The French National Reference Center for Staphylococci used whole genome sequencing (WGS) to investigate outbreaks due to a virulent MRSA clone containing the toxic shock syndrome toxin-1 (TSST-1+, sequence type 5, Geraldine clone) increasingly reported in neonatal intensive care units (ICUs).
We analyzed 48 isolates previously characterized by spa typing: 31 isolates from outbreak #1 (infected or colonized patients, healthcare workers carriage and environment), 12 isolates from 4 distinct outbreaks (#2, #3, #4, #5) that occurred in geographically independent neonatal ICUs, and 5 sporadic strains. We performed WGS using a de novo assembly approach to perform comparisons between isolates (EpiSeq®, bioMérieux). A phylogenetic analysis was constructed by comparing single nucleotide variations (SNVs) in 2020 core-genes using a cutoff of 40 SNVs for defining isolates belonging to the same transmission cluster. We detected in silico resistance and virulence markers using the same bioinformatic pipeline.
For outbreak #1, 25/31 isolates with 2 distinct but related spa types t002 and t111 were highly related (<13 SNVs), suggesting the transmission of the same strain; 6/31 isolates were genetically distinct (> 80 SNVs) from the previous cluster of 25 isolates suggesting their origin from separate sources. Interestingly the 3 isolates of outbreak #2 with a spa t111 differed by less than 22 SNVs from the main cluster of the 25 isolates of outbreak #1. This suggested origin from the same transmission cluster. The other 3 outbreaks showing respectively a spa t002 for outbreak #3 and outbreak #4 and a spa t045 for outbreak #5 were not affiliated to the main cluster of outbreak #1. The isolates carry numerous virulence factors (including TSST-1) and resistance markers confering a peculiar antibiotic resistance profile to the Geraldine clone.
WGS provides the resolution power to reveal unsuspected transmission events not indicated by conventional methods (different spa type). Based on its high resolution WGS is an all in one tool for epidemiology, virulence and resistance analysis. It really transforms outbreak management and infection control practice for an early response and should replace conventional methods for detection of MRSA transmission.
M. Bes, None
F. Laurent, None
F. Vandenesch, None
A. Tristan, None
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