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JCM Accepts, published online ahead of print on 1 December 2010
J. Clin. Microbiol. doi:10.1128/JCM.01773-10
Copyright © 2010, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.
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Revised JCM-01773-10 Version 3
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How to detect NDM-1 producers?
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Patrice Nordmann,1* Laurent Poirel,1 Amélie Carrër,1
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Mark A. Toleman,2 and Timothy R. Walsh2
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Service de Bactériologie-Virologie, INSERM U914 “Emerging Resistance to
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Antibiotics”, Hôpital de Bicêtre, Assistance Publique/Hôpitaux de Paris, Faculté de
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Médecine Paris Sud, K.-Bicêtre, France1 ; Department of Immunology, Immunity and
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Biochemistry, School of Medicine, Cardiff University, UK2
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Corresponding author : [email protected]; Service de Bactériologie-Virologie,
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hôpital de Bicêtre, 78 rue du Général Leclerc, 94275 K-Bicêtre, France. Tel. 33 1 45 21 36 32
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1
2
Enterobacterial isolates expressing the carbapenemase NDM-1 are emerging
3
worldwide. Twenty seven NDM-1-positive isolates of worldwide origin were included in
4
the study to identify these strains as not only pathogens, but also as colonizers of normal
5
flora for infection control screening purposes. Although susceptibility to carbapenems
6
varied, a combined test (IMP/IMP + EDTA), the Etest MBL and automated
7
susceptibility testing by Vitek2 (bioMérieux) identified those NDM-1 producers as
8
ratified by PCR using specific primers. Screening of carriers of NDM-1 producers may
9
be based on media such as ChromID ESBL culture medium routinely used for screening
10
extended spectrum ß-lactamase producers giving excellent detection levels with low
11
limits of detection ranging from 8 x 100 to 5 x 102 CFU/ml. The CHROMagar KPC
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culture medium had higher limits of detection (1 x 101 to 5 x 105 CFU/mL) and may be
13
proposed for the follow-up of outbreaks with NDM-1 producers. Colonies growing on
14
these screening media can be verified as NDM-1 producers with molecular methods as
15
described herein.
2
1
2
NDM-1 is a broad spectrum ß-lactamase (carbapenemase) that is able to inactivate all
3
ß-lactams except aztreonam (18). However, most NDM-1-positive strains also express CMY-
4
4 and CTX-M-15 ß-lactamases thus conferring resistance to all ß-lactams (8). Although
5
discovered in 2008, NDM-1-positive Enterobacteriaceae has attracted worldwide media
6
attention due to its high incidence in India and that many UK isolates can be directly tracked
7
to India and Pakistan (5, 8). Several reports indicate further spread of this resistance
8
determinant worldwide including in the USA (3 isolates [3]) and Australia (11) with
9
relationships in most of the cases with the Indian subcontinent. By contrast to many other
10
resistance mechanisms, NDM-1 is not associated to a single strain but has spread very rapidly
11
to non-clonally related isolates (8). It has been identified mostly in Escherichia coli and
12
Klebsiella pneumoniae and to a lesser degree in other enterobacterial species (5, 8). Plasmids
13
carrying the blaNDM-1 gene also carry a number of other resistance genes conferring resistance
14
to all aminoglycosides, macrolides and sulfamethoxazole thus making these isolates multi-
15
drug resistant or, because of other non-plasmid mediated resistances, resistant in some cases
16
to all antibiotics including tigecycline and colistin (8). Although carbapenemase-producing
17
Enterobacteriaceae isolates have been increasingly identified worldwide such as KPC
18
producers (9, 10), NDM-1 producers bring several additional factors which are deeply
19
disconcenting for public health worldwide. These factors are: (i) identification of the blaNDM-1
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gene in not a single species but in unrelated species (including Acinetobacter spp. [7])
21
indicating that this gene can spread at an unprecedent rate; (ii) it is present not only in K.
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pneumoniae, a typical nosocomial pathogen, but also in E. coli which is also a main
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community-acquired pathogen. E. coli is also the number one cause of diarrhoea in children in
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India/Pakistan, increasing the risk of resistant strains being released into the environment; iii)
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currently, the blaNDM-1 gene is primarily identified from the Indian subcontinent, which has
3
1
the second largest population in the world (1.3 billion people). Overpopulation, lack of basic
2
sanitation and access to clean water, tropical climate (Southern part of the peninsula), and
3
poor control of antibiotic usage, are all compounding factors that may promote the transfer of
4
NDM-1 positive bacteria among the Indian/Pakistanese population and then internationally.
5
Therefore, there is urgent international need to detect NDM-1 producers in any healthcare
6
facility to prevent its further spread.
7
We report here several techniques for the detection of NDM-1 producers - whether
8
this will be used for managing clinical infections or screening colonizers. We have gathered a
9
collection of international non-clonal strains including several enterobacterial species
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demonstrating various susceptibilities to carbapenems which were used to assess these
11
methods (Table).
12
Identification of NDM-1 producers. Susceptibility testing were performed by
13
determining MIC values by Etest (AB bioMérieux; Solna, Sweden) on Mueller-Hinton agar
14
plates at 37°C and results of susceptibility testing were recorded according to the CLSI
15
guidelines as modified in June 2010 (4). Those breakpoints are for imipenem susceptible (S)≤
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1, ≥ 4 µg/ml/resistant (R), for meropenem S≤ 1, ≥4 µg/ml R, for ertapenem S≤ 0.25, ≥1 µg/ml
17
R, and for doripenem S≤ 1, ≥4 µg/ml R. Twenty six out of the 27 NDM-1 strains were
18
resistant to at least one carbapenem, and 8 were resistant only to ertapenem (Table). A single
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isolate (Providencia rettgeri A) was only of intermediate susceptibility to imipenem and
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ertapenem (Table). Various susceptibility to carbapenems has been reported for producers of
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other types of carbapenemases such as KPC and VIM producers (9, 10, 12,15) in particularly
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in E. coli. Ertapenem has been also proposed to be a most appropriate carbapenem for
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detecting KPC producers with low-level resistance to carbapenems (2, 15), and seems to be
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also the most appropriate carbapenem for detecting NDM-1 producers.
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1
The Etest MBL strip is one of the methods advocated for detecting metallo-ß-
2
lactamase producers based on inhibition of metallo ß-lactamase (MBL) activity by EDTA
3
(16). The Etest MBL using imipenem and imipenem/EDTA was reliable for that detection
4
except in two cases (Enterobacter cloacae D and K. pneumoniae E) for which the
5
interpretation of the results was not possible due to too low MIC values for imipenem (Table).
6
Therefore we have evaluated another technique, the combined disk test, based also on
7
inhibition of MBL activity by EDTA (6). Two imipenem disks (10 µg), one containing 10 µl
8
of 0.1 M EDTA (292 µg) anhydrous EDTA, were placed 25 mm apart onto a Mueller-Hinton
9
plate (6). A diameter superior to 4 mm around the IMP-EDTA as compared to that of the IMP
10
disk alone was considered positive for MBL. All 27 NDM-1 producers were positively
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detected by this technique (Table) which is reliable for detecting those MBL producers on a
12
daily basis. The E test MBL may be used in labs which do not screening for MBL producers
13
on a daily basis of for those which performed susceptibility testing using liquid medium
14
techniques and rarely used disk diffusion susceptility techniques.
15
The collection of NDM-1 producers was then examined by a commercial and
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automated system designed for antibiotic susceptibility testing, Vitek 2 (bioMérieux, La-
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Balme-Les-Grottes, France, expert system version 04.02). The tested carbapenem in card
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AST-N128 is imipenem with breakpoints for susceptibilty ≤ 2, and > 8 µg/ml for resistance.
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All NDM-1 producers had higher values of MICs of imipenem by Vitek2 as compared to
20
those obtained by the Etest method. They were of intermediate susceptibility or resistant to
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carbapenems and flagged as producers of carbapenemases. Our data mirror and extend the
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results obtained by another study that evaluated three automated systems BD Phoenix (BD
23
Diagnostics), Microscan (Siemens) and Vitek 2 (bioMerieux) for detection and inference of
24
mechanisms
25
Enterobacteriaceae (17). That study included six NDM-1 producers likely of UK origin (17).
responsible
for
carbapenem
resistance
in
carbapenem-resistant
5
1
Although carbapenemase detection by spectrophotometric assay has been suggested for
2
detecting carbapenemase producers of (10, 17) (and results were positive for all NDM-1
3
producers we tested here [data not shown]), we do not recommend this method on a routine
4
basis as it is time-consuming and does not discriminate between NDM-1 and other metallo-ß-
5
lactamases. Similarly, we do not recommend the Hodge test for detecting metallo-ß-lactamases
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activity which is not only time consuming but may also lack of specificity (15). Finally, the
7
detection of the blaNDM-1 gene based on a PCR molecular technique was established. Primers
8
assessed in this study were NDM-Fm (5’-GGTTTGGCGATCTGGTTTTC-3’, positions 133-
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153) and NDM-Rm (5’-CGGAATGGCTCATCACGATC-3’, positions 734-754) that amplified
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an internal fragment of 621 bp of the blaNDM-1 gene. Primers were designed according to the
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sequence of the blaNDM-1 gene of the GenBank database under accession n°FN392876. Total
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DNA from bacterial isolates was extracted by alkaline lysis. Negative controls include reference
13
strains producing the metallo-ß-lactamase blaIMP, blaVIM, blaSPM, blaGIM, and blaSIM genes. Two
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microliters of extracted total DNA were subjected to PCR in a 50-µl reaction mixture. The PCR
15
mixture for the detection of metallo-ß-lactamase genes was: 1× PCR buffer (10 mM Tris-HCl
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[pH 8.3], 50 mM KCl), 1.5 mM of MgCl2, 0.125 mM of each deoxynucleotide triphosphate, 10
17
µM of each primer, and 2 U of AmpliTaq Gold Polymerase (Roche, Meylan, France).
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Amplification were carried out with the following thermal cycling conditions: 10 min at 94°C
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and 36 cycles of amplification consisting of 30 sec at 94°C, 40 sec at 52°C, and 50 sec at 72°C,
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with 5 min at 72°C for the final extension. DNA fragments were visualized by electrophoresis in
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a 2% agarose gel at 100 V for 1 h in 1× TAE (40 mM Tris-HCl [pH 8.3], 2 mM Acetate, 1 mM
22
EDTA) containing 0.05 mg/L ethidium bromide. Using this technique the blaNDM-1-positive
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isolates were detected within less than 3 hours with 100% sensitivity and an excellent specificity
24
as deduced by testing a few reference strains expressing other types of carbapenemase genes
25
(data not shown).
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1
Screening of NDM-1 producers as a carriage state. The efficient prevention of
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spread of NDM-1 producers requires a rapid screening method that can detect NDM-1
3
producers as colonizer (mostly in the gastrointestinal tract) when the patient/carrier is
4
admitted to any health care facility. We have shown recently that the screening culture
5
medium ChromID ESBL culture medium (bioMérieux) containing cefpodoxime as a selector,
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and that is routinely used for screening extended spectrum ß-lactamase (ESBL) producers
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(13) may be used also for detecting carbapenemase-producing Enterobacteriaceae (1). This
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culture medium may also provide a preliminary bacterial identification (E. coli; K.
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pneumoniae…) at species level based on differential chromogenic properties of the
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enterobacterial species (13). Producers of IMP-, VIM- and KPC-type carbapenemases with
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high level of resistance to cephalosporins and to carbapenems were easily detected by
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ChromID ESBL (1). In this same study, we had evaluated another screening medium
13
CHROMagar KPC (CHROMagar company, Paris, France) which contains a carbapenem as
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the selector for resistance and was first specifically designed for screening KPC producers (1,
15
13). Using the CHROM agar medium, carbapenemase-producing isolates with MIC values <
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4 µg/mL were detecteda with much higher levels of detection limits (1).
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Since NDM-1-producers were not included in that study, we have now evaluated both
18
screening media using our collection of NDM-1 producers. An inoculum of ~ 2 x 106 CFU/ml
19
(range, 1.5 x 105 to 3.5 x 107 CFU/ml) was used and serial 10-fold dilution were made in
20
normal saline buffer, then 100 µl were plated onto sheep blood-containing tryptic soy agar,
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ChromID ESBL medium and Chromagar KPC media. Viable bacteria were counted after 24
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hours and 48 hours of culture at 37°C and growth on selective media was compared to growth
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on standard culture medium. The lowest limit of detection of NDM-1 producers ranged from
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8 x 100 to 5 x 102 CFU/ml for ChromID ESBL (Table). The ability of that medium to detect
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NDM-1 producers is based on the fact that those producers are also resistant to expanded-
7
1
spectrum cephalosporins which is in part due to the broad-spectrum hydrolytic properties of
2
ß-lactamase NDM-1 (Table). Therefore this detection was possible using ChromID ESBL
3
even though strain may not express an ESBL (E. coli B for example, [data not shown]). For
4
CHROMagar KPC, the lowest limit of detection of NDM-1 producers ranged between 1 x 101
5
to 4 x 105 CFU/ml (table). Those detection limits were higher than those of the ChromID
6
ESBL medium, especially for several strains with low MICs for carbapenems (E. coli B, E.
7
coli H, E. coli J, E. cloacae C, Klebsiella oxytoca A, Providencia rettgeri A). After the
8
screening of putative NDM-1 producers, definitive identification of the NDM-1 producers is
9
needed using the techniques developed above (susceptibility testing, Etest, and PCR)
10
(Figure). This detection strategy may help to prevent the development of clinically significant
11
outbreaks with NDM-1 positive clinical isolates, in particularly with NDM-1 (+) K.
12
pneumoniae.
CONCLUSION
13
14
Early identification of NDM-1 producers both in bacteria causing clinical infections
15
and/or colonizers is mandatory to prevent their spread. Identification of NDM-1 producers in
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clinical infections shall be suspected on any decreased susceptibility to carbapenems in
17
Enterobacteriacae especially in E. coli where resistance to carbapenems may not always be
18
apparent. The ChromID ESBL is a reliable culture media for screening NDM-1 producers as a
19
carriage state. Since ChromID ESBL may detect also ESBL producers, its usage for detecting
20
carbapenemase producers may be the source of extra workload. However the higher
21
sensitivity of the Chrom ID ESBL than the CHROMagar argues for its usage. In addition, the
22
ChromID ESBL offers the economical advantage to use a single plate for detecting ESBL
23
and carbapenemase producers.
24
The CHROMagar culture medium may be proposed for the follow up of an outbreak of
25
NDM-1 producers after identification of the first cases usingthe ChromID ESBL and after
8
1
checking that this medium is sensitive enough for detecting the specific NDM-1 producer
2
strain responsible for the outbreak. We believe that a screening strategy based on early
3
detection of NDM-1 producers for any international transfer of hospitalized patients at a
4
worldwide scale, and for at-risk patients in endemic areas may prevent the emergence of
5
outbreaks of NDM-1 producers.
6
7
ACKNOWLEDGMENTS
8
9
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This work was funded mostly by a grant from the INSERM (U914), by a grant-in-aid of the
11
Ministère de l’Education Nationale et de la Recherche (UPRES-EA3539), Université Paris
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XI, Paris, France and by a grant of the European Community (TEMPOtest-QC, HEALTH-
13
2009-241742). We thank Dr. A. Ros for gift of clinical isolate.
14
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of
CHROMagar
KPC
for
rapid
detection
of
carbapenem-resistant
Thomson, K. S. 2010. Extended-spectrum ß-lactamase, AmpC and carbapenemase
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lactamases: the quiet before the storm? Clin. Microbiol. Rev. 18:306-325.
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Woodford, N., A. T. Eastaway, M. Ford, A. Leanord, C. Keane, R. M. Quayle, J.
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A Steer, J. Zhang, and D. M. Livermore. 2010. Comparison of BD Phoenix, Vitek2, and
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Microscan automated systems for detection and inference of mechanisms responsible for
22
carbapenem resistance in Enterobacteriaceae. J. Clin. Microbiol. 48:2999-3002.
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Yong, D., M. A. Toleman, C. G. Giske, H. S. Cho, K. Sundman, K. Lee, and T. R.
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Walsh. 2009. Characterization of a new metallo-ß-lactamase gene, blaNDM-1, and a novel
25
erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae
11
1
sequence type 14 from India. Antimicrob. Agents Chemother. 53:5046-5054.
2
12
1
Table. Sensitivity of detection for ChromID ESBL medium and CHROMagar KPC medium
2
for 27 NDM-1 producers and the results of the combined disk test (IMP, IMP + EDTA) and
3
the
4
ceftazidime; IMP, imipenem; ETP, ertapenem; MER, meropenem, DOR, doripenem).
Etest MBL. MICs of several ß-lactams are also shown (CTX, cefotaxime, CAZ;
5
6
Figure legend. Strategy for identification of NDM-1 producers as a source of clinical
7
infections and for detecting NDM-1 producers at the carrier state. * This culture medium can
8
be used for surveillance of outbreak of NDM-1 producers after validation of its detection
9
sensitivity for a specific strain responsible of an outbreak. ** Etest MBL is reliable when
10
MIC of imipenem is not too low.
11
13
Isolate
MICs
µg/ml
Country of Isolation
CTX
CAZ
IMP
E test
ETP
MER
DOR
E. coli A
Australia
> 32
> 256
6
4
4
> 32
E. coli B
France
> 32
> 256
3
3
2
2
E. coli C
India
> 32
> 256
2
> 32
24
6
E. coli D
India
> 32
> 256
16
> 32
16
3
E. coli E
India
> 32
> 256
32
> 32
> 32
24
E. coli F
India
> 32
> 256
> 32
> 32
16
16
E. coli G
India
> 32
> 256
4
> 32
8
3
E. coli H
India
> 32
> 256
1.5
8
2
1
E. coli I
India
> 32
> 256
3
> 32
6
2
E. coli J
India
> 32
> 256
2
4
2
1.5
E. cloacae A
India
> 32
> 256
8
6
6
4
E. cloacae B
India
> 32
> 256
> 32
12
8
12
E. cloacae C
India
> 32
> 256
2
16
2
1
E. cloacae D
India
> 32
> 256
0.75
1.5
1
K. pneumoniae A
K. pneumoniae J
Kenya
Sultanate of Oman
Sultanate of Oman
India
India
India
India
India
India
India
K. oxytoca A
3
MBL
IMP/IMP+
EDTA
Lowest limit of detection
(CFU/ml)
Chrom ID ESBL
CHROMagar KPC
2 x 101
3 x 101
2 x 10 1
3 x 105
3 x 101
3 x 101
1 x 101
1 x 101
2 x 102
1 x 101
1 x 101
3 x 101
3 x 101
4 x 101
1 x 101
2 x 105
1 x 101
1 x 101
8 x 100
1 x 104
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
-*
+
+
+
+
1 x 101
5 x 101
1 x 101
1 x 101
3 x 102
4 x 104
1 x 101
1 x 102
+
+
+
+
+
+
+
+
+
+
2 x 101
1 x 101
1 x 101
2 x 101
1 x 101
3 x 102
2 x 101
3 x 101
1 x 101
3 x 102
1 x 101
8 x 101
1 x 101
1 x 102
1 x 101
5 x 102
1 x 101
5 x 102
1 x 101
1 x 101
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
1
6
2
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
8
2
1.5
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
2
6
2
1.5
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
> 32
> 32
> 32
> 32
> 32
> 256
6
> 32
16
12
+
+
+
+
-*
+
+
+
+
+
India
> 32
> 256
2
4
3
3
+
+
1 x 101
1 x 104
C. freundii A
France
> 32
> 256
> 32
> 32
> 32
> 32
+
+
1 x 101
1 x 101
P. rettgeri A
India
> 32
> 256
3
+
+
5 x 102
5 x 105
K. pneumoniae B
K. pneumoniae C
K. pneumoniae D
K. pneumoniae E
K. pneumoniae F
K. pneumoniae G
K. pneumoniae H
K. pneumoniae I
* No interpretable
0.75
0.5
1.5
2
0.75
Screening
of carrriers
Detection of
infecting
strains
ChromID ESBL
(CHROMagar KPC*)
Susceptibility testing
(disk diffusion, Vitek 2 and
other automated systems)
IMP/IMP +EDTA
(E-test MBL**)
Molecular identification of carbapenemase genes