U.S. patent application number 14/658206 was filed with the patent office on 2015-07-30 for quick method for detecting enyzmes and microorganisms.
The applicant listed for this patent is Bio-Rad Innovations. Invention is credited to Caroline DALLENNE, Christine FAVIER.
Application Number | 20150211044 14/658206 |
Document ID | / |
Family ID | 43216363 |
Filed Date | 2015-07-30 |
United States Patent
Application |
20150211044 |
Kind Code |
A1 |
DALLENNE; Caroline ; et
al. |
July 30, 2015 |
QUICK METHOD FOR DETECTING ENYZMES AND MICROORGANISMS
Abstract
The present invention concerns an in vitro method for detecting
an enzyme or a microorganism in a biological sample, comprising the
steps of: a1) concentrating the microorganisms present in the
biological sample, optionally after a a0) culture step of the
microorganisms; b1) placing in suspension the microorganisms
concentrated at step a1) in a solution containing at least one
chromogenic or fluorogenic substrate capable of releasing a
chromophore or fluorophore after hydrolysis by the enzyme to be
detected; c1) detecting potential release of the chromophore or
fluorophore obtained at step b1); the release of the chromophore or
fluorophore detected at step c1) indicating the presence of the
enzyme to be detected.
Inventors: |
DALLENNE; Caroline;
(Sainghin-en-Weppes, FR) ; FAVIER; Christine;
(Wormhout, FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Bio-Rad Innovations |
Marnes La Coquette |
|
FR |
|
|
Family ID: |
43216363 |
Appl. No.: |
14/658206 |
Filed: |
March 15, 2015 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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13582681 |
Dec 18, 2012 |
9012167 |
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PCT/FR2011/050417 |
Mar 1, 2011 |
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14658206 |
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Current U.S.
Class: |
435/30 |
Current CPC
Class: |
C12Q 1/34 20130101; C12Q
1/44 20130101; C12Q 1/04 20130101; C12Q 1/24 20130101 |
International
Class: |
C12Q 1/24 20060101
C12Q001/24 |
Foreign Application Data
Date |
Code |
Application Number |
Mar 1, 2010 |
FR |
10 5144 |
Claims
1-12. (canceled)
13. A method for the in vitro preparation of a blood culture sample
containing microorganisms, comprising the steps of: A) lysing or
agglutinating the red blood cells present in the blood culture
sample, without lysing the microorganisms present in the blood
culture sample, B) separating the microorganisms present in the
blood culture sample from the red blood cells lysed or agglutinated
at step A), and C) washing the microorganisms of the blood culture
sample separated at step B).
14. The method according to claim 13, wherein the microorganisms
are microorganisms resistant to 3rd generation cephalosporins.
15. The method according to claim 13, wherein the lysis step A)
comprises placing the blood culture sample in contact with a lysis
buffer of red blood cells for a suitable time at a suitable
temperature to allow lysis of the red blood cells.
16. The method according to claim 13, wherein the agglutination
step A) is implemented by placing the blood culture in contact with
at least one agglutinating agent.
17. The method according to claim 16, wherein the agglutinating
agent is polyethylene glycol (PEG).
18. The method according to claim 13, wherein the separation step
B) is implemented by centrifugation, filtration or removing the
aqueous phase, preferably after decantation.
19. The method according to claim 18, wherein the separation step
B) is implemented by centrifugation.
20. The method according to claim 13, wherein the washing step C)
is performed by re-suspending the separated microorganisms in a
washing buffer, incubating for a suitable time, at a suitable
temperature and further separating the microorganisms.
Description
[0001] The present invention concerns quick methods for detecting
enzymes and microorganisms.
[0002] Methods for detecting microorganisms in a clinical sample
generally comprise the following steps:
[0003] 1) Optionally treating the sample to promote bacterial
growth, the length of this step varying in relation to the type of
sample (blood, urine, stools, cerebrospinal fluid, other puncture
fluids) and in relation to the bacterial load;
[0004] 2) Seeding one or more agar growth media which may or may
not be selective;
[0005] 3) Incubating for 18 to 48 h at 37.degree. C.;
[0006] 4) Observing the different types of colonies obtained (size,
appearance, colour . . . );
[0007] 5) Collecting one or more isolates of each type of
colony;
[0008] 6) Actual identification, if necessary using an automated
system or an identification gallery;
[0009] 7) Obtaining an antibiogram in parallel which requires a
minimum time of 16 h, or obtaining an antibiogram consecutively
which requires an additional time of 18 h to determine the profile
of the microorganism with respect to antibiotics and/or
antifungals.
[0010] The diagnosis of an infection by microorganisms is therefore
generally long, the time notably depending on the type of sample to
be analysed. This waiting time is particularly problematic if the
sample to be analysed is a blood sample. If it is sought to
identify the presence of microorganisms in blood, the first
treatment step of the sample by blood culture which allows the
detection threshold of the microorganisms to be reached, may take
up to 7 days. The duration of this first treatment step cannot be
reduced since it is dependent on automated systems. On the
slightest sign of culture positivity, Gram staining is performed on
a sample taken by aseptic puncture of the film using a sterile
syringe. This direct examination will allow recognition of the
morphology of the bacterial agent present in the bottle which may
guide towards identification of the germ. The information is then
immediately transmitted to the clinician since it may allow the
start of an antibiotic treatment that has not yet been initiated or
the correction of probabilistic antibiotherapy. Nevertheless, no
precise characterization of the microorganism under consideration
is possible at this level, and even less so a profile of particular
resistance. It is therefore particularly useful to be subsequently
able to identify rapidly the microorganisms present in the
biological sample together with their possible resistance
phenotypes so as to initiate or rectify antibiotic treatment.
[0011] Different types of microorganisms can be present in positive
blood cultures. It is a fact that staphylococci (not only
Staphylococcus aureus but also negative coagulase staphylococci)
are regularly found. Gram-negative bacilli especially Escherichia
coli (and more generally enterobacteriaceae), anaerobic bacteria of
the colon, members of the groups Klebsiella/Enterobacter,
Pseudomonas aeruginosa, Proteus spp and Providencia spp, have been
detected for example after traumatic injury or after surgery on an
already contaminated body region. The detection of salmonella in
the blood of individuals suffering from systemic salmonellosis is
not unusual. Numerous other microbial genii have been found in
cultures of blood samples such as streptococci, enterococci,
Brucella, Pasteurella, pneumococci, Neisseria, Listeria,
Clostridium, corynebacteria, Bacteroids, bacteria in the hacek
group but also yeasts and parasites.
[0012] Different techniques are used for precise identification of
these microorganisms and their possible resistance phenotypes, but
the results are generally only obtained after a relatively long
period.
[0013] Samples are coated on a medium containing fresh blood and
chocolate blood agar to which other media may be added depending on
the results of microscopy examinations.
[0014] For each positive bottle, the following are carried out:
[0015] determining the morphology of the colonies, [0016] oxidase
and catalase testing, [0017] biochemical and antigenic
identification to identify the microorganism, [0018] susceptibility
tests, evaluation of Minimum Inhibitory Concentrations (MIC).
[0019] It has been shown that it is possible to obtain an
antibiogram directly from a positive blood culture using an
inoculum equivalent to 0.5 McF from the blood culture broth. A
Mueller-Hinton agar is inoculated using the
<<flooding>> technique. The correlation with the
standard antibiogram is apparently found in 95% of cases. The
result appears no earlier than 16 h after evidencing of the
positive blood culture (Antibiotics In Laboratory Medicine, Victor
Lorian, M.D. Editor, 5.sup.th Edition; Doern et al., 1981,
Antimicrob Agents Chemother. 20(5): 696-698. Antimicrobial
Agents).
[0020] There is therefore a major need for new, more rapid methods
for detecting microorganisms, and/or their possible associated
resistances, in a biological sample, these methods having to
maintain satisfactory susceptibility and specificity.
[0021] .beta.-lactams represent the largest family of antibiotics
on account of the large number of molecules belonging thereto, and
on account of their associated pharmacological properties and
spectra which allow the combating of most bacterial species.
.beta.-lactams are rightly the antibiotics that are the most
prescribed in general medicine. Their spectrum of activity varies
as a function of their class (penicillins or cephalosporins) and at
times as a function of the molecules in each class. For example,
the G and V penicillins are rather more active on Gram-positive
cocci and anaerobic bacteria, whilst the spectrum of
aminopenicillins extends to a few Gram-negative bacilli. The
addition of a .beta.-lactamase inhibitor also leads to observing
activity on some bacteria producing these .beta.-lactamases.
Cephalosporins further extend the spectrum of activity to
Gram-negative bacilli but are a little less active on Gram-positive
cocci.
[0022] Among the .beta.-lactams, cephalosporins account for the
category of antibiotics that is most often prescribed. The frequent
use of cephalosporins has led to the spreading of strains resistant
to these molecules. These strains in particular manage to survive
the pressure of cephalosporin selection through .beta.-lactamase
activity. The detection of combined resistances against 1.sup.st,
2.sup.nd and 3.sup.rd generation (C3G) cephalosporins in
Enterobacteriaceae is becoming of major therapeutic importance. The
increasing resistance of Enterobacteriaceae to antibiotics is of
world concern with an increasing impact of extended spectrum
.beta.-lactamases (ESBLs), spreading in the community in
particular. In 2002, less than 1% of Enterobacteriaceae strains
produced an ESBL. In 2006, they represented 1 to 5% of strains.
[0023] The resistance to C3Gs whether due to ESBLs or to other
.beta.-lactamases (cephalosporinase or carbapenemase) is therefore
on the increase and has become significant in particular for
Escherichia coli and Klebsiella pneumoniae. The emergence of these
enzymes has recently been reported in non-fermenting Gram-negative
bacilli such as Acinetobacter baumannii, Pseudomonas aeruginosa and
Stenotrophomonas maltophilia. It is therefore of increasingly
greater importance to be able to detect these ESBLs.
[0024] The detection of ESBLs in Enterobacteriaceae is simple to
perform in most cases; it is implemented by synergy between a
mixture of [amoxicillin+clavulanic acid (AMC)] and a C3G
(ceftazidime is the most susceptible) or aztreonam. Nonetheless,
obtaining a result requires much time. The synergy test is
performed by arranging discs of AMC and the chosen C3G (or
aztreonam) at a distance of 30 mm away from each other, centre to
centre. The detection of ESBLs on the other hand is more difficult
for strains which are also hyper-productive of cephalosporinase
(AmpC) such as Enterobacter. In this latter case, it is easier to
visualize the synergy between AMC and cefepime or cefpirome.
Finally, in some species such as Proteus mirabilis, Proteus
vulgaris, Proteus penneri, Morganella morganii, Providencia
stuartii and Providencia rettgeri, ESBLs are weakly expressed and
are therefore even more difficult to detect. In these cases, the
synergy test is optimized by placing the discs at a distance of
40-45 mm, instead of 30 mm, following CA-SFM recommendations
(Comite de l'antibiogramme de la Societe francaise de
microbiologie) in 2007. Automated bacteriological systems for
identification and antibiograms are increasingly more used
(Mini-Api.RTM. marketed by bioMerieux Clinical Diagnostics,
Phoenix.RTM. marketed by BD Diagnostics, MicroScan.RTM. marketed by
Siemens, Vitek.RTM., Vitek-2.RTM. and Vitek Compact.RTM. marketed
by bioMerieux). In general, these automated systems detect ESBLs
relatively well in strains which do not usually hyper-produce
cephalosporinases (E. coli, K. pneumoniae, K. oxytoca). For the
other species (Enterobacter, Citrobacter, Serratia, etc.), their
susceptibility and especially their specificity are not quite as
good as those of manual methods. Additional tests prove to be
necessary.
[0025] The detection of strains resistant to C3Gs may therefore be
easy for some resistances related to some species, but in general
no procedure has 100% sensitivity or allows a rapid result to be
obtained.
[0026] Numerous improvements have been proposed to accelerate the
process of detecting and identifying microorganisms present in
blood cultures in particular. First, the improvements in culture
media and growth techniques have reduced culture times. The latest
generation of automated machines even allows the detection of small
bacterial growth. Independently of conventional techniques, when
growth is detected by an automated system, it is also possible to
perform direct identification of bacteria by molecular biology
(amplification and sequencing, FISH, DNA chips or specific probes .
. . ). Nonetheless, most of these systems are usually not open
systems and only allow the detection of one or of a small number of
specific microorganisms. In addition, they possibly may not provide
information on susceptibility or presumed resistance against an
antibiotic. Also, these methods are efficient but expensive and/or
require highly qualified laboratory technicians.
[0027] Attempts to accelerate more specific detection of
microorganisms resistant to a family of antibiotics have been
described. For example, Weinbren and Borthwick (Weinbren and
Borthwick, 2005, J. Antimicrob. Chemother. 55:131-132) have
described a method for the non-chromogenic detection of
ESBL-producing microorganisms, in a blood culture whereby a sample
of blood culture is taken and transferred onto an agar medium,
discs of cefpodoxime and cefpodoxime-clavulanate then being applied
to the medium. Nevertheless, this culture step on an agar medium
requires an additional minimum time wait of 3.5 h to 6 h before it
is possible to obtain initial results after the completion of blood
culture treatment.
[0028] Navon-Venezia et al. (Navon-Venezia et al., 2005, J. Clin.
Microb. 43:439-441) have described a method for detecting
ESBL-producing bacteria from positive blood cultures consisting of
taking a sample of blood culture broth and seeding it directly onto
a Mueller-Hinton medium containing discs of cefpodoxime and
cefpodoxime+clavulanate, without including an isolation step on
agar medium. No chromogenic agent is used in this method which
necessitates a culture step of 16 h to 18 h following the
recommendations of the American reference work CLSI/NCCLS (Clinical
and Laboratory Standards Institute/National Committee on Clinical
Laboratory Standards).
[0029] Chapin and Musgnug (2003) (Chapin and Musgnug, 2003, J. Clin
Microb. 41:4751-4754) have described a direct method for testing
susceptibility to antimicrobials on positive blood cultures
consisting of centrifuging 10 ml of inoculated blood culture in a
serum separating tube containing a gel. The microorganisms
remaining on the surface of the gel are then collected and replaced
in suspension to inoculate microplates containing different
dilutions of specific antibiotics. The result is only obtained
however 18 to 24 h after inoculation.
[0030] Chen et al. (2008) (Chen et al., 2008, J. Microbiol.
Immunol. Infect. 41:259-264) have described a method for
identifying the susceptibility of microorganisms to a group of
antibiotics using positive blood cultures which entails taking a
sample of positive blood culture, removing the red blood cells by
lysis and centrifugation, placing in suspension the bacterial
residue in a saline solution and testing using a Vitek-2.RTM.
system or AST (antimicrobial susceptibility testing). It is
nevertheless necessary to wait between 2 h30 and 16 h15 after
loading the Vitek-2.RTM. or AST system before it is possible to
observe initial results.
[0031] The team Jain et al. (Jain et al., 2007, J. Antimicrob.
Chemother. 60:652-654) has also described a relatively rapid method
for detecting extended spectrum .beta.-lactamases (ESBLs) by colour
change of a supernatant of blood culture broth after
centrifugation. On account of haemolysis problems interfering with
the change in colour of the chromogenic agent, the authors proposed
the prior conducting of a sub-culture in a fresh medium, thereby
lengthening the time of the test method.
[0032] These techniques whereby resistant microorganisms are
detected after a sub-culture step therefore remain relatively
lengthy techniques.
[0033] The inventors have developed a method for quicker detection
allowing the detection of specific resistance phenotypes such as
those conferred on Gram-negative bacteria against 3.sup.rd
generation cephalosporins, that is performed directly on the
clinical sample or after a sub-culture step but without including
an isolate selection step on agar medium, and using a chromogenic
or fluorogenic substrate.
[0034] The present invention concerns an in vitro detection method
for detecting an enzyme of a microorganism from a biological
sample, comprising the steps of:
[0035] a1) concentrating the microorganisms present in the
biological sample, optionally after a a0) culture step of the
microorganisms;
[0036] b1) placing in suspension the microorganisms concentrated at
step a1) in a solution containing at least one chromogenic of
fluorogenic substrate capable of releasing a chromophore or
fluorophore after hydrolysis by the enzyme to be detected;
[0037] c1) detecting potential release of the chromophore or
fluorophore obtained at step b1);
[0038] the release of the chromophore or fluorophore detected a
step c1) indicating the presence of the enzyme to be detected.
[0039] The present invention also concerns a method for the in
vitro preparation of a blood culture sample containing
microorganisms, comprising the steps of:
[0040] A) lysing or agglutinating the red blood cells present in
the blood culture sample without lysing the microorganisms present
in the blood culture sample,
[0041] B) separating the microorganisms present in the blood
culture sample from the red blood cells lysed or agglutinated at
step A), and
[0042] C) optionally washing the microorganisms of the blood
culture sample separated at step B).
[0043] The present invention additionally concerns an in vitro
detection method for detecting microorganisms in a biological
sample using the above enzyme detection method.
DETAILED DESCRIPTION OF THE INVENTION
[0044] Within the context of the invention a <<biological
sample>> refers to a substance of biological origin.
Preferably, the biological sample is a sample of biological fluid.
Examples of biological samples include but are not limited to
blood, and the components thereof, urine, stools, cerebrospinal
fluid or other puncture fluids. Preferably, the biological sample
of the invention is selected from the group formed by a blood
sample and a urine sample.
Enzymes
[0045] Within the context of the invention, the expression
<<enzyme of a microorganism>> refers to a macromolecule
of protein type expressed by a microorganism and which is
characterized by its catalytic activity governing specific
biochemical reactions inside the microorganism or outside the
microorganism when this enzyme is secreted by the
microorganism.
[0046] Preferably the enzyme of the invention is chosen from the
group formed by glycosidases, esterases, phosphatases,
.beta.-lactamases, in particular penicillinases, cephalosporinases,
carbenicillinases, oxacillinases, carbapenemases,
metallo-.beta.-lactamases and extended spectrum .beta.-lactamases.
More preferably, the enzyme of the invention is chosen from the
group formed by extended spectrum .beta.-lactamases,
cephalosporinases, carbapenemases, glycosidases and esterases.
Further preferably, the enzyme of the invention is chosen from the
group formed by extended spectrum .beta.-lactamases,
cephalosporinases and carbapenemases. Preferably, the enzyme is an
enzyme capable of hydrolysing 3rd generation cephalosporins.
[0047] By "glycosidase" is meant herein an enzyme from the group of
hydrolases acting on the glycosidic bond of oligosides and
glycosides. As is well known to persons skilled in the art, the
specificity of a glycosidase is a function of the type of sugar
linked by a glycosidic bond. Under the nomenclature of enzymes,
glycosidases belong to class 3 (corresponding to hydrolases),
sub-class 2 (code EC3.2). Glycosidases particularly comprise
glucosidases, xylanases, galactosidases, lactases, amylases,
chitinases, fructosidases, maltases, neuraminidases, invertases,
hyaluronidases and lysozymes.
[0048] More particularly, glycosidases are chosen from the group
formed by N-acetyl-.beta.-galactosaminidase,
N-acetyl-.beta.-glucosaminidase, .alpha.-amylase,
.alpha.-arabinofuranosidase, .alpha.-arabinosidase,
.beta.-cellobiosidase, .beta.-chitobiosidase, .alpha.-fucosidase,
.beta.-fucosidase, .alpha.-galactosidase, .beta.-galactosidase,
.alpha.-glucosidase, .beta.-glucosidase, .beta.-glucuronidase,
.alpha.-maltosidase, .beta.-maltosidase, .alpha.-mannosidase,
.beta.-mannosidase and .beta.-xylosidase.
[0049] By "esterase" is meant herein an enzyme from the group of
hydrolases splitting esters into an acid and an alcohol. As is well
known to persons skilled in the art, esterases differ according to
their substrate specificity, their protein structure and their
biological function. Under the nomenclature of enzymes, esterases
belong to class 3 (corresponding to hydrolases), sub-class 1 (code
EC3.1). Esterases particularly comprise triphosphoric monoester
hydrolases, sulfatases, diphosphoric monoester hydrolases,
phosphoric triester hydrolases, exodeoxyribonucleases,
exoribonucleases, exonucleases, deoxyribonucleases, ribonucleases,
endodeoxyribonucleases and endoribonucleases.
[0050] By "phosphatase" is meant herein an enzyme removing a
phosphate group from a simple molecule or from a biological
macromolecule, by hydrolysing the monoesters of phosphoric acid to
a phosphate ion and a molecule having a free hydroxyl group. Under
the nomenclature of enzymes, phosphatases belong to class 3
(corresponding to the hydrolases), sub-class 1.3 (code EC3.1.3). As
is well known to persons skilled in the art, phosphatases differ
according to their substrate specificity. Phosphatases particularly
comprise tyrosine phosphatases, serine/threonine phosphatases,
phosphatases having double specificity, histidine phosphatases and
lipid phosphatases.
[0051] By ".beta.-lactamase" is meant herein an enzyme which
hydrolyses .beta.-lactams breaking open the .beta.-lactam ring with
the production of inactive derivatives. .beta.-lactamases are
generally secreted within the outer medium in Gram-positive
bacteria, and within the periplasmic space in Gram-negative
bacteria. They group together inter alia cephalosporinases,
extended spectrum .beta.-lactamases and carbapenemases.
.beta.-lactamases are divided into two main classifications: [0052]
the Bush classification determined in 1989, and updated in 1995 and
again in 2009, classifies .beta.-lactamases in relation to their
preferred substrate from among penicillin, oxacillin,
carbenicillin, cefaloridine, cefotaxime and imipenem, and in
relation to their susceptibility to clavulanic acid, a
.beta.-lactamase inhibitor; [0053] the Ambler classification
proposed in 1980 is based on the protein sequence of
.beta.-lactamases. It is broken down into four classes of enzymes:
A, B, C and D. The .beta.-lactamases in classes A, C and D have a
serine at the active site which forms a transient covalent bond
with .beta.-lactam, leading to opening of the .beta.-lactam ring.
These .beta.-lactamases are also called serine .beta.-lactamases.
Class B groups together metallo-enzymes requiring a zinc ion to
hydrolyse the .beta.-lactam ring.
[0054] .beta.-lactamases are numerous and diversified in relation
to the properties thereof. They are responsible for resistance to
.beta.-lactams such as penicillins, cephalosporins, monobactams,
cephamycins, and carbapenems. They inactivate these antibiotics via
hydrolysis of the .beta.-lactam ring. Among the .beta.-lactamases,
.beta.-lactamase TEM-1 is most widespread in the different
bacterial species. It hydrolyses penicillins most efficiently, but
not 3.sup.rd generation cephalosporins, and it is susceptible to
inhibition by clavulanic acid. Bacteria producing .beta.-lactamases
in this category can therefore easily be treated with 3.sup.rd
generation cephalosporins (C3G). On the other hand, ESBLs, some
cephalosporinases and carbapenemases, when produced by bacteria,
make them resistant to 3.sup.rd generation cephalosporins
(C3GR).
[0055] The amino acid sequences of .beta.-lactamases are very close
to each other within one same family. The substitution of a small
number of amino acids was therefore sufficient to enable
.beta.-lactamases of type TEM-1, initially inactive, to hydrolyse
cephalosporins (.beta.-lactamases of ESBL type for example), or to
become resistant to the inhibitors.
[0056] Table 1 below describes the properties of the different
types of .beta.-lactamases, in particular of cephalosporinases,
extended spectrum .beta.-lactamases and carbapenemases.
TABLE-US-00001 TABLE 1 A summary, non-exhaustive table describing
the properties of major .beta.-lactamases conferring (C3GR) or not
conferring C3G resistance Inhibited by Molecular class Examples
clavulanate (Ambler) C3GR broad spectrum .beta.- TEM-1, TEM-2,
SHV-1 +++ A No lactamase (penicillinases) OXA (OXA-1) family + D No
extended spectrum TEM, SHV, CTX-M families ++++ A Yes
.beta.-lactamase (ESBL) OXA (OXA-11, -14, -15, -16, -17) + D Yes
family cephalosporinases Chromosomics 0 C No or AmpC Hyper-produced
Plasmidic: 0 C Yes ACC-1; CMY family, DHA-1 carbapenemases IMP, VIM
families 0 B Yes (metallo-.beta.-lactamases) KPC family +++ A Yes
OXA (OXA 23-27, + D Yes OXA-40, OXA-48) family
Microorganisms
[0057] By "microorganism" is meant herein a living organism having
an eukaryote or prokaryote cell structure, or which is akaryotic,
and is characterized in that it is unicellular, microscopic or
ultramicrosopic in size and having metabolic and reproductive
potential. The microorganisms of the invention particularly
comprise bacteria in particular Gram-negative bacteria and
Gram-positive bacteria, and fungi in particular yeasts (e.g. of
Candida genus). More specifically, they may be a bacterium chosen
from the group formed by: [0058] Enterobacteriaceae such as strains
of genus Klebsiella, in particular Klebsiella pneumoniae and
Klebsiella oxytoca; the strains of genus Escherichia, in particular
Escherichia coli; the strains of genus Enterobacter, in particular
Enterobacter cloacae, Enterobacter asburiae and Enterobacter
aerogenes; the strains of genus Citrobacter, in particular
Citrobacter freundii and Citrobacter koseri; the strains of genus
Proteus, in particular Proteus mirabilis, Proteus vulgaris and
Proteus rettgeri; the strains of genus Serratia, in particular
Serratia marcescens; the strains of genus Salmonella, the strains
of genus Providencia, the strains of genus Shigella and the strains
of genus Kluyvera, Morganella morganii and Hafnia alvei; [0059]
non-fermenting Gram-negative bacilli such as the strains of genus
Acinetobacter, in particular Acinetobacter baumannii; the strains
of genus Pseudomonas, in particular Pseudomonas aeruginosa, the
strains of genus Stenotrophomonas, and the strains of genus
Burkholderia; [0060] anaerobic Gram-negative bacteria such as
Bacteroides fragilis; [0061] Gram-negative coccobacilli or cocci
such as Haemophilus influenzae, Bordetella and Neisseria spp;
[0062] Gram-positive bacilli or cocci such as the strains of genus
Lactobacillus; the strains of genus Enterococcus; the strains of
genus Streptococcus; the strains of genus Staphylococcus, in
particular the strains of Staphylococcus aureus whether or not
resistant to meticillin; the strains of genus Listeria; and the
strains of genus Clostridium.
[0063] Preferably, the microorganisms of the invention are chosen
from the group formed by microorganisms carrying or which may
acquire resistance to 3.sup.rd generation cephalosporins. In
particular, the microorganisms of the invention are chosen from the
group formed by Klebsiella pneumoniae, Escherichia coli, Proteus
mirabilis, Proteus rettgeri, Proteus vulgaris, Enterobacter
cloacae, Enterobacter aerogenes, Klebsiella oxytoca, Salmonella
spp., Pseudomonas aeruginosa, Acinetobacter baumannii,
Stenotrophomonas maltophilia, Serratia marcescens, Citrobacter
freundii, Citrobacter koseri, Morganella morganii, and Providencia
sp.
[0064] Further preferably, the microorganisms of the invention are
microorganisms resistant to 3.sup.rd generation cephalosporins.
[0065] Preferably, when the microorganism of the invention is
resistant to 3.sup.rd generation cephalosporins, and hence in
general is also resistant to 1.sup.st and 2.sup.nd generation
cephalosporins, and to penicillins, the enzyme such as defined
above is chosen from the group formed by extended spectrum
.beta.-lactamases, cephalosporinases and carbapenemases.
[0066] Preferably, when the microorganism of the invention is
resistant to 3.sup.rd generation cephalosporins, the enzyme is
capable of hydrolysing the 3.sup.rd generation cephalosporins. Most
preferably, when the microorganism of the invention is resistant to
3.sup.rd generation cephalosporins, the enzyme of the invention is
an extended spectrum .beta.-lactamase.
[0067] Within the context of the invention, the expression
"microorganism resistant to 3.sup.rd generation cephalosporins"
refers to microorganisms which, through the specific activity of
their .beta.-lactamase(s), continue to proliferate and/or do not
die when cultured in the presence of a conventional inhibiting
concentration of 3.sup.rd generation cephalosporins.
[0068] Preferably, the "microorganisms resistant to 3.sup.rd
generation cephalosporins" according to the present invention are
chosen from the group formed by Klebsiella pneumoniae, Escherichia
coli, Proteus mirabilis, Enterobacter cloacae, Enterobacter
aerogenes, Klebsiella oxytoca, Salmonella spp., Pseudomonas
aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia,
Proteus rettgeri, Proteus vulgaris, Serratia marcescens,
Citrobacter freundii, Citrobacter koseri, Morganella morganii and
Providentia sp.
Chromogenic or Fluorogenic Substrate
[0069] Within the context of the invention the expression
"chromogenic substrate" refers to a molecule which can be split or
modified by an enzyme and which comprises or is coupled to a
chromophore.
[0070] By "chromophore" is meant herein a group of atoms within a
molecule which is responsible for the light absorption and/or
emission properties in the ultraviolet, visible or infrared range
of this molecule. These properties result from the capacity to
absorb the energy of photons over a range of the visible spectrum
whilst the other wavelengths are transmitted or scattered.
[0071] The chromogenic substrate according to the invention can be
coloured or colourless. This chromogenic substrate releases its
chromophore under the action of a specific enzyme.
[0072] Within the context of the invention, the expression
"fluorogenic substrate" refers to a molecule which can be split or
modified by an enzyme and which comprises or is coupled to a
fluorophore. This fluorogenic substrate releases its fluorophore
under the action of a specific enzyme.
[0073] By "fluorophore" is meant herein a group of atoms within a
molecule which is responsible for the capability of this molecule
to emit fluorescence light after excitation. They are generally
substances composed of several conjugated aromatic rings, or they
are planar or cyclic molecules having one or more .pi. bonds.
[0074] Chromophores or fluorophores are well known to those skilled
in the art and have routinely been used in laboratories for many
years (see for example Vinazzer (1975) Haemostasis 4:101-9, Manafi
(2000) Int. J. Food Microbiol. 60:205-218, Orenga et al. (2009) J.
Microbiol. Methods 79:139-155).
[0075] The chromophore may correspond for example to a derivative
of indoxyl (for example 3-indolyl-R, 5-bromo-3-indolyl-R,
5-bromo-4-chloro-3-indoxyl, 5-bromo-6-chloro-3-indoxyl or
6-chloro-3-indoxyl), to a derivative of indol (for example
7-amido-5-bromoindole), to nitrophenol or a derivative thereof (for
example paranitrophenol, orthonitrophenol or orthofluorophenol), to
chlorophenol or a derivative thereof (for example
4-amino-2,6-dichlorophenol), to naphthol or a derivative thereof
(for example 1-naphthol or 2-naphtylamide), to
5-(4-hydroxy-3-methoxyphenylmethylene)-2-thioxothiazolidin-4-one-3-ethano-
ate, 3,4-cyclohexenoesculetine, 2-alizarine or
7-amido-1-pentyl-phenoxazin-3-one.
[0076] The fluorophore may correspond for example to coumarin or a
derivative thereof (e.g. hydroxycoumarin, laminocoumarin,
7-amido-4-methylcoumarin, methoxycoumarin,
7-nitrocoumarin-3-carboxylic acid, phycoerythrin, fluorescein or a
derivative thereof (e.g. 5-dodecanoylaminofluorescein),
4-methyl-umbelliferyl, resofurin, rhodamine, allophycocyanine,
2-(5'-chloro-2'-hydroxyphenyl)-6-chloro-4-(3H)-quinazolinone.
[0077] Within the context of the invention, the expression
"chromogenic or fluorogenic substrate able to release a chromophore
or fluorophore after hydrolysis by the enzyme to be detected"
refers to a chromogenic or fluorogenic substrate such as defined
above which, when contacted with the enzyme to which it is
specific, releases the chromophore or fluorophore that it contains
or to which it is coupled.
[0078] The release of the chromophore or fluorophore may be due
directly or indirectly to hydrolysis of the substrate by the enzyme
to be detected. For example the enzyme to be detected may hydrolyse
the bond linking the substrate to the chromophore or fluorophore,
thereby releasing the chromophore or fluorophore from the
substrate. This direct action of the enzyme is typically observed
with substrates coupled to a chromophore or fluorophore. The enzyme
to be detected may also hydrolyse a domain of the substrate not
involving the chromophore or fluorophore.
[0079] Therefore, detection of the release of the chromophore or
fluorophore from the chromogenic or fluorogenic substrate of the
invention indicates that this substrate has been hydrolysed by a
specific enzyme.
[0080] Preferably, the release of the chromophore or fluorophore
leads to a change in colour of the chromogenic substrate or to the
emission of fluorescence by the fluorogenic substrate. As a result,
the detection of the release of the chromophore or fluorophore may
in particular be carried out by observing the change in colour of
the chromogenic substrate or the emission of fluorescence by the
fluorogenic substrate.
[0081] Preferably the chromogenic or fluorogenic substrate of the
invention is a substrate or a derivative of a substrate of an
enzyme such as defined above. In particular, a chromogenic or
fluorogenic substrate according to the invention is a substrate or
a derivative of a substrate of an enzyme chosen from the group
formed by glycosidases, esterases, phosphatases, .beta.-lactamases,
in particular penicillinases, cephalosporinases, carbenicillinases,
oxacillinases, carbapenemases including the
metallo-.beta.-lactamases, and extended spectrum .beta.-lactamases.
More particularly, a chromogenic or fluorogenic substrate according
to the invention is a substrate or a derivative of a substrate of
an enzyme chosen from the group formed by cephalosporinases,
carbapenemases including the metallo-.beta.-lactamases, and
extended spectrum .beta.-lactamases.
[0082] By "derivative of a substrate of an enzyme" is meant herein
a compound derived from a substrate of an enzyme, capable of being
hydrolysed by the same enzymes as the substrate from which it was
produced. Preferably, a derivative of a substrate of an enzyme
according to the invention is a substrate that is modified so as to
contain or to be coupled to a chromophore or fluorophore.
[0083] Enzyme-specific substrates are well known to those skilled
in the art. Examples of glycosidase substrates therefore comprise
glycosides, uronic acids, amino sugars and acetylated sugars.
Examples of esterase substrates particularly comprise butyrates,
palmitates, stearates, oleates, laurates and caprylates. Examples
of phosphatase substrates particularly comprise phosphate esters of
alkyl alcohol, aryl phosphate esters, arylalkyl phosphate esters,
enol phosphates, aryl phosphates, diaryl phosphates, inorganic
pyrophosphate, organic pyrophosphate, phosphamides and thioesters.
Examples of penicillinase substrates comprise penicillins and
nitrocefin. Cephalosporinase substrates for example comprise
nitrocefin, penicillins, 1.sup.st generation cephalosporins and
some 2.sup.nd generation and 3.sup.rd generation cephalosporins
(such as the 3.sup.rd generation cephalosporins defined below).
Examples of carbenicillinase substrates include nitrocefin,
carbenicillins, penicillins and cloxacillins. Examples of
oxacillinase substrates included nitrocefin, cloxacillins,
penicillins and carbenicillins. Examples of carbapenemases include
penicillins, cephalosporins, carbapenemes and nitrocefin. Examples
of metallo-.beta.-lactamase substrates particularly comprise
nitrocefin, penicillins, cephalosporins and carbapenemes. Examples
of extended spectrum .beta.-lactamase substrates include
nitrocefin, penicillins and cephalosporins, in particular 3.sup.rd
generation cephalosporins such as defined below.
[0084] In one preferred embodiment, when the enzyme to be detected
is chosen from the group formed by extended spectrum
.beta.-lactamases, cephalosporinases and carbapenemases, the
chromogenic or fluorogenic substrate comprises a .beta.-lactam
ring.
[0085] By ".beta.-lactam ring" is meant herein a cyclic
heteroatomic structure consisting of three carbon atoms and one
nitrogen atom. Preferably the .beta.-lactam ring of the chromogenic
or fluorogenic substrate of the invention is hydrolysed by the
enzyme to be detected.
[0086] Further advantageously when the enzyme to be detected is
chosen from the group formed by extended spectrum
.beta.-lactamases, cephalosporinases and carbapenemases, the
chromogenic or fluorogenic substrate of the invention is a
derivative of .beta.-lactam.
[0087] Par ".beta.-lactam" is meant herein an antibiotic containing
a 3-lactam ring in its molecular structure. As is well known to
those skilled in the art, .beta.-lactams encompass for example
derivatives of penicillin, cephalosporins, monobactams and
carbapenemes.
[0088] Further preferably, when the enzyme to be detected is chosen
from the group formed by extended spectrum .beta.-lactamases,
cephalosporinases and carbapenemases, the chromogenic or
fluorogenic substrate of the invention is a derivative of
cephalosporin.
[0089] By "derivative of cephalosporin" is meant herein a molecule
composed firstly of a group derived from a cephalosporin, or part
of a cephalosporin, capable of being hydrolysed by a
.beta.-lactamase, and secondly of a chromophore of fluorophore
group. Preferably the derivative of cephalosporin according to the
invention is a cephalosporin modified so as to contain or be
coupled to a chromophore.
[0090] Cephalosporins are usually classified into cephalosporins of
first, second, third or fourth generation based on their spectrum
of activity and their greater or lesser resistance or stability
against .beta.-lactamases. This classification is well known to
persons skilled in the art (see for example Thompson (1987) Mayo
Clin Proc. 62:821-34; Gustaferro and Steckelberg (1991) Mayo Clin
Proc. 66:1064-73; and Barber et al. (2004) Adv Biochem Eng
Biotechnol. 88:179-215). Examples of 1.sup.st generation
cephalosporins particularly include cephazolin, cephalothin,
cephapirin, cephaloridin, cephalexin Keforal.RTM., cephradine
Zeefra.RTM. and cefadroxil Oracefal.RTM.. Examples of 2.sup.nd
generation cephalosporins include inter alia cefamandole,
cefuroxime Zinnat.RTM., cefonicide, ceforanide, cefatrizine,
cefotiam, cefprozil, loracarbef, cefotetan, cefotixin and cefaclor
Alfatil.RTM.. Examples of 4.sup.th generation cephalosporins
particularly include cefepime and cefpirome.
[0091] Most preferably, the chromogenic or fluorogenic substrate of
the invention is a derivative of a 3.sup.rd generation
cephalosporin.
[0092] By "derivative of a 3.sup.rd generation cephalosporin" is
meant herein a derivative of cephalosporin such as defined above
capable of being hydrolysed by the same enzymes as the 3.sup.rd
generation cephalosporins. Preferably, a derivative of a 3.sup.rd
generation cephalosporin according to the invention is a 3.sup.rd
generation cephalosporin, or part of a 3.sup.rd generation
cephalosporin, modified so as to contain or to be coupled to a
chromophore or a fluorophore. More preferably, the derivative of a
3.sup.rd generation cephalosporin of the invention is a 3.sup.rd
generation cephalosporin or part of a 3.sup.rd generation
cephalosporin modified so as to contain or to be coupled to a
chromophore.
[0093] The 3.sup.rd generation cephalosporins generally include the
compounds in particular whose English names are the following:
Cefcapene (CAS Reference: 135889-00-8), Cefcapene Pivoxil (CAS
Reference: 105889-45-0), Cefcapene Pivoxil Hydrochloride (CAS
Reference: 147816-23-7), Cefcapene Pivoxil Hydrochloride
Monohydrate (CAS Reference: 147816-24-8), Cefdaloxime (CAS
Reference: 80195-36-4), Cefdaloxime Pivoxil, Cefdinir (CAS
Reference: 91832-40-5), Cefditoren (CAS Reference: 104146-53-4),
Cefditoren Sodium (CAS Reference: 104146-53-4), Cefditoren Pivoxil
(CAS Reference: 117467-28-4), Cefetamet Pivoxil Hydrochloride,
Cefetamet Pivoxyl (CAS Reference: 65243-33-6), Cefetamet (CAS
Reference: 65052-63-3), Cefixime (CAS Reference: 79350-37-1),
Cefixime Trihydrate, Cefmenoxime Hydrochloride (CAS Reference:
75738-58-8), Cefmenoxime (CAS Reference: 65085-01-0), Cefodizime
Sodium (CAS Reference: 86329-79-5), Cefodizime (CAS Reference:
69739-16-8), Cefoperazone Sodium (CAS Reference: 62893-20-3),
Cefoperazone A, Cefoperazone (CAS Reference: 62893-19-0),
Cefotaxime Sodium (CAS Reference: 64485-93-4), Cefotaxime S-oxide,
Cefotaxime (CAS Reference: 63527-52-6), Benzathine Cefotaxime,
Desacetylcefotaxime, Cefpimizole Sodium, Cefpimizole, Cefpiramide
Sodium (CA Reference: 74849-93-7), Cefpiramide (CAS Reference:
70797-11-4), Cefpodoxime Proxetil (CAS Reference: 87239-81-4),
Cefpodoxime (CAS Reference: 80210-62-4), Cefpodoxime Hydrate,
Cefsulodin Sodium, Cefsulodin, Ceftazidime Pentahydrate (CAS
Reference: 78439-06-2), Ceftazidime (CAS Reference: 72558-82-8),
Cefteram, Cefteram Pivaloyloxymethyl Ester, Ceftibuten,
Trans-ceftibuten, Ceftiofur, Ceftiofur Sodium (CAS Reference:
80370-57-6), Ceftiofur Hydrochloride, Ceftiofur Sodium,
Desfuroylceftiofur, Ceftiolene, Ceftizoxime Alapivoxil, Ceftizoxime
Sodium, Ceftizoxime, Ceftriaxone Disodium (CAS Reference:
74578-69-1), Ceftriaxone Sodium, Ceftriaxone (CAS Reference:
73384-59-5) and the salts of these compounds. The structure and
IUPAC name of these compounds can be found for example on the
website chemicalland21.com.
[0094] In one particular embodiment, the 3.sup.rd generation
cephalosporin is chosen from among ceftriaxone (Rocephin.RTM.),
cefotaxime (Claforan.RTM.), ceftazidime (Fortum.RTM.), cefixime
(Oroken.RTM.), cefpodoxime proxetil (Orelox.RTM.), cefotiam or
cefotiam hexetil (Taketiam.RTM.), Cefpirome (Cefrom.RTM.), Cefepime
(Axepim.RTM.), Cefsulodine (Pyocefal.RTM.), cefatamet, ceftizoxime,
cefoperazone, cefsulodin, ceftibuten and the salts of these
compounds.
[0095] Examples of chromogenic substrates specific to
.beta.-lactamases are well known to those skilled in the art and
particularly include nitrocefin
((3-[2,4-dinitrostyryl]-7-(2-thienylacetamido)3-cephem-4-carboxylic
acid), PADAC.RTM. (Pyridinium-2-azo-p-dimethylaniline chromophore),
CENTA.TM., HMRZ-86
(7R)-7-[2-(aminothiazol-4-yl)-(z)-2-(1-carboxy-1-methylethoxyimino)acetam-
ido]-3-(2,4-dinitrostyryl)-3-cephem-4-carboxylic acid
trifluoroacetate, E-isomer) and cefesone or S1
(3-(2,4-dinitrostyryl)-(6R,7R)-7-phenylacetamido-ceph-3-em-4-carboxylate)-
.
[0096] Examples of fluorogenic substrates specific to
.beta.-lactamases are well known to those skilled in the art and
include in particular Fluorocillin Green 495/525 and Fluorocillin
Green 345/350 Live Blazer.TM.-FRET B/G.
[0097] In one embodiment of the invention, the derivative of a
3.sup.rd generation cephalosporin containing or coupled to a
chromophore is one of the compounds described in European patent
application no 1325923. These compounds are represented by formula
(I):
##STR00001##
[0098] where: [0099] R.sub.1 and R.sub.2 may be the same or
different and each representing a hydrogen atom or a nitro or cyano
group; [0100] R.sub.3 is a C.sub.1-C.sub.6 alkyl group, optionally
substituted by a carboxyl group; [0101] R.sub.4 is a hydrogen atom
or an amino group; [0102] X is --S-- or --SO--; and [0103] R.sub.1
and R.sub.2 cannot simultaneously represent a hydrogen atom.
[0104] Therefore the derivative of a 3rd generation cephalosporin
containing or coupled to a chromophore may for example be the
compound: [0105]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)aceta-
mido]-3-(2,4-dinitrostyryl)-3-cephem-4-carboxylic acid, [0106]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acetamido]-3-
-(2,6-dinitrostyryl)-3-cephem-4-carboxylic acid, [0107]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acetamido]-3-
-(4-nitrostyryl)-3-cephem-4-carboxylic acid, [0108]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acetamido]-3-
-(2,4-dicyanostyryl)-3-cephem-4-carboxylic acid, [0109]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acetamido]-3-
-(4-cyanostyryl)-3-cephem-4-carboxylic acid, [0110]
7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acetamido]-3-
-(2-cyanostyryl)-3-cephem-4-carboxylic acid, [0111]
7-[2-(1-carboxy-1-methylethoxyimino)-2-(thiazol-4-yl)acetamido]-3-(2,4-di-
nitrostyryl)-3-cephem-4-carboxylic acid, [0112]
1-oxide-7-[2-(2-aminothiazol-4-yl)-2-(1-carboxy-1-methylethoxy-imino)acet-
amido]-3-(2,4-dinitrostyryl)-3-cephem-4-carboxylic acid, [0113]
7-[2-(2-aminothiazol-4-yl)-2-methoxyiminoacetamido]-3-(4-nitrostyryl)-3-c-
ephem-4-carboxylic acid, [0114]
7-[2-(2-aminothiazol-4-yl)-2-methoxyiminoacetamido]-3-(2,4-dicyanostyryl)-
-3-cephem-4-carboxylic acid, [0115]
7-[2-(2-aminothiazol-4-yl)-2-methoxyiminoacetamido]-3-(2,6-dicyanostyryl)-
-3-cephem-4-carboxylic acid, [0116]
7-[2-(2-aminothiazol-4-yl)-2-methoxyiminoacetamido]-3-(2-cyanostyryl)-3-c-
ephem-4-carboxylic acid, [0117]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2,4-dinitr-
ostyryl)-3-cephem-4-carboxylic acid, [0118]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2,6-dinitr-
ostyryl)-3-cephem-4-carboxylic acid, [0119]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(4-nitrosty-
ryl)-3-cephem-4-carboxylic acid, [0120]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2-nitrosty-
ryl)-3-cephem-4-carboxylic acid, [0121]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2,4-dicyan-
ostyryl)-3-cephem-4-carboxylic acid, [0122]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(4-cyanosty-
ryl)-3-cephem-4-carboxylic acid, [0123]
7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2-cyanosty-
ryl)-3-cephem-4-carboxylic acid, [0124]
[2-carboxymethoxyimino-2-(thiazol-4-yl)acetamido]-3-(2,4-dinitrostyryl)-3-
-cephem-4-carboxylic acid, [0125]
1-oxide-7-[2-(2-aminothiazol-4-yl)-2-carboxymethoxyimino-acetamido]-3-(2,-
4-dinitrostyryl)-3-cephem-4-carboxylic acid,
[0126] or a salt thereof,
[0127] such as described in European patent application no
1325923.
[0128] In one preferred embodiment of the invention, the
chromogenic substrate is the HMRZ-86 compound
(7R)-7-[2-(aminothiazol-4-yl)-(z)-2-(1-carboxy-1-methylethoxyimino)acetam-
ido]-3-(2,4-dinitrostyryl)-3-cephem-4-carboxylic acid
trifluoroacetate, E-isomer) (Hanaki et al. (2004) Journal of
Antimicrobial Chemotherapy 53:888-889). This compound is
represented by the following formula (II):
##STR00002##
Culture Step
[0129] In some embodiments of the invention, the number of
microorganisms present in the biological sample is insufficient to
observe the release of the chromophore or fluorophore from the
chromogenic or fluorogenic substrate of the invention. It may
therefore be necessary to culture the biological sample so as to
allow microorganism growth, before concentrating the microorganisms
which may be present and to a obtain a number of microorganisms
that is sufficient to observe the release of the chromophore or
fluorophore from the chromogenic or fluorogenic substrate of the
invention.
[0130] Therefore, in one preferred embodiment of the invention, the
method of the invention comprises a prior a0) culture step of the
microorganisms. This prior a0) culture step of the microorganisms
is performed under suitable conditions to allow the growth of the
microorganisms.
[0131] By "suitable conditions to allow the growth of the
microorganisms" is meant herein suitable conditions of temperature,
oxygenation and agitation, a suitable medium and a suitable period
so that the microorganisms present in the biological sample are
able to proliferate. The suitable conditions to allow the growth of
the microorganisms are dependent on the microorganisms to be
detected and are well known those skilled in the art. Typically,
the culture step takes placed in a non-selective culture medium,
preferably a liquid culture medium such as the Trypto-Casein-Soy
medium (TCS) at 37.degree. C., for a time allowing a final
concentration to be obtained allowing the conducting of the
test.
[0132] Preferably, when the biological sample is a blood sample;
the culture step a0) is a blood culture step.
[0133] By "blood culture" is meant herein the culture of a sample
of circulating blood. The conditions for blood cultures are well
known to those skilled in the art and are described for example in
"Hemocultures, Garnier F. and Denis F., In: Bacteriologie medicale:
techniques usuelles (2007) Ed. Masson 11:107-116". Typically the
blood sample is placed in culture in a non-selective liquid medium
such as brain-heart medium, trypticase soy medium or broth of the
type Wilkins Chalgren medium, supplemented with nutrients and
growth factors (for example vitamins, hemin, carbon hydrates,
cystein, etc. . . . ), optionally comprising an anticoagulant such
as sodium polyanethol sulfonate (SPS) and/or an antibiotic
neutralizer such as cation adsorbing resins or activated charcoal.
Preferably, the blood culture is performed in an automated system.
Automated blood culture systems are well known to those skilled in
the art and comprise Bactec.RTM. for example marketed by
Becton-Dickinson and BacT/ALERT.RTM. marketed by bioMerieux. These
systems ensure continuous monitoring, agitation and incubation of
the blood cultures. As it grows a microorganism produces CO.sub.2
inducing a drop in pH, which is detected by the automated system by
means of a sensor, either via fluorescence or via reflectometry.
The system alerts to any positive result by means of a visual
and/or sound alarm when the concentration of microorganisms reaches
a threshold concentration.
[0134] It is to be noted that the procedures of the invention are
particularly advantageous for detecting the presence of an enzyme
of a microorganism in a blood sample after a blood culture step.
The methods of the invention effectively allow the detection of
resistance in only 30 min after the blood culture step, whereas
prior art methods only allowed results to be obtained after a
minimum time of 16 h following after the blood culture step. This
reduction in waiting time obtained with the methods of the
invention is partly due to the fact that they do not contain a
culture step on an agar medium.
Concentration Step
[0135] By "to concentrate" or "concentration" is meant herein the
operation whereby the volume of a solution containing
microorganisms is reduced by removing the aqueous part so that its
microorganism content is increased. Concentration techniques are
well known to persons skilled in the art and for example include
centrifugation and filtration. Preferably, the concentration step
comprises the centrifuging of the biological sample followed by
removal of the supernatant obtained. Typically, centrifugation is
conducted at a rate of about 3000 g for 2 to 10 min so as to obtain
a bacterial residue. The supernatant derived from centrifugation is
then removed. Filtration is performed for example through a
membrane whose pore size is smaller than 1 .mu.m (e.g. 0.45 .mu.m).
The microorganisms are then concentrated and collected on the
membrane. The concentration step may also be performed in a tube
with serum-separating gel such as the serum separating tube
marketed by Becton Dickinson. After centrifugation, typically at
1300 g for 10 min, the microorganisms are recovered on the surface
of the gel.
[0136] In addition, the concentrating of the microorganisms can be
obtained by centrifuging after lysis and/or agglutination of the
blood cells and/or filtration allowing the passing of the
microorganisms.
[0137] The concentrated microorganisms can also be the subject of
one or more washings in a buffered medium (for example a phosphate
buffer).
Lysis Step
[0138] If the biological sample is a sample containing blood or red
blood cells, the concentration step can be preceded by a lysis step
of the red blood cells present in the blood culture. This lysis
step must allow the removal of the red blood cells without the
microorganisms themselves being lysed. Suitable lysis conditions
for red blood cells are well known to skilled persons and for
example comprise the contacting of the biological sample with a red
blood cell lysis buffer (RBC buffer: 150 mM NH.sub.4Cl, 10 mM
KHCO.sub.3, 0.01 mM EDTA) for a suitable time, for example 10 min
at a suitable temperature for example between 15 and 40.degree. C.,
to permit lysis of the red blood cells. Other lysis buffers which
may be used herein are known to persons skilled in the art (Chen et
al., (cited above); Moreau et al., 2002, J Drug Target.
10(2):161-73).
[0139] This lysis step can be renewed or followed by a washing step
before the concentration step.
Agglutination Step
[0140] If the biological sample is a sample containing blood or red
blood cells, the concentration step can be preceded by a step a')
to prepare the biological sample, comprising:
[0141] (i) agglutination of the red blood cells, and
[0142] (ii) separation of the agglutinated red blood cells from the
microorganisms present in the sample.
[0143] By "to agglutinate" or "agglutination" is meant herein the
operation consisting of precipitating cells, in particular blood
cells and preferably red blood cells.
[0144] Preferably, agglutination is carried out by placing the
biological sample in contact with at least one agglutinating
agent.
[0145] By "agglutinating agent" is meant herein a molecule inducing
cell agglutination. The agglutinating agent of the invention is
preferably chosen from the group formed by lectins, including
concanavalin A, abrin, ricin and agglutinins such as wheat germ
agglutinin and soy agglutinins; polymeric amino acids such as
polylysine and polyarginine; cationic polymers such as
polyethylenimine; natural or synthetic water-soluble polymers such
as hexadimethirine bromide, polyvinylpyrrolidone (PVP) and
polyethylene glycols (PEG); polycations such as protamine sulfate;
gelatins, dextrans, fibrinogen, urea, glycerol, sodium chloride and
antibodies.
[0146] Preferably the agglutinating agent used in the invention is
a polyethylene glycol (PEG).
[0147] Red blood cell agglutination techniques using an
agglutinating agent such as defined above are well known to persons
skilled in the art and are described for example in applications WO
03/025207 and U.S. Pat. No. 4,753,776. Typically, the biological
sample to be prepared is contacted with PEG at a sufficient
concentration and for a sufficient time to allow the agglutination
of the red blood cells present in the biological sample, for
example for 1 to 30 min, preferably between 5 and 15 min.
[0148] Within the context of the invention, the step for
"separation of the agglutinated red blood cells from the
microorganisms present in the sample" consists of removing the
agglutinated red blood cells and of retaining the microorganisms
present in the treated sample. Such separation techniques are well
known to persons skilled in the art and for example comprise
filtration, centrifugation and/or decantation.
[0149] Filtration for example consists of contacting the biological
sample and the agglutinating agent on the surface of the filter
before centrifugation so as to separate the agglutinated red blood
cells (which remain on the filter) from the microorganisms which
are collected in the filtrate.
[0150] Decantation for example consists of contacting the
biological sample and the agglutinating agent, and of removing the
supernatant after agglutination and decantation.
[0151] Preferably, the separation of the agglutinated red blood
cells is performed using centrifugal filters.
[0152] Step a') to prepare the biological sample such as defined
above can also be preceded or followed by one or more red blood
cell lysis steps of the red blood cells such as defined under the
above paragraph "Lysis step".
Suspending Step
[0153] The protocols of the present invention are characterized in
particular by the fact that the microorganisms, after
concentration, are placed in suspension in a solution containing at
least one chromogenic or fluorogenic substrate such as defined
above. In this manner, the chromogenic or fluorogenic substrate is
placed in contact in a solution with the concentrated
microorganisms and not on a solid medium such as an agar
medium.
[0154] By "placing the microorganisms in suspension" is meant
herein the decreasing of bacterial aggregates by dissolving in a
solution, the bacterial aggregates being derived either from
natural sedimentation or from deliberate sedimentation for example
by centrifugation. The end purpose of placing the microorganisms in
suspension according to the present invention is to tend towards a
solution in which the microorganisms are all separated from one
another.
[0155] The solution in which the microorganisms are replaced in
suspension contains at least one chromogenic or fluorogenic
substrate such as defined above. It may also contain at least one
lysing agent. The lysing agent of the invention may be a bacterial
or fungal lysing agent. Preferably, the lysing agent lyses the
bacterial or fungal wall without hydrolysing the chromogenic or
fluorogenic substrate.
[0156] The said at least one lysing agent can be chosen from the
group formed by a detergent, an enzyme which degrades the bacterial
or fungal wall, an antibiotic active on the bacterial wall such as
a polymyxin, and combinations thereof. Advantageously, the lysing
agent can be combined with or replaced by mechanical lysing means,
such as beads or ultrasound.
[0157] Within the context of the invention, a "detergent" or
"surfactant" is a chemical compound having surfactant
properties.
[0158] Examples of detergent are well known to skilled persons and
particularly comprise those described on the Sigma website
(http://www.sigmaaldrich.com/life-science/life-science-catalog/product-ca-
talog.html?TablePage=20964389) and the following compounds:
chenodeoxycholic acid; chenodeoxycholic sodium salt; cholic acid;
dehydrocholic acid; deoxycholic acid; deoxycholic acid methyl
ester; digitonin; digitoxigenin; N,N-dimethyldodecylamine oxide;
sodium docusate; glycochenodeoxycholic acid sodium salt;
glycocholic acid hydrate; glycocholic acid hydrate sodium salt;
glycodeoxycholic acid monohydrate; glycodeoxycholic acid sodium
salt; 3-sulfate disodium salt of glycolithocholic acid;
glycolithocholic acid ethyl ester; sarkosyl, N-lauroylsarcosine
sodium salt; N-lauroylsarcosine; lithium dodecyl sulfate; lugol
solution; Niaproof 4 Type 4 (i.e., the sodium salt of
7-ethyl-2-methyl-4-undecyl sulfate); the sodium salt of
1-octanesulfonic acid; sodium 1-butanesulfonate; sodium
1-decanesulfonate; sodium 1-dodecanesulfonate; sodium
1-heptanesulfonate anhydrous; sodium 1-nonanesulfonate; sodium
1-propanesulfonate monohydrate; sodium 2-bromoethanesulfonate;
sodium cholate hydrate; sodium choleate; sodium deoxycholate;
sodium deoxycholate monohydrate; sodium dodecyl sulfate; sodium
hexanesulfonate anhydrous; sodium octyl sulfate; sodium
pentanesulfonate anhydrous; sodium taurocholate; sodium
taurodeoxycholate; taurochenodeoxycholic acid sodium salt;
taurodeoxycholic acid sodium salt hydrate; 3-sulfate
taurolithocholic acid disodium salt; tauroursodeoxycholic acid
sodium salt; Trizma.RTM. dodecyl sulfate (i.e.,
tris(hydroxymethyl)aminomethane lauryl sulfate); ursodeoxycholic
acid, alkyl trimethylammonium bromide; benzalkonium chloride;
benzyl dimethylhexadecylammonium chloride; benzyl
dimethyltetradecylammonium chloride; benzyl dodecyldimethylammonium
bromide; benzyl trimethylammonium tetrachloroiodate;
cetyltrimethylammonium bromide; dimethyl dioctadecylammonium
bromide; dodecyl ethyldimethylammonium bromide; dodecyl
trimethylammonium bromide; ethyl hexadecyldimethylammonium bromide;
Girard's T reagent; hexadecyl trimethylammonium bromide;
N,N',N'-polyoxyethylene(10)-N-tallow-1,3-diaminopropane; thonzonium
bromide; trimethyl(tetradecyl)ammonium bromide, BigCHAP
(N,N-bis[3-(D-gluconamido)propyl]cholamide); bis(polyethylene
glycol bis[imidazoyl carbonyl]); the polyoxyethylene alcohols such
as Brij@ 30 (polyoxyethylene(4) lauryl ether), Brij.RTM.35
(polyoxyethylene(23) lauryl ether), Brij@ 35P, Brij@ 52
(polyoxyethylene 2 cetyl ether), Brij@ 56 (polyoxyethylene 10 cetyl
ether), Brij@ 58 (polyoxyethylene 20 cetyl ether), Brij@ 72
(polyoxyethylene 2 stearyl ether), IBrij@ 76 (polyoxyethylene 10
stearyl ether), Brij@ 78 (polyoxyethylene 20 stearyl ether), Brij@
78P, Brij@ 92 (polyoxyethylene 2 oleyl ether); Brij@ 92V
(polyoxyethylene 2 oleyl ether), Brij@ 96V, Brij@ 97
(polyoxyethylene 10 oleyl ether), Brij@ 98 (polyoxyethylene(20)
oleyl ether), Brij@ 58P, and Brij@ 700 (polyoxyethylene(100)
stearyl ether); Cremophor.RTM. EL
(polyoxyethyleneglyceroltriricinoleate 35; polyoxyl 35 castor oil);
decaethylene glycol monododecyl ether; decaethylene glycol mono
hexadecyl ether; decaethylene glycol mono tridecyl ether;
N-decanoyl-N-methylglucamine; n-decyl alpha-D-glucopyranoside;
decyl beta-D-maltopyranoside; digitonine;
n-dodecanoyl-N-methylglucamide; n-dodecyl alpha-D-maltoside;
n-dodecyl beta-D-maltoside; heptaethylene glycol monodecyl ether;
heptaethylene glycol monododecyl ether; heptaethylene glycol
monotetradecyl ether; n-hexadecyl beta-D-maltoside; hexaethylene
glycol monododecyl ether; hexaethylene glycol monohexadecyl ether;
hexaethylene glycol monooctadecyl ether; hexaethylene glycol
monotetradecyl ether; Igepal.RTM. CA-630
(nonylphenyl-polyethyleneglycol, (octylphenoxy)polyethoxyethanol,
octylphenyl-polyethylene glycol);
methyl-6-O-(N-heptylcarbamoyl)-alpha-D-glucopyranoside;
nonaethylene glycol monododecyl ether;
N-nonanoyl-N-methylglucamine; octaethylene glycol monodecyl ether;
octaethylene glycol monododecyl ether; octaethylene glycol
monohexadecyl ether; octaethylene glycol monooctadecyl ether;
octaethylene glycol monotetradecyl ether;
octyl-beta-D-glucopyranoside; pentaethylene glycol monodecyl ether;
pentaethylene glycol monododecyl ether; pentaethylene glycol
monohexadecyl ether; pentaethylene glycol monohexyl ether;
pentaethylene glycol monooctadecyl ether; pentaethylene glycol
monooctyl ether; polyethylene glycol diglycidyl ether; polyethylene
glycol W-1 ether; polyoxyethylene 10 tridecyl ether;
polyoxyethylene 100 stearate; polyoxyethylene 20 isohexadecyl
ether; polyoxyethylene 20 oleyl ether; polyoxyethylene 40 stearate;
polyoxyethylene 50 stearate; polyoxyethylene 8 stearate;
polyoxyethylene bis(imidazolyl carbonyl); polyoxyethylene 25
propylene glycol stearate; quillaja bark saponin; esters of
sorbitan fatty acid, for example Span@ 20 (sorbitan monolaurate),
Span@ 40 (sorbitan monopalmitate), Span@ 60 (sorbitan
monostearate), Span@ 65 (sorbitan tristearate), Span@ 80 (sorbitan
monooleate) and Span@ 85 (sorbitan trioleate); the different alkyl
ethers of polyethylene glycols such as for example Tergitol.RTM.
Type 15-S-12, Tergitol.RTM. Type 15-S-30, Tergitol.RTM. Type
15-S-5, Tergitol.RTM. Type 15-S-7, Tergitol.RTM. Type 15-S-9,
Tergitol.RTM. Type NP-10 (nonylphenol ethoxylate), Tergitol.RTM.
Type NP-4, Tergitol.RTM. Type NP-40, Tergitol.RTM. Type NP-7,
Tergitol.RTM. Type NP-9 (nonylphenol polyethylene glycol ether),
Tergitol.RTM. MIN FOAM IX, Tergitol.RTM. MIN FOAM 2X, Tergitol.RTM.
Type TMN-10 (polyethylene glycol trimethylnonyl ether),
Tergitol.RTM. Type TMN-6 (polyethylene glycol trimethylnonyl
ether), Triton@ 770, Triton@ CF-10 (benzyl-polyethylene glycol
tert-octylphenyl ether), Triton@ CF-21, Triton@ CF-32, Triton@
DF-12, Triton@ DF-16, Triton@ GR-5M, Triton@ N-42, Triton@ N-57,
Triton@ N-60, Triton@ N-101 (polyethylene glycol nonyl phenyl
ether; polyoxyethylene branched nonyl phenyl ether), Triton.RTM.
QS-15, Triton.RTM. QS-44, Triton.RTM. RW-75 (polyethylene glycol
260 mono(hexadecyl/octadecyl) ether and 1-octadecanol), Triton.RTM.
SP-135, Triton.RTM. SP-190, Triton.RTM. W-30, Triton.RTM. X-15,
Triton.RTM. X-45 (polyethylene glycol 4-tert-octylphenyl ether;
4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol),
Triton.RTM. X-100 (t-octylphenoxypolyethoxyethanol; polyethylene
glycol tert-octylphenyl ether;
4-(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol),
Triton.RTM. X-102, Triton.RTM. X-114 (polyethylene glycol
tert-octylphenyl ether;
(1,1,3,3-tetramethylbutyl)phenyl-polyethylene glycol), Triton.RTM.
X-165, Triton.RTM. X-305, Triton.RTM. X-405 (polyoxyethylene(40)
isooctylcyclohexyl ether; polyethylene glycol tert-octylphenyl
ether), Triton.RTM. X-705-70, Triton.RTM. X-151, Triton.RTM. X-200,
Triton.RTM. X-207, Triton.RTM. X-301, Triton.RTM. XL-80N and
Triton.RTM. XQS-20; tetradecyl-beta-D-maltoside; tetraethylene
glycol monodecyl ether; tetraethylene glycol monododecyl ether;
tetraethylene glycol monotetradecyl ether; triethylene glycol
monodecyl ether; triethylene glycol monododecyl ether; triethylene
glycol monohexadecyl ether; triethylene glycol monooctyl ether;
triethylene glycol monotetradecyl ether; polyoxyethylene sorbitan
fatty acid esters, for exampleTWEEN.RTM. 20 (polyethylene glycol
sorbitan monolaurate), TWEEN.RTM. 20 (polyoxyethylene (20) sorbitan
monolaurate), TWEEN.RTM. 21 (polyoxyethylene (4) sorbitan
monolaurate), TWEEN.RTM. 40 (polyoxyethylene (20) sorbitan
monopalmitate), TWEEN.RTM. 60 (polyethylene glycol sorbitan
monostearate; polyoxyethylene (20) sorbitan monostearate),
TWEEN.RTM. 61 (polyoxyethylene (4) sorbitan monostearate),
TWEEN.RTM. 65 (polyoxyethylene (20) sorbitan tristearate),
TWEEN.RTM. 80 (polyethylene glycol sorbitan monooleate;
polyoxyethylene (20) sorbitan monooleate), TWEEN.RTM. 81
(polyoxyethylene (5) sorbitan monooleate) and TWEEN.RTM. 85
(polyoxyethylene (20) sorbitan trioleate); tyloxapol; n-undecyl
beta-D-glucopyranoside, CHAPS
(3[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate); CHAPSO
(3-[(3-cholamidopropyl)dimethylammonio]-2-hydroxy-1-propanesulfonate);
N-dodecylmaltoside; alpha-dodecyl-maltoside;
beta-dodecyl-maltoside; the inner salt of
3-(decyldimethylammonio)propanesulfonate (SB3-10), the inner salt
of 3-(decyldimethylammonio)propanesulfonate (SB3-10), the inner
salt of 3-(dodecyldimethylammonio)propanesulfonate (SB3-12), the
inner salt of 3-(N,N-dimethylmyristylammonio)propanesulfonate
(SB3-14), the inner salt of
3-(N,N-dimethylpalmitylammonio)propanesulfonate (SB3-16), the inner
salt of 3-(N,N-dimethyloctadecylammonio)propanesulfonate (SB3-18);
MEGA-8; MEGA-9; MEGA-10; methylheptylcarbamoyl glucopyranoside;
N-nonanoyl N-methylglucamine; octyl-glucopyranoside;
octyl-thioglucopyranoside; octyl-beta-thioglucopyranoside;
3[N,N-dimethyl(3-myristoylaminopropyl)ammonio]propanesulfonate or
am idosulfobetain-14 (ASB-14); amidosulfobetain-16 (ASB-16);
EMPIGEN.RTM. BB; Cymal-1, Cymal-2, Cymal-5, Cymal-6 and deoxycholic
acid.
[0159] Preferably, in the methods of the invention, the detergent
is chosen from the group formed by CHAPS, Tween 20, Tween 80,
c7bzo, octylglucoside, octylthioglucopyranoside, ASB-14, SB3-10,
sodium dodecyl sulfate, digitonin, sarkosyl and tergitol.
[0160] The lysing agent can also be an enzyme which degrades the
bacterial wall such as lysozyme, lysostaphin, achromopeptidase,
mutanolysin, labiase, chitinase, glucanase, glucosaminidase,
muramidase, lytic transglycosylase, amidase and endopeptidase.
[0161] The lysing agent may be an agent causing the formation of
pores in the bacterial wall or the cell membrane such as a
polymyxin for example, in particular a polymyxin A, B, C, D, E (or
colistin), F, K, M, P, S or T. Polymyxins are cyclic peptide
antibiotics which act as cationic detergents and insert themselves
among the phospholipids of the bacterial wall. They may also be
.beta.-lactams, glycopeptides, fosfomycin, cycloserine, bacitracin,
fusidic acid or neomycin.
[0162] At step b1) for placing in suspension, the chromogenic or
fluorogenic substrate can also be placed in the presence of a least
one .beta.-lactamase inhibitor. The solution in which the
microorganisms are placed in suspension may therefore further
comprise at least one .beta.-lactamase inhibitor, in particular at
least one .beta.-lactamase inhibitor chosen from the group formed
by a cephalosporinase inhibitor, a serine .beta.-lactamase
inhibitor, a metal chelator and a ESBL inhibitor.
[0163] Examples of .beta.-lactamase inhibitors are well known to
persons skilled in the art and particularly include cloxacillin,
the syn2190 compound, aztreonam, boronic acid and derivatives
thereof such as 3-aminophenyl boronic acid, phenyl boronic acid,
benzo(b)thiophene-2-boronic acid, meta-carboxyphenylboronic acid;
clavulanic acid, salts of clavulanic acid, tazobactam and
sulbactam; dipicolinic acid (DPC), diethyldithiocarbamate (DEDTC),
N,N,N',N'-tetrakis-(2-pyridylmethyl)-ethylenediamine (TPEM),
ethylene diamine tetra acetic acid (EDTA), 2,3-dimercapto-1-propane
sulfonic acid (DMPS) and 1,10-phenanthroline; ceftazidime, a salt
of ceftazidime, cefotaxime and a salt of cefotaxime; BAL30072
siderophore monobactam, 2-amino-4-thiazolyl methoxyimino-penicillin
(ATMO-penicillin); C-6-mercaptomethyl penicillinate; BRL 42715
methylidene penem; BLI-489 methylidene penem; alkylidene penems;
tri- and bicyclic methylidene penems; LK-157 tricycylic carbapenem;
1-b-methylcarbapenem 225; Ro 48-1220 penam sulfone; LN-1-255 penam
sulfone; sodium salt of
trans-7-oxo-6-(sulfooxy)-1,6-diazabicyclo[3.2.1]octan-2-carboxamide
(NXL104); the phosphonates and derivatives thereof such as the
cyclic acyl phosphonates; penicillins such as JDB/LN-I-255; the
sulfonic cephalosporins such as JBB/DVR-II-214. It is known that
the choice of the inhibitors which can be used may depend on the
type of enzyme it is desired to detect (WO2009/051838).
[0164] Preferably, the microorganisms are left in suspension in the
solution comprising a chromogenic or fluorogenic substrate
according to the invention at a suitable temperature and for a
suitable time to allow the hydrolysis of the substrate by the
enzyme and the detection of any release of the chromophore or
fluorophore. Such conditions are well known to skilled persons and
are a function of the chromogenic or fluorogenic substrate used.
Typically, the microorganisms are left to incubate for 5 min to 2
h, at a temperature of between 15 and 42.degree. C. The release of
the chromophore or fluorophore, which is characterized by a change
in colour of the chromogenic substrate or fluorescence emission by
the fluorogenic substrate, can then be directly observed in
solution.
[0165] The methods of the invention have the advantage of largely
reducing the time after which it is possible to detect the presence
of an enzyme of a microorganism in a biological sample. This saving
in time is due in particular to the fact that the methods of the
invention do not comprise any culture step of the microorganisms in
a selective medium containing a specific antibiotic. In particular,
they do not comprise any selection step or microorganism inducing
step on an agar medium.
[0166] If the biological sample is a sample containing blood or red
blood cells, the detection method of the invention may further
comprise a step to lyse the red blood cells present in the
biological sample before the suspending step as described above in
the section titled "Lysis step".
Method for Preparing a Blood Culture Sample
[0167] A further subject of the present invention is a method for
the in vitro preparation of a blood culture sample containing
microorganisms, comprising the steps of: [0168] A) lysing or
agglutinating the red blood cells present in the blood culture
without lysing the microorganisms present in the blood culture
sample, [0169] B) separating the microorganisms present in the
blood culture sample from the red blood cells lysed or agglutinated
at step A), and [0170] C) optionally washing the microorganisms of
the blood culture sample separated at step B).
[0171] Preferably, the above preparation method allows
microorganisms to be obtained on which it is possible to apply step
a1) of the detection methods such as defined above.
[0172] The lysis step A) of the red blood cells can typically be
implemented as indicated above under the paragraph "Lysis step", by
placing the blood culture sample in contact with a lysis buffer of
red blood cells, RBC lysis buffer, for a suitable time for example
between 1 min and 10 min, at a suitable temperature, for example
ambient temperature or at 37.degree. C., to allow lysis of the red
blood cells.
[0173] The agglutination step A) of the red blood cells can
typically be implemented as indicated above under the paragraph
"Agglutination step" placing the blood culture in contact with at
least one agglutinating agent such as defined above.
[0174] The separation step B) to separate the microorganisms
present in the blood culture sample can be implemented using any
suitable technique well known to persons skilled in the art. The
step to separate the microorganisms can be performed in particular
by centrifugation, filtration or removing the aqueous phase, for
example after decantation. Preferably the step to separate the
microorganisms is implemented by centrifugation.
[0175] The optional washing step may typically be performed by
re-suspending the separated microorganisms in a washing buffer,
such as the RBC lysis buffer, incubating for a suitable time, at a
suitable temperature and further separation of the microorganisms,
for example by centrifugation.
In Vitro Detection Method of Microorganisms
[0176] As indicated above, with the in vitro methods for detecting
enzymes according to the invention, the enzymes to be detected are
produced by particular microorganisms. The presence of the enzyme
to be detected therefore means that the microorganism producing
this enzyme is present in the biological sample.
[0177] Therefore, the present invention also concerns an in vitro
method for detecting microorganisms in a biological sample using
the enzyme detecting method such as defined above.
[0178] In particular, one embodiment of the invention concerns an
in vitro method for detecting a microorganism in a biological
sample comprising the steps of:
[0179] a1) concentrating the microorganisms present in the
biological sample, optionally after a a0) culture step of the
microorganisms such as defined above;
[0180] b1) placing the microorganisms concentrated at a1) in
suspension in a solution comprising at least one chromogenic or
fluorogenic substrate capable of releasing a chromophore or a
fluorophore after hydrolysis by an enzyme of the microorganism to
be detected such as defined above;
[0181] c1) detecting any release of the chromophore or fluorophore
obtained at step b1);
[0182] the release of the chromophore or the fluorophore detected
at step c1) indicating the presence of the microorganism to be
detected.
[0183] The detection of the release of the chromophore or the
fluorophore from the chromogenic or fluorogenic substrate according
to the invention is therefore indicative of the presence of
microorganisms expressing the enzyme specific to the chromogenic or
fluorogenic substrate of the invention.
[0184] The following examples illustrate the invention without
limiting the scope thereof.
Example 1
Detection of 13-Lactamase Conferring Resistance to 3.sup.rd
Generation Cephalosporins Upon Microorganisms Producing this
.beta.-Lactamase, Directly from Urines without any Bacterial Growth
Step
[0185] This example shows that it is possible to identify
Enterobacteriaceae resistant to 3.sup.rd generation cephalosporins
(C3G), directly from urine.
[0186] Two urines were collected from healthy volunteers (one male
and one female). These urines were each separately inoculated with
different loads of two strains of Escherichia coli (T434=resistant
to C3G having major .beta.-lactamase activity; ATCC
25922=susceptible).
[0187] Briefly, 1 ml of urine was inoculated with 1, 10 or 100
.mu.L of a 0.5 McFarland (McF) bacterial suspension. The tubes were
centrifuged at 3000 g or 6000 g optionally with washings.
[0188] To the bacterial residue obtained were added 20 .mu.L of a
solution containing 0.8 g/L of HMRZ-86 substrate and 20 .mu.L of
CHAPS at 20 g/L. After vortexing for 10 seconds the tube was left
30 min at ambient temperature.
[0189] The inventors observed a positive reaction for the strongest
inoculum. A change from yellow to orange was observed with the
resistant strain when its number reached 6.10.sup.6 cfu/mL whereas
no change was visible with the susceptible strain.
Example 2
Detection of .beta.-lactamase Conferring Resistance to 3.sup.rd
Generation Cephalosporins Upon Microorganisms Producing this
.beta.-lactamase, with a Bacterial Growth Step
[0190] This test was performed in a microplate.
[0191] Each well contained: [0192] 50 .mu.L of HMRZ-86 dissolved in
buffered TCS medium 60 g/L (0.2 M phosphate buffer, pH 6), [0193]
40 .mu.L of CHAPS or H.sub.2O, [0194] 10 .mu.L of a dense bacterial
suspension (5 McF, >10.sup.8 cfu/ml).
[0195] The microplates were observed every hour to detect any
colour change.
[0196] After 3 h, for example out of a panel of 8 resistant strains
and 4 susceptible strains, with 0.4 g/L of HMRZ-86 and between 10
and 20 g/L of CHAPS, and a strong inoculum, the results given in
Table 2 were obtained.
TABLE-US-00002 TABLE 2 Water CHAPS Resistant Susceptible Resistant
Susceptible strains strains strains strains Significant 3 5 change
Uncertain change 1 No change 4 4 3 4
[0197] After 3 h30, in another example, out of a panel of 8
resistant strains and 4 susceptible strains using 0.4 g/L of
HMRZ-86, in or not in the presence of 5 g/L CHAPS and using a
strong inoculum, the results given in Table 3 were obtained.
TABLE-US-00003 TABLE 3 With CHAPS Without CHAPS Resistant
Susceptible Resistant Susceptible strain strain strain strain
Significant 4 6 change Uncertain change 1 1 No change 3 3 2 4
[0198] Therefore, the presence of CHAPS promotes the reaction if a
prior bacterial growth step is conducted.
Example 3
Detection of .beta.-Lactamase Conferring Resistance to 3.sup.rd
Generation Cephalosporins Upon Microorganisms Producing this
.beta.-Lactamase, Directly from a Blood Culture
[0199] This example shows that it is possible to identify
Enterobacteriaceae resistant to 3.sup.rd generation cephalosporins
(C3G) directly from a blood culture.
[0200] To examine the possibility of detecting strains resistant to
C3Gs in blood cultures, the adopted protocol was the following (NB:
variants of the protocol not leading to any variation in the
results obtained are given between square brackets. They were
applied to 2 strains, a susceptible strain and a resistant strain.
A change in colour was observed for the resistant strain and no
change was observed for the susceptible strain):
[0201] To 7.5 mL of medium from the blood culture bottle
(bacTAlert; ref 259791 or 259793) were added 2.5 mL of defibrinated
sheep blood. 25 .mu.L of a 0.5 McF bacterial suspension were added.
After homogenising by vortexing and incubation for 18-20 h at
37.degree. C., 500 .mu.L were sampled. 0.5 mL [or 1 mL] of modified
red blood cell lysis solution containing NH.sub.4Cl in particular
but not containing EDTA (SL) were added. After homogenising by
vortexing, the tube was incubated 10 min at 37.degree. C., [or 1
min at 37.degree. C. or 1 min at ambient temperature]. A residue
collected after centrifugation at 750 g for 5 min [or 2 min] was
re-suspended in 200 .mu.L of SL and left 2 min at ambient
temperature. 1 mL of 0.1 M PBS was then added. The tube was again
centrifuged at 750 g for 5 min [or 2 min], and the residue was
dissolved in a solution comprising 50 .mu.L of HMRZ-86 substrate
(1.2 g/L) and 50 .mu.L of CHAPS (30 g/L). After homogenising
vortexing, the tube was left to incubate for 15 min at ambient
temperature. After centrifuging at 750 g for 5 min [or 2 min], the
change in colour was observed.
[0202] The test was conducted on 4 strains of which 3 strains were
resistant C3G (including 2 metallo-.beta.-lactamases whose reaction
was inhibited in the presence of the culture medium) and one
susceptible strain.
[0203] A test was conducted on the two blood culture media (aerobic
and anaerobic) over a wider panel. In the aerobic medium 17 C3G
resistant strains out of 18 responded positively to the test and 6
susceptible strains out of 8 did not show any significant colour
change. In the anaerobic medium, 16 C3G resistant strains out of 18
responded positively to the test and 6 out of 8 susceptible strains
did not show any significant colour change.
[0204] Tests were similarly conducted using bottles of blood
culture medium supplemented with whole human blood.
[0205] Different protocols were followed:
[0206] To 7.5 mL of medium derived from the blood culture bottle
(bacTAlert; ref 259791 or 259793) were added 2.5 mL of whole human
blood. 25 .mu.L of a 0.5 McF bacterial suspension were added. After
homogenising by vortexing, the tube was incubated 18-20 h at
37.degree. C.
[0207] Lysis Protocol
[0208] 0.5 ml of blood culture were sampled and 0.5 mL of lysis
buffer was added thereto. The mixture was left in contact for 10
min then centrifuged for 2 min at 750 g. The residue was subjected
twice again to the same protocol (addition of lysis buffer then
centrifugation). It was then dissolved in a solution containing 50
.mu.L of HMRZ-86 substrate (1.2 g/L) and 50 .mu.L of CHAPS (30
g/L). After homogenising by vortexing, the tube was incubated 15
min at ambient temperature. Any change in colour was noted after
centrifuging 2 min at 750 g.
[0209] Protocol for <<Agglomeration--Filtration on
Centrifugal Filter>>
[0210] 50 mg of PEG were deposited on a centrifugal filter of the
type: <<Millipore Ultrafree MC centrifugal filter units 5
.mu.m>>. 0.5 mL of blood culture were taken and deposited on
the filter and left in contact with the PEG for 5 min. After
centrifuging 5 min at 5500 g (which allowed filtration) and removal
of the supernatant above the filter, the filtrate was treated with
1 mL of lysis buffer for 10 min. The tube was centrifuged 5 min at
5500 g, the supernatant was removed.
[0211] The residue was then dissolved in a solution containing 50
.mu.L of HMRZ-86 substrate (0.8 g/L) and 50 .mu.L of CHAPS (20
g/L). After homogenising by vortexing, the tube was incubated 15
min at ambient temperature then any change in colour was noted.
[0212] Protocol for <<Agglomeration--Decantation>>
[0213] 1 ml of blood culture was taken and 200 mg PEG added
thereto. The mixture was left to decant for 15 min. 500 .mu.L of
supernatant was placed in another tube. After centrifuging 5 min at
5500 g and removal of the supernatant, the residue was treated with
1 mL of lysis buffer and after 10 min it was again centrifuged for
5 min at 5500 g.
[0214] The residue was then dissolved in a solution containing 50
.mu.L of HMRZ-86 substrate (0.8 g/L) and 50 .mu.L of CHAPS (20
g/L). After homogenising by vortexing followed by incubation 15 min
at ambient temperature, any change in colour was noted.
[0215] All these three protocols allow limiting of red colouring
due to the blood culture, and rapid C3GR identification.
[0216] They were applied to a C3GR strain and a C3GS strain: the
test with the C2GR strain showed bright red colouring whereas the
test with the C3GS strain remained orangish-yellow.
Example 4
Detection of the Glycosidase Activity of Candida tropicalis
(Substrate: 5-Bromo 4-chloro 3-indolyl .alpha.-glucoside) of
Enterococcus faecalis (Substrate: 5-Bromo 4-chloro 3-indolyl
.beta.-Glucoside) and the Esterase Activity of Pseudomonas
aeruginosa or Salmonella enteritidis (Substrate: 5-bromo 4-chloro
3-indolyl butyrate), Directly from Urine
[0217] Urines from healthy individuals were artificially
contaminated. For this purpose, a 0.5 McF bacterial suspension
(about 10.sup.78 cfu/ml) was prepared in physiological water. This
suspension was centrifuged for 5 min at 6000 g and the supernatant
was removed. The residue was then dissolved in 1 mL of urine to
obtain a concentration of about 10.sup.78 cfu/ml urine. The
contaminated urine was incubated for 15 to 30 min. It was then
centrifuged for 5 min at 6000 g and the supernatant removed. The
residue was dissolved in a solution containing 50 .mu.L of
chromogenic substrate 2.times. and 50 .mu.L of detergent 2.times..
The change in colour was observed after an incubation time of 30
min at ambient temperature.
[0218] The results obtained with the test to detect glycosidase
activity are given in Tables 4 and 5.
TABLE-US-00004 TABLE 4 Candida tropicalis ATCC 750 Substrate
X-.alpha.-glucoside Read time 30 min 0.1M phosphate buffer pH 7
(Bp) White Bp + Digitonin 0.5 g/L Blue Bp + OTG 5 g/L Blue (OTG =
Octyl-.beta.-thioglucopyranoside; X = 5-bromo 4-chloro
3-indolyl).
TABLE-US-00005 TABLE 5 Enterococcus faecalis ATCC 29212 Substrate
X-.beta.-glucoside Read time 30 min at AT 0.1M phosphate buffer pH
7 Blue reflections/light blue
[0219] The results obtained with the test for detecting the
esterase activity are given in Tables 6 and 7.
TABLE-US-00006 TABLE 6 P. aeruginosa RDC 45 Substrate X-butyrate
Read time 45 min at 37.degree. C. 0.1M phosphate buffer H7 (Bp)
White Bp + PolyB 250 mg/L Blue Bp + CHAPS 10 g/L White Bp + CHAPS +
PolyB Blue (polyB = polymyxine B)
TABLE-US-00007 TABLE 7 Salmonella enteritidis ATCC 13076 Substrate
X-butyrate Buffer 0.1M phosphate buffer pH 7 (Bp) Read time 1 h at
AT Bp + PolyB 250 mg/L Blue reflections (BR)/light blue Bp + CHAPS
10 g/L BR Bp + Tween 20 0.2% BR Bp + CHAPS + PolyB BR/light blue Bp
+ Tween 20 + PolyB BR/light blue
[0220] The influence of temperature and incubation time was tested
(see Table 8).
TABLE-US-00008 TABLE 8 P. aeruginosa RDC45 Substrate X-butyrate
Read time 1 h at 45 min at 1 h 15 at AT 37.degree. C. 37.degree. C.
Negative bacteria-free control in ND White Blanc Bp (0.1M phosphate
buffer pH 7) Bp ND White Blue reflectn. (BR) Bp + CHAPS 10 g/L
White White BR Bp + PolyB 250 mg/L BR- Light blue Blue Bp + CHAPS +
PolyB BR- Light blue Blue - ND: not determined
Example 5
Detection of .beta.-lactamase Conferring Resistance to 3.sup.rd
Generation Cephalosporins Upon Microorganisms Producing this
.beta.-lactamase, Directly from Blood Cultures Positive to
Gram-Negative Bacilli
[0221] This example shows that it is possible to detect resistance
to 3.sup.rd generation cephalosporins (C3G) in Enterobacteriaceae
or other Gram-negative bacilli such as Pseudomonas, directly from a
blood culture.
[0222] The study was a prospective study on blood cultures positive
to aerobic Gram-negative bacilli. The protocol below was conducted
on the same day as the blood cultures were detected to be positive
by an automated system (BacT/ALERT by Biomerieux).
[0223] Lysis Protocol
[0224] 0.5 ml of blood culture was taken and 0.5 mL of lysis buffer
was added thereto. The mixture was briefly vortexed then left in
contact for 10 min at ambient temperature. A centrifuging step (2
min at 3000 rpm) was then performed and the supernatant removed.
The residue was subjected twice to the following steps: addition of
1 mL of lysis buffer, short vortexing, 10 min wait, then
centrifuging 2 min at 3000 rpm and removal of the supernatant. The
residue was then dissolved in a solution containing 50 .mu.L of
HMRZ-86 substrate (1.2 g/L) and 50 .mu.L of CHAPS (30 g/L). After
homogenising by vortexing, the tube was incubated 15 min at ambient
temperature. Any change in colour was noted after centrifuging 2
min at 3000 rpm.
[0225] The detected strains are given in Table 9.
TABLE-US-00009 TABLE 9 Susceptible strains Resistant strains (C3GS)
(C3GR) Acinetobacter baumannii 1 -- Citrobacter freundii 1 --
Escherichia coli 10 3 Klebsiella oxytoca -- 1 Klebsiella pneumoniae
1 -- Pseudomonas aeruginosa 1 -- Yersinia enterocolitica 1 -- TOTAL
15 4
[0226] The results are given in Table 10.
TABLE-US-00010 TABLE 10 Resistant Susceptible strains strains
Significant change 4 1 Uncertain change -- -- No change -- 14
[0227] This example therefore shows that the lysis protocol allows
the detection of .beta.-lactamase conferring resistance to 3.sup.rd
generation cephalosporins upon aerobic Gram-negative bacilli
producing this .beta.-lactamase, directly from positive blood
cultures. Aside from one C3GS strain which was detected as
<<false positive>>, the test conducted with the C3GS
strains showed pale yellow to orangish-yellow colouring, whereas
the test with the C3GR strains changed from yellow to bright
red.
* * * * *
References