Lineage specific recombination and positive selection in coding and intragenic regions contributed to evolution of the main Listeria monocytogenes virulence gene cluster

Abstract

The major virulence cluster of Listeria monocytogenes harbors six virulence genes that encode proteins critical for the intracellular life cycle of this human and animal pathogen. In this study, we determined the sequence (8709nt) of the virulence gene cluster (including the six main virulence genes) in 40 L. monocytogenes isolates from different source populations (human clinical cases, animal clinical cases, foods, and natural environments). An alignment of the full length cluster as well as individual gene alignments and alignments of intragenic regions were used for phylogenetic, recombination, and positive selection analyses. Initial phylogenetic analyses showed that the sequences represented two main clusters, consistent with previously defined L. monocytogenes phylogenetic lineages. The 40 sequences represented 25 distinct allelic types and the overall alignment included 592 polymorphic sites. Overall, our data show that (i) virulence genes in the main L. monocytogenes virulence gene cluster include highly conserved genes (i.e., hly and prfA) as well as diverse genes that appear to have evolved by positive selection (mpl, actA, and plcA), (ii) recombination has played an important role in the evolution of the virulence gene cluster, but is limited to lineage II isolates, and (iii) the promoter region driving the transcription of virulence genes transcribed early in intracellular infection (i.e., hly and plcA) has evolved by positive selection. The genes and intragenic regions in the L. monocytogenes virulence gene cluster thus have evolved independently, despite their close physical linkage, likely reflecting distinct selective pressures associated with expression and function of the proteins encoded in this region.

Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics

“…Initial studies focused on either probing for presence/absence of selected genes among different strains (e.g., virulence genes) or characterizing allelic variation of these genes (Chen et al, 2005;Jacquet et al, 2004;Nightingale et al, 2005b;Orsi et al, 2008b;Vines et al, 1992;Ward et al, 2004;Wiedmann et al, 1997). Subsequently, genomic microarray studies have been used to probe for genome-wide gene presence/absence patterns Call et al, 2003;Doumith et al, 2006;Zhang et al, 2003).…”

Stress Survival Islet 1 (SSI-1) Survey in Listeria monocytogenes Reveals an Insert Common to Listeria innocua in Sequence Type 121 L. monocytogenes Strains

“…Serotype 4c belongs to lineage IIIA, whereas serotype 1/2a belongs to lineage II. Recombination rates are higher in lineage II strains, and a large number of imports from lineage IIIA to lineage II was observed (8,23,24). In addition, SSI-1 is located within a 616-kbp region in the first third of the genome, which may be a hot spot for horizontal gene transfer (3).…”

Significant Shift in Median Guinea Pig Infectious Dose Shown by an Outbreak-AssociatedListeria monocytogenesEpidemic Clone Strain and a Strain Carrying a Premature Stop Codon Mutation ininlA

“…Molecular subtyping studies (i.e., DNA band-and sequencebased typing studies) consistently showed that L. monocytogenes isolates cluster into four divergent genetic lineages, termed lineages I, II, III, and IV (2,26,32,34,48,49). Previous molecular epidemiology studies suggest that L. monocytogenes genetic lineages and clonal groups within those lineages differ in their associations with human disease and isolation from foods (12,15,25,26,27,39,40,47,48,49).…”