Scientists have described the main lessons learned from the use of whole genome sequencing (WGS) of E. coli in France.
WGS is routine for surveillance of Shiga toxin–producing E. coli (STEC) human isolates. Experts assessed implementation of WGS between 2018 and 2022 for 1,002 sequenced isolates. From genomic distances of serotypes O26:H11, O157:H7, O80:H2, and O103:H2, they determined thresholds for cluster determination and compared those with 5 allelic differences (HC5) clusters. A cluster is defined as cases grouped in space, time, or both. An outbreak is cases for which an epidemiologic link is identified.
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