Sentinel surveillance study Shigella species from the Amsterdam region

In the Netherlands, more than half of domestic shigellosis cases are among men who have sex with men (MSM). Since there is no laboratory surveillance based on whole genome sequencing (WGS), there is no insight in the relatedness of these cases. Here, we report the results of a regional genomic surveillance study in which Shigella isolates were subjected to WGS to gain insight into the relatedness of circulating isolates including antimicrobial resistance markers. Shigellosis cases with cultured isolates from the Amsterdam region from February 2019 to October 2021 were included. All isolates were subjected to Illumina WGS at the RIVM. Raw data was quality-checked and assembled using our in-house bioinformatic pipeline based on SPAdes. The Shigella serotype was determined in-silico by read mapping to known O-antigen genes and antimicrobial resistance markers were detected using ResFinder and PointFinder. Relatedness of isolates, including 21 international reference genomes, was assessed with core genome multi-locus sequence typing (cgMLST), using the Enterobase Escherichia/Shigella V1 scheme and a cluster cut-off of =5 alleles. This study shows that multiple clones of Shigella are present in the Netherlands. A majority of the clusters contain isolates originating from MSM and some of these clusters match with international MSM sequences indicating widespread international circulation. These results led to the implementation of a national WGS-based laboratory surveillance for Shigella that started in April 2022.