Using core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak

Hansen, Svend E.; Andersen, Lise Lotte Torvin; Detlefsen, Mette; Holm, Anette; Roer, Louise; Antoniadis, Panagiotis; Skov, Marianne Nielsine; Hammerum, Anette M.; Kemp, Michael

doi:10.1016/j.jgar.2021.02.007

Cited by 13 publications

(7 citation statements)

References 15 publications

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“…Despite these limitations, our study shed lights on the factors responsible for the recent expansion of specific sub-populations of VREfm within clade A1 that were not explained so far. Recently, other studies reported the spread of specific lineages throughout Europe ( Bender et al, 2016 ; Papagiannitsis et al, 2017 ; Abdelbary et al, 2019 ; Falgenhauer et al, 2019 ; Liese et al, 2019 ; Pinholt et al, 2019 ; Eisenberger et al, 2020 ; Weber et al, 2020 ), amongst which ST117/CT24 has been sporadically identified carrying the vanA operon ( Kjær Hansen et al, 2021 ). However, to the best of our knowledge, this is the first study reporting the molecular characterisation of the ST117/CT24- vanB clone and the relative contribution of its MGEs and accessory genes, therefore broadening the currently available epidemiological data.…”

Section: Discussionmentioning

confidence: 99%

Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks

et al. 2021

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Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis.Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content.Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes.Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.

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Section: Discussionmentioning

confidence: 99%

Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks

et al. 2021

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“…The phylogenetic tree was visualized using iTOL ( Letunic and Bork, 2019 ). Additionally, multilocus sequence typing (MLST) ( Larsen et al, 2012 ), based on seven housekeeping genes ( adk, fumC , gyrB , icd , mdh , purA , and recA ) and core genome (cgMLST) ( Hansen et al, 2021 ) were performed using the Center for Genomic Epidemiology website 1 . The isolates also were characterized by Clermont phylogenetic typing by EzClermont web ( Waters et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador

et al. 2021

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In cities across the globe, the majority of wastewater – that includes drug resistant and pathogenic bacteria among other contaminants – is released into streams untreated. This water is often subsequently used for irrigation of pastures and produce. This use of wastewater-contaminated streams allows antibiotic-resistant bacteria to potentially cycle back to humans through agricultural products. In this study, we investigated the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli isolated from produce and irrigation water across 17 provinces of Ecuador. A total of 117 vegetable samples, 119 fruit samples, and 38 irrigation water samples were analyzed. Results showed that 11% of the samples were positive for E. coli including 11 irrigation water samples (29%), and samples of 13 vegetables (11%), and 11 fruits (9%). Among the 165 E. coli isolates cultured, 96 (58%) had the ESBL phenotype, and 58% of ESBL producing E. coli came from irrigation water samples, 11% from vegetables, and 30% from fruits. The blaCTX–M–55, blaCTX–M 65, and blaCTX–M 15 genes were the most frequently found gene associated with the ESBL phenotype and coincided with the blaCTX–M alleles associated with human infections in Ecuador. Three isolates had the mcr-1 gene which is responsible for colistin resistance. This report provides evidence of the potential role of irrigation water in the growing antimicrobial resistance crisis in Ecuador.

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“…Susceptibility to vancomycin was tested according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST; www.eucast.org) guidelines. In cases of uncertainty, in-house PCR was applied for detecting the presence of the vancomycin-resistance genes vanA , vanB and vanX [23]. Successively, presence of vancomycin-resistance genes was crosschecked against the WGS data (see below) and for VSEfm used for discarding isolates found false susceptible by the EUCAST susceptibility test or PCR.…”

Section: Methodsmentioning

confidence: 99%

Vancomycin-sensitive Enterococcus faecium bacteraemia – hospital transmission and mortality in a Danish University Hospital

Hansen

Roer

Karstensen

et al. 2023

Journal of Medical Microbiology

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Introduction. The emergence of vancomycin-resistant Enterococcus faecium (VREfm) has left the vancomycin-sensitive E. faecium (VSEfm) strains almost unnoticed. Hypothesis. Molecular characteristics, hospital transmission patterns and clinical impact of VSEfm have changed, and VSEfm is a predictor of VREfm introduction. Aim. We wanted to do a molecular characterization of VSEfm to identify hospital transmissions and links between VSEfm and VREfm, and to investigate the demographics, treatment and impact on mortality of VSEfm bacteraemia. Methodology. VSEfm and VREfm blood culture isolates from Odense University Hospital, Denmark, from 2015 to 2019 were characterized using whole-genome sequencing and core-genome multilocus sequence typing (cgMLST). Clonal shifts and diversity of the VREfm isolates were compared to the VSEfm isolates. Hospital records were used for clinical data and transmission investigation of VSEfm cases. Results. Six-hundred and thirty VSEfm isolates from 599 patients belonged to 42 sequence types (STs) and 131 complex types (CTs) in several clusters. Multiple types were involved in putative transmission, occurring over the entire period. Twenty-seven VREfm bacteraemia cases were included. No correlation between the VSEfm and VREfm clones was identified. The 30 day mortality was 40 %, but only in 6.3 % of the cases, VSEfm bacteraemia was the likely cause of death. Conclusion. The molecular types of VSEfm bacteraemia isolates are changing and diverse. No direct correlation between VSEfm and the introduction of VREfm was found, but widespread hospital transmission indicates a presence of risk factors that could facilitate transmission of other micro-organisms as well. VSEfm bacteraemia is rarely the cause of death, indicating that 30 day mortality does not reflect the cause of death.

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Using core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak

Cited by 13 publications

References 15 publications

Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks

Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks

Extended-Spectrum Beta-Lactamase Producing-Escherichia coli Isolated From Irrigation Waters and Produce in Ecuador

Vancomycin-sensitive Enterococcus faecium bacteraemia – hospital transmission and mortality in a Danish University Hospital

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