Whole genome genetic variation and linkage disequilibrium in a diverse collection ofListeria monocytogenesisolates

We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180Listeria monocytogenesstrains having diverse geographical and temporal origins. The subtyping data was used for characterizing genetic variation and evaluating patterns of linkage disequilibrium in the pan-genome ofL. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium inL. monocytogenes, with ∼99% of genes showing significant non-random associations with a large majority of other genes in the genome. Twenty-seven loci having lower levels of association with other genes were considered to be potential “hot spots” for horizontal gene transfer (i.e., recombination via conjugation, transduction, and/or transformation). The patterns of linkage disequilibrium inL. monocytogenessuggest limited exchange of foreign genetic material in the genome and can be used as a tool for identifying new recombinant strains. This can help understand processes contributing to the diversification and evolution of this pathogenic bacteria, thereby facilitating development of effective control measures.