Phylogenomic investigation of increasing fluoroquinolone resistance among Belgian cases of Shigellosis between 2013 and 2018 indicates both travel-related imports and domestic circulation

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.SUPPLEMENTARY MATERIAL : FIGURE S1: Occurrence of gyrA p83, gyrA p87 and parC p80 mutations associated with ciprofloxacin resistance in the background collection. FIGURE S2: Network representation of minimum spanning trees for S. sonnei (A) and S. flexneri (B), TABLE S1: Accession number and metadata for the Belgian samples, TABLE S2: Read trimming statistics, TABLE S3: Assembly and coverage statistics, TABLE S4: Percentage of cgMLST alleles identified, TABLE S5: In silico determined serotypes for all S. flexneri samples, TABLE S6: Detected AMR genes for all samples, TABLE S7: Detected AMR point mutations for all samples, TABLE S8: Detected qnr genes, TABLE S9: Classification of contigs carrying qnr genes, TABLE S10: Lineage and PG classification, and ciprofloxacin resistance for the Belgian samples and background collection.The NRC is partially supported by the Belgian Ministry of Social Affairs through a fund within the Health Insurance System.https://www.mdpi.com/journal/microorganismsam2022Genetic