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Genetic features associated with the blaNDM-1 gene were investigated in 6 Escherichia coli, 7 Klebsiella pneumoniae, 1 Citrobacter freundii, 1 Proteus mirabilis, and 1 Providencia stuartii isolate of worldwide origin. Clonal diversity was observed for both E. coli and K. pneumoniae. The blaNDM-1 gene was carried by different plasmid types (IncA/C, IncF, IncL/M, or untypeable) and was likely chromosome borne in two isolates. The blaNDM-1 plasmids coharbored a variety of resistance determinants, including β-lactamase genes, quinolone resistance genes, and 16S RNA methylase genes.
Recent reports showed that the plasmid-mediated blaNDM-1 gene encoding the metallo-β-lactamase (MBL) NDM-1 is spreading worldwide, mainly in members of the Enterobacteriaceae originating primarily from the Indian subcontinent (10, 14, 28).
Our aim was to compare the genetic features of NDM-1-producing strains recovered from unrelated countries by analyzing a collection of 16 multidrug-resistant and blaNDM-1-pos-itive enterobacterial isolates (Table 1). The genetic context and plasmid support of the blaNDM-1 gene were investigated, and the main broad-spectrum resistance determinants to non-β-lactam antibiotics were also examined.
Multilocus sequence typing (MLST) was performed as described previously (7, 26) for Escherichia coli and Klebsiella pneumoniae isolates. Five MLST types were identified among the six E. coli isolates, showing that diverse NDM-1-positive clones were circulating (Table 1). Only one out of the six E. coli isolates was an ST131 type, which is the major clone carrying the extended-spectrum ß-lactamase (ESBL) blaCTX-M-15 gene worldwide (4, 13). Similarly, four MLST types were identified among the seven K. pneumoniae isolates (Table 1). The ST14 type that corresponds to that of the first described NDM-1-producing K. pneumoniae isolate recovered in Sweden from an Indian patient (29) was also identified in three isolates, one each from India, Oman, and Kenya. Pulsed-field gel electrophoresis (PFGE) performed as described previously (4) and interpreted according to the criteria of Tenover et al. (27) showed that isolates from Oman, Kenya, and Sweden were clonally related, whereas the remaining ST14 isolate from India had a significantly different pattern (data not shown). In addition, the two ST147 K. pneumoniae isolates, one each from Switzerland and Iraq, were clonally related. The ST258 type known to carry the blaKPC genes worldwide was not identified here (5).
Just by analyzing strains isolated in India or elsewhere but from patients previously hospitalized on the Indian subcontinent, a large variety of ST types was evidenced, emphasizing the diversity of clones carrying the blaNDM-1 gene. This interesting feature is highlighted in Fig. 1, which includes data from our study but also from other studies in which information about MLST typing was available.
PCR was used with primers specific for many resistance genes (Table 2) (1, 3, 23). Most of the blaNDM-1-positive isolates coharbored an ESBL gene, mostly the blaCTX-M-15 gene. The blaTEM-1, blaOXA-1, and blaOXA-10 genes were also frequently detected. Cooccurrence of 16S RNA methylase genes encoding broad-spectrum aminoglycoside resistance was often observed, being of different types (armA, rmtA, rmtB, and rmtC). Among the plasmid-mediated quinolone resistance genes, a qnr-type gene was identified in a few cases, as well as the aac(6′)-Ib-cr gene encoding reduced susceptibility to ciprofloxacin and the qepA efflux pump-encoding gene (Table 1). These results indicate that the NDM-1 producers have gathered uncommon and unrelated broad-spectrum resistance genes, suggesting that they have been selected by broad-spectrum antibiotics. These high levels of resistance did not result from single genetic events.
Mating-out assays performed as described previously (24) with NDM-1 producers as the donors and azide-resistant E. coli J53 as the recipient and using a selection based on cefoxitin (10 μg/ml) (cefoxitin being a substrate of NDM-1 but not of ESBLs) and azide (100 μg/ml) produced transconjugants except for two strains (Table 1). Analysis of plasmid DNAs as reported previously (9) identified a variety of plasmid supports in those transconjugants according to their sizes, which ranged from 35 to 170 kb (Table 1). No blaNDM-1-carrying plasmid was identified in two isolates (E. coli RKI and Providencia stuartii PS1), suggesting the presence of a chromosomal support. Some transconjugants possessed two plasmids, indicating that several blaNDM-1-positive plasmids were likely not self-conjugative and required a helper plasmid for their mobilization. This was confirmed by electrotransformation experiments using plasmid extracts from donors and electrocompetent E. coli TOP10 as the recipient and a selection based on cefoxitin (10 μg/ml). Transformants were obtained for all strains except for E. coli RKI and P. stuartii PS1.
Plasmid incompatility groups were then assigned by using the PCR-based replicon typing method (2), identifying a variety of plasmid scaffolds carrying the blaNDM-1 gene. Our data indicate that its current spread is therefore not related to a single plasmid. Several plasmids were of narrow host range, such as the IncF plasmids, and thus able to disseminate among Enterobacteriaceae only; others were of broad host range, such as the IncA/C types, able to also replicate in Acinetobacter and Pseudomonas species.
We previously identified insertion sequences (IS) located on both extremities of the blaNDM-1 gene in E. coli 271 (19). In that isolate, the blaNDM-1 gene was bracketed by ISEc33 and ISSen4 (19) (Fig. 2). Further analysis performed on that isolate identified that part of ISAba125, an IS element that had been previously identified in blaNDM-1-negative Acinetobacter strains (8, 12) was present upstream of blaNDM-1. Primers specific for ISAba125 were designed, targeting its right end comprising the promoter sequence as well as its left end (Table 2; Fig. 2). We also identified a gene we named bleMBL which encoded a 122-amino-acid-long protein and conferred putative resistance to bleomycin immediately downstream of the blaNDM-1 gene in E. coli GUE. Thus, primers specific for this bleMBL gene were also designed (Table 2), and their locations are indicated in Fig. 2.
Genetic structures surrounding the blaNDM-1 gene showed that at least a remnant of insertion sequence ISAba125 was systematically present upstream of the blaNDM-1 gene. The entire ISAba125 element was identified upstream of the blaNDM-1 gene in most isolates, except in three cases (E. coli 271 and K. pneumoniae Kp7 and 601) (Table 1). However, the ISEc33 identified in E. coli 271 was absent in K. pneumoniae Kp7 and 601 (Fig. 2). These results suggest that ISAba125 was likely at the origin of the original mobilization of the blaNDM-1 from its progenitor.
Downstream of the blaNDM-1 gene, the bleMBL gene was quite systematically identified in most isolates; it was not amplified by PCR in four isolates only (Table 1). Those isolates were from France and Switzerland, and the source of contamination could be traced back to India, Pakistan, and Serbia (21; this study). This would suggest that an ISAba125-related initial mobilization mechanism had been responsible for an acquisition en bloc of both the blaNDM-1 and bleMBL genes. Therefore, our working hypothesis is that both the blaNDM-1 and the bleMBL gene originated from the same progenitor.
This study showed that almost all NDM-1 producers coexpressed plasmid-mediated AmpCs or ESBLs, which may have initially contributed to the frequent use of carbapenems for treating related infections. As opposed to what has been observed for CTX-M-15 or KPC-2, NDM-1 is not associated with certain clones, plasmids, or transposons. The only common features identified here correspond to an ISAba125 element and a bleMBL gene identified upstream and downstream, respectively, of the blaNDM-1 gene. The diversity of genetic features associated with the blaNDM-1 gene may explain its current high rate of spread worldwide.
The research leading to these results received funding from the INSERM (U914), Paris, France, and the European Community's Seventh Framework Programme FP7/2007-2013 under grant agreement no. 241742 (TEMPOtest-QC).
Published ahead of print on 22 August 2011.