Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129067 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR32158403_1.fastq.gz | Fastqsanger.gz | |||
| SRR32158404_1.fastq.gz | Fastqsanger.gz | |||
| SRR32158405_1.fastq.gz | Fastqsanger.gz | |||
| SRR32158406_1.fastq.gz | Fastqsanger.gz |
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Project description:In this study, we used an -omics approach coupled with high resolution mass spectrometry to characterize twenty F. graminearum isolates collected from five distinct regions across Manitoba, containing both 3-acetyl deoxynivalenol (3ADON) and 15-acetyl deoxynivalenol (15ADON) chemotypes. These data identified regional F. graminearum populations within Manitoba that demonstrate distinct genomic variation and patterns of gene expression, particularly within pathogenicity associated processes. Further, we identified genetic variation and differential expression between isolates showing high and low levels of pathogenicity, allowing for the identification of previously characterized and novel putative pathogenicity factors, as well as regions of genetic diversity between these groups. Lastly, we detected production of 3ANX and/or NX mycotoxins within the majority of our twenty characterized F. graminearum isolates, suggesting the 3ANX chemotype may be more prevalent than previously expected in Canada. These findings highlight the diversity of F. graminearum across Manitoba, and more importantly uncover specific genomic regions and candidate pathogenicity factors influenced by this diversity. These data can ultimately help researchers develop improved disease management strategies against FHB and the dynamic populations of F. graminearum.
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Project description:Methicillin-resistant Staphylococcus aureus (MRSA) is the causative agent of serious hospital- and community-associated infections. Due to the global rise in community-associated MRSA, the respective lineages are increasingly introduced into hospitals. This raises the question whether and, if so, how they adapt to this new environment. The present study was aimed at investigating how MRSA isolates of the USA300 lineage, infamous for causing infections in the general population, have adapted to the hospital environment. To this end, a collection of community- and hospital-associated USA300 isolates was compared by RNA-sequencing. Here we report that merely 460 genes were differentially expressed between these two epidemiologically distinct groups, including genes for virulence factors, oxidative stress responses and the purine, pyrimidine and fatty acid biosynthetic pathways. Differentially regulated virulence factors included leukotoxins and phenol-soluble modulins, implicated in staphylococcal escape from immune cells. We therefore investigated the ability of the studied isolates to survive internalization by human neutrophils. This showed that the community-associated isolates have the highest neutrophil-killing activity, while the hospital-associated isolates are better adapted to intra-neutrophil survival. Importantly, the latter trait protects internalized staphylococci against a challenge with antibiotics. We therefore conclude that prolonged intra-neutrophil survival serves as a relatively simple early adaptation of S. aureus USA300 to the hospital environment where antibiotic pressure is high.
2016-11-02 | GSE89394 | GEO
Project description:Staphylococcus aureus is the most common cause of hospital-acquired infection. In healthy hosts outside of the health care setting, S.aureus is a frequent colonizer of the human nose but rarely causes severe invasive infection such as bacteremia, endocarditis, or osteomyelitis. To identify genes associated with community-acquired invasive isolates, regions of genomic variability, and the S.aureus population structure, we compared 61 community-acquired invasive isolates of S.aureus and 100 nasal carriage isolates from healthy donors using a microarray spotted with PCR products representing every gene from the seven S.aureus sequencing projects. The core genes common to all strains were identified, and 10 dominant lineages of S.aureus were clearly discriminated. Each lineage carried a unique combination of hundreds of core variable (CV) genes scattered throughout the chromosome, suggesting a common ancestor but early evolutionary divergence. Many CV genes are regulators of virulence genes or known or predicted to be expressed on the bacterial surface and to interact with the host during nasal colonization and infection. Within each lineage, isolates showed substantial variation in the carriage of mobile genetic elements and their associated virulence and resistance genes, indicating frequent horizontal transfer. However, we were unable to identify any association between lineage or gene and invasive isolates. We suggest that the S.aureus gene combinations necessary for invasive disease may also be necessary for nasal colonization and that community-acquired invasive disease is strongly dependent on host factors. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-33
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Project description:Introduction Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) are increasingly isolated, with USA300-0114 being the predominant clone in the USA. Comparative whole genome sequencing of USA300 isolates collected in 2002, 2003 and 2005 showed a limited number of single nucleotide polymorphisms and regions of difference. This suggests that USA300 has undergone rapid clonal expansion without great genomic diversification. However, whole genome comparison of CA-MRSA has been limited to isolates belonging to USA300. The aim of this study was to compare the genetic repertoire of different CA-MRSA clones with that of HA-MRSA from the USA and Europe through comparative genomic hybridization (CGH) to identify genetic clues that may explain the successful and rapid emergence of CA-MRSA. Materials and Methods Hierarchical clustering based on CGH of 48 MRSA isolates from the community and nosocomial infections from Europe and the USA revealed dispersed clustering of the 19 CA-MRSA isolates. This means that these 19 CA-MRSA isolates do not share a unique genetic make-up. Only the PVL genes were commonly present in all CA-MRSA isolates. However, 10 genes were variably present among 14 USA300 isolates. Most of these genes were present on mobile elements. Conclusion The genetic variation present among the 14 USA300 isolates is remarkable considering the fact that the isolates were recovered within one month and originated from a confined geographic area, suggesting continuous evolution of this clone. Data is also available from <ahref=http://bugs.sgul.ac.uk/E-BUGS-108 target=_blank>BuG@Sbase</a>
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