Descriptive genomic analysis of antibiotic resistance in Pasteurella multocida isolates from India

Antibiotic resistance in Pasteurella multocida (P. multocida) poses a significant threat to both animal and public health. This study investigates the genomic mechanisms underlying antibiotic resistance in P. multocida strains isolated from various hosts in India, including buffalo, cattle, sheep, and pigs, as well as other species such as ducks and deer. A total of 40 whole genome sequences of P. multocida strains were analyzed, revealing that 17.5% harbored resistance genes, with notable resistance to antibiotics such as streptomycin, sulfamethoxazole, and trimethoprim. The ResFinder tool and Comprehensive Antibiotic Resistance Database (CARD) were employed to identify resistance genes. The presence of integrative and conjugative elements (ICEs) was detected using the ICEfinder tool, while MobileElementFinder was used to identify mobile genetic elements associated with resistance genes. Origins of transfer (oriT) were determined using oriTfinder, and efflux pumps were identified using resources from the Bacterial and Viral Bioinformatics Resource Center. Prophage sequences were annotated using PHASTEST. The study highlights the significant role of efflux pumps and oriT in the survival of resistant strains. The IncQ1 plasmid, identified in buffalo-derived strains such as PmBUFF2016HRY and ABT/RAWAL/2015/HSR, indicates a potential for multi-drug resistance spread across bacterial populations. Additionally, sheep-derived strains exhibited a high prevalence of prophages and genetic elements like integrase and transposase, making them key reservoirs for resistance evolution. This work provides valuable insights into the genomic mechanisms driving antibiotic resistance in P. multocida, offering a foundation for developing targeted strategies to curb resistance spread.