Burden and genomic characterisation of Shigella-associated diarrhoea in children younger than 5 years in Lusaka, Zambia: a prospective cohort study.
BACKGROUND Shigella is a leading cause of childhood diarrhoea in low-income and middle-income countries and is increasingly resistant to first-line antibiotics. We conducted a surveillance study to assess the incidence, genomic characteristics, and antimicrobial resistance (AMR) profiles of Shigella infections in children younger than 5 years with moderate-to-severe diarrhoea (MSD) in Lusaka, Zambia. METHODS Between Sept 15, 2020, and Nov 30, 2021, a prospective cohort study was conducted, which included 1400 children younger than 5 years enrolled during a community census in a periurban setting and passively followed up for 9·5 months for MSD. During enrolment, sociodemographic data were collected using electronic questionnaires, whereas clinical data were collected through the DHIS platform. The main outcome, Shigella in diarrhoeal stool in children younger than 5 years, was detected using culture and loop-mediated isothermal amplification targeting the ipaH gene. Cox proportional hazards models were used to assess the incidence and risk factors of Shigella (ipaH) infections. Whole-genome sequencing was used to characterise the genomic diversity and AMR genes, complemented by phenotypic antibiotic susceptibility testing. FINDINGS 230 first episodes of Shigella were noted over a follow-up time of 9581·7 child-months, yielding an incidence of 24·0 (95% CI 21·1-27·3) cases per 1000 child-months, with the highest incidence among children aged 2-3 years. The key risk factors identified were the water source (p=0·025) and age group (p=0·014). Genotypic characterisation revealed ten Shigella flexneri, nine Shigella sonnei, and three Shigella boydii isolates. The S sonnei isolates formed two clusters, differing in virulence factors and plasmid profiles, indicating two possible circulating strains. Shigella isolates showed phenotypic and genotypic multidrug resistance (MDR), including against trimethoprim, aminoglycosides, and β-lactams. Plasmid-mediated quinolone resistance (qnrS1) was identified in four S flexneri isolates, with these genes located on the IncFIB(K) plasmid, highlighting the potential for horizontal transmission and spread of quinolone resistance in this region. No phenotypic and genotypic resistance to macrolides, the first-line treatment for Shigella infection in Zambia, was observed. INTERPRETATION We report a high burden of Shigella with MDR, including resistance to fluoroquinolones. These findings highlight the increasing resistance of Shigella to first-line antibiotics and underscore the importance of developing safe and effective vaccines, improving water, sanitation, and hygiene conditions, and ongoing AMR surveillance. FUNDING The EDCTP2 programme, supported by the EU, the Faculty for the Future Foundation, The Netherlands Organisation for Health Research and Development, and Health-Holland AMR-Global, Gloria, and Track-AMR.