Investigating contagious transmission of Mannheimia haemolytica in feedlot calves by leveraging whole genome sequences of a unique isolate collection

The role of specific strains of Mannheimia haemolytica (Mh) acting as contagious pathogens in the bovine respiratory disease complex remains debated. This study evaluated the contagious spread of Mh within and between adjacent feedlot pens using whole-genome-sequencing (WGS) to assess microbial genetic relationships. Deep-nasopharyngeal swabs were collected from auction-market calves entering a Saskatchewan feedlot in fall 2020; Mh isolates from 400 steers housed in four contiguous pens (100 steers per pen) were sequenced. All calves received standard arrival vaccinations (modified live 5-way viral vaccine with Mh toxoid, and a clostridial vaccine) and metaphylaxis with tulathromycin. Swabs were collected at 1, 13, and 36 days on feed (DOF). A total of 485 Mh isolates were identified, and WGS was performed to characterize phylogeny and antimicrobial resistance (AMR) genes. Before metaphylaxis at 1 DOF, isolates showed high genetic diversity, which decreased markedly by 13 DOF, with one or two genetic clusters becoming dominant within each pen. At 1 and 13 DOF, herd-of-origin was associated with genetic cluster, but this association disappeared by 36 DOF. Seven AMR genes were detected: strA, aphA1, strB, mphE, msrE, estT, sul2, and tetH. All dominant clusters carried AMR genes, typically three, although some carried five. These findings demonstrate that selection for and expansion of dominant Mh strains can occur shortly after feedlot arrival. Marked genetic shifts and reduced diversity during the first weeks on feed provide evidence of contagious spread of Mh within and between neighboring pens.