Genomics

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Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes


ABSTRACT: Full title: Probing the pan genome of a foodborne bacterial pathogen Listeria monocytogenes: Implications for its niche adaptation, pathogenesis, and evolution Listeria monocytogenes is a foodborne bacterial pathogen well known for adaptability to diverse environmental and host niches, and a high fatality rate among infected, immuno-compromised individuals. Three genetic lineages have been identified within this species. Strains of genetic lineages I and II account for more than ninety percent of foodborne disease outbreaks worldwide, whereas strains from genetic lineage III are rarely implicated in human infectious for unknown, yet intriguing, reasons. Here we have probed the genomic diversity of 26 L. monocytogenes strains using both whole-genome sequences and a novel 385,000 probe pan-genome microarray, fully tiling the genomes of 20 representative strains. Using these methods to identify genes highly conserved in lineages I and II but rare in lineage III, we have identified 86 genes and 8 small RNAs that play roles in bacterial stress resistance, pathogenicity, and niche, potentially explaining the predominance of L. monocytogenes lineages I and II in foodborne disease outbreaks. Extending gene content analysis to all lineages revealed a L. monocytogenes core genome of approximately 2,350 genes (80% of each individual genome) and a pan-genomic reservoir of >4,000 unique genes. Combined gene content data from both sequences and arrays was used to reconstruct an informative phylogeny for the L. monocytogenes species that confirms three distinct lineages and describes the relationship of 9 new lineage III genomes. Comparative analysis of 18 fully sequenced L. monocytogenes lineage I and II genomes shows a high level of genomic conservation and synteny, indicative of a closed pan-genome, with moderate domain shuffling and sequence drift associated with bacteriophages is present in all lineages. In contrast with lineages I and II, notable genomic diversity and characteristics of an open pan-genome were observed in the lineage III genomes, including many strain-specific genes and a more complex conservation pattern. This indicates that the L. monocytogenes pan-genome has not yet been fully sampled by genome sequencing, and additional sequencing of lineage III genomes is necessary to survey the full diversity of this intriguing species and reveal its mechanisms for adaptability and virulence.

ORGANISM(S): Listeria monocytogenes FSL R2-503 Listeria monocytogenes J0161 Listeria monocytogenes FSL N3-165 Listeria monocytogenes F6900 Listeria monocytogenes 10403S Listeria monocytogenes FSL J2-071 Listeria monocytogenes FSL F2-515 Listeria monocytogenes serotype 1/2a str. F6854 Listeria monocytogenes FSL F2-208 Listeria monocytogenes FSL J1-208 Listeria monocytogenes FSL J2-064 Listeria monocytogenes HPB2262 Listeria monocytogenes LO28 Listeria monocytogenes FSL J2-003 Listeria monocytogenes J2818 Listeria monocytogenes Listeria monocytogenes FSL N1-017 Listeria monocytogenes FSL J1-175 Listeria monocytogenes serotype 4b str. H7858 Listeria monocytogenes EGD-e Listeria monocytogenes FSL J1-194 Listeria monocytogenes serotype 4b str. F2365

PROVIDER: GSE20367 | GEO | 2010/04/06

SECONDARY ACCESSION(S): PRJNA125465

REPOSITORIES: GEO

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