Abstract
Invasive nontyphoidal Salmonella (iNTS) infections remain a critical public health concern in sub-Saharan Africa (SSA) and South Africa (SA), where high human immunodeficiency virus (HIV) prevalence and socioeconomic disparities contribute to elevated disease burden. In SSA, iNTS is a leading cause of community-acquired bloodstream infections, with Salmonella Typhimurium ST313 and S. Enteritidis ST11 being the most prevalent serovars implicated in severe systemic disease. Compounding this threat is the increasing emergence of multidrug-resistant (MDR) strains, often associated with mobile genetic elements that facilitate the dissemination of antimicrobial resistance.
Methods
This descriptive study investigated the genomic epidemiology and AMR profiles of iNTS isolates collected in SA between January 2020 and December 2022 through the National Institute for Communicable Diseases GERMS-SA Laboratory Surveillance Network. Utilising whole-genome sequencing (WGS), the study characterised circulating Salmonella serovars, sequence types, and resistance determinants. Descriptive statistics, including frequencies and percentages, were used to describe isolate characteristics, patient demographics, and clinical outcomes. Associations between categorical variables were assessed using the Chi-squared test, including the relationship between HIV status and the distribution of serovars and AMR.
Results
A total of 1 308 cases of iNTS was identified from 2020 to 2022. In total, 76.9% (1 006/1 308) underwent WGS. Gauteng reported the highest number of iNTS cases. Most cases (609/1 006; 60.5%) were identified in the 25-59-year age group, followed by 18.8% (189/1 006) in the 0-4-year age group. Where HIV status was known, 54.4% (711/1 308)
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were identified as HIV-infected. Overall case report forms of S. Enteritidis (705/1 006; 70.0%) and S. Typhimurium (182/1 006; 18.1%) accounted for >80% of iNTS cases. MDR was identified in 2.8% (28/1 006) of isolates; 7.7% (14/182) of S. Typhimurium and 100.0% (12/12) of S. Isangi isolates were MDR. S. Isangi showed the highest levels of AMR. Notably, resistance to third-generation cephalosporins and fluoroquinolones was also identified. WGS enabled the identification of key resistance genes and provided insights into potential transmission pathways and clonal expansion events. The burden of disease was disproportionately higher among HIV-infected individuals, underscoring the intersection between immunosuppression and invasive salmonellosis.
Conclusion
This study provides critical insights into the molecular landscape of Salmonella infections in SA. The findings highlight the urgent need for ongoing epidemiological and genomic surveillance to monitor disease burden and case fatality rates, identify high-risk groups and to monitor circulating serovars and AMR trends. Improved access to diagnostics, initiatives to improve water, sanitation and hygiene, implementation of HIV and malaria control programmes and the development of targeted public health interventions, including vaccine development and antimicrobial stewardship, will be critical in mitigating the impact of iNTS in SA and high burden countries. This study contributes to the growing body of knowledge on iNTS in SA and highlights the importance of integrating genomic data into national public health responses.