Phenotypic and Genotypic Characterization of Drug Resistant Shigella Species Isolated from North-East, Nigeria

Abstract

Nigeria’s high age-standardized AMR related mortality rate could lead to a 5-7% loss in GDP by 2050. This highlights the urgent need for coordinated efforts to develop effective tools to tackle the growing threat of AMR and address the rapid adaptation of Shigella spp. to changing environments. This study aims to isolate and characterize Shigella species, determine their resistance profile and phylogeny as an essential guide to informing effective treatment measures in northeast Nigeria. Diarrhoeagenic stools samples were collected and cultured on selective media. Colonic phenotypic identification was done using classical microbiology, biochemical testing and molecular methods. The generated partial sequences aligned and phylogenetic tree constructed. Out of 324 diarrhoeagenic samples collected, 30 (9%) Shigella species confirmed include Shigella boydii (13), Shigella flexneri (15) and Shigella Sonnei (2). The high resistance was against Cefuroxime (100%), Ampicillin (80%), Amoxicillin-Clavulanic Acid (78%) while high susceptibility observed were against Amikacin (93%), Chloramphenicol (90%) and Azithromycin (85%). All five MDR phenotypes, one of which showed XDR potential and high MAR indices (0.2-0.9) including Shigella boydii and Shigella flexneri showed 16S rRNA amplicon around 720bp with sequences clustered within reference strains from China, Iran and U.S.A. Shigella strains in this study favours Amikacin, Chloramphenicol and Azithromycin as possible empirical treatment option and call for compulsory AST before shigellosis treatment due high MAR indices for the MDR Shigella species and XDR Shigella flexneri high risk. The guidelines recommend molecular diagnostics, genotypic high-risk strains tracking to help clinicians tailor therapy and limit outbreaks of MDR Shigella spp. There is need for coordinated national strategy to drive intentional collaboration with research institutions to meet the targets for AMR research in Nigeria. These findings underscore the urgent need for WGS-enhanced surveillance and regional antibiotic stewardship for better genomic information.