Genomic analysis revealed distinct transmission clusters of vancomycin-resistant Enterococcus faecium ST80 in Stockholm, Sweden

Fang, Hong; Fröding, Inga; Ullberg, Måns; Giske, Christian G.

doi:10.1016/j.jhin.2020.10.019

Cited by 15 publications

(11 citation statements)

References 14 publications

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“…53 The two VRE isolates we recovered and sequenced belonged to ST80, a highly-prevalent MDR strain which has been reported across Europe. 52 , 54 , 55 …”

Section: Discussionmentioning

confidence: 99%

A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

Madhav,

Bousfield,

Pereira-Dias

et al. 2024

Gut Microbes

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Two-thirds of small-bowel transplantation (SBT) recipients develop bacteremia, with the majority of infections occurring within 3 months post-transplant. Sepsis-related mortality occurs in 31% of patients and is commonly caused by bacteria of gut origin, which are thought to translocate across the implanted organ. Serial post-transplant surveillance endoscopies provide an opportunity to study whether the composition of the ileal and colonic microbiota can predict the emergence as well as the pathogen of subsequent clinical infections in the SBT patient population. Five participants serially underwent aspiration of ileal and colonic bowel effluents at transplantation and during follow-up endoscopy either until death or for up to 3 months post-SBT. We performed whole-metagenome sequencing (WMS) of 40 bowel effluent samples and compared the results with clinical infection episodes. Microbiome composition was concordant between participants and timepoint-matched ileal and colonic samples. Four out of five (4/5) participants had clinically significant infections thought to be of gut origin. Bacterial translocation from the gut was observed in 3/5 patients with bacterial infectious etiologies. In all three cases, the pathogens had demonstrably colonized the gut between 1–10 days prior to invasive clinical infection. Recipients with better outcomes received donor grafts with higher alpha diversity. There was an increase in the number of antimicrobial resistance genes associated with longer hospital stay for all participants. This metagenomic study provides preliminary evidence to support the pathogen translocation hypothesis of gut-origin sepsis in the SBT cohort. Ileal and colonic microbiome compositions were concordant; therefore, fecal metagenomic analysis could be a useful surveillance tool for impeding infection with specific gut-residing pathogens.

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“…53 The two VRE isolates we recovered and sequenced belonged to ST80, a highly-prevalent MDR strain which has been reported across Europe. 52 , 54 , 55 …”

Section: Discussionmentioning

confidence: 99%

A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

Madhav,

Bousfield,

Pereira-Dias

et al. 2024

Gut Microbes

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“…First, we divided isolates into WGS clusters and then searched for variable loci based on this clustering, so the MLST scheme proposed here reflects the individual STs true genetic relatedness to the maximum extent possible. As the strains classified according to the original scheme to ST80, ST17, and ST117 belong to the most clinically significant strains ( 17 – 19 ), it is likely that dividing them into the new STs can significantly affect further epidemiology studies and epidemiological measures in relation to E. faecium . Certain E. faecium isolates lack the pstS gene and belong to a specific group, which is assigned the pstS 0 allele for the purpose of the MLST typing.…”

Section: Discussionmentioning

confidence: 99%

“…These CCs are still frequently used by epidemiologists despite their relatively low discriminative power. Specifically in E. faecium , the globally widespread CC17 (the original MLST scheme) includes a substantial part of the most widespread STs and thus unites genetically distant strains into 1 complex ( 17 , 31 ). As part of the proposed MLST scheme design, CCs were also determined on the pilot genome group.…”

Section: Discussionmentioning

confidence: 99%

New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data

et al. 2023

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“…Clonal complex 17 (CC17) is a well-documented global polyclonal cluster of hospital adapted vancomycin-resistant Enterococcus faecium (5). So far, several sequence types (ST) have been described for their multidrug resistance ability and different levels of virulence (5,22,23). ST17 and ST117 are among the most well-studied clones involved in in-hospital outbreaks and have been shown to express high levels of antimicrobial resistance and virulence (4,5).…”

Section: Signi Cance Of Environmental Hygienementioning

confidence: 99%

First Report of Nosocomial Outbreak of Vancomycin-Resistant Enterococcus Faecium Infection Among COVID-19 Patients Hospitalized in a Non-Intensive Care Unit Ward in Central Europe

Jalali¹,

Šturdík

Jalali

et al. 2021

Preprint

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Background: The COVID-19 pandemic in 2020 exerted immense pressure on health care systems worldwide, causing substantial resources to be diverted to respond to the pandemic. These changes raise the concern about the potential for reduction in adherence to long-established measures in the prevention of healthcare-associated infections (HAI). Enterococcus species account for most of human enterococcal HAI and multidrug-resistant infections and have become a major threat to modern public health. We examine the rise in the number of vancomycin resistant E. faecium blood stream and urinary tract infections in a COVID-19 department during an epidemiologic outbreak investigation to detect and eliminate nosocomial clusters of the bacteria. Methods: Strain identification was performed by classical isolation and biochemical and cultivation methods. Antibiotic testing results were interpreted according to European committee on antimicrobial susceptibility testing (EUCAST) guidelines. Six isolated samples underwent whole genome sequencing (WGS) during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing.Results: WGS revealed two genotypically distinct VRE clusters, one of which had genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control strategies.Conclusions: This study provides the first description of an outbreak caused by vanA-ST17 E. faecium strains among COVID-19 patients in central Europe, and the first description of an outbreak caused by vanB-ST117 and vanA-ST17 E. faecium strains in Slovakia. This study can help raise awareness about the need for strict adherence to infection control measures and the implementation of rational antimicrobial stewardship as a routine part of COVID-19 management.

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Genomic analysis revealed distinct transmission clusters of vancomycin-resistant Enterococcus faecium ST80 in Stockholm, Sweden

Abstract: Genomic analysis revealed distinct transmission clusters of vancomycin-resistant Enterococcus faecium ST80 in

Cited by 15 publications

References 14 publications

A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation

New Multilocus Sequence Typing Scheme for Enterococcus faecium Based on Whole Genome Sequencing Data

First Report of Nosocomial Outbreak of Vancomycin-Resistant Enterococcus Faecium Infection Among COVID-19 Patients Hospitalized in a Non-Intensive Care Unit Ward in Central Europe

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