Skip to main content
NCBI home page
Antimicrobial Agents and Chemotherapy logoLink to Antimicrobial Agents and Chemotherapy
. 2015 Dec 31;60(1):136–141. doi: 10.1128/AAC.01243-15

Genomic Characteristics of NDM-Producing Enterobacteriaceae Isolates in Australia and Their blaNDM Genetic Contexts

Alexander M Wailan a, David L Paterson a,b, Karina Kennedy c, Paul R Ingram d, Evan Bursle a,e, Hanna E Sidjabat a,✉
PMCID: PMC4704237  PMID: 26482302

Abstract

blaNDM has been reported in different Enterobacteriaceae species and on numerous plasmid replicon types (Inc). Plasmid replicon typing, in combination with genomic characteristics of the bacterial host (e.g., sequence typing), is used to infer the spread of antimicrobial resistance determinants between genetically unrelated bacterial hosts. The genetic context of blaNDM is heterogeneous. In this study, we genomically characterized 12 NDM-producing Enterobacteriaceae isolated in Australia between 2012 and 2014: Escherichia coli (n = 6), Klebsiella pneumoniae (n = 3), Enterobacter cloacae (n = 2) and Providencia rettgeri (n = 1). We describe their blaNDM genetic contexts within Tn125, providing insights into the acquisition of blaNDM into Enterobacteriaceae. IncFII-type (n = 7) and IncX3 (n = 4) plasmids were the most common plasmid types found. The IncHI1B (n = 1) plasmid was also identified. Five different blaNDM genetic contexts were identified, indicating four particular plasmids with specific blaNDM genetic contexts (NGCs), three of which were IncFII plasmids (FII-A to -C). Of note, the blaNDM genetic context of P. rettgeri was not conjugative. Epidemiological links between our NDM-producing Enterobacteriaceae were established by their acquisition of these five particular plasmid types. The combination of different molecular and genetic characterization methods allowed us to provide insight into the spread of plasmids transmitting blaNDM.

INTRODUCTION

Plasmids have received increased attention in the last decade due to their ability to acquire genes conferring antibiotic resistance and to transfer them between different bacterial hosts. Plasmids of the family Enterobacteriaceae have been categorized into replicon (Inc) types via PCR-based replicon typing (PBRT) (1–3). PBRT, in combination with other characteristics of the bacterial host, such as serotype, sequence type (ST) via multilocus sequence typing (MLST), and resistance gene profiles, is used to demonstrate the spread of antimicrobial resistance determinants between genetically unrelated bacterial hosts (4).

New Delhi metallo-β-lactamase gene (blaNDM)-harboring plasmids have been extensively characterized. Genetic variations in the accessory regions of plasmids have contributed to the complexity that underlies the spread of antimicrobial resistance determinants between bacterial hosts. Since its first description (5), blaNDM has been reported on various plasmid Inc types (6), including IncA/C (7, 8), IncF types (9), IncL/M (10), IncH (11), IncN types (12–14), IncX types (15), and IncHI1 types (16), of the family Enterobacteriaceae. However, it may be misleading to assume that all plasmids of the same replicon type are identical, especially among the IncA/C (7, 17–19) and IncFII (9, 20) plasmids. For Enterobacteriaceae plasmids harboring blaNDM, the variation in the genetic context of blaNDM generally involves two features. First, blaNDM is frequently observed in the 10,099-bp transposon Tn125 (with two flanking ISAba125 elements) within NDM-producing species of the genus Acinetobacter (17, 21–24). The blaNDM gene was hypothesized to originate in the genus Acinetobacter (25). In Enterobacteriaceae, the Tn125 structure carrying blaNDM is frequently truncated (ΔTn125) at various lengths (17). Second, the sequence flanking the ΔTn125 structure involves various mechanisms of gene acquisition, including different ISCR elements (18), class 1 integrons (19), flanking insertion sequence (IS) elements (18), miniature inverted-repeat transposable elements (MITEs) (26), and singleton IS elements, present in close proximity (8, 10). The variations observed in these two features have contributed to the different blaNDM genetic contexts reported, even on the same plasmid type.

The blaNDM genetic contexts of NDM producers from Singapore, Japan, Hong Kong, Thailand, and Taiwan have been described (10, 12–14, 18). Additionally, NDM-producing Enterobacteriaceae have been reported in Australia (27, 28). Limited studies have described the plasmid features and genetic contexts of NDM producers from Australia (29–31). Here, we analyze the blaNDM genetic contexts of 12 NDM-producing Enterobacteriaceae isolates from Australia between 2012 and 2014 to provide insights into their likely acquisition.

(Part of this study was presented as a poster presentation at the Gram-Negative Superbugs Gold Coast in 2013.)

MATERIALS AND METHODS

Isolates.

Twelve clinical or screening isolates producing NDM in this study from Queensland, Australian Capital Territory, and Western Australia were referred to the University of Queensland Centre for Clinical Research for detailed molecular characterization between 2012 and 2014. The isolates included Escherichia coli (n = 6), Klebsiella pneumoniae (n = 3), Enterobacter cloacae (n = 2), and Providencia rettgeri (n = 1) (Table 1). The work was approved by the human research ethics committee (HREC/13/QRBW/391: epidemiology, clinical significance, treatment, and outcome of infections by carbapenem-resistant Enterobacteriaceae and Acinetobacter spp. in Queensland).

TABLE 1.

Specimens, sequence types, resistance determinants, and plasmid types of Enterobacteriaceae strains that acquired plasmids harboring blaNDMf

graphic file with name zac00116-4694-t01.jpg

Open in a new tab
a

Isolates from this study.

b

Strain was first described in this study.

c

M, male; F, female; R, rectal swab; U, urine; B, blood; S, swab. Age (in years) is given in parentheses.

d

ST, sequence type, determined by available MLST schemes; N/A, not available.

e

Responsible for aminoglycoside and quinolone resistance.

f

Shaded boxes indicate the replicon types and genes present in each strain as determined by PlasmidFinder and ResFinder.

Antimicrobial susceptibility testing.

Antimicrobial susceptibility and MIC characterization was performed by Etest (bioMérieux, Marcy l'Etoile, France). The antimicrobial agents tested were ceftazidime, cefotaxime, ceftriaxone, cefepime, aztreonam, amikacin, doripenem, ertapenem, meropenem, imipenem, and tetracycline. Susceptibility results were interpreted according to the 2015 EUCAST clinical breakpoint guidelines (http://www.eucast.org/clinical_breakpoints/).

Plasmid experiments.

Plasmid transfer experiments by conjugation and transformation were performed on all NDM producers using a previously described technique (32). Sodium azide-resistant E. coli J53 and E. coli Top10 were used as the recipients for conjugation and transformation experiments, respectively. The transconjugants and transformants acquiring blaNDM-harboring plasmids were examined phenotypically and confirmed by PCR for blaNDM. PBRT was used to identify the plasmid Inc type carrying blaNDM as previously described (1–3).

Whole-genome sequencing.

Paired-end libraries of whole genomic DNA of all 12 isolates were prepared and sequenced by Illumina HiSeq2000 (Illumina, San Diego, CA, USA). All sequences were de novo assembled using CLC Genomic Workbench v7.5 (CLC Bio, Aarhus, Denmark). Reannotated sequences from the GenBank database, which included pNDM-BJ01 (GenBank accession no. JQ001791) (24), were used as a reference for manual annotation. CLC Genomic Workbench was further used to BLAST search (http://blast.ncbi.nlm.nih.gov/Blast.cgi), analyze, and manually annotate the blaNDM-1 genetic context according to the above-mentioned reference sequences. IS element identification within each context was achieved via IS finder (https://www-is.biotoul.fr/). Contigs containing blaNDM from each isolate were named as follows: pCR7-EC-NDM-1 (E. coli CR7), pCR15-EC-NDM-4 (E. coli CR15), pCR16-ECL-NDM-1 (E. cloacae CR16), pCR37-ECL-NDM-7 (E. cloacae CR37), pCR38-KP-NDM-1 (K. pneumoniae CR38), pCR53-EC-NDM-4 (E. coli CR53), pCR58-PR-NDM-1 (P. rettgeri CR58), pCR63-KP-NDM-1 (K. pneumoniae CR63), pWA1-EC-NDM-4 (E. coli WA1), pWA2-KP-NDM-7 (K. pneumoniae WA2), and pACT1-EC-NDM-1 (E. coli ACT1). pCR694-EC-NDM-5 (E. coli CR694) had previously been submitted to the GenBank database (GenBank accession no. KP178355) (31). Contigs of the entire genome were submitted to the Center for Genomic Epidemiology (http://www.genomicepidemiology.org/) to identify the plasmid replicons and the resistance genes of each clinical isolate, as well as its ST via an available MLST scheme. Specifically, the databases Plasmid finder 1.2 (33), Resfinder 2.1 (34), and MLST 1.7 (35) were used.

Nucleotide sequence accession numbers.

Contigs containing blaNDM from each isolate were annotated and deposited into the GenBank database with the following accession numbers: pCR7-EC-NDM-1, KP826713; pCR15-EC-NDM-4, KP826709; pCR16-ECL-NDM-1, KP826704; pCR37-ECL-NDM-7, KP826705; pCR38-KP-NDM-1, KP826710; pCR53-EC-NDM-4, KP826711; pCR58-PR-NDM-1, KP826706; pCR63-KP-NDM-1, KP826712; pWA1-EC-NDM-4, KP826707; pWA2-KP-NDM-7, KP826708; and pACT1-EC-NDM-1, KP826702.

RESULTS AND DISCUSSION

In comparison to other geographical regions, such as the United Kingdom, China, and the Indian subcontinent (21, 36–39), there are relatively few reports of NDM-producing Enterobacteriaceae from Australia. In the majority of the cases preceding 2014, patients had a history of travel to high-incidence countries (32). Investigations of plasmid-mediated blaNDM involving the description of carbapenem-resistant species within Australia have rarely included genetic-context characterization. By utilizing genetic-context characterization in our study, we provide insights into the acquisition of blaNDM through five groups of plasmids, each carrying a specific blaNDM genetic context (NGC) type.

Phenotypic characterization of the NDM-producing Enterobacteriaceae.

All the isolates were nonsusceptible to all the tested carbapenems, with meropenem, ertapenem, imipenem, and doripenem MICs of >32 μg/ml. All the isolates were resistant to the 3rd and 4th generation cephalosporins, with cefotaxime and ceftriaxone MICs of >32 μg/ml and ceftazidime and cefepime MICs of >256 μg/ml. Interestingly, aztreonam MICs were generally >256 μg/ml, except in NDM-5-producing E. coli, with a MIC of 24 μg/ml. Variability of the amikacin MICs was observed and was correlated with the presence or absence of 16S rRNA methylase. The amikacin MICs of NDM-producing Enterobacteriaceae possessing 16S rRNA methylase genes were >256 μg/ml. In contrast, isolates without 16S rRNA methylase genes had amikacin MICs between 1 and 2 μg/ml.

Genotypic characterization of the NDM-producing Enterobacteriaceae.

In silico analysis of the molecular characteristics of the isolates, STs, antibiotic resistance determinant genes, plasmid replicons, and blaNDM genetic context are tabulated in Table 1. The ST of CR58 is not provided, as there was no available MLST scheme for P. rettgeri. Common antimicrobial resistance determinants identified among the isolates included the following four blaNDM variants described here, i.e., blaNDM-1 in 6 strains, blaNDM-4 in 3 strains, blaNDM-5 in 1 strain (6), and blaNDM-7 in 2 strains (Table 1). Each clinical isolate except CR53, CR58, and CR694 carried blaCTX-M-15 and at least one aminoglycoside resistance gene, including 16S rRNA methylase genes, rmtB, rmtC, aac(6′)Ib-cr, or armA. CR38 also coharbored the carbapenemase gene blaOXA-48. There was no correlation between the blaNDM variants and the replicon types. Among NDM producers with FII plasmids, two variants, blaNDM-1 and blaNDM-4, were identified. Four variants, blaNDM-1, blaNDM-4, blaNDM-5, and blaNDM-7, were identified on replicon type X3 blaNDM-harboring plasmids. Comparisons of plasmid replicon types and their blaNDM genetic contexts enabled us to identify links between genetically unrelated bacterial species, regardless of their STs and resistance determinant profiles.

Characterization of plasmids harboring blaNDM.

Six blaNDM-harboring plasmids that underwent plasmid transfer experiments by transformation—CR15, CR16, CR37, CR694, WA1, and WA2—were successfully transferred into E. coli TOP10. Multiple attempts to transfer blaNDM-harboring plasmids by transformation to the rest of the NDM-producing Enterobacteriaceae were not successful. In conjugation experiments, of the 12 NDM-producing Enterobacteriaceae, 10 blaNDM-harboring plasmids were transferred. Of note, the conjugation experiment with K. pneumoniae CR38 resulted in the transfer of a blaOXA-48-harboring plasmid, but not a blaNDM-harboring plasmid, into E. coli J53. The blaNDM gene of P. rettgeri CR58 was not transferred by conjugation and transformation. This may indicate the potential location of blaNDM on a nonconjugative plasmid or a potential chromosomal location. The replicons of plasmids harboring blaNDM extracted from transformed E. coli TOP10 and E. coli J53 transconjugants acquiring blaNDM-harboring plasmids are listed in Table 1.

Utilizing the WGS data, blaNDM genetic-context characterization of each strain identified a truncated Tn125 (ΔTn125) structure carrying blaNDM. pNDM-BJ01 was used as the reference sequence (26). The left-hand ISAba125 of the ΔTn125 structure was truncated, and the ΔTn125 sequence ends at various lengths downstream of blaNDM (Fig. 1). The sizes of the ΔTn125 structure ranged from 1,769 bp to 8,046 bp. Characterizing the flanking regions of each ΔTn125 structure identified two recurrent genetic contexts repeated in two clinical isolates and three distinct genetic contexts, each found in a separate clinical isolate. Five different types or groups of NGCs were determined. They were used to categorize each NDM-producing strain into five blaNDM-harboring plasmid groups according to their respective NGC. There are three types of NGCs within FII-type plasmids (FII-A to -C). The other two types were X3-A and HI1B-A (Fig. 1). The strains, NDM plasmid type, and NGC type of each group are described below.

FIG 1.

FIG 1

Open in a new tab

Schematic representation of all the NGCs in the study and the reference sequence pNDM-BJ01 (GenBank accession no. JQ001791). The blaNDM genetic contexts and their GenBank accession numbers are as follows: IncFII plasmids with NGC type FII-A (pCR53-EC-NDM-4 [KP826711], pWA1-EC-NDM-4 [KP826707], pACT1-EC-NDM-1 [KP826702], and pCR7-EC-NDM-1 [KP826713]), with NGC type FII-B (pCR16-ECL-NDM-1 [KP826704] and pCR63-KP-NDM-1 [KP826712]), and with NGC type FII-C (pCR38-KP-NDM-1 [KP826710]); IncX3 plasmids with NGC type X3-A (pCR37-ECL-NDM-7 [KP826705], pWA2-KP-NDM-7 [KP826708], and pCR15-EC-NDM-4 [KP826709]); and an IncHI1B plasmid with NGC type HI1B-A (pCR58-PR-NDM-1 [KP826706]). Δ, truncated gene. IS elements are represented as block arrows. The vertical black arrows indicate insertion of IS elements. Reference sequences from GenBank for each genetic context are in boldface: pGUE-NDM (GenBank accession no. NC_019089), pECL3-NDM-1 (GenBank accession no. KC887917), pKOX-NDM-1 (GenBank accession no. JQ314407), pNDM_MGR194 (GenBank accession no. KF220657), pTR3 (GenBank accession no. JQ349086), and PittNDM01 (GenBank accession no. CP006799). The gray box highlights blaNDM in each genetic context.

Strains harboring FII-type plasmids.

The IncFII type was the most frequent Inc type, identified in 7 of the 12 plasmids harboring blaNDM (Table 1). Three of the five plasmid groups were NGC FII type. The strains harboring IncFII types were categorized into three different FII groups according to the three different FII blaNDM genetic contexts (NGC types FII-A to -C). The strains and their FII plasmid subtypes and corresponding NGC types were identified as follows. Four E. coli strains, CR7, CR53, WA, and ACT1, carried an FII subtype plasmid harboring NGC type FII-A. NGC type FII-A had a 3,328-bp ΔTn125 structure, flanked upstream by a truncated ISEcp1 and the right end of IS26 and downstream by an ISCR1 element and is very similar to the blaNDM genetic context on IncFII pGUE-NDM (GenBank accession no. NC_019089) of an E. coli ST131 strain isolated in France (20) and IncFII pMC-NDM (GenBank accession no. HG003695) of an E. coli ST410 strain isolated in Poland (40).

The second plasmid group had strains with an FIIY plasmid with NGC type FII-B. Two strains, E. cloacae ST265 strain CR16 and K. pneumoniae ST45 strain CR63, were included in the group. NGC type FII-B involved a 7,977-bp ΔTn125 structure with IS903B and an IS1 family element upstream and was very similar to pECL3-NDM-1 (direct-submission GenBank accession no. KC887917) of E. cloacae ECL3 isolated in Australia.

The third group carried an FIIY plasmid with NGC type FII-C with K. pneumoniae ST15 strain CR38. NGC type FII-C is a 5,947-bp ΔTn125 structure flanked by two identical 256-bp MITEs. The aminoglycoside resistance determinant rmtC was also identified upstream of the ΔTn125 structure of NGC type FII-C and is very similar to IncFII pKOX_NDM1 (GenBank accession no. JQ314407) of Klebsiella oxytoca isolated in Taiwan (26).

Strains harboring IncX3 and IncHI1B.

Similar to the analysis of IncFII blaNDM plasmids, blaNDM genetic-context groups were established with the remaining clinical strains that harbored IncX3 and IncHI1B plasmids. The fourth plasmid group is composed of strains carrying an IncX3 plasmid with the NGC type X3-A. The four clinical isolates in this group are E. cloacae ST127 strain CR37, E. coli ST101 strain CR15, E. coli ST648 strain CR694, and K. pneumoniae ST15 strain WA2. NGC type X3-A involved a 3,167-bp ΔTn125 structure flanked by an IS5 upstream and an IS26 downstream and was similar to the IncX3 plasmid pNDM-MGR194 (accession no. KF220657) of K. pneumoniae isolated in India (41).

The last plasmid group carried an IncHI1B plasmid with NGC type HI1B containing P. rettgeri strain CR58. NGC type HI1B-A consists of an 8,046-bp ΔTn125 sequence with a partial sequence of ISEc33 upstream and is identical to IncHI1B pPKPN1 of K. pneumoniae strain PittNDM01 ST14 (GenBank accession no. CP006799) isolated in Pittsburgh, PA (42).

Although this study had a small sample size, it could indicate further potential wide dissemination of blaNDM by IncFII-type and IncX3 plasmids in Australia. Geographically specific dissemination of blaNDM by a certain group of plasmid types has been previously reported with five identical IncN2 plasmids harboring blaNDM in four K. pneumoniae and one E. coli ST131 isolates in two countries in Southeast Asia (13, 14). The characterization presented here would indeed help to track the horizontal movement of blaNDM among members of the family Enterobacteriaceae.

While the mechanism and factors through which these genetic contexts originated and the source and environment in which the strains have acquired these plasmids remain unknown, the five groups of plasmids carrying these specific blaNDM genetic contexts within different bacterial species highlight the role of plasmids in transmitting mechanisms of carbapenem resistance. Genetic-context characterization was an accurate method, allowing us to refine epidemiological links between strains established by the acquisition of plasmids carrying a specific blaNDM genetic context. We suggest genetic-context characterization as an additional tool in combination with other molecular methods, such as plasmid replicon typing and sequence typing via MLST, when conducting epidemiology studies involving NDM producers of the family Enterobacteriaceae and possibly other promiscuous antimicrobial resistance determinants.

In conclusion, we have identified five particular plasmids with specific blaNDM genetic contexts conferring carbapenem resistance in the family Enterobacteriaceae through genetic-context characterization in combination with other epidemiological molecular methods. IncFII-type and IncX3 plasmids were the most frequent plasmids carrying blaNDM within our study, with three different blaNDM genetic contexts identified among the IncFII-type plasmids. By combining different molecular and genetic characterization methods, epidemiological investigations can provide better insight into the spread of plasmids transmitting blaNDM and possibly other, similar promiscuous resistance mechanisms to genetically unrelated bacterial species.

ACKNOWLEDGMENTS

We thank all the microbiology laboratory staff who referred the isolates.

The funding for the whole-genome sequencing was partially provided by the Australian Infectious Diseases Research Centre.

REFERENCES

  • 1.Carattoli A, Bertini A, Villa L, Falbo V, Hopkins KL, Threlfall EJ. 2005. Identification of plasmids by PCR-based replicon typing. J Microbiol Methods 63:219–228. doi: 10.1016/j.mimet.2005.03.018. [DOI] [PubMed] [Google Scholar]
  • 2.Johnson TJ, Bielak EM, Fortini D, Hansen LH, Hasman H, Debroy C, Nolan LK, Carattoli A. 2012. Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae. Plasmid 68:43–50. doi: 10.1016/j.plasmid.2012.03.001. [DOI] [PubMed] [Google Scholar]
  • 3.Villa L, Garcia-Fernandez A, Fortini D, Carattoli A. 2010. Replicon sequence typing of IncF plasmids carrying virulence and resistance determinants. J Antimicrob Chemother 65:2518–2529. doi: 10.1093/jac/dkq347. [DOI] [PubMed] [Google Scholar]
  • 4.Carattoli A. 2013. Plasmids and the spread of resistance. Int J Med Microbiol 303:298–304. doi: 10.1016/j.ijmm.2013.02.001. [DOI] [PubMed] [Google Scholar]
  • 5.Yong D, Toleman MA, Giske CG, Cho HS, Sundman K, Lee K, Walsh TR. 2009. Characterization of a new metallo-beta-lactamase gene, bla(NDM-1), and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14 from India. Antimicrob Agents Chemother 53:5046–5054. doi: 10.1128/AAC.00774-09. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 6.Wailan AM, Paterson DL. 2014. The spread and acquisition of NDM-1: a multifactorial problem. Expert Rev Anti Infect Ther 12:91–115. doi: 10.1586/14787210.2014.856756. [DOI] [PubMed] [Google Scholar]
  • 7.Carattoli A, Villa L, Poirel L, Bonnin RA, Nordmann P. 2012. Evolution of IncA/C blaCMY-2-carrying plasmids by acquisition of the blaNDM-1 carbapenemase gene. Antimicrob Agents Chemother 56:783–786. doi: 10.1128/AAC.05116-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Hudson CM, Bent ZW, Meagher RJ, Williams KP. 2014. Resistance determinants and mobile genetic elements of an NDM-1-encoding Klebsiella pneumoniae strain. PLoS One 9:e99209. doi: 10.1371/journal.pone.0099209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Hishinuma A, Yoshida A, Suzuki H, Okuzumi K, Ishida T. 2013. Complete sequencing of an IncFII NDM-1 plasmid in Klebsiella pneumoniae shows structural features shared with other multidrug resistance plasmids. J Antimicrob Chemother 68:2415–2417. doi: 10.1093/jac/dkt190. [DOI] [PubMed] [Google Scholar]
  • 10.Ho PL, Lo WU, Yeung MK, Lin CH, Chow KH, Ang I, Tong AH, Bao JY, Lok S, Lo JY. 2011. Complete sequencing of pNDM-HK encoding NDM-1 carbapenemase from a multidrug-resistant Escherichia coli strain isolated in Hong Kong. PLoS One 6:e17989. doi: 10.1371/journal.pone.0017989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 11.Villa L, Poirel L, Nordmann P, Carta C, Carattoli A. 2012. Complete sequencing of an IncH plasmid carrying the blaNDM-1, blaCTX-M-15 and qnrB1 genes. J Antimicrob Chemother 67:1645–1650. doi: 10.1093/jac/dks114. [DOI] [PubMed] [Google Scholar]
  • 12.Chen CJ, Wu TL, Lu PL, Chen YT, Fung CP, Chuang YC, Lin JC, Siu LK. 2014. Closely related NDM-1-encoding plasmids from Escherichia coli and Klebsiella pneumoniae in Taiwan. PLoS One 9:e104899. doi: 10.1371/journal.pone.0104899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Chen YT, Lin AC, Siu LK, Koh TH. 2012. Sequence of closely related plasmids encoding blaNDM-1 in two unrelated Klebsiella pneumoniae isolates in Singapore. PLoS One 7:e48737. doi: 10.1371/journal.pone.0048737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Netikul T, Sidjabat HE, Paterson DL, Kamolvit W, Tantisiriwat W, Steen JA, Kiratisin P. 2014. Characterization of an IncN2-type blaNDM-1-carrying plasmid in Escherichia coli ST131 and Klebsiella pneumoniae ST11 and ST15 isolates in Thailand. J Antimicrob Chemother 69:3161–3163. doi: 10.1093/jac/dku275. [DOI] [PubMed] [Google Scholar]
  • 15.Wang X, Xu X, Li Z, Chen H, Wang Q, Yang P, Zhao C, Ni M, Wang H. 2014. An outbreak of a nosocomial NDM-1-producing Klebsiella pneumoniae ST147 at a teaching hospital in mainland China. Microb Drug Resist 20:144–149. doi: 10.1089/mdr.2013.0100. [DOI] [PubMed] [Google Scholar]
  • 16.Dolejska M, Villa L, Poirel L, Nordmann P, Carattoli A. 2013. Complete sequencing of an IncHI1 plasmid encoding the carbapenemase NDM-1, the ArmA 16S RNA methylase and a resistance-nodulation-cell division/multidrug efflux pump. J Antimicrob Chemother 68:34–39. doi: 10.1093/jac/dks357. [DOI] [PubMed] [Google Scholar]
  • 17.Partridge SR, Iredell JR. 2012. Genetic contexts of blaNDM-1. Antimicrob Agents Chemother 56:6065–6067, 6071. doi: 10.1128/AAC.00117-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 18.Sekizuka T, Matsui M, Yamane K, Takeuchi F, Ohnishi M, Hishinuma A, Arakawa Y, Kuroda M. 2011. Complete sequencing of the blaNDM-1-positive IncA/C plasmid from Escherichia coli ST38 isolate suggests a possible origin from plant pathogens. PLoS One 6:e25334. doi: 10.1371/journal.pone.0025334. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 19.McGann P, Hang J, Clifford RJ, Yang Y, Kwak YI, Kuschner RA, Lesho EP, Waterman PE. 2012. Complete sequence of a novel 178-kilobase plasmid carrying blaNDM-1 in a Providencia stuartii strain isolated in Afghanistan. Antimicrob Agents Chemother 56:1673–1679. doi: 10.1128/AAC.05604-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 20.Bonnin RA, Poirel L, Carattoli A, Nordmann P. 2012. Characterization of an IncFII plasmid encoding NDM-1 from Escherichia coli ST131. PLoS One 7:e34752. doi: 10.1371/journal.pone.0034752. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 21.Jones LS, Toleman MA, Weeks JL, Howe RA, Walsh TR, Kumarasamy KK. 2014. Plasmid carriage of blaNDM-1 in clinical Acinetobacter baumannii isolates from India. Antimicrob Agents Chemother 58:4211–4213. doi: 10.1128/AAC.02500-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 22.Zong Z, Zhang X. 2013. blaNDM-1-carrying Acinetobacter johnsonii detected in hospital sewage. J Antimicrob Chemother 68:1007–1010. doi: 10.1093/jac/dks505. [DOI] [PubMed] [Google Scholar]
  • 23.Pfeifer Y, Wilharm G, Zander E, Wichelhaus TA, Gottig S, Hunfeld KP, Seifert H, Witte W, Higgins PG. 2011. Molecular characterization of blaNDM-1 in an Acinetobacter baumannii strain isolated in Germany in 2007. J Antimicrob Chemother 66:1998–2001. doi: 10.1093/jac/dkr256. [DOI] [PubMed] [Google Scholar]
  • 24.Hu H, Hu Y, Pan Y, Liang H, Wang H, Wang X, Hao Q, Yang X, Yang X, Xiao X, Luan C, Yang Y, Cui Y, Yang R, Gao GF, Song Y, Zhu B. 2012. Novel plasmid and its variant harboring both a blaNDM-1 gene and type IV secretion system in clinical isolates of Acinetobacter lwoffii. Antimicrob Agents Chemother 56:1698–1702. doi: 10.1128/AAC.06199-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 25.Toleman MA, Spencer J, Jones L, Walsh TR. 2012. blaNDM-1 is a chimera likely constructed in Acinetobacter baumannii. Antimicrob Agents Chemother 56:2773–2776. doi: 10.1128/AAC.06297-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 26.Huang TW, Wang JT, Lauderdale TL, Liao TL, Lai JF, Tan MC, Lin AC, Chen YT, Tsai SF, Chang SC. 2013. Complete sequences of two plasmids in a blaNDM-1-positive Klebsiella oxytoca isolate from Taiwan. Antimicrob Agents Chemother 57:4072–4076. doi: 10.1128/AAC.02266-12. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 27.Shoma S, Kamruzzaman M, Ginn AN, Iredell JR, Partridge SR. 2014. Characterization of multidrug-resistant Klebsiella pneumoniae from Australia carrying blaNDM-1. Diagn Microbiol Infect Dis 78:93–97. doi: 10.1016/j.diagmicrobio.2013.08.001. [DOI] [PubMed] [Google Scholar]
  • 28.Rogers BA, Sidjabat HE, Paterson DL. 2011. Escherichia coli O25b-ST131: a pandemic, multiresistant, community-associated strain. J Antimicrob Chemother 66:1–14. doi: 10.1093/jac/dkq415. [DOI] [PubMed] [Google Scholar]
  • 29.Espedido BA, Dimitrijovski B, van Hal SJ, Jensen SO. 2015. The use of whole-genome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J Clin Pathol 68:835–838. doi: 10.1136/jclinpath-2015-203044. [DOI] [PubMed] [Google Scholar]
  • 30.Poirel L, Lagrutta E, Taylor P, Pham J, Nordmann P. 2010. Emergence of metallo-beta-lactamase NDM-1-producing multidrug-resistant Escherichia coli in Australia. Antimicrob Agents Chemother 54:4914–4916. doi: 10.1128/AAC.00878-10. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 31.Wailan AM, Paterson DL, Caffery M, Sowden D, Sidjabat HE. 2015. Draft genome sequence of NDM-5-producing Escherichia coli sequence type 648 and genetic context of blaNDM-5 in Australia. Genome Announc 3:e00194-15. doi: 10.1128/genomeA.00194-15. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 32.Sidjabat HE, Townell N, Nimmo GR, George NM, Robson J, Vohra R, Davis L, Heney C, Paterson DL. 2015. Dominance of IMP-4-producing enterobacter cloacae among carbapenemase-producing Enterobacteriaceae in Australia. Antimicrob Agents Chemother 59:4059–4066. doi: 10.1128/AAC.04378-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 33.Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, Moller Aarestrup F, Hasman H. 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58:3895–3903. doi: 10.1128/AAC.02412-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 34.Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, Aarestrup FM, Larsen MV. 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67:2640–2644. doi: 10.1093/jac/dks261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 35.Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, Jelsbak L, Sicheritz-Ponten T, Ussery DW, Aarestrup FM, Lund O. 2012. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 50:1355–1361. doi: 10.1128/JCM.06094-11. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 36.Day KM, Ali S, Mirza IA, Sidjabat HE, Silvey A, Lanyon CV, Cummings SP, Abbasi SA, Raza MW, Paterson DL, Perry JD. 2013. Prevalence and molecular characterization of Enterobacteriaceae producing NDM-1 carbapenemase at a military hospital in Pakistan and evaluation of two chromogenic media. Diagn Microbiol Infect Dis 75:187–191. doi: 10.1016/j.diagmicrobio.2012.11.006. [DOI] [PubMed] [Google Scholar]
  • 37.Kumarasamy KK, Toleman MA, Walsh TR, Bagaria J, Butt F, Balakrishnan R, Chaudhary U, Doumith M, Giske CG, Irfan S, Krishnan P, Kumar AV, Maharjan S, Mushtaq S, Noorie T, Paterson DL, Pearson A, Perry C, Pike R, Rao B, Ray U, Sarma JB, Sharma M, Sheridan E, Thirunarayan MA, Turton J, Upadhyay S, Warner M, Welfare W, Livermore DM, Woodford N. 2010. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect Dis 10:597–602. doi: 10.1016/S1473-3099(10)70143-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 38.Qin S, Fu Y, Zhang Q, Qi H, Wen JG, Xu H, Xu L, Zeng L, Tian H, Rong L, Li Y, Shan L, Xu H, Yu Y, Feng X, Liu HM. 2014. High incidence and endemic spread of NDM-1-positive Enterobacteriaceae in Henan Province, China. Antimicrob Agents Chemother 58:4275–4282. doi: 10.1128/AAC.02813-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 39.Nordmann P, Poirel L, Toleman MA, Walsh TR. 2011. Does broad-spectrum beta-lactam resistance due to NDM-1 herald the end of the antibiotic era for treatment of infections caused by Gram-negative bacteria? J Antimicrob Chemother 66:689–692. doi: 10.1093/jac/dkq520. [DOI] [PubMed] [Google Scholar]
  • 40.Fiett J, Baraniak A, Izdebski R, Sitkiewicz I, Zabicka D, Meler A, Filczak K, Hryniewicz W, Gniadkowski M. 2014. The first NDM metallo-β-lactamase-producing Enterobacteriaceae isolate in Poland: evolution of IncFII-type plasmids carrying the blaNDM-1 gene. Antimicrob Agents Chemother 58:1203–1207. doi: 10.1128/AAC.01197-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 41.Krishnaraju M, Kamatchi C, Jha AK, Devasena N, Vennila R, Sumathi G, Vaidyanathan R. 2015. Complete sequencing of an IncX3 plasmid carrying blaNDM-5 allele reveals an early stage in the dissemination of the blaNDM gene. Indian J Med Microbiol 33:30–38. doi: 10.4103/0255-0857.148373. [DOI] [PubMed] [Google Scholar]
  • 42.Doi Y, Hazen TH, Boitano M, Tsai YC, Clark TA, Korlach J, Rasko DA. 2014. Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob Agents Chemother 58:5947-5953. doi: 10.1128/AAC.03180-14. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Antimicrobial Agents and Chemotherapy are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES