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115 results for “virulence factors”
Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection [Primary data]
<p>Primary data underlying journal article titled "<strong>Murine norovirus virulence factor 1 (VF1) protein contributes to viral fitness during persistent infection</strong>"</p>
Genomic Typing, Antimicrobial Resistance Gene, Virulence Factor and Plasmid Replicon Dataset for the Important Pathogenic Bacteria Klebsiella pneumoniae
<p>The infections caused by various bacterial pathogens both in clinical and community settings represent a significant threat to public healthcare worldwide. The growing resistance to antimicrobial drugs acquired by bacterial species causing healthcare-associated infections has already become a life-threatening danger noticed by the World Health Organization. Several groups or lineages of bacterial isolates usually called 'the clones of high risk' often drive the spread of resistance within particular species. </p> <p>Thus, it is vitally important to reveal and track the spread of such clones and the mechanisms by which they acquire antibiotic resistance and enhance their survival skills. Currently, the analysis of whole genome sequences for bacterial isolates of interest is increasingly used for these purposes, including epidemiological surveillance and developing of spread prevention measures. However, the availability and uniformity of the data derived from the genomic sequences often represents a bottleneck for such investigations. </p> <p>In this dataset, we present the results of a genomic epidemiology analysis of 61,857 genomes of a dangerous bacterial pathogen <em>Klebsiella pneumoniae</em> obtained from NCBI Genbank database. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), capsular (KL) and oligosaccharide (OL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to clonal groups (CG). The presence of antimicrobial resistance and virulence genes, as well as plasmid replicons, within the genomes is also reported. </p> <p>These data will be useful for researchers in the field of <em>K. pneumoniae</em> genomic epidemiology, resistance analysis and prevention measure development.</p>
Data for "Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton"
<p>This publication contains 27 coral reef bacterioplankton metagenome-assembled genomes (MAGs) from the following paper: </p> <p>Cárdenas, A., Neave, M. J., Haroon, M. F., Pogoreutz, C., Rädecker, N., Wild, C., Gärdes, A., & Voolstra, C. R. (2018). Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton. <em>The ISME Journal</em>, <em>12</em>(1), 59–76. https://doi.org/10.1038/ismej.2017.142</p> <p> </p>
Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis
<p>Citrus canker is a major disease affecting citrus production in Brazil. Its mainly caused by <em>Xanthomonas citri </em>subsp. <em>citri</em> strain 306 pathotype A (Xac). We analysed the differential expression of proteins secreted by wild type Xac and an asymptomatic mutant for <em>hrpB4</em> (<em>ΔhrpB4</em>) grown in Nutrient Broth (NB) and a medium mimicking growth conditions in the plant (XAM1). This allowed the identification of 55 secreted proteins, of which 37 were secreted by both strains when cultured in XAM1. In this secreted protein repertoire, the following stand out: Virk, Polyphosphate-selective porin, Cellulase, Endoglucanase, Histone-like protein, Ribosomal proteins, five hypothetical proteins expressed only in the wild type strain, Lytic murein transglycosylase, Lipoprotein, Leucyl-tRNA synthetase, Co-chaperonin, Toluene tolerance, C-type cytochrome biogenesis membrane protein, Aminopeptidase and two hypothetical proteins expressed only in the <em>ΔhrpB4 </em>mutant. Furthermore, Peptidoglycan-associated outer membrane protein, Regulator of pathogenicity factor, Outer membrane proteins, Endopolygalacturonase, Chorismate mutase, Peptidyl-prolyl cis-trans isomerase and seven hypothetical proteins were detected in both strains, suggesting that there was no relationship with the secretion mediated by the type III secretory system, which is not functional in the mutant strain. Also worth mentioning is the Elongation factor Tu (EF-Tu), expressed only the wild type strain, and Type IV pilus assembly protein, Flagellin (FliC) and Flagellar hook-associated protein, identified in the wild-type strain secretome when grown only in NB. Noteworthy, that FliC, EF-Tu are classically characterized as PAMPs (Pathogen-associated molecular patterns), responsible for a PAMP-triggered immunity response. Therefore, our results highlight proteins potentially involved with the virulence. Overall, we conclude that the use of secretome data is a valuable approach that may bring more knowledge of the biology of this important plant pathogen, which ultimately can lead to the establishment of new strategies to combat citrus canker.</p>
Pseudomonas syringae virulence factors identified by HMMER
<p>JSON object containing Pseudomonas syringae accession numbers as primary keys, containing protein accession numbers, e-value, and NCBI annotations for every HMMER hit for common <em>P. syringae</em> virulence factors. includes: canonical type III secretion system genes, type III effector subfamilies as described by the <em>Pseudomonas syringae</em> effector compendium, and ewoody host or Pseudomonas (WHOP) genes.</p>
Infection of mice by the enteroaggregative E. coli strain 042 and two mutant derivatives overexpressing virulence factors: impact on disease markers, gut microbiota and concentration of SCFAs in feces
<p>This dataset contains raw sequencing data from the microbiota analysis conducted in the enteroaggregative E. coli strain 042 study. The data includes FASTQ files generated from Illumina sequencing, along with metadata describing the sample collection and processing methods.</p>
Supplementary File S2 for the publication 'Predicting Bacterial Virulence Factors - Evaluation of Machine Learning and Negative Data Strategies' by Rentzsch, R et al.
<p>Supplementary File S2 for the publication 'Predicting Bacterial Virulence Factors - Evaluation of Machine Learning and Negative Data Strategies' by Robert Rentzsch, Carlus Deneke, Andreas Nitsche, and Bernhard Y. Renard</p>
Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus
<p><em>Staphylococcus aureus</em> uses quorum sensing and nutrient availability to control the expression of <em>agr</em>-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at high concentration, reduces expression of surface attachment proteins (<em>coa</em>, <em>fnbpA</em>), and increases expression of exotoxins (<em>lukS</em>) and proteases (<em>splA</em>). Nutrient availability can be sensed through the <em>saeS</em>/<em>saeR</em> system. Low nutrients increase expression of <em>saeR</em>, which augments expression of <em>coa</em> and <em>fnbpA</em> distinct from AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. This may impact quorum sensing and/or nutrient acquisition, and thus affect the expression of <em>agr</em>-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of <em>S. aureus</em> using a physical force affects the expression of <em>agr</em>-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of <em>coa</em>, <em>fnbpA</em>, <em>lukS</em>, and <em>splA</em>. Disturbance into a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of <em>coa</em> and <em>fnbpA</em> but increased expression of <em>lukS</em> and <em>splA</em>. Interestingly, at an intermediate amplitude, the overall expression of <em>agr-</em>regulated virulence factors was the lowest; expression of <em>lukS</em> and <em>splA</em> remained unchanged relative to an undisturbed biofilm while expression of <em>coa</em> and <em>fnbpA</em> significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to disturbance.</p>
Data files and taxonomic classifiers for Pseudomonas syringae classification and virulence factor prediction
<p>PSSC.tree : core-genome tree of 2,161 high quality <em>Pseudomonas syringae</em> genomes</p> <p>metadata.csv: A CSV file containing taxonomic data, type strain designations, phylogroups as assigned in this study, LIN clusters assigned for classification purposes, presence/absence of key virulence factors, and metadata found in each genome’s Biosample record for all genomes found in PSSC.tree</p> <p>CLASSIFIER_xxx: QIIME 2 classifier artifacts trained on amplicons generated from primer sets indicated in file name</p> <p>xxx_VFOC.JSON: HMMER results for T3SS and effectors and WHOP genes, structured with both genome and gene product accession numbers as primary key, depending on file</p> <p> </p> <p> </p>
Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus
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Characterization of virulence factors and antibiotic resistance pattern of uropathogenic Escherichia coli strains in a tertiary care center
<p><strong>Background</strong>: Urinary tract infections (UTIs) are the most prevalent bacterial infection in humans. The uropathogenic E. <em>coli </em>(UPEC) express a wide range of virulence factors that contribute to their pathogenicity<span>.</span><span> The emergence of Multidrug resistance(MDR)-associated UTI is increasing off late</span>. Hence this study was undertaken to monitor the distribution of virulence factors among UPEC strains and to note the antibiogram, outcome and type of associated UTI.</p> <p><strong>Methods</strong>: A prospective cross-sectional time-bound study of 6 months was done on clinically significant <span>urinary </span>isolates of <em>Escherichia</em> <em>coli</em>. <span>Detection of haemolysin production and serum resistance</span><span> was done by </span><span>phenotypic methods. Genotypic characterization of the virulence genes (papC, iutA, hlyA, cnf1) was done by multiplex PCR. </span>Demographic data, clinical history, antibiogram and type of UTI were collected from clinical case records.</p> <p><strong>Results</strong>: 75 <em>E</em>. <em>coli</em> isolates from patients with suspected urinary tract infections were included. <span>Females had a higher preponderance of UTI (66.7%).93% of the patients were adults and the remaining 7% were from the paediatric population. 24 (32%) isolates showed haemolysis by plate haemolysis method, and all 75 (100%) isolates were serum resistant. </span>Out of 75 isolates, 65 were positive for at least one of the four targeted genes, while the remaining 10 isolates were negative for all 4 genes. <span>Multidrug resistance was found in 40 (53.3%) isolates. 97.4% of the UTI cases had a favourable clinical outcome at discharge. Mortality due to urosepsis was 2.6%.</span></p> <p><strong>Conclusion</strong>:<span> The association of hemolysin production with resistance to imipenem and norfloxacin in UPEC strains was significant. T</span><span>he presence of the hlyA gene is positively associated with ceftazidime resistance. </span><span>Nitrofurantoin, piperacillin tazobactam and cefaperazone sulbactam maybe suitable candidates for empirical therapy of UTIs. Drugs like aminoglycosides, carbapenems and fosfomycin may be used as reserve drugs in the treatment of MDR-UTI</span><span>. However, inappropriate usage can gradually increase antibiotic resistance. Hence, proper selection of antibiotics in hospitals taking into account the local antibiogram is needed to reduce the emergence of antibiotic resistance.</span></p>
Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa
<p>The opportunistic pathogen <em>Pseudomonas aeruginosa</em> uses quorum sensing to control the expression of multiple virulence factors. In this dataset, we provide raw data demonstrating that periodically disturbing biofilms composed of <em>P. aeruginosa</em> using a physical force reduces the expression of multiple quorum sensing regulated virulence factors from the three major regulons. This dataset also contains cell density measurements of bacteria both the in biofilm and planktonic state under a variety of conditions that use physical force to manipulate the spatial positioning of bacteria. Finally, the data set contains raw outputs from a network logic model that described the core quorum sensing network. This data is affiliated with the manuscript entitled "Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in <em>Pseudomonas aeruginosa</em>."</p>
Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa
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Characterization of virulence factors and antibiotic resistance pattern of uropathogenic Escherichia coli strains in a tertiary care center
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Data from: Manipulating virulence factor availability can have complex consequences for infections
Given the rise of bacterial resistance against antibiotics, we urgently need alternative strategies to fight infections. Some propose we should disarm rather than kill bacteria, through targeted disruption of their virulence factors. It is assumed that this approach (i) induces weak selection for resistance because it should only minimally impact bacterial fitness, and (ii) is specific, only interfering with the virulence factor in question. Given that pathogenicity emerges from complex interactions between pathogens, hosts, and their environment, such assumptions may be unrealistic. To address this issue in a test case, we conducted experiments with the opportunistic human pathogen Pseudomonas aeruginosa, where we manipulated the availability of a virulence factor, the iron-scavenging pyoverdine, within the insect host Galleria mellonella. We observed that pyoverdine availability was not stringently predictive of virulence, and affected bacterial fitness in non-linear ways. We show that this complexity could partly arise because pyoverdine availability affects host responses and alters the expression of regulatorily linked virulence factors. Our results reveal that virulence-factor manipulation feeds back on pathogen and host behavior, which in turn affects virulence. Our findings highlight that realizing effective and evolutionarily robust anti-virulence therapies will ultimately require deeper engagement with the intrinsic complexity of host-pathogen systems.
Data from: Manipulating virulence factor availability can have complex consequences for infections
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An aphid lncRNA is a member of an aphid-specific family that translocates into plant and is a virulence factor [HostSwap Expt]
GEO Series GSE129667. Myzus persicae. 45 samples. Type: Expression profiling by high throughput sequencing.
Pseudomonas virulence factor controls expression of virulence genes in Pseudomonas entomophila
GEO Series GSE216056. Pseudomonas entomophila L48. 12 samples. Type: Expression profiling by high throughput sequencing.
General response of Salmonella enterica serovar Typhimurium to desiccation: A new role for the virulence factors sopD and sseD in survival.
GEO Series GSE86580. Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028. 2 samples. Type: Expression profiling by high throughput sequencing.
Plasmodium falciparum Heterochromatin Protein 1 Marks Genomic Loci Linked to Phenotypic Variation of Exported Virulence Factors
GEO Series GSE17029. Plasmodium falciparum. 1 samples. Type: Genome binding/occupancy profiling by genome tiling array.
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Allen Brain Atlas
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International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.