Emerging Genomic Mechanisms of Multidrug-Resistant Salmonella enterica in Poultry Supply Chains: Implications for One Health Strategies

Abstract

Multidrug resistant (MDR) Salmonella enterica is a growing serious issue in poultry supply chain (particularly in India) due to the escalating level of poultry consumption in India with minimal checks. The proposed research includes whole-genome sequencing (WGS) of 100 isolates (poultry farm, processing plant, and retail market) in Haryana that will help to unveil the new genomic pathways that lead to antimicrobial resistance (AMR). Multi-locus sequence typing (MLST) revealed dominating classes of sequences (STs) including ST48 and ST32 and comparative genomics revealed novel plasmids with copies of blaTEM and tetA and mcr-1 genes and integrons (class 1 and 2) favouring horizontal gene transfer. MDR displaying phenotypic resistance under ANOVA was found to have significant difference (F=12.45, p< 0.001) between levels in the supply chain. The farm isolates and those of retail were then grouped into other phylogenetic trees that showed contamination during processing. Findings indicate zoonotic threats in One Health systems, indicating the need to enhance the genomic surveillance, phage therapy, and vaccine development against adhesins (including fimH). The novelty of the research is the combination of WGS and supply chain mapping in the Indian case which did not involve regional data. These lessons suggest integrated measures in order to curb the AMR transmission between poultry and human population. (248 words)