Geographic clustering and population structures ofandin South and Southeast Asian poultry systems.

Abstract

Poultry production is rapidly expanding across South and Southeast Asia to meet rising demand for human consumption.andare the leading causes of human bacterial gastroenteritis worldwide, with poultry serving as a primary reservoir posing significant risks to food safety and public health. This study investigated the genetic diversity ofandisolates from chicken sampled in farms, along with markets (live bird markets and shops) and slaughtering facilities from Bangladesh, India, Sri Lanka and Vietnam. Core-genome multilocus sequence typing revealed strong geographical clustering ofisolates, dominated by ST-828 clonal complex lineages largely confined within national borders. In contrast,isolates clustered more diffusely into multiple clonal complexes (ST-21, ST-45 and ST-257) that were shared between countries, reflecting greater ecological adaptability and frequent gene flow. Permutational multivariate ANOVA (PERMANOVA) supported these patterns; geography explained more genomic variation forthanwhile poultry breed type and production site contributed little overall. An exception was Sri Lanka, whereshowed an apparent ecological segregation between markets and slaughtering facilities, albeit with a limited within-country sample size. Genomic SNP-based analysis highlighted recombination as a significant evolutionary force maintaining distinct country-specific lineages in, while supporting a broader geographic mixing of. Pangenome analyses were consistent with more geographically structured accessory profiles inand a more dispersed pattern in, compatible with broader regional dissemination. Comparison with global reference genomes showed these isolates clustered with strains from diverse host species, highlighting the ability ofto occupy multiple ecological niches and spread across borders. The distinct patterns of spatially clustered and dispersed lineage distributions forand, respectively, highlight the importance of understanding species-specific transmission dynamics to inform targeted intervention strategies. This understanding underscores the need for interventions along poultry production and distribution networks that can effectively mitigate the risks associated with campylobacteriosis.