The present study was designed to understand the population structure of Salmonella and genotypic diversity, in order to inform control strategies of poultry salmonellosis in Sri Lanka. The study included a cross-sectional survey of broiler farms and associated hatcheries from poultry-dense areas as well as an outbreak study, based on isolates and metadata from poultry salmonellosis outbreaks. Altogether 164 pure Salmonella isolates; 128 from the cross-sectional survey and 36 from farm outbreaks, were included following PCR confirmation. High-quality genomic DNA were extracted, sequencing libraries prepared and assessed for quality before being sent for Illumina sequencing.
The Salmonella in Silico Typing Resource (Sistr) identified fifteen different serovars of Salmonella enterica belonging to diverse serogroups such as B, C1, C2-C4, D1, E1 and E4. The majority of Isolates comprised Kentucky 44 (27%), Enteritidis 37 (23%) and Typhimurium 22 (13%) while Bareilly, Gallinarum, Corvallis, Braenderup, Butanatan, Senftenberg, Paratyphi B var.Java 1, Chester, Durban, Virchow, Weltevreden and Tennessee were also present. Notably, Enteritidis, Gallinarum and Typhimurium were responsible for more than 80% of outbreaks and serovars Tennessee and Gallinarum could be seen only among outbreak isolates. According to Multi Locus Sequence Typing (MLST) there are 18 different sequence types (STs) while three isolates displayed likelihood of being a new ST. The latest version of the program fast-GeP is underway to perform whole-genome MLST analysis for the acquired genomic assemblies and the study is being continued with further bioinformatics- based analysis on the genetic distances of the isolates.