Abstract:
Background: Nontyphoidal Salmonella remains a leading cause of foodborne illness globally, yet transmission pathways at human-poultry interfaces in sub-Saharan Africa are poorly characterized. Backyard poultry systems are suspected reservoirs, but direct genomic evidence of cross-host clonal transmission in community settings is lacking.
Aim: To investigate backyard poultry as a potential source of human Salmonella infection through integrated genomic analysis of epidemiologically linked isolates from poultry, their human cohabitants, and clinical patients.
Methods: We conducted a cross-sectional One Health study in Teshie, Accra. A total of 315 fecal samples were collected from backyard poultry (185), their human cohabitants(48), and febrile clinical patients at LEKMA Hospital (82). Salmonella was isolated per ISO 6579 and confirmed by MALDI-TOF MS. Whole-genome sequencing of 26 isolates (11 poultry, 6 cohabitants, 9 clinical) was performed on an Illumina MiSeq platform. Bioinformatic analyses included MLST, core-genome MLST (cgMLST), phylogenomics, resistome profiling, and pangenome analysis.
Results: Salmonella was detected in 34/315 samples. Of the Salmonella-positive samples, 26 isolates were sequenced, comprising 11 poultry, 6 human cohabitants, and 9 clinical isolates. From these 9 Salmonella sequence types were identified. S. Corvallis ST3962 predominated, accounting for 10 of 26 isolates (38%) from poultry (n=5), human cohabitants (n=2), and clinical patients (n=3). Core-genome analysis revealed ≤10 single-nucleotide polymorphism (SNP) differences between isolates from different hosts and 99.2% core genome conservation across all the ST3962 isolates. The plasmid-mediated colistin resistance gene mcr-9 was detected in 2/6 human cohabitants. Other resistance genes included aac(6')-Ib-cr (present in all 26 isolates), blaCTX-M-9 (n=2), and blaTEM-1B (n=1). Virulence genes associated with systemic infection (spvB, spvC, and spvR) were detected only in clinical isolates (n=3). Other serovars identified included S. typhi ST2 (n=2, clinical only), S. Enteritidis ST11 (n=1, clinical), S. Agona ST13 (n=2, cohabitants only), and S. Stanleyville ST2562 (n=2, clinical and cohabitant).
Conclusion: We provide direct genomic evidence of clonal Salmonella transmission across backyard poultry, human cohabitants, and clinical patients in urban Ghana. mcr-9 detection signals emerging community-level colistin resistance. The genomic overlap between human and animal reservoirs emphasizes the urgent need for integrated One Health antimicrobial stewardship programs that extend beyond commercial agriculture to include peri-urban backyard farming.
Biography:
Peter Ofori Appiah is a Medical Microbiologist specializing in One Health, antimicrobial resistance, and microbial genomics. He holds an MPhil in Medical Microbiology from the University of Ghana Medical School and a BSc in Biochemistry from the University of Cape Coast. As an NIH DS-ZOOFOOD Fellow, he has published extensively on zoonotic pathogens, environmental contamination, and host-pathogen interactions. Peter founded the MedCraft Systematic Review Group to build research capacity among medical students and is currently seeking PhD opportunities to advance interdisciplinary research at the human-animal-environment interface.
