reproducible. Another,
unexpected advantage of the methods is the extreme sensitivity that
may be ascertained by using a single swab sample. Unlike other
methods know in the art, the methods are capable of detecting less
than 210 CFU/sample (and in some instance less than 15 CFU/sample)
without the need to culture the sample.
[0177] Once the bacterial DNA is extracted from the biological
sample, an enrichment step is performed prior to the detection of
the MDRO associated genes. Enrichment is accomplished for example
by performing multiplex PCR. After enrichment, detection is
performed for example by using real time PCR using primers that are
specific to the MDRO associated gene being detected. Optionally, an
internal amplification control is included to guard against false
negatives associated with PCR inhibition. Additionally, appropriate
positive, negative, and no-template control (NTC) samples are
included during each performance run of the assay.
[0178] For example, in block 600 of FIG. 6, a first target MDRO
gene (e.g., KPC) is selected, and a sample is enriched for the
target MDRO gene. Primers specific to the target MDRO gene are used
in pre-amplification for ultra-high sensitivity to the target MDRO
gene. In block 602, primers and probes (e.g., a multiplex DNA
probe) are designed to detect broad subtypes of the target MDRO
gene. In block 604, multiplex PCR detection is performed, with MDRO
test results and sample information, as shown in block 606,
obtained in less than three hours according to some embodiments.
Thus, the systems, apparatus, and methods described herein may
yield ultra-high sensitivity and resolution of MDRO-associated
genes and throughput in less time at lower cost.
[0179] FIG. 6 also shows an analysis platform for generating an
outcome (e.g., a resistome profile, infection state, or infection
outbreak classification) according to some embodiments as described
herein. For example, the analysis platform may use an analysis
engine and cloud database technology to extend a gene detection
system with databases and advanced analytics. Powerful new
capabilities include monitoring and tracking bacterial gene
subtypes of antibiotic resistance on global and local levels
through the assignment of resistome profiles. In block 608, a
resistome profile is constructed for each isolate based on the MDRO
test results, metadata, and clinical observations.
[0180] The MDRO test results may include DNA sequence data for an
entire genome, for targeted regions of a genome, and/or for
antibiotic resistance genes of interest. If sequence data is
available, a resistome profile may include information indicating
differences in the nucleotide sequences from nearest neighbors,
including, but not limited to, the number and locations of these
differences in the nucleotide sequences. A nearest neighbor
indicator may be included in a resistome profile as a component of
the profile uniqueness identifier, or may be included in the
resistome profile as a separate classification parameter.
[0181] In block 610, an antibiotic resistance is characterized
according to a typing algorithm, described further herein. In block
612, the resistome profile and type contribute to the larger
identification and analysis of trends over time, geographical
locations, and other factors. For example, prevalence in a
particular location (e.g., a facility) may result automatically in
the generation of a dynamic, real-time alert and/or report.
Minimum Inhibitory Concentrations and Resistome Scores
[0182] In some embodiments, minimum inhibitory concentrations
(MICs) for antibiotics are determined--the levels of MICs
including, but not limited to, resistance (R), intermediate (I), or
susceptible (S)--and used for genotype/phenotype associations and
other forms of matching.
[0183] For example, MICs of some antibiotics for
carbapenem-resistant Enterobacteriaceae are shown in TABLE 9 in
accordance with some embodiments.
TABLE-US-00009 TABLE 9 CRE MICs Susceptible Intermediate Resistant
Current Breakpoints (M100-S22) MIC (.mu.g/mL) Doripenem .ltoreq.1 2
.gtoreq.4 Ertapenem .ltoreq.0.5 1 .gtoreq.2 Imipenem .ltoreq.1 2
.gtoreq.4 Meropenem .ltoreq.1 2 .gtoreq.4 Revised (M100-S20) MIC
(.mu.g/mL) Cefotaxime .ltoreq.1 2 .gtoreq.4 Ceftazidime .ltoreq.4 8
.gtoreq.16 Ceftriaxone .ltoreq.1 2 .gtoreq.4
[0184] MICs of some antibiotics for cephalosporin-resistant (3rd or
4th generation) Gram-negative bacillus are shown in TABLE 10 in
accordance with some embodiments.
TABLE-US-00010 TABLE 10 CephR-GNB MICs Susceptible Intermediate
Resistant Revised (M100-S20) MIC (.mu.g/mL) Cefepime .ltoreq.8 16
.gtoreq.32 Ceftazidime .ltoreq.4 8 .gtoreq.16
[0185] In some embodiments, a resistome profile for a sample is
converted to a resistome score by assigning respective weights to
genes across the entire resistome profile based on associated
phenotypes. Higher weights may be assigned to genes of lower
antibiotic susceptibility or higher antibiotic resistance (i.e.,
resistant MICs), and lower weights may be assigned to genes with
lower antibiotic resistance or higher antibiotic susceptibility
(i.e., resistant MICs). This provides a user with the ability to
correlate or illustrate associations between genotypic resistome
data and phenotypic antibiotic susceptibility or resistance. For
example, FIGS. 7 and 8 exhibit good correlation between Resistome
Scores and phenotypic antibiotic susceptibility test results.
Resistome Scores also may be weighted by other information,
including, but not limited to, genomic and/or pathogenicity
information, such as the location of a gene on a plasmid, mobile
element, or chromosome, and other factors affecting negative
clinical outcomes.
[0186] FIG. 7 illustrates associations between genotypic resistome
results (e.g., a gene test) 700 and antibiotic susceptibility test
results 702 for a set of thirty-three Pseudomonas aeruginosa
culture isolates. Each row in FIG. 7 represents an individual
bacterial isolate 704. The isolates 704 were sorted according to
antibiotic susceptibility test results (i.e., phenotypic antibiotic
MIC values) 702 with more antibiotic resistant isolates (in darker
shades) at the top of the graph. More heavily weighted positive
resistome genes are shown (in darker shades) among the genotypic
resistome results 700. According to some embodiments, a Resistome
Score 706 was calculated for each isolate by weighting each gene
700 in a Resistome Test, with higher scores shown (in darker
shades) at the top of the Resistome Score scale 706.
[0187] Similarly, FIG. 8 illustrates associations between genotypic
resistome results (e.g., a gene test) 800 and antibiotic
susceptibility test results 802 for a set of eighty-six Klebsiella
pneumoniae culture isolates. Each row in FIG. 8 represents an
individual bacterial isolate 804. The isolates 804 were sorted
according to antibiotic susceptibility test results (i.e.,
phenotypic antibiotic MIC values) 802 with more antibiotic
resistant isolates (in darker shades) at the top of the graph. More
heavily weighted positive resistome genes are shown (in darker
shades) among the genotypic resistome results 800. According to
some embodiments, a Resistome Score 806 was calculated for each
isolate by weighting each gene 800 in a Resistome Test, with higher
scores shown (in darker shades) at the top of the Resistome Score
scale 806. In particular, an isolate that was positive for KPC and
CTX-M-1 was assigned a Resistome Score of 1100 through weights of
1000 and 100 for KPC and CTX-M-1, respectively.
Varied Data Classes & Typing
[0188] In some embodiments, a resistome profile include various
test results or sources of data (i.e., data classes), including
results from one or more of a gene test (e.g., MDRO detection), a
Resistome Test, identification and antibiotic susceptibility test,
sequencing (e.g., whole genome), in silico profiles (e.g.,
generated from well-documented reference organisms in outbreaks
from individual facilities or geographical regions), mass
spectrometry (e.g., MALDI-TOF.TM.), phenotype, and sample
metadata.
[0189] In some embodiments, information gathered from existing
systems may be referenced, including information based on at least
one of a mass spectrometry spectra (e.g., MALDI-TOF.TM.) database,
multi-locus sequence typing (MLST), single nucleotide polymorphism
(SNP) schemes, and ribosomal MLST (rMLST). Species-specific MLST
may be used as a basis for backwards compatibility reasons. MLST
sequence types (ST) may be extracted from next generation
sequencing (NGS) data. The pan-bacterial ribosomal MLST may be
used. Genome-wide gene by gene bacterial typing (i.e., core genome
MLST or MLST+) may be an extension of the traditional MLST concept.
These methods may be standardized (in contrast to lineage specific
schemes based on explorative SNPs or lineage specific allele typing
schemes). Lineage specific SNP/allele approaches may be layered on
top of the standardized schemes for local or ad hoc analysis to
gain even more discriminatory power.
[0190] FIG. 9 is a flowchart illustrating methods of using a gene
detection system and analysis platform in accordance with some
embodiments. Data representative of at least one measure of
antibiotic resistance of an organism is obtained from a sample 902
obtained from a subject. The data may be obtained using a variety
of test results or sources of data (i.e., data classes), including
at least one of an MDRO gene test 904 applied to the sample 902 and
an identification and antibiotic susceptibility test 906 performed
on bacterial isolates 908 from the sample 902. The MDRO gene test
904 may result in detection of hundreds of MDRO genes. Together,
results from the MDRO gene test 904 and/or the identification and
antibiotic susceptibility test 906 may be used to generate a
resistome profile for each bacterial isolate of the subject as
described hereinabove. The resistome profile(s) may be stored in
database 910. As also described hereinabove, additional sample data
912 associated with the sample from the subject, including, but not
limited to, information associated with resistance, phenotype,
patient history, and metadata, also may be included in the
resistome profile(s) and/or stored in database 910. As shown in
FIG. 9, the information 912 associated with the sample may be
obtained from facility 914 (e.g., a hospital). In some embodiments,
in silico profiles may be created from well-documented reference
organisms in outbreaks from individual hospitals or countries.
[0191] According to some embodiments, analysis engine 916 accesses
the resistome profile(s) and/or other data in database 910 to
generate any outcome (e.g., a resistome profile, infection state,
or infection outbreak classification) described herein. For
example, FIG. 9 lists some information that may be communicated to
a user using interface 918. As non-limiting examples, the user may
use the interface to interact with analysis engine 916 and database
910, including, but not limited to, identifying a resistome profile
in database 910 that, for example, meets a parameter according to a
search of database 910, viewing a history of a resistome profile in
database 910, analyzing trends among resistome profiles in database
910, obtaining and/or transmitting a resistome profile in database
910, ascertaining a prevalence of a resistome profile in database
910, and obtaining and/or transmitting an indication of an active
alert and/or report.
[0192] As shown in FIG. 9, a report 920 and/or an alert 922 may be
communicated to facility 914. For example, a potential for an
outbreak at a facility may be determined based on application of
analysis engine 916 to the resistome profiles stored in database
910. The report 920 and/or alert 922 may include information
indicating the potential for an outbreak at facility 914 or another
facility.
[0193] Information provided by facility 914 may be communicated
back to analysis engine 916 and database 910. As shown in block
924, the platform may provide a capability for facility 914 to
interact with analysis engine 916 by sharing real-time, dynamic
data and aggregates.
[0194] The generation and assignment of a "type" to indicate the
uniqueness of each pattern (e.g., the Unique Profile No. of the
profile uniqueness identifier) may be challenging when varied test
results or sources of data (i.e., data classes) are involved.
Current data classes may include, but are not limited to, gene test
(e.g., MDRO detection) results, resistome results, identification
and antibiotic susceptibility test results, sequencing results, in
silico results, mass spectrometry (e.g., MALDI-TOF.TM.) results,
phenotype results, and sample metadata. Any given sample for which
a resistome profile is generated may have results from one or more
of these data classes.
[0195] According to some embodiments, comparison of two or more
resistome profiles requires that the type of each resistome profile
must be derived from the same data classes. For example, if a first
sample has only resistome results and a second sample has only MDRO
gene detection and identification and antibiotic susceptibility
test results, both samples may be assigned resistome profiles, but
the types associated with those profiles may be different. Instead
of just a numeric identifier, the types for each sample may be
expressed in terms of the data class. Some non-limiting examples of
data class codes are shown below in TABLE 11:
TABLE-US-00011 TABLE 11 Test Results/Sources of Data Data Class
Code Antibiotic Susceptibility Test Results A Gene Test Results G
Resistome Results R Sequencing Results S
[0196] For example, TABLE 12 shows two examples of resistome
profiles for the same sample according to some embodiments. Ex. 12A
only requires a numeric type, but Ex. 12B expresses type in terms
of the underlying tests.
TABLE-US-00012 TABLE 12 Resistome Profiles Pattern Profile
Uniqueness Resistance N.sup.th Member Ex. Organism ID Phenotype
Genes Type of Type 12A K1:CRE:KPC_NDM 2-5 12B K1:CRE:KPC_NDM
G2-15_R5-9_A6-4_S19-2
[0197] Although Ex. 12A and Ex. 12B share the same pattern, Ex. 12B
expresses multiple profile uniqueness identifiers linked to the
underlying tests or sources of data according to some embodiments.
For Ex. 12A, the pattern (K1:CRE:KPC_NDM) is compared to known
patterns, for example, in a database and according to a similarity
metric, assigned a profile uniqueness identifier of 2-5, indicating
that the pattern has already been assigned Unique Profile No. 2 and
has been observed five times in total (i.e., four known patterns in
the database share this pattern or a sufficiently similar pattern).
For Ex. 12B, the same pattern (K1:CRE:KPC_NDM) may compared to
known patterns, for example, even in the same database, except that
the comparison depends on profiles with the same type. Thus, the
pattern of Ex. 12B is compared to known patterns with the same data
classes.
[0198] For example, the pattern of Ex. 12B was obtained at least in
part from gene test results and therefore may be compared to known
patterns also obtained at least in part from gene test results,
according to a similarity metric, and assigned a profile uniqueness
identifier component G2-15, indicating that, among sufficiently
similar patterns obtained at least in part from gene test results,
Ex. 12B is being assigned Unique Profile No. 2 and has appeared
fifteen times in the database.
[0199] The pattern of Ex. 12B also was obtained at least in part
from resistome results, antibiotic susceptibility test results, and
sequencing results and therefore may be compared to known patterns
respectively obtained at least in part from resistome results,
antibiotic susceptibility test results, and sequencing results,
according to one or more similarity metrics. Thus, Ex. 12B may be
assigned the profile uniqueness identifier component R5-9,
indicating that, among sufficiently similar patterns obtained at
least in part from resistome results, Ex. 12B is being assigned
Unique Profile No. 5 and has appeared nine times in the database.
Ex. 12B also may be assigned the profile uniqueness identifier
component A6-4, indicating that, among sufficiently similar
patterns obtained at least in part from antibiotic susceptibility
test results, Ex. 12B is being assigned Unique Profile No. 6 and
has appeared four times in the database. Ex. 12B further may be
assigned the profile uniqueness identifier component S19-2,
indicating that, among sufficiently similar patterns obtained at
least in part from sequencing results, Ex. 12B is being assigned
Unique Profile No. 6 and has appeared only once before in the
database.
[0200] In another example, TABLE 13 shows two examples of partial
resistome profiles according to some embodiments.
TABLE-US-00013 TABLE 13 Ex. Resistome Profile 13A :
:KPC_NDM:G2-15_R5-9_A6-4_S19-2 13B : :KPC_NDM:G3-2
[0201] While the identity and the phenotype of the organism are not
shown, both Ex. 13A and Ex. 13B have the same key resistance genes
KPC and NDM. Ex. 13A has gene test, resistome, antibiotic
susceptibility test, and sequencing results, but Ex. 13B has only
gene test results. According to some embodiments, it need not
matter that Ex. 13B has no resistome, antibiotic susceptibility
test, or sequencing results, as long as Ex. 13A and Ex. 13B are
compared on only common data classes (i.e., gene test results).
[0202] According to some embodiments, a resistome profile may be
formatted as: [0203] Species ID:Phenotype:Positive Genes:
[Testtype]Subtypenumber-Count_[Testtype]Subtypenumber-Count_[Testtype]Sub-
typenumber-Count Examples of test types in use are A17 (antibiotic
susceptibility test or AST with 17 antibiotics, as shown below in
TABLE 14) and R70 (i.e., Resistome Test with 70 target genes, as
shown below in TABLE 15); however, the above format may be
modified, for example, to be re-ordered or to include fewer or
additional tests, target genes, and/or antibiotics.
[0204] According to some embodiments, a phenotype in a resistome
profile may be determined according to the antibiotic
susceptibility test rules defined in TABLE 14:
TABLE-US-00014 TABLE 14 Phenotype AST Rule CRE [Enterobacteriaceae]
&& (<Imipenem> || <Meropenem>) CR-P.aeru
[Pseudomonas] && (<Imipenem> || <Meropenem>)
MDR-Acin var count=0; if (<Imipenem> || <Meropenem>)
count++; if (<Piperacillin>) count++; if (<Amikacin> ||
<Gentamicin> || <Tobramycin>) count++; if
(<Ciprofloxacin> || <Levofloxacin>) count++; if
(<Ampicillin>) count++; ([Acinetobacter] && count
> 2) CR-GNB [GNB] && (<Imipenem> ||
<Meropenem>) CephR-GNB [GNB] && (<Ceftazidime>
|| <Ceftriaxone> || <Cefotaxime> || <Cefepime>)
S-GNB [GNB] && !(<Imipenem> || <Meropenem> ||
<Ceftazidime> || <Ceftriaxone> || <Cefepime>)
[0205] According to some embodiments, a positive gene in a
resistome profile may be determined according to the Resistome Test
priorities defined in TABLE 15:
TABLE-US-00015 TABLE 15 Target Genes Priority Genotype Code KPC-1 1
KPC1 NDM-1 2 NDM1 VIM-1 3 VIM1 VIM-2 4 VIM2 VIM-5 5 VIM5 VIM-13 6
VIM13 IMP-1 7 IMP1 IMP-2 8 IMP2 IMP-5 9 IMP5 SME-1 10 SME1 IMI-1 11
IMI1 NMC-A 12 NMCA OXA-2 13 OXA2 OXA-10 14 OXA10 OXA-18 15 OXA18
OXA-23 16 OXA23 OXA-24 17 OXA24 OXA-45 18 OXA45 OXA-48 19 OXA48
OXA-50 20 OXA50 OXA-51 21 OXA51 OXA-54 22 OXA54 OXA-55 23 OXA55
OXA-58 24 OXA58 OXA-60 25 OXA60 OXA-62 26 OXA62 CTX-M-1 27 CTXM1
CTX-M-2 28 CTXM2 CTX-M-8/25 29 CTXM8 CTX-M-9 30 CTXM9 VEB-1 31 VEB1
PER-1 32 PER1 GES-1 33 GES1 BES-1 34 BES1 TLA-1 35 TLA1 SFC-1 36
SFC1 SHV-G238S&E240K 37 SHV4 SHV-G238S&E240 38 SHV2
SHV-G238&E240K 39 SHV3 SHV-G156D 40 SHV6 TEM-G238S&E240K 41
TEM10 TEM-G238S&E240 42 TEM8 TEM-G238&E240K 43 TEM9
TEM-R164H 44 TEM4 TEM-R164C 45 TEM5 TEM-R164S 46 TEM6 TEM-E104K 47
TEM2 SHV-G238&E240 (WT) 48 SHV1 SHV-G156 (WT) 49 SHV5
TEM-G238&E240 (WT) 50 TEM7 TEM-R164 (WT) 51 TEM3 TEM-E104 (WT)
52 TEM1 BEL-1 53 BEL1 GIM-1 54 GIM1 SPM-1 55 SPM1 DHA-1 56 DHA1
FOX-1 57 FOX1 SIM-1 58 SIM1 ACC-1 59 ACC1 ACC-3 60 ACC3 ACT-1 61
ACT1 ACT-5 62 ACT5 MIR-1 63 MIR1 MO.chi.-1 64 MOX1 MO.chi.-5 65
MOX5 CMY-1 66 CMY1 CMY-2 67 CMY2 CFE-1 68 CFE1 CMY-47 69 CMY47
CMY-70 70 CMY70
[0206] Each unique combination of positive values for a test type
is assigned a sequential subtype number. In the example below in
TABLE 16, using the Resistome Test, a third unique combination of
positive Resistome gene results was found and therefore assigned
the number 3. For the AST result, a second unique combination was
observed and therefore assigned the number 2. Count is the number
of occurrences across the database of that particular subtype
number at the time the type is assigned. In the example below, both
the Resistome and AST subtypes were the first occurrence.
TABLE-US-00016 TABLE 16 Unique No. of Subtype Organisms Resistance
No. (Count) Example Resistome Species Phenotype Genes RXX AXX RXX
AXX Profile K. CRE SHV- 3 2 1 1
K1:CRE:KPC1_SHV1_TEM4:[RXX]3-1_[AXX]2-1 pneumoniae G238&E240
(WT) and TEM-R164H
Communication of Outcomes
[0207] In some embodiments, systems, apparatus, and/or methods
communicate value-added information to stakeholders (e.g., a
facility agent, a physician, an infection control professional, or
a public health agency) concerning a resistome profile, an
infection state, and/or an outbreak classification.
[0208] According to some embodiments, an individual resistome
profile is interrogated for valuable clinical therapeutic insights
regarding diagnosis, clinical significance, and treatment
decisions. Execution of processor-executable instructions may lead
a processor to interrogate a computer database based on a resistome
profile and, if a match is identified, indicate a level of clinical
significance of the match (a similarity metric above a threshold).
For example, a K1:CRE:KPC:1-1 profile (K. pneumonia with a
carbapenem-resistant phenotype and a KPC plasmid gene) may be
ranked in a database as a more critical infection or colonization
than an E1:ESBL:C1:1-1 profile (E. coli with an ESBL phenotype and
a CTX group 1 genotype). For example, a stakeholder may be informed
that, based on a resistome profile that indicates an organism with
both a VIM or IMP metalloproteinase carbapenem genotype and an ESBL
genotype, the respective subject may not be responsive to
Aztreonam, one of a few choices for treating the infection.
[0209] Some embodiments are configured to provide guidance
regarding in silico data, such as published results from expert
observations and research in the field. In silico data may be used
to augment unique resistome profiles by comparing them to
well-characterized reference strains. For example, an in silico
comparison may be made between the clone ST258 and various KPC
subtypes such as KPC-2 or KPC-3 that are geographically
predominant, known to come from local facilities, etc.
[0210] In addition to facilitating rapid diagnosis and/or treatment
decisions, systems, apparatus, and methods may be configured to
indicate that there is a potential outbreak or common source of
infection according to some embodiments. Using resistome profiles,
systems, apparatus, and methods may be configured to search
geographical and/or facility-based demographic data. Systems,
apparatus, and methods may be configured to generate a map of a
geographical area or facility (including, but not limited to, ICU
rooms) where various resistome profiles have been identified, to
classify the facility according to micro-geographic matches. The
example resistome profiles may be used to provide statistical data
and tracking data. In some embodiments, systems, apparatus, and
methods automatically transmit and/or display an alert or report.
For example, an alert or report may be transmitted or displayed
when resistome profiles K1:CRE:KPC:1-1, K1:CRE:KPC:1-2, and
K1:CRE:KPC:1-3 have been identified for subjects in a single
facility (including, but not limited to, an individual ICU). The
alert or report may include at least one of a resistome profile, an
infection state, a classification, a map, statistical data, and
tracking data.
[0211] In some embodiments, information indicating an outcome
(e.g., a resistome profile, infection state, or potential outbreak
classification) may be stored or output via a network or displayed
to a user. For example, information indicating a resistome profile
may be compressed, stored, transmitted, applied, and/or displayed
as one or more numbers, textual symbols, graphical images, or some
combination thereof. In some embodiments, a graphical image
includes, but is not limited to, a two-dimensional code (e.g., a QR
code), a tube graph, and an epidemiology star chart. In further
embodiments, alerts or reports as to an outcome also may be
compressed, stored, transmitted, applied, and/or displayed as one
or more numbers, textual symbols, graphical images, or some
combination thereof. In addition, alerts or reports as to an
outcome may be accompanied by audio or tactile output, depending on
the user device.
[0212] As shown in FIG. 9, a user and/or facility may communicate
over interface 918 to identify a resistome profile in database 910
that, for example, meets a parameter according to a search of
database 910, view a history of a resistome profile in database
910, analyze trends among resistome profiles in database 910,
obtain and/or transmit a resistome profile from database 910,
ascertain a prevalence of a resistome profile in database 910, and
obtain and/or transmit an indication of an active report 920 and/or
an alert 922. The report 920 and/or alert 922 may include
information indicating the potential for an outbreak at facility
914 or another facility.
[0213] FIG. 10A illustrates a non-limiting example of a graphical
representation of a resistome profile 1000 according to some
embodiments. In this example, resistome profile
E1:KPC_O48:EPN_MPN_CTD:24-3 is represented. A large green circle
1002 represents the organism identification code E1 (indicating E.
coli), the small red circle 1004 and small purple circle 1006
respectively represent the presence of KPC and OXA-48 resistance
genes while the blue square 1008, yellow square 1010 and brown
square 1012 respectively represent resistance to the antibiotics
EPN (Ertapenem), MPN (Meropenem), and CTD (Ceftazidime). The number
"3" in circle 1002 indicates three occurrences of organisms in a
known database with this pattern. The graphical display may be
further configured to display any other database information not
included in the pattern or profile uniqueness identifier.
[0214] FIG. 10B illustrates an alternative non-limiting example of
a graphical representation of a resistome profile using a QR code
1050 according to some embodiments. The QR code represents a
resistome profile for a K. pneumoniae organism with a CRE phenotype
and resistance genes VIM and CTX-M-1, that is non-susceptible to
Doripenem, Imipenem and Meropenem, and assigned a profile
uniqueness code indicating that it is Unique Profile #34 with two
other known organisms in the database with this pattern. The QR
code may also be coded to include any other database information
not included in the pattern or profile uniqueness identifier.
[0215] In some embodiments, an indication of a classification of a
population (e.g., a facility) as to a potential for infection
outbreak may be displayed using a graphical representation similar
to the non-limiting examples shown in FIGS. 10A and 10B.
[0216] In some embodiments, systems, apparatus, and/or methods
facilitate choosing a naming convention that, for example, is
consistent with a different classification system, thus reducing
the need for translation, and thereby saving memory and processing
time. In some embodiments, the codes used to generate patterns in a
first database of known patterns differ from the codes used to
generate patterns in a second database of known patterns. The codes
may differ by at least one of the organism identification code, the
phenotype code, the genotype code, and the susceptibility code. At
least one conversion table may correlate the codes for the first
database to the codes for the second database. According to some
embodiments, the systems, apparatus, and methods described herein
are configured to apply at least one conversion table to known
patterns in the first or second database in order to perform any
comparison described herein.
[0217] The ability to view additional or varied information may be
set by a user as a preference on a customized basis, or the
information may be hidden and made available based on a request or
selection from a user according to some embodiments. For example, a
display interface may be configured such that the user can make a
selection on a short form name or symbol to expand a field or open
a new window on the display that provides detailed antibiotic
resistance data or other diagnostically useful information for a
subject sample. For example, in TABLE 17, the differences in
minimum inhibitory concentration (MIC) results for two isolate
species are provided.
TABLE-US-00017 TABLE 17 Isolate No. 850707 850793 MIC Value (mg/L)
MIC Value (mg/L) Amikacin 32 32 Amoxicillin 16 16 Clavulanic Acid
Ampicillin 32 32 Cefepime 16 16 Ceftazidime 16 128 Ceftazidime 16
128 Clavulanic Colistin/TWEEN 0.12 0.12 Doripenem 32 4 Ertapenem 6
1 Imipenem 2 8 Levofloxacin 1 0.5 Meropenem 32 8 Piperacillin 64
128 Tazobactam Teicoplanin -- -- Tigecycline 2 1 Vancomycin --
--
[0218] In TABLE 18, the isolates are numbered and linked to an
isolate species (K. pneumoniae); resistome profiles including the
species (K1), phenotype (CRE), genotype (IMP and C1), and profile
uniqueness identifiers indicating sequential unique patterns
compared to an associated database (1-1 and 2-1, respectively);
Acuitas MDRO Gene Test results (IMP(A) and CTX-M(A)); and reported
genotypes listed in rank order of clinical importance (IMP-26,
CTX-M-15, and SHV-28(u), and IMP-4, CTX-M-15, SHV-1(b), and TEM,
respectively). The trailing "1s" in the assigned resistome profiles
(i.e., the second digit of each profile uniqueness identifier)
reflect the first occurrences of these patterns/profiles derived
based on data collected from subject sample measurements. In this
example, the tests are not designed to detect SHV, TEM, ACT/MIR,
CMY-2, DHA-1, ACT-16, or VEB-1.
TABLE-US-00018 TABLE 18 Isolate Acuitas MDRO No. Isolate Species
Resistome Profile Gene Test Results Reported Genotype 850707 K.
pneumoniae K1:CRE:IMP_C1:1-1 IMP(A) and IMP-26, CTX-M-15, CTX-M(A)
and SHV-28(u) 850793 K. pneumoniae K1:CRE:IMP_C1:2-1 IMP(A) and
IMP-4, CTX-M-15, CTX-M(A) SUV-1(b), and TEM
CONCLUSION
[0219] While various inventive embodiments have been described and
illustrated herein, those of ordinary skill in the art will readily
envision a variety of other means and/or structures for performing
the function and/or obtaining the results and/or one or more of the
advantages described herein, and each of such variations and/or
modifications is deemed to be within the scope of the inventive
embodiments described herein. More generally, those skilled in the
art will readily appreciate that all parameters, dimensions,
materials, and configurations described herein are meant to be
exemplary and that the actual parameters, dimensions, materials,
and/or configurations will depend upon the specific application or
applications for which the inventive teachings is/are used. Those
skilled in the art will recognize, or be able to ascertain using no
more than routine experimentation, many equivalents to the specific
inventive embodiments described herein. It is, therefore, to be
understood that the foregoing embodiments are presented by way of
example only and that, within the scope of the appended claims and
equivalents thereto, inventive embodiments may be practiced
otherwise than as specifically described and claimed. Inventive
embodiments of the present disclosure are directed to each
individual feature, system, article, material, kit, and/or method
described herein. In addition, any combination of two or more such
features, systems, articles, materials, kits, and/or methods, if
such features, systems, articles, materials, kits, and/or methods
are not mutually inconsistent, is included within the inventive
scope of the present disclosure.
[0220] The above-described embodiments may be implemented in any of
numerous ways. For example, implementations of the subject matter
described herein may be realized in digital electronic circuitry,
integrated circuitry, specially designed ASICs (application
specific integrated circuits), computer hardware, firmware,
software, and/or combinations thereof. When implemented in
software, the software code may be executed on any suitable
processor or collection of processors, whether provided in a single
computer or distributed among multiple computers.
[0221] Further, it should be appreciated that a computer may be
embodied in any of a number of forms, such as a rack-mounted
computer, a desktop computer, a laptop computer, or a tablet
computer. Additionally, a computer may be embedded in a device not
generally regarded as a computer but with suitable processing
capabilities, including a Personal Digital assistant (PDA), a smart
phone, or any other suitable portable or fixed electronic
device.
[0222] Also, a computer may have one or more input and output
devices. These devices may be used, among other things, to present
a user interface. Examples of output devices that may be used to
provide a user interface include printers or display screens, such
as CRT (cathode ray tube) or LCD (liquid crystal display) monitors,
for visual presentation of output and speakers or other sound
generating devices for audible presentation of output. Examples of
input devices that may be used for a user interface include
keyboards, and pointing devices, such as mice, touch pads, and
digitizing tablets. As another example, a computer may receive
input information through speech recognition or in other audible
format. Other kinds of devices may be used to provide for
interaction with a user as well; for example, feedback provided to
the user may be any form of sensory feedback (e.g., visual
feedback, auditory feedback, or tactile feedback); and input from
the user may be received in any form, including acoustic, speech,
or tactile input.
[0223] Such computers may be interconnected by one or more networks
in any suitable form, including a local area network or a wide area
network, such as an enterprise network, and intelligent network
(IN) or the Internet. Such networks may be based on any suitable
technology and may operate according to any suitable protocol and
may include wireless networks, wired networks or fiber optic
networks.
[0224] The subject matter described herein may be implemented in a
computing system that includes a back-end component (e.g., as a
data server), or that includes a middleware component (e.g., an
application server), or that includes a front-end component (e.g.,
a client computer having a graphical user interface or a Web
browser through which a user may interact with an implementation of
the subject matter described herein), or any combination of such
back-end, middleware, or front-end components. The components of
the system may be interconnected by any form or medium of digital
data communication (e.g., a communication network). Examples of
communication networks include a local area network ("LAN"), a wide
area network ("WAN"), and the Internet.
[0225] The computing system may include clients and servers. A
client and server are generally remote from each other and
typically interact through a communication network. The
relationship of client and server arises by virtue of computer
programs running on the respective computers and having a
client-server relationship to each other.
[0226] The various methods or processes outlined herein may be
coded as software that is executable on one or more processors that
employ any one of a variety of operating systems or platforms.
Additionally, such software may be written using any of a number of
suitable programming languages and/or programming or scripting
tools, and also may be compiled as executable machine language code
or intermediate code that is executed on a framework or virtual
machine. As used herein, "machine-readable medium" refers to any
computer program product or apparatus (e.g., a magnetic disc, an
optical disk, memory, a Programmable Logic Device (PLD)) used to
provide machine instructions and/or data to a programmable
processor, including a machine-readable medium that receives
machine instructions as a "machine-readable signal," which includes
any signal used to provide machine instructions and/or data to a
programmable processor.
[0227] Also, various inventive concepts may be embodied as one or
more methods, of which an example has been provided. The acts
performed as part of the method may be ordered in any suitable way.
Accordingly, embodiments may be constructed in which acts are
performed in an order different than illustrated, which may include
performing some acts simultaneously, even though shown as
sequential acts in illustrative embodiments.
[0228] All publications, patent applications, patents, and other
references mentioned herein are incorporated by reference in their
entirety.
* * * * *