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“Comparative genomics and pangenomics of vancomycin resistant and susceptible Enterococcus faecium from Irish hospitals across 20 years”

View ORCID ProfileR.J. Leigh, C. McKenna, R. McWade, B. Lynch, View ORCID ProfileF. Walsh
doi: https://doi.org/10.1101/2021.11.22.469549
R.J. Leigh
1Department of Biology, Maynooth University
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C. McKenna
1Department of Biology, Maynooth University
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R. McWade
2Department of Microbiology, Mater Misericordiae University Hospital
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B. Lynch
2Department of Microbiology, Mater Misericordiae University Hospital
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F. Walsh
1Department of Biology, Maynooth University
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Abstract

Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland exhibits a recalcitrant vancomycin resistant bloodstream infection rate compared to other developed countries. A set of 28 vancomycin resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in-silico methodologies and uncovered distinct evolutionary, coevolutionary, and clinically relevant population trends. These results suggest that a stable (in terms of genome size, GC%, and number of genes), yet genetically diverse population (in terms of gene content) of Enterococcus faecium persist in Ireland with acquired resistance arising via plasmid acquisition (vanA) or to a lesser extent, chromosomal recombination (vanB). Population analysis described five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation mediated resistance, and chromosomal harboured arsenals of virulence factors. Comparative phagomics revealed a core prophagome of three prophages throughout the dataset. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates. These results highlight the evolutionary history of Irish Enterococcus faecium isolates and may provide an insight into underlying infection dynamics in a clinical setting.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted November 22, 2021.
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“Comparative genomics and pangenomics of vancomycin resistant and susceptible Enterococcus faecium from Irish hospitals across 20 years”
R.J. Leigh, C. McKenna, R. McWade, B. Lynch, F. Walsh
bioRxiv 2021.11.22.469549; doi: https://doi.org/10.1101/2021.11.22.469549
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“Comparative genomics and pangenomics of vancomycin resistant and susceptible Enterococcus faecium from Irish hospitals across 20 years”
R.J. Leigh, C. McKenna, R. McWade, B. Lynch, F. Walsh
bioRxiv 2021.11.22.469549; doi: https://doi.org/10.1101/2021.11.22.469549

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