Listeria monocytogenes isolate:foodborne outbreak
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PROVIDER: PRJNA858193 | ENA |
REPOSITORIES: ENA
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Project description: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. This is a Listeria monocytogenes pan-genome tilling array designed using PanArray algorithm. 9 experimental strains (F2-569, M1-002, F2-208, J2-071, J1-208, W1-111, W1-110, F2-524, F2-501) vs reference (EGD-e) strain.
2010-04-06 | E-GEOD-20367 | biostudies-arrayexpress
Project description: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.
2010-04-06 | GSE20367 | GEO
Project description:Among the three major genetic lineages of L. monocytogenes (i.e. LI, LII, and LIII), LI and LII are predominantly associated with foodborne listeriosis outbreaks, whereas LIII is rarely implicated in human infections. In a previous study, we identified a Crp/Fnr family transcription factor lmo0753 that was highly specific to outbreak-associated LI and LII but absent from LIII. Lmo0753 shares two conserved functional domains including a DNA-binding domain with the well-characterized master virulence regulator PrfA in L. monocytogenes. In this study, we constructed a lmo0753 deletion and complementation mutants of the fully sequenced L. monocytogenes LII strain EGDe. We found that deletion of lmo0753 led to the loss of L-rhamnose utilization in EGDe. Transcriptomic comparison of the EGDe lmo0753 deletion mutant and the wild type incubated in phenol-red medium containing L-rhamnose as the sole carbon source revealed 126 (4.5%) and 546 (19.5%) out of 2,798 genes in the EGDe genome that were up- and down-regulated for more than 2-fold, respectively. Genes involved in biotin biosynthesis, general stress response and rhamnose metabolism were shown to be differentially regulated by Lmo0753. Findings from this study may partially explain why LIII of L. monocytogenes is underrepresented in the environment and rarely associated with human listeriosis outbreaks due to the inability of rhamnose utilization. We report the transcriptomic profile of L. monocytogenes Δlmo0753 LII strain (EGDe) in broth media with L-rhamnose as the sole carbon source.
2013-07-17 | GSE47721 | GEO
Project description:Among the three major genetic lineages of L. monocytogenes (i.e. LI, LII, and LIII), LI and LII are predominantly associated with foodborne listeriosis outbreaks, whereas LIII is rarely implicated in human infections. In a previous study, we identified a Crp/Fnr family transcription factor lmo0753 that was highly specific to outbreak-associated LI and LII but absent from LIII. Lmo0753 shares two conserved functional domains including a DNA-binding domain with the well-characterized master virulence regulator PrfA in L. monocytogenes. In this study, we constructed a lmo0753 deletion and complementation mutants of the fully sequenced L. monocytogenes LII strain EGDe. We found that deletion of lmo0753 led to the loss of L-rhamnose utilization in EGDe. Transcriptomic comparison of the EGDe lmo0753 deletion mutant and the wild type incubated in phenol-red medium containing L-rhamnose as the sole carbon source revealed 126 (4.5%) and 546 (19.5%) out of 2,798 genes in the EGDe genome that were up- and down-regulated for more than 2-fold, respectively. Genes involved in biotin biosynthesis, general stress response and rhamnose metabolism were shown to be differentially regulated by Lmo0753. Findings from this study may partially explain why LIII of L. monocytogenes is underrepresented in the environment and rarely associated with human listeriosis outbreaks due to the inability of rhamnose utilization. We report the transcriptomic profile of L. monocytogenes M-NM-^Tlmo0753 LII strain (EGDe) in broth media with L-rhamnose as the sole carbon source. Examination of deletion of Lmo0753 on L-rhamnose utilization in L. monocytogenes. Two biological replicates per WT and M-NM-^Tlmo0753.
2013-07-17 | E-GEOD-47721 | biostudies-arrayexpress
Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator HrcA, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DhrcA stationary phase cells were compared to wt to identify hrcA-dependent genes. We identified 61 HrcA-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression between ΔhrcA and wt. Combined with microarray analysis, Hidden Markov Model searches show HrcA directly repress at least 8 genes. Keywords: Listeria monocytogenes, HrcA regulon, stationary phase
2007-11-03 | GSE7517 | GEO
Project description:The foodborne pathogen Listeria monocytogenes uses a number of transcriptional regulators, including the negative regulator CtsR, to control gene expression under different environmental conditions and in response to stress. Gene expression patterns of DctsR log phase cells were compared to both wt and ictsR-mcsA log phase cells grown with 0.5mM IPTG to identify CtsR-dependent genes.We identified 62 CtsR-dependent genes that showed significant expression ratios (adj. P < 0.05), with ≥ 1.5-fold differential expression either between ΔctsR and wt or between ΔctsR and ictsR-mcsA. Keywords: Listeria monocytogenes, CtsR regulon, log phase
2007-10-14 | GSE7514 | GEO
Project description:Survival of the foodborne pathogen Listeria monocytogenes in acidic environments (e.g., stomach and low pH foods) is vital to its transmission. L. monocytogenes grows at temperatures as low as 2°C, and refrigerated, ready-to-eat foods have been sources of L. monocytogenes outbreaks. The purpose of this study was to determine whether growth at a low temperature (i.e., 7°C) affects the response of L. monocytogenes to sudden acid shock.
2011-07-01 | GSE22672 | GEO
Project description:Listeria monocytogenes is the ubiquitous food-borne pathogen which causes listeriosis, a disease with a high mortality rate, mostly transmitted through contaminated ready-to-eat foods (EFSA, 2018). To better understand the systemic response of such microorganism exposed at three environmental factors (T, pH and NaCl), the proteome of a L. monocytogenes strain, which was isolated from a meat product (Coppa di testa) linked to a listeriosis outbreak occurred in Marche region (Italy) in 2016, was investigated in order to identify differences in its protein patterns.
2022-08-12 | PXD033519 | Pride
Project description:Listeria monocytogenes, a silent foodborne pathogen in Ecuador.
| PRJEB48671 | ENA
Project description:Listeria monocytogenes strain F2365 was the first strain representative of serotype 4b (lineage I) to be sequenced in 2004, suggesting it could become the model organism for this serotype, which is associated with most human outbreaks of listeriosis worldwide to date. F2365 itself is an outbreak strain involved in the Mexican-style soft cheese outbreak in California in 1985. In this study we show through phenotypic and transcriptomic analysis that L. monocytogenes strain F2365 has reduced ability to respond to stress due to the absence of a functional σB-dependent stress response system. F2365 shows no B-dependent ability to survive acid or oxidative stress nor B-dependent ability to infect Caco-2 epithelial cell in vitro or guinea pigs in vivo. Therefore, there is substantial evidence that F2365 is an atypical strain and is not a suitable representative of outbreak-associated serotype 4b strains.
2013-06-01 | GSE42730 | GEO