Genome Diversification in Phylogenetic Lineages I and II ofListeria monocytogenes: Identification of Segments Unique to Lineage II Populations

Abstract

Thirteen different serotypes of Listeria monocytogenes can be distinguished on the basis of variation in somatic and flagellar antigens. Although the known virulence genes are present in all serotypes, greater than 90% of human cases of listeriosis are caused by serotypes 1/2a, 1/2b, and 4b and nearly all outbreaks of food-borne listeriosis have been caused by serotype 4b strains. Phylogenetic analysis of these three common clinical serotypes places them into two different lineages, with serotypes 1/2b and 4b belonging to lineage I and 1/2a belonging to lineage II. To begin examining evolution of the genome in these serotypes, DNA microarray analysis was used to identify lineage-specific and serotype-specific differences in genome content. A set of 44 strains representing serotypes 1/2a, 1/2b, and 4b was probed with a shotgun DNA microarray constructed from the serotype 1/2a strain 10403s. Clones spanning 47 different genes in 16 different contiguous segments relative to the lineage II 1/2a genome were found to be absent in all lineage I strains tested (serotype 4b and 1/2b) and an additional nine were altered exclusively in 4b strains. Southern hybridization confirmed that conserved alterations were, in all but two loci, due to absence of the segments from the genome. Genes within these contiguous segments comprise five functional categories, including genes involved in synthesis of cell surface molecules and regulation of virulence gene expression. Phylogenetic reconstruction and examination of compositional bias in the regions of difference are consistent with a model in which the ancestor of the two lineages had the 1/2 somatic serotype and the regions absent in the lineage I genome arose by loss of ancestral sequences.Listeria monocytogenes is a ubiquitous gram-positive bacterium that can cause life-threatening infections including meningitis, septicemia, abortion, and fetal death. Its primary route of transmission to humans is through contaminated food and despite the relatively low incidence of listeriosis in humans, outbreaks of listeriosis often have high associated morbidity, particularly among pregnant women, unborn fetuses, and immunocompromised individuals (24). These characteristics, coupled with its physiological durability and its ubiquitous distribution in nature have propelled L. monocytogenes to the forefront of food safety research and the regulatory arena.Pathogenesis of listeriosis is a consequence of the organism's ability to invade and replicate within several different cell types in mammalian tissues, including intestinal, liver, and neural tissues. During the course of food-borne infections, the bacteria penetrate the intestinal lining through cell invasion and translocation and use the lymphatic system as a conduit to reach the main target tissues within the liver and spleen (41). Prolonged replication in the liver, facilitated by depressed cell mediated immunity, is thought to be an antecedent to spread of the bacteria to brain tissue and breach of the placental barrier in pregnant wo...

Functional Consequences of Genome Evolution inListeria monocytogenes: the lmo0423 and lmo0422 Genes Encode σCand LstR, a Lineage II-Specific Heat Shock System

“…Lineage II includes serotype 1/2a, one of the most commonly found in foods (43,47,48,59), and it is possible that the sigC region contributes to physiological characteristics important to survival in the food production environment. Analysis of compositional bias in sigC and the adjacent lmo0422-lmo0421 region is consistent with the region being ancestral to the species and subsequently lost during the divergence of phylogenetic lineage I (65). Indeed, orthologous genes are also found in the Listeria innocua genome at the same relative position, further underscoring the conclusion that it is ancestral to the genus.…”

“…Based on phylogenetic analysis of genome composition, we have recently shown that a previously unknown sigma factorlike gene, lmo0423 (herein referred to as sigC), is part of a three gene region that is carried only by L. monocytogenes strains comprising phylogenetic lineage II of the species (65). Lineage II includes serotype 1/2a, one of the most commonly found in foods (43,47,48,59), and it is possible that the sigC region contributes to physiological characteristics important to survival in the food production environment.…”

Selective Discrimination of Listeria monocytogenes Epidemic Strains by a Mixed-Genome DNA Microarray Compared to Discrimination by Pulsed-Field Gel Electrophoresis, Ribotyping, and Multilocus Sequence Typing

“…DNA subtyping with DNA microarrays may provide an improved alternative to resolve genetic differences that exist among isolates (4,9,28). This technique has the added advantage that, unlike PFGE, ribotyping, and MLST, it can identify specific or unique genes associated with strains of interest.…”

Characterization of the Genome Composition of Bartonella koehlerae by Microarray Comparative Genomic Hybridization Profiling

“…Comparative whole-genome microarray hybridization has revealed differences in the contents of genes and genomic islands (GEIs) in closely related strains or species with different host ranges and virulence characteristics (11,15,17,22,23,25,29,35,44,52,55). The GEIs may contain bacteriophage and plasmid genes and are typically flanked on one side by a tRNA gene and on the other by an integrase gene (21).…”