Whole genome sequencing of Moraxella bovis strains from North America reveals two genotypes with different genetic determinants

Abstract

Background: Moraxella bovis and Moraxella bovoculi both associate with infectious bovine keratoconjunctivitis (IBK), an economically significant and painful ocular disease that affects cattle worldwide. There are two genotypes of M. bovoculi (genotypes 1 and 2) that differ in their gene content and potential virulence factors, although neither have been experimentally shown to cause IBK. M. bovis is a causative IBK agent, however, not all strains carry a complete assortment of known virulence factors. The goals of this study were to determine the population structure and depth of M. bovis genomic diversity, and to compare core and accessory genes and predicted outer membrane protein profiles both within and between M. bovis and M. bovoculi.

Results: Phylogenetic trees and bioinformatic analyses of 36 M. bovis chromosomes sequenced in this study and additional available chromosomes of M. bovis and both genotype 1 and 2 M. bovoculi, showed there are two genotypes (1 and 2) of M. bovis. The two M. bovis genotypes share a core of 2015 genes, with 121 and 186 genes specific to genotype 1 and 2, respectively. The two genotypes differ by their chromosome size and prophage content, encoded protein variants of the virulence factor hemolysin, and by their affiliation with different plasmids. Eight plasmid types were identified in this study, with types 1 and 6 observed in 88 and 56% of genotype 2 strains, respectively, and absent from genotype 1 strains. Only type 1 plasmids contained one or two gene copies encoding filamentous haemagglutinin-like proteins potentially involved with adhesion. A core of 1403 genes was shared between the genotype 1 and 2 strains of both M. bovis and M. bovoculi, which encoded a total of nine predicted outer membrane proteins.

Conclusions: There are two genotypes of M. bovis that differ in both chromosome content and plasmid profiles and thus may not equally associate with IBK. Immunological reagents specifically targeting select genotypes of M. bovis, or all genotypes of M. bovis and M. bovoculi together could be designed from the outer membrane proteins identified in this study.

Keywords: Core genome; Genotype; Infectious bovine keratoconjunctivitis; Moraxella bovis; Moraxella bovoculi; Outer membrane protein.

Fig. 1

M. bovis genotype 1 and 2 differences. A Whole genome tree of M. bovis and M. bovoculi constructed in EDGAR using 1220 genes per genome, 1,278,792 bp per genome, with CP087830 as a reference. B Whole genome tree of M. bovis constructed with Parsnp using 74% of CP030241 as a reference and viewed with Ginger. The alleles of 11,070 polymorphisms separate the two genotype clades. ANI values were calculated using the whole genome sequence of M. bovis type strain CCUG 2133 M. Hemolysin protein variant sequences are provided in Supplementary Fig. S1. Isoform sequences of PilA are provided in Supplementary Fig. S3. PilA protein variant sequences connected to serotypes are represented with letters whereas isoforms without corresponding serotypes are represented with numbers

Fig. 2

Core genome and OMP comparisons of M. bovis genotypes 1 and 2 and M. bovoculi genotypes 1 and 2. A Exclusive core genome of all combinations for genotypes of M. bovis and M. bovoculi. Genes represented in each slice of the Venn diagram are found in 95% of the genomes of samples from that group of genotypes and no genomes of samples from outside of that group of genotypes B Predicted OMPs shared between all combinations of genotypes of M. bovis and M. bovoculi

Fig. 3

Core genome and OMP comparisons of M. bovis and M. bovoculi. A M. bovis genotypes 1 and 2 core genomes. B M. bovoculi genotypes 1 and 2 core genomes. C M. bovis genotype 1 and 2 core genome predicted OMPs. D M. bovoculi genotype 1 and 2 core genome predicted OMPs