Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

Johnson, Timothy J.; Bielak, Eliza Maria; Fortini, Daniela; Hansen, Lars Hestbjerg; Hasman, Henrik; DebRoy, Chitrita; Nolan, Lisa K.; Carattoli, Alessandra

doi:10.1016/j.plasmid.2012.03.001

Cited by 238 publications

(212 citation statements)

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“…PCR-based replicon typing (PBRT) was performed, as previously described (26), with additional primers to detect FII, FII K (27), and IncX subtypes (28) and the IncL/M plasmid variant known to carry bla (29) (now designated IncL [30]). …”

Section: Methodsmentioning

confidence: 99%

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

et al. 2016

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cThe minimal concentration of antibiotic required to inhibit the growth of different isolates of a given species with no acquired resistance mechanisms has a normal distribution. We have previously shown that the presence or absence of transmissible antibiotic resistance genes has excellent predictive power for phenotype. In this study, we analyzed the distribution of six ␤-lactam antibiotic susceptibility phenotypes associated with commonly acquired resistance genes in Enterobacteriaceae in Sydney, Australia. Escherichia coli (n ‫؍‬ 200) and Klebsiella pneumoniae (n ‫؍‬ 178) clinical isolates, with relevant transmissible resistance genes (bla TEM , n ‫؍‬ 33; plasmid AmpC, n ‫؍‬ 69; extended-spectrum ␤-lactamase [ESBL], n ‫؍‬ 116; and carbapenemase, n ‫؍‬ 100), were characterized. A group of 60 isolates with no phenotypic resistance to any antibiotics tested and carrying none of the important ␤-lactamase genes served as comparators. The MICs for all drug-bacterium combinations had a normal distribution, varying only in the presence of additional genes relevant to the phenotype or, for ertapenem resistance in K. pneumoniae, with a loss or change in the outer membrane porin protein OmpK36. We demonstrated mutations in ompK36 or absence of OmpK36 in all isolates in which reduced susceptibility to ertapenem (MIC, >1 mg/liter) was evident. Ertapenem nonsusceptibility in K. pneumoniae was most common in the context of an OmpK36 variant with an ESBL or AmpC gene. Surveillance strategies to define appropriate antimicrobial therapies should include genotype-phenotype relationships for all major transmissible resistance genes and the characterization of mutations in relevant porins in organisms, like K. pneumoniae. E scherichia coli and Klebsiella pneumoniae are among the most important pathogens in community and hospital settings, and their increasing resistance to extended-spectrum (third-and fourth-generation) cephalosporin and carbapenem antibiotics is a major health threat. In Gram-negative bacteria, such as these, a variety of mechanisms may confer ␤-lactam resistance (1), but the spread of transmissible genes encoding extended-spectrum ␤-lactamases (ESBLs) (2), plasmid-mediated AmpC ␤-lactamases (pAmpCs) (3), and carbapenemases (4) is particularly significant. Carbapenems have been the antibiotics of choice for treating ESBLs and other multidrug-resistant strains, but carbapenem resistance is increasingly common (5). This is mostly attributed to the production of specific carbapenemases (6), but the expression of AmpC or ESBL enzymes in isolates with altered outer membrane porins is also associated with decreased susceptibility to carbapenems (7-9). Mutations in major outer membrane porins may be required for clinically relevant carbapenem resistance in K. pneumoniae isolates expressing carbapenemases, such as KPC and OXA-48-like enzymes, which rarely elicit clinically important antibiotic resistance in E. coli (6).The clinical definitions of antibiotic susceptibility are developed by the collection and analysis of...

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Section: Methodsmentioning

confidence: 99%

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

et al. 2016

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“…The IncX group of plasmids are narrow-host-range plasmids common in Enterobacteriaceae, and they exist even in isolates from the preantibiotic era (53). They are known to encode type IV fimbriae enabling their own conjugative transfer, and they provide accessory functions to their host bacteria such as biofilm formation and resistance to antimicrobial agents (54). IncX plasmids possess highly syntenic plasmid backbones but are quite divergent with respect to nucleotide and amino acid similarity (54).…”

Section: Characteristics Of Clinical Isolatesmentioning

confidence: 99%

“…They are known to encode type IV fimbriae enabling their own conjugative transfer, and they provide accessory functions to their host bacteria such as biofilm formation and resistance to antimicrobial agents (54). IncX plasmids possess highly syntenic plasmid backbones but are quite divergent with respect to nucleotide and amino acid similarity (54). Based on phylogenetic comparisons of sequenced IncX plasmids, the IncX plasmid group has been divided into at least four subgroups, IncX1 to IncX4 (54).…”

Section: Characteristics Of Clinical Isolatesmentioning

confidence: 99%

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Complete Nucleotide Sequences of bla _KPC-4 - and bla _KPC-5 -Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey

Chen

Chavda

Fraimow

et al. 2013

Antimicrob Agents Chemother

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h Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have emerged as major nosocomial pathogens. bla KPC , commonly located on Tn4401, is found in Gram-negative bacterial strains, with the two most common variants, bla KPC-2 and bla KPC-3 , identified in plasmids with diverse genetic backgrounds. In this study, we examined bla KPC-4 -and bla KPC-5 -bearing plasmids recovered from two K. pneumoniae strains, which were isolated from a single New Jersey hospital in 2005 and 2006, respectively. IncN plasmid pBK31551 is 84 kb in length and harbors bla KPC-4 , bla TEM-1 , qnrB2, aac(3)-Ib, aph(3=)-I, qacF, qacE⌬1, sul1, and dfrA14, which confer resistance to ␤-lactams, quinolones, aminoglycosides, quaternary ammonium compounds, and co-trimoxazole. The conserved regions within pBK31551 are similar to those of other IncN plasmids. Surprisingly, analysis of the Tn4401 sequence revealed a large IS110-and Tn6901-carrying element (8.3 kb) inserted into the istA gene, encoding glyoxalase/bleomycin resistance, alcohol dehydrogenase, and S-formylglutathione hydrolase. Plasmid pBK31567 is 47 kb in length and harbors bla KPC-5 , dfrA5, qacE⌬1, and sul1. pBK31567 belongs to a novel IncX subgroup (IncX5) and possesses a highly syntenic plasmid backbone like other IncX plasmids; however, sequence similarity at the nucleotide level is divergent. The bla KPC-5 gene is carried on a Tn4401 element and differs from the genetic environment of bla KPC-5 described in Pseudomonas aeruginosa strain P28 from Puerto Rico. This study underscores the genetic diversity of multidrug-resistant plasmids involved in the spread of bla KPC genes and highlights the mobility and plasticity of Tn4401. Comparative genomic analysis provides new insights into the evolution and dissemination of KPC plasmids belonging to different incompatibility groups.

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“…The transconjugants and transformants acquiring blaNDM-harbouring plasmids were examined phenotypically and confirmed by PCR for blaNDM. PBRT was used to identify the plasmid Inc type carrying blaNDM as previously described (58,222,223). …”

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The genetic analysis of Enterobacteriaceae plasmids to provide insights into the acquisition and spread of the blaNDM gene

Wailan¹

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Treatment options for infections caused by pathogenic Gram-negative bacteria, especially those of the Enterobacteriaceae family, are becoming limited with the increase of antimicrobial resistance (AMR). β-lactamases are a major mechanism for AMR within the Enterobacteriaeae. The most problematic β-lactamases are carbapenemases, which confer resistance to carbapenems, the major last-line antimicrobial. A recently emerged carbapenemase that has globally disseminated is the NDM carbapenemase, provided by blaNDM genes. These blaNDM genes (and other AMR genes) are able to transmit between strains when inserted on extrachromosomal self-replicating DNA molecules known as 'plasmids'. AMR genes within Enterobacteriacae are frequently associated with specific bacterial species, clonal lineage, plasmid Incompatibility (Inc) types or transposable elements. The blaNDM genes however do not have this association when oberserved in the Enterobacteriaceae family. To address and characterise this new paradigm presented by blaNDM genes, this thesis presents the bioinformatic analysis of plasmids associated with the Enterobacteriaceae to provide insights into the acquisition and spread of the blaNDM gene and an epidemiological approach to assess its plasmid-mediated dissemination between genetically unrelated species.Specifically these aims were achieved by; firstly, the establishment of a recent account of the blaNDM gene from an epidemiological perspective using a novel genetic/molecular approach. This would identify the spread of individual plasmids carrying blaNDM across multiple species and patients, both within a single facility and across multiple national facilities. The approach combined in-depth bioinformatic analysis of blaNDM genetic contexts (NGCs) with common molecular epidemiology techniques. IncN2 (n=4) and IncA/C (n=3) were identified as the most common plasmids types carrying blaNDM across four patients within a Pakistani military hospital. These patients harboured between two and four NDM-1 producing Gram-negative bacilli of different ii species coresident in their stool samples. IncFII-types (n=7) and IncX3 (n=4) were the most common plasmid types carrying blaNDM amongst 12 Enterobacteriaceae isolates, each from different patients across multiple Australian healthcare facilities. These isolates each carried one plasmid harbouring blaNDM but only five different blaNDM genetic contexts were identified, indicating five particular plasmids with a specific NGC had disseminated amongst these 12 isolates.Secondly, to investigate transposable elements involved for insertion of the blaNDM gene into different plasmid types, the complete sequence of four plasmids carrying blaNDM (two IncA/C2 and two IncFIIY) was bioinformatically analysed. These plasmids were from four different clinical samples of four patients, comprised of Klebsiella pneumoniae, Enterobacter cloacae, and Escherichia coli. Each plasmid was observed to acquire blaNDM by different mechanisms on very similar plasmid backbones. Transposable elements ...

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Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

Cited by 238 publications

References 47 publications

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

Complete Nucleotide Sequences of bla _KPC-4 - and bla _KPC-5 -Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey

The genetic analysis of Enterobacteriaceae plasmids to provide insights into the acquisition and spread of the blaNDM gene

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Expansion of the IncX plasmid family for improved identification and typing of novel plasmids in drug-resistant Enterobacteriaceae

Cited by 238 publications

References 47 publications

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

Predictability of Phenotype in Relation to Common β-Lactam Resistance Mechanisms in Escherichia coli and Klebsiella pneumoniae

Complete Nucleotide Sequences of bla KPC-4 - and bla KPC-5 -Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey

The genetic analysis of Enterobacteriaceae plasmids to provide insights into the acquisition and spread of the blaNDM gene

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Complete Nucleotide Sequences of bla _KPC-4 - and bla _KPC-5 -Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey