Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes

Authors: Clawson, Michael - Mike; MURRAY, ROBERT - Zoetis; SWEENEY, MICHAEL - Zoetis; APLEY, MICHAEL - Kansas State University; DEDONDER, KEITH - Kansas State University; CAPIK, SARAH - Kansas State University; LARSON, ROBERT - Kansas State University; LUBBERS, BRIAN - Kansas State University; WHITE, BRAD - Kansas State University; KALBFLEISCH, THEODORE - University Of Louisville; Schuller, Genevieve - Gennie; Dickey, Aaron; Harhay, Gregory; Heaton, Michael - Mike; Chitko-Mckown, Carol; Harhay, Dayna; Bono, James - Jim; Smith, Timothy - Tim

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/18/2016
Publication Date: 11/29/2016
Citation: Clawson, M.L., Murray, R.W., Sweeney, M.T., Apley, M.D., DeDonder, K.D., Capik, S.F., Larson, R.L., Lubbers, B.V., White, B.J., Kalbfleisch, T.S., Schuller, G., Dickey, A.M., Harhay, G.P., Heaton, M.P., Chitko-McKown, C.G., Brichta-Harhay, D.M., Bono, J.L., Smith, T.P.L. 2016. Genomic signatures of Mannheimia haemolytica that associate with the lungs of cattle with respiratory disease, an integrative conjugative element, and antibiotic resistance genes. BMC Genomics. 17:982. doi: 10.1186/s12864-016-3316-8.

Interpretive Summary: Bovine respiratory disease is a worldwide animal health and welfare problem. There are multiple causes of bovine respiratory disease, including environmental stress, viral, and bacterial infections. Mannheimia haemolytica is the predominant bacterial agent that causes bovine respiratory disease. An opportunistic pathogen, M. haemolytica is normally found in the upper respiratory tract of cattle that show no signs of disease. However, when cattle are stressed or immunocompromised, M. haemolytica can infect their lungs and cause illness and death. The literature has indicated for some time that not all strains of M. haemolytica associate equally with bovine respiratory disease or have the same level of antibiotic resistance. To investigate this, the genomes of 1,133 M. haemolytica isolates from North American cattle were sequenced and used to develop a new, high-resolution typing system for M. haemolytica. The typing system showed that the isolates classified into two major genetic types, or “genotypes” (1 and 2), which were each composed of multiple subtypes. Only genotype one M. haemolytica were found to associate with the lungs of cattle afflicted with respiratory disease. Importantly, this genotype also associated with an integrative conjugative element (ICE), which is a mobile genetic element that can carry virulence factors and pass between bacteria. Additionally, isolates classified to one particular subtype of genotype 2 (subtype b) were found to have up to 12 different antibiotic resistance genes, known to be carried on ICEs, that collectively encoded resistance to six different classes of antibiotics. These findings show how genetically distinct types, or strains of M haemolytica associate with the lungs of cattle with respiratory disease and antibiotic resistance. Tests that rapidly identify virulent antibiotic resistant genotype 2 M. haemolytica in cattle could facilitate management interventions to reduce the prevalence of bovine respiratory disease caused by this pathogen, and subsequent needs for antibiotic treatments. Additionally, new generation vaccines developed against genotype 2 M. haemolytica could effectively protect cattle from respiratory disease involving this pathogen.

Technical Abstract: Background: Mannheimia haemolytica typically resides in cattle as a commensal member of the upper respiratory tract microbiome. However, some strains can invade their lungs and cause respiratory disease and death, including those with multi-drug resistance. A nucleotide polymorphism typing system was developed for M. haemolytica from the genome sequences of 1,133 North American isolates, and used to identify genetic differences between isolates from the lungs and upper respiratory tract of cattle with and without clinical signs of respiratory disease. Results: A total of 26,081 nucleotide polymorphisms were characterized after quality control filtering of 48,403 putative polymorphisms. Phylogenetic analyses of nucleotide polymorphism genotypes split M. haemolytica into two major genotypes (1 and 2) that each were further divided into multiple subtypes. Multiple polymorphisms were identified with alleles that tagged genotypes 1 or 2, and their respective subtypes. Only genotype 2 M. haemolytica associated with the lungs of diseased cattle and the sequence of a particular integrative and conjugative element (ICE). Additionally, isolates belonging to one subtype of genotype 2 (2b), had the majority of antibiotic resistance genes detected in this study, which were assorted into seven combinations that ranged from one to twelve resistance genes. Conclusions: Typing of diverse M. haemolytica by nucleotide polymorphism genotypes successfully identified associations with diseased cattle lungs, ICE sequence, and antibiotic resistance genes. Management of cattle by their carriage of M. haemolytica could be an effective intervention strategy to reduce the prevalence of respiratory disease and supplemental needs for antibiotic treatments in North American herds.