Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center

Abstract

The French National Reference Center for Staphylococci currently uses DNA arrays and spa typing for the initial epidemiological characterization of Staphylococcus aureus strains. We here describe the use of whole-genome sequencing (WGS) to investigate retrospectively four distinct and virulent S. aureus lineages [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 on de novo assembly (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-resistant S. 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-susceptible S. 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, spa type, 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 of S. aureus lineages. Our findings underscore the importance of adding WGS for (inter-)national surveillance of infections caused by virulent clones of S. aureus but 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.

Microbial Contamination of Fresh Produce: What, Where, and How?

“…This is a serious concern, as it hinders the implementation of targeted protective measures and mitigation strategies. Whole genome sequencing has recently been adopted by a number of health agencies to help establish a link between contaminated foodstuffs and possible sources of contamination, making epidemiological studies easier (Dallman et al., ; Durand et al., ; Inns et al., ).…”

Methotrexate and melanoma‐specific mortality

“…Staphylococcus aureus sent to the National Reference Laboratory Centre for Staphylococcus (Lyon, France) were analysed according to the method previously detailed. 2 From January 2009 to August 2016, 13 cases were included ( Table 1). None of the children were premature.…”

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Surveillance-embedded genomic outbreak resolution of methicillin-susceptibleStaphylococcus aureusin a neonatal intensive care unit

“…Given the vast genetic diversity observed in the circulating MSSA population, we considered that these isolates were very likely to be closely related. Likewise, previous studies identified many unsuspected transmission clusters upon re-assessment of S. aureus cohorts using WGS (28,29). Accordingly, in our genomic view time-linkage was not regarded as a prerequisite for outbreak clustering.…”