Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.

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Serval ID
serval:BIB_3F15E371F699
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Whole-Genome Sequencing Reveals the Contribution of Long-Term Carriers in Staphylococcus aureus Outbreak Investigation.
Journal
Journal of clinical microbiology
Author(s)
Gordon N.C., Pichon B., Golubchik T., Wilson D.J., Paul J., Blanc D.S., Cole K., Collins J., Cortes N., Cubbon M., Gould F.K., Jenks P.J., Llewelyn M., Nash J.Q., Orendi J.M., Paranthaman K., Price J.R., Senn L., Thomas H.L., Wyllie S., Crook D.W., Peto TEA, Walker A.S., Kearns A.M.
ISSN
1098-660X (Electronic)
ISSN-L
0095-1137
Publication state
Published
Issued date
07/2017
Peer-reviewed
Oui
Volume
55
Number
7
Pages
2188-2197
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
Whole-genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at a high resolution, thereby helping to characterize outbreaks. However, for javax.xml.bind.JAXBElement@716d6b2f , the accumulation of within-host diversity during carriage might limit the interpretation of sequencing data. In this study, we hypothesized the converse, namely, that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analyzed WGS data from 20 historical outbreaks and applied phylogenetic methods to assess genetic relatedness and to estimate the time to most recent common ancestor (TMRCA). The findings were compared with the routine investigation results and epidemiological evidence. Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% highest posterior density interval [HPD], 143 to 343 days) compared with 55 days (95% HPD, 28 to 81 days) for outbreaks lacking epidemiological evidence for an LTC ( javax.xml.bind.JAXBElement@ad698a = 0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1. We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles; however, these had only modestly increased pairwise diversity (mean 17.5 single nucleotide variants [SNVs] [95% confidence interval {CI}, 17.3 to 17.8]) compared with isolates with identical antibiograms (12.7 SNVs [95% CI, 12.5 to 12.8]) ( javax.xml.bind.JAXBElement@485b341e < 0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates that were genetically distinct despite having the outbreak pulsed-field gel electrophoresis (PFGE) pulsotype. The duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g., in health care workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.
Keywords
Adult, Carrier State/epidemiology, Carrier State/microbiology, Disease Outbreaks, Electrophoresis, Gel, Pulsed-Field, Genotype, Humans, Microbial Sensitivity Tests, Molecular Typing, Phylogeny, Staphylococcal Infections/epidemiology, Staphylococcal Infections/microbiology, Staphylococcus aureus/classification, Staphylococcus aureus/genetics, Staphylococcus aureus/isolation & purification, Whole Genome Sequencing, MRSA, Staphylococcus aureus, outbreaks, whole-genome sequencing
Pubmed
Web of science
Open Access
Yes
Create date
16/05/2017 18:50
Last modification date
01/02/2020 7:19
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