Whole genome sequencing analysis of non-typhoidal and typhoidal Salmonella enterica of chicken meat and human origin under surveillance in Sri Lanka

A total of seventy-nine Salmonella enterica isolates, thirty-three from raw chicken meat from Colombo and forty-six from clinical specimen, were collected in a pilot surveillance study from eight cities in Sri Lanka, between time periods in 2015 and 2016. The isolates were characterized by conventional serotyping and whole genome sequencing. The raw sequenced data were assembled and analysed to determine multilocus sequence typing (ST) profiles of genome and plasmid, and predicted serotypes, and to identify plasmid replicon sequences and antimicrobial resistance (AMR) genes.