Application of Whole-Genome Sequencing Data for O-Specific Antigen Analysis and In Silico Serotyping of Pseudomonas aeruginosa Isolates.
Accurate typing methods are required for efficient infection control. The emergence of whole-genome sequencing (WGS) technologies has enabled the development of genome-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 facilitates 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 1,649 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 nontypeable isolates found using PAst was the result of either a 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.
Technical University of Denmark, Department of Systems Biology, Kgs. Lyngby, Denmark.
Sandra Wingaard
SW
Thrane
University of Guelph, Department of Molecular and Cellular Biology, Guelph, Canada.
Véronique L
VL
Taylor
Technical University of Denmark, Center for Biological Sequence Analysis, Department of Systems Biology, Kgs. Lyngby, Denmark.
Ole
O
Lund
University of Guelph, Department of Molecular and Cellular Biology, Guelph, Canada.
Joseph S
http://orcid.org/0000-0002-1822-1165
JS
Lam
Technical University of Denmark, Department of Systems Biology, Kgs. Lyngby, Denmark lj@bio.dtu.dk.
Lars
http://orcid.org/0000-0002-5759-9769
L
Jelsbak
D019295:Computational Biology; D016680:Genome, Bacterial; D006801:Humans; D019081:O Antigens / Q000235:genetics*; D011550:Pseudomonas aeruginosa / Q000145:classification* / Q000235:genetics*; D019666:Rubiaceae; D012680:Sensitivity and Specificity; D012703:Serotyping / Q000379:methods*
D019081:O Antigens; C095976:O antigen, Pseudomonas