Whole Genome Sequencing Analysis of a Recent Multi-Drug Resistant Shigella sonnei Outbreak Among Tunisian Children

Abstract

BackgroundShigella sonnei, a leading cause of shigellosis, is a global health concern, particularly affecting children under five. The emergence of multidrug-resistant (MDR) strains, including resistance to key antibiotics like ciprofloxacin and third-generation cephalosporins, exacerbates treatment challenges. This study investigates the genetic and antimicrobial resistance profiles of S. sonnei isolates from Tunisia, focusing on an outbreak of extended-spectrum beta-lactamase (ESBL)-producing strains. MethodsWe analysed nine S. sonnei isolates collected between September 2022 and January 2023 from Tunisian hospitals, using whole genome sequencing (WGS). Standard bacterial identification and serotyping methods were employed alongside antimicrobial susceptibility testing. We examined the genetic relatedness of the isolates, identified resistance genes, and characterised virulence factors. ResultsAll the isolates were confirmed as S. sonnei H6, biotype a, and belonged to lineage 3, clade 6 and sub-lineage 3. All harboured blaCTX-M-15, conferring resistance to third-generation cephalosporins. These were chromosomally integrated, suggesting stable resistance. Five isolates exhibited fluoroquinolone resistance associated with the qnrS1 gene, and all isolates had a single quinolone resistance-determining region mutation (GyrA-D87Y). Additionally, the plasmid-borne mphA gene, conferring resistance to macrolides, was prevalent. Single-linkage hierarchical clustering analysis indicated close genetic relationships with S. sonnei strains from Europe, particularly France and the UK (0 to 31 core genome MLST allele differences), indicating recent international dissemination. ConclusionThis study provides the first comprehensive molecular characterisation of MDR S. sonnei in Tunisia, highlighting a significant public health threat. The findings underscore the importance of continuous genomic surveillance to track the spread of resistant strains and inform public health interventions.