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

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 1133 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.ResultsA 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 1 to 12 resistance genes.ConclusionsTyping 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3316-8) contains supplementary material, which is available to authorized users.

Probiotic bacteria inhibit the bovine respiratory pathogenMannheimia haemolyticaserotype 1in vitro

“…; Clawson et al . ) which may reduce the efficacy of current antimicrobials used to treat BRD. Novel methods to mitigate BRD‐related pathogenic bacteria are therefore needed.…”

“…Treatment and control of BRD in the beef sector are aimed mainly at bacterial pathogens, through use of antimicrobials. However, studies have shown that antimicrobial resistance in BRD pathogens has increased (Portis et al 2012) and multiresistance has been identified on mobile elements (Klima et al 2014;Clawson et al 2016) which may reduce the efficacy of current antimicrobials used to treat BRD. Novel methods to mitigate BRD-related pathogenic bacteria are therefore needed.…”

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

“…Primers and probes were designed using Geneious 8.1.9 (Biomatters Ltd., Newark, NJ, USA) and verified using the NCBI BLAST nucleotide collection (nt/rt) reference sequence database ( Table 2 (Figure 1). While ICEs differ among strains, the presence of tet(H) (conferring tetracycline resistance) was found in 100% of AMR M. haemolytica strains associated with BRD (12). While the tet(H) gene itself is prevalent among genomes of numerous bacterial species, within ICE, tet(H) is located adjacent to a transposase (tnpA) with a conserved sequence among ICE-containing strains of M. haemolytica, P. multocida, and H. somni.…”

“…Excluding M. bovis, the genomes of BRD pathogens often contain integrative conjugative elements (ICE), mobile genetic elements that can harbor multiple AMR genes and encode the conjugation machinery required for transfer of ICE between BRD pathogens and to other bacteria (4,9). The resulting multi-drug resistance (MDR) among some BRD pathogens containing ICE presents a significant challenge for the efficacy of antimicrobial therapy as a treatment for BRDClawson et al (12) found that the gene tet(H), which confers tetracycline resistance was present in all AMR M. haemolytica strains isolated from confirmed BRD cases, and was also frequently found in P. multocida (13) and H. somni ICE (14). Furthermore, tet(H) was adjacent to the transposase gene tnpA, a core ICE gene associated with increased minimum inhibitory antimicrobial concentrations in M. haemolytica, H. somni, and P. multocida (15).…”

Development of a multiplex real-time PCR assay using two thermocycling platforms for detection of major bacterial pathogens associated with bovine respiratory disease complex from clinical samples

“…Additionally, the lktD locus of 1,133 M. haemolytica isolates sequenced in a previous study was used for screening of potential polymorphisms at the primerbinding sites. 4 Primers and probe sequences were selected that were unique and did not possess significant identity to other sequences in GenBank, with the exception of M. haemolytica (Table 2). M. haemolytica had some sequence identity with closely related species; however, some polymorphisms were present in primer and probe-binding sites for non-target species ( Supplementary Fig.…”