Evolutionary Dynamics of pSK1 Plasmids in ST239 MRSA
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ABSTRACT:
PROVIDER: PRJEB29322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| Other | ||||
| ERR2855740_1.fastq.gz | Fastqsanger.gz | |||
| ERR2855740_2.fastq.gz | Fastqsanger.gz | |||
| ERR2855750_1.fastq.gz | Fastqsanger.gz |
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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 ST239 diversity
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Project description:Long-term laboratory evolution experiments provide a controlled record of evolutionary dynamics and metabolic change in microorganisms. Nevertheless, the correspondence between genetic mutation and phenotypic adaptation remains elusive, partly because of the overwhelming number of genetic changes that accrue after tens-of-thousands of generations. Using a coarse-grained characterization of bacterial physiology applied to Lenski's laboratory-evolved strains of Escherichia coli, we identify an intermediate measure between genotype and phenotype that provides insight into the dynamics of adaptation.
2021-04-27 | MSV000087313 | MassIVE
Project description:Whole genome sequencing data of low risk neuroblastoma tumors and matching controls used to study the evolutionary dynamics of neuroblastoma.
| EGAS00001004990 | EGA
Project description:Staphylococcus aureus ST239 diversity (Turkey)
| PRJEB2173 | ENA
Project description:Previous studies have documented the diversity of genetic background of methicillin-resistant S. aureus (MRSA) strains associated with healthcare (HA-MRSA), community (CA-MRSA) and livestock (LA-MRSA). The accessory and core-variable genome content of those strains remain largely unknown. To compare the composition of accessory and core-variable genome of Belgian MRSA strains according to host, population setting and genetic background, representative strains of HA- (n=21), CA- (n = 13) and ST398 LA-MRSA (n = 18) were characterized by a DNA-microarray (StaphVar Array) composed of oligonucleotide probes targeting ~400 resistance, adhesion and virulence associated genes.ST398 strains displayed very homogenous hybridization profiles (>94% gene content homology) irrespective of their host origin. This “ST398-specific” genomic profile was not distantly demarked from those of certain human-associated lineages but lacked several virulence- and colonization-associated genes harbored by strains of human origin, such as genes encoding proteases, haemolysins or adhesins. No enterotoxin gene was found among ST398 strains. In conclusion, our findings are consistent with a non-human origin of this ST398 lineage but suggest that it might have the potential to adapt further to the human host.
2010-11-15 | GSE20541 | GEO
Project description:Long-term laboratory evolution experiments provide a controlled record of evolutionary dynamics and metabolic change in microorganisms. Nevertheless, the correspondence between genetic mutation and phenotypic adaptation remains elusive, partly because of the overwhelming number of genetic changes that accrue after tens-of-thousands of generations. Using a coarse-grained characterization of bacterial physiology applied to Lenski's laboratory-evolved strains of Escherichia coli, we identify an intermediate measure between genotype and phenotype that provides insight into the dynamics of adaptation.
2021-04-27 | MSV000087313 | GNPS
Project description:Staphylococcus aureus CN79 strain:ST239 Genome sequencing
| PRJNA178069 | ENA
Project description:Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen associated with severe morbidity and mortality and poses a significant threat to public health worldwide. The genetic diversity based on sequence types of MRSA strains was illustrated in previous studies; meanwhile, the diversity along with the predominant sequence type, especially in Egypt, remains unknown. The purpose of the current study was to determine the diversity of the predominant MRSA clone ST239-MRSA (n = 50) isolated from different hosts and clinical samples and to illustrate the correlation between the resistance patterns, toxin genes, and the genetic background in Port-said and El-Sharkia Governorates, Egypt. The ST239-MRSA clone was analyzed by phenotypic antibiotyping and various genotypic assays comprising SCCmec, agr, spa, coa, and coa-RFLP in addition to toxin gene profiles. Most of the analyzed strains (40/50, 80%) were multidrug resistant (MDR), belonged to SCCmec-III, agr-I, and coa genotype I, and harbored sea and pvl genes. A negative correlation between the toxin gene profiles and antimicrobial resistance was recorded. Meanwhile, the correlation between the toxin gene profiles and the genetic background was not observed in this study. Although ST239-MRSA strains belonged to a single sequence type, they exhibited a high degree of phenotypic and genotypic diversity, indicating weak clonality and adaptability. With such diversity, it is assumed that these strains may have undergone different evolutionary processes during transmission events among and/or within a single host or tissue niche.
| S-EPMC8990901 | biostudies-literature
Project description:The success of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) as pathogens is due to a combination of antibiotic resistance with high virulence. However, evolution of the exceptional virulence potential of CA-MRSA is not understood. Our previous study indicated that differential gene expression contributes substantially to this process. Thus, we here investigated the role of the pivotal virulence gene regulatory system agr in the most prevalent CA-MRSA strain USA300. Using a mouse subcutaneous infection model, we show that agr is essential for the development of CA-MRSA skin infections, the most frequent manifestation of disease caused by CA-MRSA. Furthermore, genome-wide analysis of gene expression revealed significant differences in agr-dependent virulence gene regulation between CA-MRSA, HA-MRSA, and laboratory strains. Our findings demonstrate that agr functionality is critical for CA-MRSA disease and indicate that an adaptation of the agr regulon to optimize expression of a broad set of virulence determinants may have contributed to the evolution of exceptionally pronounced virulence of CA-MRSA strains. Keywords: wild type vs mutant
2011-03-29 | GSE18793 | GEO