Listeria monocytogenes

Facts about listeriosis:
Immuno-compromised individuals, pregnant women, the elderly and neonates are at high risk for listeriosis, an invasive food-borne disease of humans and more than 40 animal species. Outbreaks of listeriosis have been associated with the consumption of ready-to-eat foods, especially meat and dairy products. The disease can result in abortion, stillbirths, septicemia, meningitis, encephalitis and death. In the United States, Listeria monocytogenes causes an estimated 1700 meningitis cases each year with an overall case-fatality rate of approximately 20%. Listeriosis represents the second most common cause of fatal human food-borne infections causing an estimated 28% of all fatal human food borne infections.

L. monocytogenes is a causative agent of listeriosis:
Until this data release from TIGR, only L. monocytogenes strain EGD-e (serotype 1/2a) and Listeria innocua CLIP 11262 (serotype 6a) have been sequenced. To better understand the molecular mechanisms of virulence in humans and survival in food, a genomic survey of three strains of L. monocytogenes was conducted. The strains that were chosen represent the main lineages, and have been associated with outbreaks of listeriosis in the United States since 1985:

L. monocytogenes F2365

serotype 4b
Cheese isolate from the Jalisco cheese outbreak of 1985 in California, USA
Sequenced to closure and manually annotated at TIGR.
Download the complete DNA sequence
Download the multifasta file of DNA sequences of genes
Download the multifasta file of predicted protein sequences
Find information for this sequencing project using links at the TIGR

L. monocytogenes H7858

serotype 4b
Frankfurter isolate from the multi-state outbreak of 1998-1999 in the USA.
Sequenced to 8X coverage and annotated in an automated fashion at TIGR:
Download the 180 contigs as a multifasta file
Download the DNA sequence of the pseudo-chromosome
Download the DNA sequence of the pseudo-plasmid pLM80
Download the multifasta file of DNA sequences of genes
Download the multifasta file of predicted protein sequences

L. monocytogenes F6854

serotype 1/2a
Turkey frankfurter isolate from a sporadic case in 1988 in Oklahoma, USA.
Sequenced to 8X coverage and annotated in an automated fashion at TIGR:
Download the 134 contigs as a multifasta file
Download the DNA sequence of the pseudo-chromosome
Download the multifasta file of DNA sequences of genes
Download the multifasta file of predicted protein sequences

The comparative whole genome analysis includes two strains of Listeria, which were previously sequenced outside TIGR.
To facilitate comparison with the strains sequenced at TIGR, these non-TIGR genomes were put through the same pipeline as 8X genomes. Basically, the program Glimmer was used to predict genes, which were then annotated in an automated fashion.

L. monocytogenes strain EDG-e

serotype 1/2a
Used extensively as a laboratory strain.
Sequenced to closure and published by the EC Consortium. Find information for this sequencing project, using links provided by the TIGR Comprehensive Microbial Resource.

L. innocua strain CLIP 11262

serotype 6a
Used previously for the heterologous expression of genes from L. monocytogenes.
Sequenced to closure and published by the Institut Pasteur. Find information for this sequencing project, using links provided by the TIGR Comprehensive Microbial Resource.

Comparative Genome Analysis
A match table was generated to reveal related genes in the five Listeria strains, using the parameters of synteny and BLAST score, which are described in the materials and methods of the manuscript. Each column represents one strain, and each row depicts the related genes. A dash indicates no match in that particular strain due to loss of synteny, a low BLAST score, or a missing gene translation. For L. monocytogenes strain EGD-e and L. innocua, newly identified genes have been assigned TIGR loci numbers (NT01LM and NT01LI numbers) in the tables accompanying this web site.

The five Listeria genomes were compared against each other at the protein and nucleotide level to reveal a number of significant differences that may relate to the unique pathogenic aspects of the individual strains and serotypes. For the identification of strain specific sequences, the genes from all 5 Listeria genomes were compared against each other. A second filtering step was performed to determine the true uniqueness of these genes. The nucleotide sequence of each "unique" gene (from the closed F2365 strains) was used as the query for BLASTN analysis against a WUBLAST-formatted database of the complete nucleotide sequence from each Listeria strain. Those genes that matched a non-self genomic sequence greater than 90% of its length and with more than 90% identity were considered non-unique. Newly identified strain specific genes from L. monocytogenes strain EGD-e and L. innocua strain CLIP 11262 that were not identified in the original comparisons are available in the Third Party Annotation Section of the DDBJ/EMBL/GenBank databases under the accession numbers TPA: BK005164-BK005176.
View the strain and serotype specific genes.

The chi-squared values were calculated to reveal DNA regions of atypical G+C composition, using a window size of 2000 bp and a window shift of 1000 bp. A chi-squared cutoff of 500 was chosen for identifying genes with atypical composition, compared to the rest of the genome.

Single nucleotide polymorphisms (SNPs) of L. monocytogenes were identified by comparing the closed genome of strain F2365, to those of strains H7858 (178 contigs) and F6854 (133 contigs), using MUMmer. (Strain EGD-e was not included in this analysis due to fact that we do not have access to the underlying sequence files that are necessary for this analysis).

Download all SNPs file for H7858.
Download intergenic SNPs file for H7858.
Download non-synonymous SNPs file for H7858.
Download SNPs file for H7858.

Download all SNPs file for F6854.
Download intergenic SNPs file for F6854.
Download non-synonymous SNPs file for F6854.
Download synonymous SNPs file for F6854.

The quality of sequence reads is given in the total coverage files. A key for interpreting the total coverage files is provided for the two 8X genomes:
Download the total coverage sequencing files for H7858.
Download the total coverage sequencing files for F6854.