Dataset Information

Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.

ABSTRACT: Objectives. A large OXA-48 outbreak in the Netherlands involved the spread of OXA-48producing Enterobacteriaceae among at least 118 patients, suggesting horizontal transfer of this resistance gene through one or more plasmids. Elucidating transmission dynamics of resistance plasmids is hampered by the low resolution of classic typing methods. This study aimed to investigate the molecular epidemiology of plasmids carrying OXA-48 carbapenemase using a next-generation sequencing approach.Methods. A total of 68 OXA-48-producing Enterobacteriaceae isolated from the hospital outbreak, as well as 22 non-outbreak related OXA-48-producing Enterobacteriaceae from the Netherlands, Libya and Turkey were selected. Plasmids were sequenced using the Illumina Miseq platform, and read sets were assembled and analysed.Results. In all plasmids bla OXA-48 was embedded in transposon Tn1999.2 and located on a ca. 62 kb IncL/M conjugative plasmid in 14 different species. There were a maximum of 2 SNPs (single nucleotide polymorphisms) between the core sequence alignment of all plasmids. Closely related sequence variants of this plasmid were detected in non-outbreak isolates from the Netherlands and other countries. Thirty-one of 89 OXA-48-producing isolates also harboured bla CTX-M-15, which was not located on the bla OXA-48-carrying plasmid. Sequencing of four plasmids harbouring bla CTX-M15 revealed extensive plasmid heterogeneity.Conclusions. A ca 62 kb plasmid was responsible for the OXA-48 outbreak in a Dutch hospital. Our findings provide strong evidence for both within-host inter-species and between host dissemination of plasmid-based OXA-48 during a nosocomial outbreak. These findings exemplify the complex epidemiology of carbapenemase producing Enterobacteriaceae (CPE).

SUBMITTER: Hidalgo L

PROVIDER: S-EPMC6879230 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.

Hidalgo Laura L de Been Mark M Rogers Malbert R C MRC Schürch Anita C AC Scharringa Jelle J van der Zee Anneke A Bonten Marc J M MJM Fluit Ad C AC

Antimicrobial agents and chemotherapy 20190901 12

<b>Objectives.</b> A large OXA-48 outbreak in the Netherlands involved the spread of OXA-48producing Enterobacteriaceae among at least 118 patients, suggesting horizontal transfer of this resistance gene through one or more plasmids. Elucidating transmission dynamics of resistance plasmids is hampered by the low resolution of classic typing methods. This study aimed to investigate the molecular epidemiology of plasmids carrying OXA-48 carbapenemase using a next-generation sequencing approach.<b> ...[more]

PMID: 31591122

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Project description:Klebsiella pneumoniae is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical K. pneumoniae isolates from Serbia. Consecutive non-replicate K. pneumoniae clinical isolates (n = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem (n = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates (N = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, N = 38), CG258 (ST437, N = 4; ST340, N = 1; ST258, N = 1) and CG17 (ST336, N = 1). mcr genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrBC28S being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the bla OXA- 48 genetic background. The bla OXA- 48 gene was located in a novel IncFIA-IncR hybrid plasmid, also containing the extended spectrum β-lactamase-encoding gene bla CTX-M-15 and several other AMR genes. Non-ST101 isolates presented different MgrB alterations (C28S, C28Y, K2∗, K3∗, Q30∗, adenine deletion leading to frameshift and premature termination, IS5-mediated inactivation) and expressed different carbapenemases: OXA-48 (ST437 and ST336), NDM-1 (ST437 and ST340) and KPC-2 (ST258). Our study reports the clonal expansion of the newly emerging ST101 clone in Serbia. This high-risk clone appears adept at acquiring resistance, and efforts should be made to contain the spread of such clone.

Project description:The hospital environment has been reported as a source of transmission events and outbreaks of carbapenemase-producing Enterobacterales. Interconnected plumbing systems and the microbial diversity in these reservoirs pose a challenge for outbreak investigation and control. A total of 133 clinical and environmental OXA-48-producing Enterobacter cloacae isolates collected between 2015 and 2021 were characterized by whole-genome sequencing (WGS) to investigate a prolonged intermittent outbreak involving 41 patients in the hematological unit. A mock-shower experiment was performed to investigate the possible acquisition route. WGS indicated the hospital water environmental reservoir as the most likely source of the outbreak. The lack of diversity of the blaOXA-48-like harbouring plasmids was a challenge for data interpretation. The detection of blaOXA-48-like-harboring E. cloacae strains in the shower area after the mock-shower experiment provided strong evidence that showering is the most likely route of acquisition. Initially, in 20 out of 38 patient rooms, wastewater traps and drains were contaminated with OXA-48-positive E. cloacae. Continuous decontamination using 25% acetic acid three times weekly was effective in reducing the trap/drain positivity in monthly environmental screening but not in reducing new acquisitions. However, the installation of removable custom-made shower tubs did prevent new acquisitions over a subsequent 12-month observation period. In the present study, continuous decontamination was effective in reducing the bacterial burden in the nosocomial reservoirs but was not sufficient to prevent environment-to-patient transmission in the long term. Construction interventions may be necessary for successful infection prevention and control. IMPORTANCE The hospital water environment can be a reservoir for a multiward outbreak, leading to acquisitions or transmissions of multidrug-resistant organisms in a hospital setting. The majority of Gram-negative bacteria are able to build biofilms and persist in the hospital plumbing system over a long period of time. The elimination of the reservoir is essential to prevent further transmission and spread, but proposed decontamination regimens, e.g., using acetic acid, can only suppress but not fully eliminate the environmental reservoir. In this study, we demonstrated that colonization with multidrug-resistant organisms can be acquired by showering in showers with contaminated water traps and drains. A construction intervention by installing removable and autoclavable shower inserts to avoid sink contact during showering was effective in containing this outbreak and may be a viable alternative infection prevention and control measure in outbreak situations involving contaminated shower drains and water traps.

Dataset Information

Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.

Publications

Sequence-based epidemiology of an OXA-48 plasmid during a hospital outbreak.

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