Moraxella catarrhalis (M. catarrhalis) is a bacterial respiratory pathogen, which commonly causes otitis media and pneumonia. The species comprises a sero-sensitive clade of moderate virulence and a more pathogenic sero-resistant lineage. Since few genomic studies have been performed on M. catarrhalis, the aim of the present work was to characterise molecular epidemiology of M. catarrhalis in Western Australia (WA) using a whole genome sequence approach. In addition, no bacteriophages (phages) have yet been reported for this species. As phages often play important roles in pathogenicity of their hosts, the second aim of the project was to determine whether integrated phage genomes (prophages) exist within M. catarrhalis genomic sequences.
Analysis of eight housekeeping (MLST) genes of 339 strains in the M. catarrhalis database using goeBurst analysis revealed no relationship between the strains at single, double and triple locus variant levels. Sequence alignment and phylogeny of the MLST data from 310 strains categorised them into sero-sensitive and sero-resistant lineages. Eighty strains from WA were sequenced using Illumina base-pair technology, and were mapped unto the phylogenetic tree. Four isolates were found to be in the sero-sensitive clade, while the remainders in the sero-resistant clade. Phage annotation was performed on all 80 genomes, manually and using the programmes PHAST and PhageFinder. Twenty-four strains were found to harbour an intact prophage each, with sizes ranging from 17 kbp to 54 kbp. The 24 phages display a large diversity according to sequence of homologous phage genes as well as the synteny of phage genes. An alignment of blocks of genes using Mauve resulted in four possible clades of phages. A pan-genome of the phages has been constructed, and used as a reference sequence for comparison of individual phages.These data provide the first evidence of phages in M. catarrhalis.