A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid

Yamagishi, Takashi; Matsui, Mari; Sekizuka, Tsuyoshi; Ito, Hiroaki; Fukusumi, Munehisa; Uehira, Tomoko; Tsubokura, Miyuki; Ogawa, Yoshihiko; Miyamoto, Atsushi; Nakamori, Shoji; Tawa, Akio; Yoshimura, Takahisa; Yoshida, Hideki; Hirokawa, Hidetetsu; Suzuki, Satowa; Matsui, Takeshi; Shibayama, Keigo; Kuroda, Makoto; Oishi, Kazunori

doi:10.1038/s41598-020-60659-2

Cited by 30 publications

(26 citation statements)

References 47 publications

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“…The single amino acid variant, IMP-6, was identified in 2001 (18). IMP-1 producers have disseminated mainly in eastern Japan, including Tokyo (24,34), whereas IMP-6 producers have been almost exclusively found in western Japan, including Osaka (7,10,11,25). Consistent with these findings, in the present study only one K. pneumoniae isolate carrying bla IMP-1 , E105, was isolated in hospital A, where CRE carrying pKPI-6 were dominant.…”

Section: Discussionsupporting

confidence: 87%

“…Therefore, genetic tracking of plasmids encoding carbapenemase genes has allowed the monitoring of the spread of CRE isolates. For example, structural similarities among plasmids from isolates obtained in a single hospital outbreak allowed elucidating links between patients carrying the isolates (5)(6)(7), and plasmid data accumulated globally revealed the worldwide spread of an epidemic plasmid carrying bla KPC. (8).…”

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confidence: 99%

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Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-ResistantEnterobacteriaceae

et al. 2020

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Carbapenem-resistant Enterobacteriaceae (CRE) infections, high in morbidity and mortality, pose serious clinical challenges due to limited treatment options. A previous CRE surveillance study on 1,507 patients from 43 hospitals in Osaka, Japan, revealed that 12% of patients carried CRE and that 95% of the CRE isolates were IMP-type carbapenemase producers. Here, the mechanisms for this regional dissemination of a single carbapenemase gene were investigated. Since the dissemination of CRE is primarily due to the transmission of carbapenemase genes located on plasmids, we analyzed the plasmidome of 230 CRE isolates carrying blaIMP by whole-genome sequencing and Southern blotting. blaIMP-6 was found to be predominantly disseminated among chromosomally distinct isolates through the pKPI-6 plasmid. Underlying the vast clonal dissemination of pKPI-6, various subpopulations deriving from pKPI-6 were identified, which had acquired advantages for the dissemination of CRE isolates. A cluster exhibiting heteroresistance against meropenem by the transcriptional regulation of blaIMP-6 caused an outbreak likely through covert transmission of blaIMP-6. For stable carriage of blaIMP-6, they occasionally integrated blaIMP-6 on their chromosomes. In addition, we detected one isolate that broadened the range of antimicrobial resistance through a single point mutation in blaIMP-6 on pKPI-6. Multifaceted analysis of the plasmidome granted us more accurate perspectives on the horizontal spread of CRE isolates, which is difficult to trace only by comparing the whole genomes. This study revealed the predominant spread of a specific carbapenemase-encoding plasmid accompanying the emergence of phenotypically diverse derivatives, which may facilitate further dissemination of CRE in various environments. IMPORTANCE Global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the efficacy of antibiotics even against common bacterial infections. Carbapenem resistance, mainly due to carbapenemase, is generally encoded on plasmids and is spread across bacterial species by conjugation. Most CRE epidemiological studies have analyzed whole genomes or only contigs of CRE isolates. Here, plasmidome analysis on 230 CRE isolates carrying blaIMP was performed to shed light into the dissemination of a single carbapenemase gene in Osaka, Japan. The predominant dissemination of blaIMP-6 by the pKPI-6 plasmid among genetically distinct isolates was revealed, as well as the emergences of pKPI-6 derivatives that acquired advantages for further disseminations. Underlying vast clonal dissemination of a carbapenemase-encoding plasmid, heteroresistance was found in CRE offspring, which was generated by the transcriptional regulation of blaIMP-6, stabilization of blaIMP-6 through chromosomal integration, or broadened antimicrobial resistance due to a single point mutation in blaIMP-6.

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Section: Discussionsupporting

confidence: 87%

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confidence: 99%

Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-ResistantEnterobacteriaceae

et al. 2020

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“…The single amino-acid variant, IMP-6, was identi ed in 2001 [17]. IMP-1 producers have disseminated mainly in eastern Japan, including Tokyo [23,24,33], whereas IMP-6 producers have been almost exclusively found in western Japan, including Osaka [7,10,11,24]. Consistent herewith, in this study, only one K. pneumoniae isolate carrying bla IMP−1 , E105, was isolated in hospital A, where CRE carrying pKPI-6 were dominant.…”

Section: Discussionsupporting

confidence: 86%

“…Genetic tracking of plasmids encoding carbapenemase genes has allowed monitoring the spread of CRE isolates. For example, structural similarities among plasmids from isolates obtained in a single hospital outbreak allowed elucidating links between patients carrying the isolates [5][6][7], and plasmid data accumulated globally revealed the worldwide spread of an epidemic plasmid carrying bla KPC . [8].…”

Section: Introductionmentioning

confidence: 99%

Regional Dissemination of a Carbapenemase-encoding Plasmid: Plasmidome analysis Reveals Diverse Adaptations of Carbapenemase-Producing Enterobacteriaceae

Abe¹,

Akeda²,

Sugawara³

et al. 2020

Preprint

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Background. The global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens human health by limiting the range of usable antibiotics even against common bacterial infections. The spread of CRE is primarily due to the transmission of carbapenemase genes located on plasmids. However, few studies have comprehensively identified regionally spreading carbapenemase-encoding plasmids because of the difficulty to determine the complete sequence of a plasmid encoding carbapenemases. In a CRE surveillance study of 1,507 patients from 43 hospitals in northern Osaka, Japan, we previously found that 12% of the patients carried CRE and 95% of CRE isolates were IMP-6 producers. This result suggested a vast horizontal spread of a clonal plasmid carrying blaIMP-6 among Enterobacteriaceae in this region. In the current study, we aimed to describe the dynamics of this regional horizontal plasmid transmission.Results. We systematically analysed the plasmids of 230 CRE isolates carrying blaIMP obtained in our previous surveillance study by using whole genome sequencing and Southern blotting. We detected a major population (187 out of 230 blaIMP-positive CRE isolates, 85.6%) that carried blaIMP-6 on the IncN plasmid pKPI-6, along with diverse minor subpopulations. Among the subpopulations, we identified a novel cluster carrying an IncF plasmid that leads to heteroresistance due to amplification of blaIMP-6, resulting in covert transmission of blaIMP-6 or occasional chromosomal integration of blaIMP-6. In addition, we detected one isolate that harboured blaIMP-1, which is identical to blaIMP-6 except for a single point mutation, on pKPI-6 and thus had acquired a broader range of antimicrobial resistance. Conclusions. Carbapenemase-encoding plasmid tracking revealed the clonal dissemination of pKPI-6 among chromosomally distinct isolates. Focusing on the mode of carbapenemase gene carriage is helpful for monitoring of horizontal spread of CRE isolates that is difficult to trace only by the comparisons of the whole genomes. A seemingly clonal horizontal dissemination of the predominant plasmid had embraced heterogenous subpopulations that contribute to diverse adaptations including covert transmission, stable chromosomal integration of blaIMP-6, or broadened antimicrobial resistance patterns, ultimately leading to treatment failure.

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“…In contrast, most of the IMP-6 producers coharbored CTX-M-2, and both the IMP-6 and CTX-M-2 genes were transferable with high frequency. Yamagishi et al ( 15 ) reported IMP-6-carrying IncN plasmids isolated from 2013 to 2014 in Japan, including three strains of K. pneumoniae . In Japan, the IMP-6-carrying IncN plasmids may have been predominant since 2013.…”

Section: Discussionmentioning

confidence: 99%

Molecular and Epidemiological Characteristics of Carbapenemase-Producing Klebsiella pneumoniae Clinical Isolates in Japan

Yonekawa

Mizuno

Nakano

et al. 2020

mSphere

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Carbapenemase-producing Enterobacteriaceae represent a serious public health threat worldwide. Carbapenemase genes, harbored on a transferable plasmid, have been isolated globally with distinct geographical features. Klebsiella pneumoniae, included in Enterobacteriaceae, also produces carbapenemase and often shows hypervirulence. Overlapping carbapenem resistance and hypervirulence in K. pneumoniae have been reported, but such strains have not yet been found in Japan. Here, we screened 104 carbapenemase-producing K. pneumoniae isolates collected from 37 hospitals and outpatient clinics in Japan between September 2014 and July 2015. PCR and DNA sequencing demonstrated IMP-1 in 21 isolates and IMP-6 in 83 isolates, 77 of which coharbored CTX-M-2. Most of the isolates showed low MICs toward imipenem and meropenem but high MICs toward penicillin and cephalosporins. Conjugation experiments with an Escherichia coli J53 recipient showed that most of the plasmids in IMP-6 producers were transferable, whereas only one-half of the plasmids in IMP-1 producers were transferable. PCR-based replicon typing and multiplex PCR identified five isolates belonging to the CG258 non-tonB79 cluster and no isolate belonging to the CG258-tonB79 cluster or sequence type 307 (ST307). Four K1-ST23 isolates, 10 K2-ST65 isolates, and 7 K2-ST86 isolates were detected that harbored virulence genes. The resistance genes in 85 isolates were transferable, but the virulence genes were not transferred. These results demonstrate the acquisition of IMP-type carbapenemase genes and CTX-M-type genes among hypervirulence isolates in Japan, warranting further attention and countermeasures. In this study, we have determined the molecular characteristics and epidemiology of IMP-6 producers that coharbored various CTX-M genes in Japan. IMPORTANCE Carbapenems serve as a last resort for the clinical treatment of multidrug-resistant infections. Therefore, the rapid spread of carbapenemase-producing strains represents a serious public health threat, further limiting antibiotic choices. The current findings of hypervirulent carbapenemase-producing Klebsiella pneumoniae clinical isolates in Japan demonstrate the potential broad spread and transfer of these genes, necessitating close surveillance.

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A prolonged multispecies outbreak of IMP-6 carbapenemase-producing Enterobacterales due to horizontal transmission of the IncN plasmid

Cited by 30 publications

References 47 publications

Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-ResistantEnterobacteriaceae

Characterization of the Plasmidome Encoding Carbapenemase and Mechanisms for Dissemination of Carbapenem-ResistantEnterobacteriaceae

Regional Dissemination of a Carbapenemase-encoding Plasmid: Plasmidome analysis Reveals Diverse Adaptations of Carbapenemase-Producing Enterobacteriaceae

Molecular and Epidemiological Characteristics of Carbapenemase-Producing Klebsiella pneumoniae Clinical Isolates in Japan

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