MULTILOCUS SEQUENCE TYPING OF LISTERIA MONOCYTOGENES USING HYPERVARIABLE GENES REVEALS CLONAL AND RECOMBINATION HISTORIES OF THREE LINEAGES

Authors: Meinersmann, Richard - Rick; Phillips, Robert; WIEDMANN, MARTIN - CORNELL UNIVERSITY; Berrang, Mark

Submitted to: Applied and Environmental Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/1/2003
Publication Date: 4/1/2004
Citation: Meinersmann, R.J., Phillips, R.W., Wiedmann, M., Berrang, M.E. 2004. Multilocus sequence typing of listeria monocytogenes using hypervariable genes reveals clonal and recombination histories of three lineages. Applied and Environmental Microbiology. 70(4):2193-2203.

Interpretive Summary: Listeria monocytogenes is a common organism that occasionally causes severe disease and even death in people. Food contamination is often the source of human infection. The organism is so common in the US that it is difficult to determine if there are specific families of Listeria that are more dangerous and where these families come from. Therefore, it is important to develop methods that are accurate and repeatable to find an organism¿s subtype (the place of the organism on the family tree). We can then use the tree to identify relatives to the organism that is causing disease. Subtyping methods that make use of DNA sequencing (determining the linear structure of a specific piece of DNA) fulfill these requirements. In this study we chose eleven genes from L. monocytogenes to sequence based on large differences seen in previously known sequences. However, the ability to distinguish families with the sequences of these genes was less than expected. This occurred because of two reasons: 1. it turned out that there were two major sequence types that were different from each other with other sequences only being slightly different from the major types; and 2. there was evidence that some families share genes with other families such that the mixing of genetic parts makes differences smaller. Thus, the DNA sequence-based method for distinguishing Listeria families shows how subtypes develop in the species but is poor at discriminating strains.

Technical Abstract: In an attempt to develop a method to discriminate isolates of Listeria monocytogenes, the sequences of all the annotated genes from the fully sequenced strain, L. monocytogenes strain EGD-e, were compared by BLASTn to an unfinished file of the genomic sequence of L. monocytogenes 4B (ATCC19115). Approximately seven percent of the matching genes had 90 percent or less identity between the two strains and the lowest observed identity was 80 percent. Nine genes (hisJ, cbiE, truB, ribC, comEA, purM, aroE, hisC, addB) in the 80 to 90 percent identity group and two genes (gyrB, rnhB) with approximately 97 percent identity were selected for further study by multiple sequence analysis of the genes from two small populations of L. monocytogenes. We found three lineages of L. monocytogenes that differed in their history of apparent recombination. Lineage I appears to be completely clonal. The sequences of the genes for Lineage II were distant from those of Lineage I, but a few individual strains with most genes characteristic of Lineage II had genes that were characteristic of Lineage I. Genes from Lineage III organisms were mostly similar to Lineage I genes with numerous instances of genes appearing to be mosaics with Lineage II genes. Even though Lineage I and Lineage II had distant sequences, there was very little discriminatory power within each Lineage. The overall pattern of differences was almost identical with gyrB and rnhB sequences except that the distances were smaller. A subgroup of the tested populations of Listeria all came from one food-processing plant. This population included organisms in Lineage I and Lineage II in almost equal prevalence. Thus, it appears that lineages of L. monocytogenes can share habitats but differ in the amount that they can share genes.