(267) Unbalanced microbial genomic sequences from East Africa limits global surveillance for antimicrobial resistance in non-typhoidal Salmonella

Publication Number: 927

Background
Nontyphoidal Salmonella (NTS) is a leading cause of bacterial foodborne infection worldwide. This includes Africa where gastroenteritis—associated mortality is high. Next-generation sequencing has transformed surveillance for emerging pathogens in some parts of the world. The objective of this study is to assess the implementation of integrated genomic surveillance in Africa and elucidate its use to characterize antimicrobial resistance (AMR) in NTS and invasive infections.

Methods
We queried the Pathogen Detection Browser (at: www.ncbi.nlm.nih.gov/pathogens/) in January 2023 and downloaded NTS summary data for isolates from Kenya, Uganda, and Tanzania. Selected variables included serotype, isolation type, isolation source, single-nucleotide polymorphism (SNP) cluster, and AMR genes. Clinical isolates from normally sterile sites were defined as invasive.

Results
Of the 238 NTS isolates from Kenya, 65% (155) were clinical, and 32% (75) were from swine. No AMR genes were detected. Of the clinical isolates, 46% (71) were invasive. Uganda had 73 NTS isolates, 50 were clinical and of these, 24% (12) were invasive. Thirty of the clinical isolates had ampicillin-resistant genes (blaTEM-1, n=26 and blaOXA-1, n=4). Of 14 Ugandan NTS isolates from poultry, 10 had AMR genes including one with blaTEM-1 and another had a plasmid-mediated quinolone (PMRQ) resistant gene (qnrS1). Of the 443 NTS isolates from Tanzania, 0.5% (2) were clinical and 40.7% (180) were from meat sources, mostly (85%, 153) from unspecified animals. One Heidelberg isolate from meat had a PMRQ gene, and two heat-resistant S. senftenberg strains were isolated from the environment.

Conclusions
In these three African countries with a combined population of >160 million people, less than 800 public NTS sequences were available. NTS isolates were either predominantly clinical (Kenya and Uganda) or from animal sources (Tanzania). NTS from poultry sources and one from unknown meat type had genes that confer resistance to antibiotics recommended for severe infections. Integrated One Health surveillance in humans, animals, plants, and the environment is inadequate to detect the emergence of antimicrobial resistance strains, facilitate outbreak investigations, and guide clinical management.