Listeria monocytogenes internalins are highly diverse and evolved by recombination and positive selection

To probe the evolution of internalins with confirmed or suspected roles in Listeria monocytogenes virulence we sequenced the full inlB, inlC2, inlC, inlD, inlE, inlF, inlG, and inlH ORFs from 40 L. monocytogenes isolated from human (n = 10) and animal (n = 10) clinical cases, foods (n = 10), and the natural environment (n = 10). inlB and inlE were present in all isolates, representing 26 and 20 alleles, respectively. inlC was found in all lineage I and II isolates and represented 21 alleles. inlC2 and inlD represented 22 and 24 alleles, respectively, and were found in all L. monocytogenes isolates, with the exception of three lineage II isolates, which carried inlH, an apparent fusion of the 5′ end of inlC2 with the 3′ end of inlD. inlF and inlG were absent from lineage I isolates and represented 16 and 11 alleles, respectively. Average pairwise nucleotide differences per site (π) ranged from 0.00849 (inlF) to 0.07020 (inlE). Phylogenetic trees generally showed clustering of internalin genes into two major evolutionary lineages consistent with lineages I and II previously assigned by ribotyping. In addition to detection of recombination events within each internalin gene, inlB, inlC, inlC2, and inlF showed significant evidence for positive selection (i.e., selection for an advantageous mutant allele). Overall, our data indicated that (i) internalin genes are highly diverse, (ii) internalin gene sequences cluster consistent with the phylogenetic lineages of L. monocytogenes, (iii) both intragenic recombination and positive selection have contributed to the evolution of L. monocytogenes internalins, and (iv) L. monocytogenes internalins show distinct evolutionary histories.