Geraldine Durand, Fabien Javerliat, Michèle Bes, Jean-Baptiste Veyrieras, Ghislaine Guigon, Nathalie Mugnier, Stéphane Schicklin, Gaël Kaneko, Emmanuelle Santiago-Allexant, Coralie Bouchiat, Patrícia Martins-Simões, Frederic Laurent, Alex Van Belkum, François Vandenesch, Anne Tristan
Abstract
The French National Reference Center for Staphylococci currently uses DNA arrays andspatyping for the initial epidemiological characterization ofStaphylococcus aureusstrains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulentS. aureuslineages [clonal complexes (CCs): CC1, CC5, CC8, CC30] involved in hospital and community outbreaks or sporadic infections in France. We used a WGS bioinformatics pipeline based onde novoassembly (reference-free approach), single nucleotide polymorphism analysis, and on the inclusion of epidemiological markers. We examined the phylogeographic diversity of the French dominant hospital-acquired CC8-MRSA (methicillin-resistantS. aureus) Lyon clone through WGS analysis which did not demonstrate evidence of large-scale geographic clustering. We analyzed sporadic cases along with two outbreaks of a CC1-MSSA (methicillin-susceptibleS. aureus) clone containing the Panton-Valentine leukocidin (PVL) and results showed that two sporadic cases were closely related. We investigated an outbreak of PVL-positive CC30-MSSA in a school environment and were able to reconstruct the transmission history between eight families. We explored different outbreaks among newborns due to the CC5-MRSA Geraldine clone and we found evidence of an unsuspected link between two otherwise distinct outbreaks. Here, WGS provides the resolving power to disprove transmission events indicated by conventional methods (same sequence type,spatype, toxin profile, and antibiotic resistance profile) and, most importantly, WGS can reveal unsuspected transmission events. Therefore, WGS allows to better describe and understand outbreaks and (inter-)national dissemination ofS. aureuslineages. Our findings underscore the importance of adding WGS for (inter-)national surveillance of infections caused by virulent clones ofS. aureusbut also substantiate the fact that technological optimization at the bioinformatics level is still urgently needed for routine use. However, the greatest limitation of WGS analysis is the completeness and the correctness of the reference database being used and the conversion of floods of data into actionable results. The WGS bioinformatics pipeline (EpiSeqTM) we used here can easily generate a uniform database and associated metadata for epidemiological applications.
This research output has an Altmetric Attention Score of 2. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 05 April 2018.
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