Whole genome genetic variation and linkage disequilibrium in a diverse collection of Listeria monocytogenes isolates

We performed whole-genome multi-locus sequence typing for 2554 genes in a large and heterogenous panel of 180 Listeria monocytogenes strains 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 of L. monocytogenes. Our analysis revealed the presence of strong linkage disequilibrium in L. monocytogenes, with similar to 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 in L. monocytogenes suggest 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.

Automated summary

By conducting whole-genome multi-locus sequence typing on 180 heterogeneous Listeria monocytogenes strains, this study found that approximately 99% of genes in the genome exhibit significant non-random associations, with 27 loci considered as potential hot spots for horizontal gene transfer. The patterns of linkage disequilibrium suggest limited exchange of foreign genetic material in the L. monocytogenes genome, which can be utilized as a tool for identifying new recombinant strains.