Illumina NGS WGS sequencing of 1139 novel Salmonella enterica isolates taken from foodborne sources in Metro Manila and Pampanga in the Philippines
Salmonella enterica is a leading zoonotic cause of foodborne illness, transmitted to humans via contaminated meat. In the Philippines, rising demand for chicken and pork, limited antibiotic regulation in farming, and lower-hygiene wet markets create significant risk from antibiotic-resistant and multidrug-resistant (MDR) strains. Using Illumina whole-genome sequencing, we analysed 1,139 S. enterica isolates from chicken (n=662; 58.1%) and pork (n=477; 41.9%), collected from wet markets, slaughterhouses, and veterinary clinics in Metro Manila and Pampanga (2018–2022). Forty-five serovars were identified; S. Infantis, S. Anatum, S. Uganda, and S. London accounted for 52.9% of isolates, with clinically significant serovars S. Typhimurium (n=51) and S. Enteritidis (n=26) also detected. Leveraging the serovar-based clustering on the phylogenetic tree, Bayesian molecular clock analysis estimated an average evolutionary rate of 3.10 SNPs per year. Over half of isolates encoded resistance to at least one antibiotic class, including the last-resort antibiotic colistin, and all carried 10–15 virulence factors, with higher resistance and virulence gene counts in chicken and market isolates. Integrating publicly available data (total n=1,323), we identified over 100 potential transmission clusters at a SNP threshold of 12, including 10 large clusters (20–124 isolates; 7 serovars), suggesting shared sources. Pairwise SNP distances between these isolates and S. enterica sequences from foodborne sources across Southeast Asia (n=111) all exceeded the 12-SNP threshold; the smallest observed distance was 22 SNPs, between isolates from the Philippines and Vietnam. Our findings highlight the growing prevalence of MDR Salmonella in Philippine food supply chains and underscore the urgent need for integrated, sequencing-based surveillance across the farm-to-table continuum.
Salmonella enterica is a leading zoonotic cause of foodborne illness, transmitted to humans via contaminated meat. In the Philippines, rising demand for chicken and pork, limited antibiotic regulation in farming, and lower-hygiene wet markets create significant risk from antibiotic-resistant and multidrug-resistant (MDR) strains. Using Illumina whole-genome sequencing, we analysed 1,139 S. enterica isolates from chicken (n=662; 58.1%) and pork (n=477; 41.9%), collected from wet markets, slaughterhouses, and veterinary clinics in Metro Manila and Pampanga (2018–2022). Forty-five serovars were identified; S. Infantis, S. Anatum, S. Uganda, and S. London accounted for 52.9% of isolates, with clinically significant serovars S. Typhimurium (n=51) and S. Enteritidis (n=26) also detected. Leveraging the serovar-based clustering on the phylogenetic tree, Bayesian molecular clock analysis estimated an average evolutionary rate of 3.10 SNPs per year. Over half of isolates encoded resistance to at least one antibiotic class, including the last-resort antibiotic colistin, and all carried 10–15 virulence factors, with higher resistance and virulence gene counts in chicken and market isolates. Integrating publicly available data (total n=1,323), we identified over 100 potential transmission clusters at a SNP threshold of 12, including 10 large clusters (20–124 isolates; 7 serovars), suggesting shared sources. Pairwise SNP distances between these isolates and S. enterica sequences from foodborne sources across Southeast Asia (n=111) all exceeded the 12-SNP threshold; the smallest observed distance was 22 SNPs, between isolates from the Philippines and Vietnam. Our findings highlight the growing prevalence of MDR Salmonella in Philippine food supply chains and underscore the urgent need for integrated, sequencing-based surveillance across the farm-to-table continuum.
London School of Hygiene and Tropical Medicine