Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA674322 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12972100_1.fastq.gz | Fastqsanger.gz | |||
| SRR12972100_2.fastq.gz | Fastqsanger.gz | |||
| SRR12972101_1.fastq.gz | Fastqsanger.gz | |||
| SRR12972101_2.fastq.gz | Fastqsanger.gz | |||
| SRR12972078_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:Clonal emergence is a major driver for changes in bacterial disease epidemiology. Recently, it has been proposed that episodic emergence of novel, hypervirulent clones of group A Streptococcus (GAS) results from horizontal gene transfer (HGT) and recombination events leading to increased expression of the cytotoxins Nga (NADase) and SLO (streptolysin O). We previously described a gene fusion event involving the gene encoding the GAS M protein (emm) and an adjacent M-like protein (enn) in the emm4 GAS population, a GAS emm type that lacks the hyaluronic acid capsule. Using whole genome sequencing of a temporally and geographically diverse set of 1,127 isolates, we discovered that the North American emm4 GAS population has undergone clonal replacement with emergent GAS strains completely replacing historical isolates by 2017. Emergent emm4 GAS strains were defined by a handful of small genetic variations, including the emm-enn gene fusion, and showed a marked in vitro growth defect compared to historical strains. In contrast to other previously described GAS clonal emergence events, emergent emm4 GAS lacked significant HGT events and showed no significant increase in transcript levels of nga/slo toxin gene via RNA sequencing and quantitative real-time PCR analysis relative to historic strains. Despite the in vitro growth differences, emergent emm4 GAS strains demonstrated hypervirulence in mouse and ex vivo growth in human blood compared to historical strains. Thus, these data detail the emergence and dissemination of a hypervirulent acapsular GAS clone defined by small genetic variation thereby defining a novel model for GAS strain replacement.
2021-05-05 | GSE160737 | GEO
Project description:The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic.
2010-11-01 | GSE24034 | GEO
Project description:The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic. We used metagenomics-based technologies (the Virochip microarray) and deep sequencing to analyze nasal swab samples from individuals with 2009 H1N1 infection. This Series includes the Virochip microarray data only.
2010-11-01 | E-GEOD-24034 | biostudies-arrayexpress
Project description:Candidatus Symbiopectobacterium sp. 'North America' (SyHa):How1 (Howardula aoronymphium) Genome sequencing
| PRJNA415854 | ENA
Project description:Paleo-Eskimo genetic legacy across North America: sequence data
| PRJEB30575 | ENA
Project description:Our preliminary work demonstrates that there is buy-in from both patients and surgeons with regards to early ileostomy closure (EIC) for select rectal cancer patients undergoing restorative proctectomy (RP) and diverting loop ileostomy (DLI). The feedback from leaders in Europe further supports the need for a large scale randomized-controlled trial (RCT) on this subject in North America. Should the results of such a study be favourable, we believe it could support a change in practice that would be beneficial to patients and the health care system alike. Furthermore, our work will help identify which patients and practices are suitable for EIC.
The goal of our project is to determine whether EIC in rectal cancer patients undergoing RP with a DLI is safe, feasible and beneficial in a North American population. Specifically, our primary objective is to compare the severity of complications between patients undergoing EIC versus traditional (late) closure. Our secondary objectives include assessing the difference in quality of life (QoL), early and late bowel function, and cost of care between these two groups.
| 2388367 | ecrin-mdr-crc
Project description:Ecrobia is a genus of small brackish-water mud snails with an amphi-Atlantic distribution. Interestingly, the species occurring in the northwestern Atlantic, Ecrobia truncata, is more closely related to the Pontocaspian taxa, Ecrobia grimmi and Ecrobia maritima, than to the species occurring in the northeastern Atlantic and Mediterranean Sea. At least three colonization scenarios may account for this peculiar biogeographical pattern: (1) a recent human-mediated dispersal, (2) a historical transatlantic interchange, and (3) a historical transpolar interchange. To test these three scenarios, we used five operational criteria-time of species divergence, first appearance in the fossil record, dispersal limitation as well as environmental filtering and biotic interactions along the potential migration routes. Specifically, we inferred a time-calibrated molecular phylogeny for Ecrobia and reconstructed a paleogeographical map of the Arctic Ocean at 2.5 million years ago (Mya). Based on the five operational criteria, scenarios 1 and 2 can likely be rejected. In contrast, all criteria support scenario 3 (historical transpolar interchange). It is therefore suggested that a bird-mediated and/or ocean current-mediated faunal interchange via the Arctic Ocean occurred during the Late Pliocene or Early Pleistocene. This dispersal was likely facilitated by reduced distances between the Eurasian and North American/Greenland landmasses, marine introgressions, and/or a stepping-stone system of brackish-water habitats in northern Siberia, as well as a lack of competition along the migration route. As for the direction of dispersal, the scientific data presented are not conclusive. However, there is clearly more support for the scenario of dispersal from the Pontocaspian Basin to North America than vice versa. This is the first study providing evidence for a natural faunal exchange between the Pontocaspian Basin and North America via the Arctic Ocean.
| S-EPMC6787871 | biostudies-literature
Project description:Small RNA sequencing of historical cassave specimen
| PRJNA698751 | ENA
Project description:Background?Bayesian evolutionary analysis (coalescent analysis) based on genetic sequences has been used to describe the origins and spread of rapidly mutating RNA viruses, such as influenza, Ebola, human immunodeficiency virus (HIV), and hepatitis C virus (HCV).Methods?Full-length subtype 1a and 3a sequences from early HCV infections from the International Collaborative of Incident HIV and Hepatitis C in Injecting Cohorts (InC3), as well as from public databases from a time window of 1977-2012, were used in a coalescent analysis with BEAST software to estimate the origin and progression of the HCV epidemics in Australia and North America. Convergent temporal trends were sought via independent epidemiological modeling.Results?The epidemic of subtype 3a had more recent origins (around 1950) than subtype 1a (around 1920) in both continents. In both modeling approaches and in both continents, the epidemics underwent exponential growth between 1955 and 1975, which then stabilized in the late 20th century.Conclusions?Historical events that fuelled the emergence and spread of injecting drug use, such as the advent of intravenous medical therapies and devices, and growth in the heroin trade, as well as population mixing during armed conflicts, were likely drivers for the cross-continental spread of the HCV epidemics.
| S-EPMC5079374 | biostudies-literature
Project description:Clostridioides difficile BI/NAP1/ribotype 027 is an epidemic hypervirulent strain found worldwide, including in Latin America. We examined the genomes and exoproteomes of two multilocus sequence type (MLST) clade 2 C. difficile strains considered hypervirulent: ICC-45 (ribotype SLO231/UK[CE]821), isolated in Brazil, and NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica. C. difficile isolates were cultured and extracellular proteins were analyzed using high-performance liquid chromatography-tandem mass spectrometry. Genomic analysis revealed that these isolates shared most of the gene composition. Only 83 and 290 NAP1/027 genes were considered singletons in ICC-45 and NAP1/027, respectively. Exoproteome analysis revealed 197 proteins, of which 192 were similar in both strains. Only five proteins were exclusive to the ICC-45 strain. These proteins were involved with catalytic and binding functions and indirectly interacted with proteins related to pathogenicity. Most proteins, including TcdA, TcdB, flagellin subunit, and cell surface protein, were overrepresented in the ICC-45 strain; 14 proteins, including mature S-layer protein, were present in higher proportions in LIBA5756. These data show close similarity between the genome and proteins in the supernatant of two strains with hypervirulent features isolated in Latin America and underscore the importance of epidemiological surveillance of the transmission and emergence of new strains.
2021-07-01 | PXD026218 | Pride