Molecular Characterisation of Virulence and Antibiotic Resistance Genes in Diarrhoeal Shigella Isolates from Diwaniyah, Iraq

Abstract

Objective: Investigating the genetic diversity, virulence determinants, and resistance profiles of Shigella spp is essential to managing outbreaks and informing effective treatment measures, especially in the Iraqi setting, where such data is scarce. Methods: Stool samples from patients with acute diarrhoea were cultured on selective media. Colony phenotypic identification was based on non-lactose fermenting properties, H₂S negative behaviour, and Gram-negative, non-motile appearance. Molecular confirmation via PCR amplification of the 16S rRNA gene sequence assembly was performed using the assembly tool in CLC Genomic Workbench with default parameters, and partial sequences were aligned using ClustalW, and phylogenetic trees were constructed in MEGA11. Conventional PCR detected virulence (ipaH, invE, sigA) and resistance genes (blaTEM, aada1, qnrA). Results: All 88 isolates were positive for the 16S rRNA gene. Phylogenetic analysis revealed grouping into clusters of 3 species: S. sonnei, S. flexneri, and S. dysenteriae, each closely related to reference strains from Asia and the Middle East. The ipaH gene was universally present, whereas invE and sigA were detected in a subset of isolates. Common resistance genes included blaTEM, indicating extensive resistance to β-lactam antibiotics. Conclusion: Local isolates of Shigella spp exhibited considerable genetic diversity and harboured virulence and antimicrobial resistance genes. These findings highlight the importance of routine molecular surveillance in tracking the spread of high-risk strains and supporting public health interventions and treatment protocols tailored to specific clusters. Iraqi dysentery guidelines need to be updated to restrict ineffective antibiotics, improve hospital hygiene, and develop vaccines targeting conserved virulence genes.