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PROVIDER: PRJNA1251236 | ENA |
REPOSITORIES: ENA
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2023-09-04 | PXD045091 |
Project description:Tilapia Lake Virus (TiLV) poses a significant threat to global tilapia aquaculture, causing high mortality rates and severe economic losses. Despite its impact, the molecular mechanisms of TiLV-host interactions remain poorly understood. This study investigates the proteomic and phosphoproteomic changes in two piscine cell lines, E-11 and RHTiB, following TiLV infection.
2024-09-25 | PXD053604 | JPOST Repository
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to investigate the significantly different pathways and genes between ST398 and ST239. Methods: mRNA profiles of ST398 and ST239 at mid-logarithmic growth phase (4h) were generated by deep sequencing, respectively in quadruplicate and duplicate samples, using the Hiseq2000 (Illumina, CA) sequencer. The four samples of ST398 are J-92 (Sample1), W-604 (Sample2), R-1025 (Sample3) and R-1089 (Sample4) and grouped to G1, while the two samples of ST239 are J-95 (Sample5) and J-99 (Sample6) and grouped to G2. The sequence reads of ST398 and ST239 that passed quality filters were respectively aligned to S. aureus subsp. aureus ST398 (RefSeq accession number AM990992) and S. aureus subsp. aureus TW20 (RefSeq accession number NC _017331) using the Burrows-Wheeler Alignment tool (BWA) followed by ANOVA (ANOVA). Only the consistent data between the four ST398 samples and two ST239 samples were reserved for further analysis. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, RNA-seq analyses revealed four types of significantly differentially expressed genes between ST398 and ST239 (G1 only, G2 only, G1/G2>2, G2/G1>2), and only the type of G1/G2>2 was included in this study. The type of G1/G2>2 included 164 genes in total, in which there are 14 top genes showing G1/G2>5 including essB gene. Conclusions: Our data provide new information to the signicantly different genes between ST239 and ST398, especially the highly expressed genes in ST398 compared to ST239 which might be closely related to the high virulence of ST398.
2018-07-29 | GSE71516 | GEO
Project description:Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Δvwbp and ΔscpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation.
2015-12-31 | GSE47910 | GEO
Project description:Staphylococcus aureus is a common human and animal opportunistic pathogen. In humans nasal carriage of S. aureus is a risk factor for various infections. Methicillin-resistant S. aureus ST398 is highly prevalent in pigs in Europe and North America. The mechanism of successful pig colonization by MRSA ST398 is poorly understood. Previously, we developed a nasal colonization model of porcine nasal mucosa explants to identify molecular traits involved in nasal MRSA colonization of pigs. Here, we report the analysis of the transcriptome of MRSA ST398 strain S0462 during colonization on the explant epithelium. Major regulated genes were encoding metabolic processes and regulation of these genes represents metabolic adaptation to nasal mucosa explants. Colonization was not accompanied by significant changes in transcripts of main virulence associated genes or known human colonization factors. Here, we document regulation of two genes which have potential influence on S. aureus colonization; cysteine extracellular proteinase (scpA) and von Willebrand factor-binding protein (vwbp, located on SaPIbov5). Colonization with isogenic-deletion strains (Î?vwbp and Î?scpA) did not alter the nasal S. aureus colonization compared to wild type. Our results suggest that nasal colonization with MRSA ST398 is a complex event that is accompanied with changes in bacterial gene expression regulation and metabolic adaptation. Number of the samples: 5 (timepoint 0 min, 30 min, 60 min, 90 min and 180 min) in 4 replicates. 4 control samples
2015-12-31 | E-GEOD-47910 | biostudies-arrayexpress
Project description:Livestock-associated (LA) methicillin-resistant Staphylococcus aureus (MRSA) and strains of sequence type 398 (ST398), which first became known for its widespread colonization of pigs but are now also rapidly emerging in the number of human colonization and infections. The ability of broad host adaption in combination with a consciously evolves by acquisition of virulence gene or mobile genetic elements (MGE) have been increasingly addressed ST398 lineage a serious threat to public health. The present study was aimed to track out how the diverse ST398 lineage, which colonized or infected in a broad range of reservoirs and various geographic regions, is actually reflected in the course of virulence evolution. We therefore profiled the extracellular proteome, representing the main reservoir of virulence factors, of 30 representative clinical isolates using label-free quantitative mass spectrometry. The results show that these isolates can be divided into five distinct clusters based on their exoproteome identities and abundance signatures. The majority of proteins identified were predicted as cytoplasmic proteins showing substantial heterogeneity among our 30 investigated isolates. Only 50% of isolates their exoproteome clustering of isolates can be correlated the clustering based on genome sequences suggested that the large-scale extend of genotype changes over time. To assess the virulence and cytotoxicity of the 30 investigated isolates, we employed infection models based on Galleria mellonella and HeLa cells. The results uncovered the grouping of clinical isolates based on their virulence or cytotoxicity have apparently distinctive exoproteome signatures and particular exoproteins could play decisive roles in pathogenicity of this specific S. aureus lineage. Altogether, the combination of exoproteome and virulence analysis contribute to the comprehensive insights for the impact of genome diversity on the global production of virulence factors of this zoonotic lineage, and more importantly, our outcomes as well as our approach provided an effective pipeline to define proteomic signatures of S. aureus virulence.
2020-08-05 | PXD013951 | Pride
Project description:There is evidence that MRSA ST398 of animal origin is only capable of temporarily occupying the human nose, and it is therefore, often considered a poor human colonizer.We inoculated 16 healthy human volunteers with a mixture of the human MSSA strain 1036 (ST931, CC8) and the bovine MSSA strain 5062 (ST398, CC398), 7 weeks after a treatment with mupirocin and chlorhexidine-containing soap. Bacterial survival was studied by follow-up cultures over 21 days. The human strain 1036 was eliminated faster (median 14 days; range 2-21 days) than the bovine strain 5062 (median 21 days; range 7-21 days) but this difference was not significant (pM-bM-^@M-^J=M-bM-^@M-^J0.065). The bacterial loads were significantly higher for the bovine strain on day 7 and day 21. 4/14 volunteers (28.6%) showed elimination of both strains within 21 days. Of the 10 remaining volunteers, 5 showed no differences in bacterial counts between both strains, and in the other 5 the ST398 strain far outnumbered the human S. aureus strain. Within the 21 days of follow-up, neither human strain 1036 nor bovine strain 5062 appeared to acquire or lose any mobile genetic elements. In conclusion, S. aureus ST398 strain 5062 is capable of adequately competing for a niche with a human strain and survives in the human nose for at least 21 days. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-131]
2012-10-29 | E-BUGS-131 | biostudies-arrayexpress