Abstract
Moraxella catarrhalis is a human-adapted pathogen, and a major cause of otitis media (OM) and exacerbations of chronic obstructive pulmonary disease. The species is comprised of two main phylogenetic lineages, RB1 and RB2/3. Restriction–modification (R-M) systems are among the few lineage-associated genes identified in other bacterial genera and have multiple functions including defense against foreign invading DNA, maintenance of speciation, and epigenetic regulation of gene expression. Here, we define the repertoire of R-M systems in 51 publicly available M. catarrhalis genomes and report their distribution among M. catarrhalis phylogenetic lineages. An association with phylogenetic lineage (RB1 or RB2/3) was observed for six R-M systems, which may contribute to the evolution of the lineages by restricting DNA transformation. In addition, we observed a relationship between a mutually exclusive Type I R-M system and a Type III R-M system at a single locus conserved throughout a geographically and clinically diverse set of M. catarrhalis isolates. The Type III R-M system at this locus contains the phase-variable Type III DNA methyltransferase, modM, which controls a phasevarion (phase-variable regulon). We observed an association between modM presence and OM-associated middle ear isolates, indicating a potential role for ModM-mediated epigenetic regulation in OM pathobiology.
Highlights
Moraxella catarrhalis is a Gram-negative bacterial colonizer of the human respiratory tract
R-M systems are ubiquitous in bacteria and are abundant in naturally competent species, for example, Neisseria meningitidis (Budroni et al 2011; Kong et al 2013), Neisseria gonorrhoeae (Stein et al 1995), H. influenzae (Vasu and Nagaraja 2013), S. pneumoniae (Vasu and Nagaraja 2013), and Helicobacter pylori (Lin et al 2001; Kumar et al 2015)
Of the 51 total genomes analyzed, 26 are ribotype 1 (RB1) lineage strains, 19 are ribotype 2 and 3 (RB2/3) lineage strains, and six are divergent strains that differ in their average GC content (43.6–45.3%) relative to RB1 and RB2/3 lineage strains (41.6%), and currently classified as M. catarrhalis, are predicted to represent a different species or subspecies (Wirth et al 2007; Earl et al 2016)
Summary
Moraxella catarrhalis is a Gram-negative bacterial colonizer of the human respiratory tract. Often carried asymptomatically in the nasopharynx (Vaneechoutte et al 1990), acquisition of M. catarrhalis frequently progresses to otitis media (OM) in infants and children, and exacerbations of chronic obstructive pulmonary disease (COPD) in adults It is one of the three most prevalent bacterial causes of OM, along ß The Author(s) 2018. Evol. 10(11):2932–2946. doi:10.1093/gbe/evy226 Advance Access publication October 18, 2018
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