Antimicrobial resistance in Mannheimia haemolytica from diseased cattle: phenotypic and genotypic insights over five years (2018–2022)

Mannheimia haemolytica is a gram-negative bacterium that typically resides in the upper respiratory tract of healthy cattle but can invade the lower respiratory tract in immunocompromised cattle, contributing to bovine respiratory disease (BRD). The rise of antimicrobial resistance (AMR) in M. haemolytica strains, especially those linked to BRD, is a growing concern. This study aimed to investigate AMR phenotypes and genotypes in M. haemolytica isolates collected during the NAHLN AMR Pilot Project (2018–2022) and assess the use of a previously developed single nucleotide polymorphism genotyping scheme to classify strains and identify associations between genotypes, AMR genes, quinolone point mutations (QPMs) and mobile genetic elements in diseased cattle. Of 2743 isolates tested for antimicrobial susceptibility, 66.7% (1830/2743) were pan-susceptible, while 33.3% (913/2743) showed resistance to at least one antimicrobial, primarily tetracyclines. Among the 848 sequenced isolates, 36.7% (311/848) harbored AMR genes and/or QPMs. Of these, 59.8% (186/311) were phenotypically classified as multidrug-resistant; commonly detected AMR genes included aadA , ant(2’’)-Ia , bla OXA−2 , mph (E), msr (E), and tet (H). The study found that 88.3% (749/848) of isolates belonged to genotype 2, a group previously associated with BRD and AMR. Notably, 95.8% (298/311) of isolates harboring AMR genes were from genotype 2. Although most clinical isolates of M. haemolytica were pan-susceptible and lacked AMR genes, a substantial proportion of isolates exhibited AMR, with a high degree of concordance between genotype and phenotype across all antimicrobials tested. Most clinical isolates (749/848, 88.3%), primarily obtained from the cattle lungs rather than the upper respiratory tract, were classified as genotype 2. These isolates harbored a T4SS integrative and conjugative element (ICE, 283/848, 33.4%) as well as an integrative and mobilizable element (IME, 59/848, 7.0%) containing AMR genes. This study highlights a strong association between genotype 2 M. haemolytica and AMR, with a significant prevalence of multidrug-resistant strains. The findings underscore the importance of genotypic characterization and whole-genome sequencing (WGS) for monitoring AMR in M. haemolytica and informing future management strategies for BRD.