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Non-typeable  Haemophilus influenzae  contains an N 6 -adenine DNA-methyltransferase (ModA) that is subject to phase-variable expression (random ON/OFF switching). Five  modA  alleles,  modA2 ,  modA4, modA5 ,  modA9  and  modA10 , account for over two-thirds of clinical otitis media isolates surveyed. Here, we use single molecule, real-time (SMRT) methylome analysis to identify the DNA-recognition motifs for all five of these  modA  alleles. Phase variation of these alleles regulates multiple proteins including vaccine candidates, and key virulence phenotypes such as antibiotic resistance ( modA2 ,  modA5 ,  modA10 ), biofilm formation ( modA2 ) and immunoevasion ( modA4 ). Analyses of a  modA2  strain in the chinchilla model of otitis media show a clear selection for ON switching of  modA2  in the middle ear. Our results indicate that a biphasic epigenetic switch can control bacterial virulence, immunoevasion and niche adaptation in an animal model system.

A biphasic epigenetic switch controls immunoevasion, virulence and niche adaptation in non-typeable Haemophilus influenzae