Abstract
Shigellosis is an acute enteric infection caused mainly by the species Shigella flexneri and Shigella sonnei. Since surveillance of these pathogens indicated an increase in ciprofloxacin-resistant samples collected in Belgium between 2013 and 2018, a subset of 148 samples was analyzed with whole genome sequencing (WGS) to investigate their dispersion and underlying genomic features associated with ciprofloxacin resistance. A comparison between observed phenotypes and WGS-based resistance prediction to ciprofloxacin revealed perfect correspondence for all samples. Core genome multi-locus sequence typing and single nucleotide polymorphism-typing were used for phylogenomic investigation to characterize the spread of these infections within Belgium, supplemented with data from international reference collections to place the Belgian isolates within their global context. For S. flexneri, substantial diversity was observed with ciprofloxacin-resistant isolates assigned to several phylogenetic groups. Besides travel-related imports, several clusters of highly similar Belgian isolates could not be linked directly to international travel suggesting the presence of domestically circulating strains. For S. sonnei, Belgian isolates were all limited to lineage III, and could often be traced back to travel to countries in Asia and Africa, sometimes followed by domestic circulation. For both species, several clusters of isolates obtained exclusively from male patients were observed. Additionally, we illustrated the limitations of conventional serotyping of S. flexneri, which was impacted by serotype switching. This study contributes to a better understanding of the spread of shigellosis within Belgium and internationally, and highlights the added value of WGS for the surveillance of this pathogen.
Highlights
Shigellosis is an acute enteric infection caused by the species Shigella dysenteriae, S.flexneri, S. boydii, and S. sonnei, and transmitted via the oral-fecal route
Of the 2315 Shigella isolates received by the Belgian National Reference Centre (NRC) between January 2013 and December 2018, 1690 (73.0%) were identified as S. sonnei, 485 (21.0%) as S. flexneri, 96 (4.1%) as S. boydii, 33 (1.4%) as S. dysenteriae and 11 isolates were untypeable
We analyzed the genomic variability among 148 Shigella isolates collected during the national surveillance of shigellosis in Belgium between 2013 and 2018
Summary
Shigellosis is an acute enteric infection caused by the species Shigella dysenteriae, S. flexneri, S. boydii, and S. sonnei, and transmitted via the oral-fecal route. Phylogenetic studies have shown that serologically defined Shigella spp. comprise three clusters (C1, C2, and C3) embedded within, but distinct from E. coli lineages A, B1, and E [8]. These genomic elements were not obtained at a single point in time from a single ancestral species but were rather acquired independently on multiple occasions from multiple ancestors, and encode genes for invasive infection, siderophores, and bactericidal and immune evasion [9]
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