Bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1075815 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR15049115_1.fastq.gz | Fastqsanger.gz | |||
| SRR15049115_2.fastq.gz | Fastqsanger.gz | |||
| SRR18080511_1.fastq.gz | Fastqsanger.gz | |||
| SRR18080511_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Study on the prevalence of antibiotic resistance in foodborne bacterial pathogens in southern Vietnam
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2022-02-22 | PXD026636 | Pride
Project description:During an intracellular bacterial infection, the host cell and the infecting pathogen interact through a progressive series of events that may result in many distinct outcomes. To understand the specific strategies our immune system employs to manage attack by diverse pathogens, we sought to identify the unique and the core host and pathogen interactions that occur during infection: We compared in molecular detail the pathways induced across infection by seven diverse bacterial species that constitute many of the main human pathogens: Staphylococcus aureus, Listeria monocytogenes, Enterococcus faecalis, Group B Streptococcus, Yersinia pseudotuberculosis, Shigella flexneri and Salmonella enterica. We infected primary human macrophages with each species and used scRNA-Seq to generate a comprehensive dataset of gene expression profiles during bacterial infection. Examining the expression profiles of the infected macrophages across the pathogens, we discovered different modules of infection representing different states through which the infection progresses. The early module captures intra-cellular activity such as lysosome and degranulation, followed by type I IFN signaling, from which results in a cell death module, with a last mode of inflammatory response through response to IL-1. Comparing these modules across the pathogens, we found that their dynamics differ, with some modules active in all species and others which are present in some, but not all pathogens. Our work defines the hallmarks of host-pathogen interactions by identifying recurring properties of infection that can provide insight into diagnostics and therapeutic timing.
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