Clonal expansion of Salmonella Corvallis ST3962 across backyard poultry, household contacts and clinical patients in urban Ghana: genomic evidence of shared lineages and community mcr-9 carriage

Nontyphoidal Salmonella remains a leading cause of foodborne illness globally. While backyard poultry are suspected drivers of nontyphoidal Salmonella transmission, genomic evidence linking community carriage, shared lineages, and clinical disease within a single ecosystem remains absent. We conducted a cross-sectional One Health study in Teshie, Accra. A total of 315 fecal samples were collected from backyard poultry (185), human cohabitant (48), and clinical patients (82). Salmonella isolates were recovered per ISO 6579-1:2017 and confirmed by MALDI-TOF MS. Twenty-six isolates (11 poultry, 6 cohabitants, 9 clinical) were selected based on household epidemiological links and underwent whole-genome sequencing on an Illumina MiSeq platform. Bioinformatic analyses included MLST, core-genome MLST (cgMLST), phylogenomics, resistome profiling, and pangenome analysis. Nine defined sequence types were identified (ST2, ST11, ST13, ST455, ST516, ST584, ST8938, ST2562, and ST3962), plus untypeable isolates (NA). Salmonella Corvallis ST3962 accounted for 10 of 26 sequenced isolates (poultry ( n = 8), human cohabitants ( n = 1), and clinical patients ( n = 1)). cgMLST analysis revealed ≤ 10 allelic differences among all 10 ST3962 isolates and 99.2% core genome conservation across all 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), bla CTX-M-9 ( n = 2), and bla TEM-1B ( n = 1). Nine plasmid replicon types were identified in clinical and human cohabitant isolates, most frequently IncH2_1, IncHI2A_1, and RepA_1_pKPC_CAV1321 (each in two human cohabitant isolates); no plasmids were detected in poultry isolates. Virulence genes associated with systemic infection ( spvB , spvC , and spvR ) were detected only in clinical isolates ( n = 3). We provide genomic evidence suggestive of recent cross-host circulation of a clonal Salmonella lineage across backyard poultry, human cohabitants, and clinical patients in urban Ghana. The detection of mcr-9 in asymptomatic household contacts without prior hospitalization signals a reservoir of genetic potential for last-resort antimicrobial resistance outside clinical settings.