Identification of Phase-Variable Genes That May Contribute to Nontypeable Haemophilus influenzae Nasopharyngeal Colonization in Humans Contributes to Our Understanding of Specific Host-Pathogen Interactions

Phase variation of surface components is an important mechanism by which bacteria can adapt rapidly to an ever-changing environment. Phase variation is a reversible switching on and off of genes, resulting in the expression of phenotypes that vary within a clonal population. The rate of phase variation is variable but may occur at a high frequency. There are several known molecular mechanisms responsible for bacterial phase variation, including slipped-strand mispairing, Damdependent epigenetic DNA methylation, various types of DNA inversion, gene conversion, and site-specific recombination [1, 2]. In the human-specific opportunistic bacterialpathogenHaemophilusinfluenzae, slipped-strand mispairing is the most wellknown and studied mechanism of phase variation. Slipped-strand mispairing may occur when short or simple sequence repeats (SSRs) of nucleotides occur anywhere within the open reading frame (translational regulation) or within or upstream of the promoter region (transcriptional regulation) [3]. During DNA replication, if SSRs are present in the coding region, slippage of one DNA strand may result in the insertion or deletion of a repeat unit by excision/repair, which could then place the open reading frame out of frame with the start codon. If a stop codon occurs prematurely, translation is interrupted, resulting in a nonfunctional protein. The SSRs present in phase-variable genes usually consist of mono-, di-, or tetranucleotides, but more may occur, particularly in eukaryotic genomes [4]. Furthermore, the phase-variation rate correlates with the number of repeats present [5]. H. influenzae has a small genome (<2 Mb), and therefore phase variation through slipped-strand mispairing is a simple regulatory mechanism by which the bacteria can modify their phenotype to adapt to various niches within their host. Analysis of the genomes of sequenced bacterial strains has identified a number of genes with SSRs that would predictably undergo phase variation through slipped-strand mispairing. Such genes include those responsible for lipopolysaccharide (LPS) or lipooligosaccharide (LOS) biosynthesis, iron acquisition, fimbriae, and adhesins [3, 6, 7]. Phase variation of surface or extracellular components also results in antigenic heterogeneity, which may enable bacteria to avoid host defense mechanisms. One well-established mechanism for evading host immunity is phase variation of LOS epitopes. LOS is a type of LPS that lacks the repeating O-antigen side chain that is typical in most enteric and environmental Gram-negative bacteria. LOS is commonly expressed by some, but not all, species of Pasteurellaceae, including H. influenzae. However, the LOS of H. influenzae and others also differs from LPS by the presence of oligosaccharide side chains consisting of common hexoses and amino-hexoses extending from 3 heptose residues that are present in the inner core of the LOS [8]. One or more of these oligosaccharide side chains may Received and accepted 3 May 2013; electronically published 28 May 2013. Correspondence: Thomas Inzana, PhD, Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine and Virginia Tech-Carilion School of Medicine, Virginia Tech, Blacksburg, VA 24061 (tinzana@vt. edu). The Journal of Infectious Diseases 2013;208:713–6 © The Author 2013. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals. permissions@oup.com. DOI: 10.1093/infdis/jit243