Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources

Abstract

Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2–8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the dependency on antibiotics to treat respiratory infection in cattle.

Essential oils inhibit the bovine respiratory pathogensMannheimia haemolytica,Pasteurella multocidaandHistophilus somniand have limited effects on commensal bacteria and turbinate cellsin vitro

“…haemolytica varies among serotypes, with serotypes 1 and 6 typically being more virulent and associated with BRD cases, while serotype 2 is more prevalent in the upper respiratory tract of healthy cattle (Klima et al . ). We therefore tested the three EOs (ajowan, thyme and fennel) showing the greatest inhibition of L024A against a diverse set of M. haemolytica , varying in serotype, isolation source and antibiotic phenotype.…”

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

“…Under laboratory conditions, ICE Pmu1 was able to transfer from P. multocida to M. haemolytica by conjugation and integration [22]. Homologs of ICE Pmu1, such as ICE Mh1 , have subsequently been identified in field-collected isolates of M. haemolytica from cattle in Nebraska, Pennsylvania, and Texas [21, 23, 27, 28]. The homologs share a conserved backbone that consists of blocks of genes which are adjacent to antibiotic resistance gene regions [23].…”

“…For example, ICE Mh1 has five antibiotic resistance genes, while yet another putative homolog found in M. haemolytica strain USDA_ARS_USMARC 183 has none [23]. Homologs to ICE Pmu1 and ICE Mh1 that contain antibiotic resistance genes do not appear restricted to one geographical region of North America [21, 27, 29], and may have a wide distribution and role in M. haemolytica antibiotic resistance. Given that capsular serotypes and PFGE profiles both indicate that M. haemolytica strains do not all equally associate with BRD, it is plausible that homologs containing antibiotic resistance genes could be more prevalent in M. haemolytica strains that associate with disease, as they would be more frequently exposed to BRD prevention and control measures that include antimicrobials.…”

A Sensitive and Accurate Recombinase Polymerase Amplification Assay for Detection of the Primary Bacterial Pathogens Causing Bovine Respiratory Disease

“…In this study, RPA assays were developed to detect four bacterial BRD pathogens (M. haemolytica, M. bovis, H. somni, and P. multocida), seven AMR genes, and a region of ICE associated with BRD pathogens. Furthermore, detection of M. haemolytica was specific to serotypes A1 and A6, those most commonly associated with disease, while excluding all other serotypes, including A2 a common bovine commensal (30,31). Beker et al (13) developed a multiplex PCR assay targeting four conserved core genes required for integration and maintenance of ICE structures within the Pasteurellaceae family and demonstrated relevance of this assay to detecting these elements in P. multocida and M. haemolytica (13).…”