In an attempt to develop a method to discriminate among isolates of Listeria monocytogenes, the sequences of all of the annotated genes from the fully sequenced strain L. monocytogenes EGD-e (serotype 1/2a) were compared by BLASTn to a file of the unfinished genomic sequence of L. monocytogenes ATCC 19115 (serotype 4b). Approximately 7% of the matching genes demonstrated 90% or lower identity between the two strains, and the lowest observed identity was 80%. Nine genes (hisJ, cbiE, truB, ribC, comEA, purM, aroE, hisC, and addB) in the 80 to 90% identity group and two genes (gyrB and rnhB) with approximately 97% identity were selected for multilocus sequence analysis in two sets of L. monocytogenes isolates (a 15-strain diversity set and a set of 19 isolates from a single food-processing plant). Based on concatenated sequences, a total of 33 allotypes were differentiated among the 34 isolates tested. Population genetics analyses revealed three lineages of L. monocytogenes that differed in their history of apparent recombination. Lineage I appeared to be completely clonal, whereas representatives of the other lineages demonstrated evidence of horizontal gene transfer and recombination. Although most of the gene sequences for lineage II strains were distinct from those of lineage I, a few strains with the majority of genes characteristic of lineage II had some that were characteristic of lineage I. Genes from lineage III organisms were mostly similar to lineage I genes, with instances of genes appearing to be mosaics with lineage II genes. Even though lineage I and lineage II generally demonstrated very distinct sequences, the sequences for the 11 selected genes demonstrated little discriminatory power within each lineage. In the L. monocytogenes isolate set obtained from one food-processing plant, lineage I and lineage II were found to be almost equally prevalent. While it appears that different lineages of L. monocytogenes can share habitats, they appear to differ in their histories of horizontal gene transfer.Although disease caused by Listeria monocytogenes occurs at a low rate relative to those caused by other food-borne pathogens, the organism is second only to Salmonella spp. in the estimated number of food-related deaths in the United States (18). The majority of these deaths occur in individuals who are immunocompromised (6). With the continued high prevalence of AIDS, an increasingly elderly population, and numerous organ transplants, joint replacements, and other immunocompromising conditions, the number of people in the United States who are susceptible to listeriosis is growing.Accurate tracing of Listeria strains is important for clinical epidemiology, food safety, and public health. Molecular tracing can help to manage and contain L. monocytogenes contamination in food-processing plants by giving a means to accurately evaluate the source of a specific contaminant. The last decade has seen a flurry of published studies in which inexpensive and rapid methods to type Listeria spp. have been designed and...