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The Capital Region of Denmark - a part of Copenhagen University Hospital
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Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting

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  1. Staphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition

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  2. Azole-Resistant Aspergillus fumigatus Among Danish Cystic Fibrosis Patients: Increasing Prevalence and Dominance of TR34/L98H

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  3. Involvement of NLRP3 and NLRC4 Inflammasome in Uropathogenic E. coli Mediated Urinary Tract Infections

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  1. Staphylococcus saprophyticus Causing Infections in Humans Is Associated with High Resistance to Heavy Metals

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  2. Staphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition

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Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.

Original languageEnglish
Article number636608
JournalFrontiers in Microbiology
Volume12
Pages (from-to)1-8
Number of pages8
ISSN1664-302X
DOIs
Publication statusPublished - 1 Apr 2021

    Research areas

  • MRSA, cgMLST, nosocomial infections, pathogens, surveillance, whole-genome sequencing

ID: 65017832