Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer reviewed journal
Publication Acceptance Date: 4/1/2004
Publication Date: 4/1/2004
Citation: Nelson, K., Fouts, D., Mongodin, E., Fraser, C., Kathariou, S., Wonderling, L.D., Uhlich, G.A., Bayles, D.O., Luchansky, J.B. 2004. Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen listeria monocytogenes reveal new insights into the core genome components of this species. Proceedings Of The National Academy Of Sciences. 2004. Vol. 32. No. pg. 2386-2395. Interpretive Summary: Listeria monocytogenes remains a significant food-borne health risk and an economic burden to Americans. To better understand the molecular mechanisms of virulence in humans at various points along the food chain, The Institute for Genomic Research (TIGR) and the USDA-ARS determined the order and number of nucleic acid base pairs of the chromosome of L. monocytogenes strain F2365 (serotype 4b, Mexican-style cheese isolate). This strain is responsible for the largest outbreak of listeriosis in North America. To date, we have shown that the genome of strain F2365 (2,905,310 bp) is smaller than strain EGD-e (serotype 1/2a, animal isolate; 2,944,528 bp) as determined by a European Consortium. One major difference to account for the size discrepancy is the absence of a bacterial virus (~42 kbp). To characterize the genetic variability of listeriae, in addition to strain F2365, strain H7858 (serotype 4b, frankfurter isolate) and strain F6854 (serotype 1/2a, turkey frankfurter isolate) were recently sequenced to 8X coverage and compared to strain F2365. In general, the chromosomes of all three strains were largely similar. However, we were able to identify both strain and serotype specific differences among these strains, with most of these differences due to the presence/absence of bacterial virus, mobile genetic elements, and single base-pair differences. The availability of this new genetic information will make it possible to better address food-safety related problems through the application of the powerful tools of molecular biology.
Technical Abstract: The genomes of three strains of Listeria monocytogenes that have been associated with outbreaks of food-borne listeriosis in the United States were sequenced and subjected to whole genome comparative analyses. A total of 51, 97, and 72 strain specific genes, many of which were found in clusters, were identified in L. monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate), and H7858 (serotype 4b, meat isolate), respectively. Eighty-four genes were specific to the serotype 1/2a strain and 51 to the serotype 4b strains. The serotype 1/2a specific genes include an operon that codes for the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for 5 glycosyl transferases and an adenine-specific DNA methyltransferase. When compared to the closed genome of strain F2365, 8,603 and 105,050 high quality single nucleotide polymorphisms (SNPs) were found for strains H7858 and F6854, respectively. Of these high quality SNPs, 1,984 (23%) and 16,811 (16%) resulted in a nonsynonymous (NS) change in amino acid sequence in strains H7858 and F6854, respectively. When grouped by role category, a higher number of NS-SNPs were evident in the role categories of cell envelope and cellular processes, which includes pathogenesis and toxin production. Whole genome comparative analyses revealed that the L. monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements, and SNPs. Concerted analysis of the three L. monocytogenes genomes from the present study with those of L. monocytogenes strain EGD-e (serotype 1/2a) and the non-pathogenic L. innocua CLIP 11262 (serotype 6a) reported by other investigators revealed a small number of unique genes harbored by the L. monocytogenes strains that may contribute to the virulence of L. monocytogenes. This small number of putative pathogenicity genes suggests a limited but effective genomic investment to virulence-related functions by L. monocytogenes.