Prevalence, antimicrobial resistance, and genomic characterization of non-typhoidal Salmonella in Thai native...

Native Blackbone chickens (Gallus gallus domesticus) are increasingly consumed in Southeast Asia because of their perceived health benefits. However, information on the epidemiology, antimicrobial resistance (AMR), and genomic characteristics of non-typhoidal Salmonella associated with this traditional poultry system remains limited. This study aimed to determine the prevalence, serovar distribution, antimicrobial susceptibility patterns, and genomic features of Salmonella isolated from feces and meat of Thai native Blackbone chickens.

A prospective longitudinal study was conducted between August 2020 and July 2021 on a small-scale Blackbone chicken farm in Phitsanulok province, Thailand. A total of 2,258 samples, comprising 1,755 fecal and 503 meat samples, were collected from chickens aged 1-50 weeks. Salmonella isolation was performed using standard culture and biochemical methods, with confirmation by invA using polymerase chain reaction. Serovars were determined by slide agglutination. Antimicrobial susceptibility was assessed against 14 antimicrobial agents using disk diffusion and broth microdilution methods. Six representative isolates were subjected to whole-genome sequencing (WGS) for multilocus sequence typing, detection of AMR and virulence genes, plasmid analysis, and phylogenetic comparison.

The overall prevalence of Salmonella was 6.3% (142/2,258), with detection rates of 4.7% in fecal samples and 11.9% in meat samples. Salmonella Bovismorbificans was the predominant serovar (64.1%), followed by S. Corvallis (20.4%) and S. Weltevreden (9.2%). More than half of the isolates (52.8%) exhibited resistance to at least one antimicrobial, most commonly streptomycin (46.5%), while resistance to critically important antimicrobials was not observed. Multidrug resistance (MDR) was rare (1.4%). WGS revealed that S. Bovismorbificans isolates belonged to sequence type ST1499, whereas S. Weltevreden was identified as ST365. Despite limited AMR, all sequenced isolates carried numerous virulence-associated genes linked to adhesion, invasion, and intracellular survival.

Thai native Blackbone chickens harbor non-typhoidal Salmonella, including emerging and potentially invasive lineages, with low levels of MDR but substantial virulence potential. These findings highlight the zoonotic risk posed by traditional poultry systems and underscore the importance of continued surveillance and genomic monitoring to support food safety and One Health strategies.