Non-typeable Haemophilus influenzae isolates from patients with chronic obstructive pulmonary disease contain new phase-variable modA methyltransferase alleles controlling phasevarions

John M Atack,Timothy F Murphy,Melinda M Pettigrew,Michael P Jennings,Kate L Seib

doi:10.1038/s41598-019-52429-6

Abstract

Phasevarions (phase-variable regulons) are emerging as an important area of bacterial gene regulation. Many bacterial pathogens contain phasevarions, with gene expression controlled by the phase-variable expression of DNA methyltransferases via epigenetic mechanisms. Non-typeable Haemophilus influenzae (NTHi) contains the phase-variable methyltransferase modA, of which multiple allelic variants exist (modA1-21). We have previously demonstrated 5 of 21 these modA alleles are overrepresented in NTHi strains isolated from children with middle ear infections. In this study we investigated the modA allele distribution in NTHi strains isolated from patients with chronic obstructive pulmonary disease, COPD. We demonstrate that the distribution of modA alleles in a large panel of COPD isolates is different to the distribution seen in middle ear infections, suggesting different modA alleles may provide distinct advantages in the differing niches of the middle ear and COPD airways. We also identified two new phase-variable modA alleles – modA15 and modA18 – and demonstrate that these alleles methylate distinct DNA sequences and control unique phasevarions. The modA15 and modA18 alleles have only been observed in COPD isolates, indicating that these two alleles may be markers for isolates likely to cause exacerbations of COPD.

Highlights

Non-typeable Haemophilus influenzae (NTHi) is a major human-adapted pathogen that is the etiological agent of a number of acute and chronic diseases of the human respiratory tract[1,2], and for invasive infections such as septicaemia and meningitis[3,4,5]
In work carried out with a large panel of NTHi isolates taken from children with middle ear infection, or otitis media (OM), we have previously demonstrated that ~65% of these NTHi isolates contain one of just five phase-variable Type III N6 adenine DNA methyltransferases, ModA2, 4, 5, 9, or 10, among the 21 known modA alleles
An NTHi collection isolated from chronic obstructive pulmonary disease (COPD) patients contains different proportions of modA alleles compared to those isolated from OM patients

Summary

Introduction

Non-typeable Haemophilus influenzae (NTHi) is a major human-adapted pathogen that is the etiological agent of a number of acute and chronic diseases of the human respiratory tract[1,2], and for invasive infections such as septicaemia and meningitis[3,4,5]. Each modA allele methylates a distinct DNA sequence and controls a different set of genes, i.e., a different phasevarion[19]. Using sequenced genomes for 269 NTHi isolates from patients presenting with COPD21 we carried out BLAST analysis with our previously, well-defined modA allele sequences[19,20] to determine the modA allele distribution within this population.

Results

Conclusion