Evaluation of whole-genome sequencing for identification and typing of vibrio cholerae

Abstract

Epidemiological and microbiological data on Vibrio cholerae strains isolated between April 2004 and March 2018 (n 836) and held at the Public HealthEngland culture archive were reviewed. The traditional biochemical species identification and serological typing results were compared with the genome-derived species identification and serotype for a subset of isolates (n 152). Of the 836 isolates, 750 (89.7%) were from a fecal specimen, 206 (24.6%) belonged to serogroupO1, and 7 (0.8%) were serogroup O139; 792 (94.7%) isolates were from patients reporting recent travel abroad, most commonly to India (n 209) and Pakistan (n 104). Of the 152 V. cholerae isolates identified by use of kmer, 149 (98.1%) were concordant with those identified using the traditional biochemical approach. Traditionalserotyping results were 100% concordant with those of the whole-genome sequencing (WGS) analysis for the identification of serogroups O1 and O139 and classicaland El Tor biotypes. ctxA was detected in all isolates of V. cholerae O1 El Tor andO139 belonging to sequence type 69 (ST69) and in V. cholerae O1 classical variantsbelonging to ST73. A phylogeny of isolates belonging to ST69 from U.K. travelersclustered geographically, with isolates from India and Pakistan located on separatebranches. Moving forward, WGS data from U.K. travelers will contribute to globalsurveillance programs and the monitoring of emerging threats to public health andthe global dissemination of pathogenic lineages. At the national level, these WGSdata will inform the timely reinforcement of direct public health messaging to travelers and mitigate the impact of imported infections and the associated risks topublic health.