Analysis of Nontypeable Haemophilus influenzae Phase Variable Genes during Experimental Human Nasopharyngeal Colonization

(See the editorial commentary by Inzana on pages 713–6.) Phase variation is described as a random process by which a clonal population of microbes can present heterogeneous phenotypes as a result of a reversible genetic event [1, 2]. The process can involve several mechanisms, including slipped-strand mispairing (SSM), site-specific recombination, and epigenetic regulation mediated by DNA methylation [2]. SSM is a mechanism found in human pathogens, including pathogenic Neisseria, Bordetella pertussis, Haemophilus influenzae, and Helicobacter pylori. The resulting frame shift causes on-off changes in gene expression [3]. The process can occur at rates as high as 2–3 × 10−4 colony forming units [3]. Nontypeable H. influenzae (NTHi), which colonizes human mucosal surfaces and can cause disease, has genes with long tandem repeats that undergo high rates of phase variation [3]. In 1989, Weiser et al identified a tetranucleotide repeat region (5′-CAAT-3′) in licA that was responsible for phase-variable expression of that gene in H. influenzae type b [4]. Subsequent work showed that a number of genes in the H. influenzae chromosome had similar characteristics and underwent phase variation. These genes are associated with iron regulation, membrane protein expression, and lipooligosaccharide (LOS) biosynthesis [5–9]. The opportunity to directly study the effect of experimental human colonization on changes in the phase-on, phase-off status of NTHi phase-varying genes was presented to us. This article describes the results of that study.