Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates

Sandra Wingaard Thrane, Véronique L. Taylor, Ole Lund, Joseph S. Lam, Lars Jelsbak

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Abstract

Accurate typing methods are required for efficient infection control. The emergence of whole genome sequencing (WGS) technologies has enabled the development of genomics-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web-service, and aptly facilitate high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections, and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1649 genomes resulted in successful serogroup assignments in 99.27% of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of non-typeable isolates found using PAst was the result of either complete absence of OSA genes in the genomes or the artifact of genomic misassembly. With PAst, P. aeruginosa serotype data can be obtained from WGS information alone. PAst is a highly efficient alternative to conventional serotyping methods in relation to outbreak surveillance of serotype O12 and other high-risk clones, while maintaining backward compatibility to historical serotype data.
Original languageEnglish
JournalJournal of Clinical Microbiology
Volume54
Issue number7
Pages (from-to)1782-1788
Number of pages7
ISSN0095-1137
DOIs
Publication statusPublished - 2016

Cite this

@article{ce2cb5fe77a748dc96a1deb8290b4c97,
title = "Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates",
abstract = "Accurate typing methods are required for efficient infection control. The emergence of whole genome sequencing (WGS) technologies has enabled the development of genomics-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web-service, and aptly facilitate high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections, and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1649 genomes resulted in successful serogroup assignments in 99.27{\%} of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of non-typeable isolates found using PAst was the result of either complete absence of OSA genes in the genomes or the artifact of genomic misassembly. With PAst, P. aeruginosa serotype data can be obtained from WGS information alone. PAst is a highly efficient alternative to conventional serotyping methods in relation to outbreak surveillance of serotype O12 and other high-risk clones, while maintaining backward compatibility to historical serotype data.",
author = "Thrane, {Sandra Wingaard} and Taylor, {V{\'e}ronique L.} and Ole Lund and Lam, {Joseph S.} and Lars Jelsbak",
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language = "English",
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journal = "Journal of Clinical Microbiology",
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}

Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates. / Thrane, Sandra Wingaard; Taylor, Véronique L.; Lund, Ole; Lam, Joseph S.; Jelsbak, Lars.

In: Journal of Clinical Microbiology, Vol. 54, No. 7, 2016, p. 1782-1788.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - Application of WGS data for O-specific antigen analysis and in silico serotyping of Pseudomonas aeruginosa isolates

AU - Thrane, Sandra Wingaard

AU - Taylor, Véronique L.

AU - Lund, Ole

AU - Lam, Joseph S.

AU - Jelsbak, Lars

PY - 2016

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N2 - Accurate typing methods are required for efficient infection control. The emergence of whole genome sequencing (WGS) technologies has enabled the development of genomics-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web-service, and aptly facilitate high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections, and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1649 genomes resulted in successful serogroup assignments in 99.27% of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of non-typeable isolates found using PAst was the result of either complete absence of OSA genes in the genomes or the artifact of genomic misassembly. With PAst, P. aeruginosa serotype data can be obtained from WGS information alone. PAst is a highly efficient alternative to conventional serotyping methods in relation to outbreak surveillance of serotype O12 and other high-risk clones, while maintaining backward compatibility to historical serotype data.

AB - Accurate typing methods are required for efficient infection control. The emergence of whole genome sequencing (WGS) technologies has enabled the development of genomics-based methods applicable for routine typing and surveillance of bacterial pathogens. In this study, we developed the Pseudomonas aeruginosa serotyper (PAst) program, which enabled in silico serotyping of P. aeruginosa isolates using WGS data. PAst has been made publically available as a web-service, and aptly facilitate high-throughput serotyping analysis. The program overcomes critical issues such as the loss of in vitro typeability often associated with P. aeruginosa isolates from chronic infections, and quickly determines the serogroup of an isolate based on the sequence of the O-specific antigen (OSA) gene cluster. Here, PAst analysis of 1649 genomes resulted in successful serogroup assignments in 99.27% of the cases. This frequency is rarely achievable by conventional serotyping methods. The limited number of non-typeable isolates found using PAst was the result of either complete absence of OSA genes in the genomes or the artifact of genomic misassembly. With PAst, P. aeruginosa serotype data can be obtained from WGS information alone. PAst is a highly efficient alternative to conventional serotyping methods in relation to outbreak surveillance of serotype O12 and other high-risk clones, while maintaining backward compatibility to historical serotype data.

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