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147 results for “Bacterial pathogens”
Simulated NGS read datasets for bacterial pathogenic potential prediction
<p>## Predicting pathogenic potentials from NGS reads: novel bacterial species</p> <p>This repository contains simulated Illumina read datasets for bacterial pathogenic potential prediction and associated metadata extracted from the IMG Database (https://img.jgi.doe.gov/). The reads are 250bp long and were simulated with Mason (https://www.seqan.de/apps/mason/) from genomes downloaded from NCBI. The training-validation-test split was done on the species level to ensure "novelty" of validation and test species. The training sets contain 10 million reads per class, validation sets - 1.25 million reads per class, and test sets - 1.25 million paired reads per class. Additional, imbalanced training sets contain 2.5 million "nonpathogenic" and 17.5 million "pathogenic" reads, keeping the mean covarage constant for all species. The temporal benchmark test set contains reads from 3 additional pathogenic species in the Pantoea genus.</p> <p>## Predicting pathogenic potentials from NGS reads: novel strains of known species</p> <p>The BacPaCS datasets contain reads simulated from the dataset compiled by Barash et al. (https://doi.org/10.1093/bioinformatics/bty928). It this case, the training-validation-test split was done on the strain level (so different strains of the same species may be present in all three sets).</p>
Dataset for publication: An inter-laboratory study characterizes the impact of bioinformatic approaches on genome-based cluster detection for foodborne bacterial pathogens
<p>This dataset is part of a dry-lab interlaboratory study conducted across Germany, regarding bacterial outbreak detection based on NGS data, with a focus on bioinformatic analysis of four species to identify potential variability caused by different data analysis approaches and human interpretation. Participants were asked to follow their usual in-house protocols while adhering to the general guidelines. A quality assessment (with sample exclusion) was followed by 7-gene Multilocus-Sequence Typing (MLST), core genome Multilocus Sequencing Typing (cgMLST), and SNP calling. The participants were then asked to identify clusters. The study was not intended to resemble a standard proficiency test with a passing/failing grade, but rather to investigate and quantify obvious variability in the results and, where possible, the reasons for it. For this purpose, the datasets included borderline cases in terms of quality.</p>
Data for 'Genetic variation in trophic avoidance shows fruit flies are generally attracted to bacterial pathogens'
<p>Raw data dn R code for the analysis of data dn generation of all figures in the above referenced paper. Descriptions of each data file are included wihtin the R script. </p>
Supplementary dataset for the publication "Prevalence of tick-borne bacterial pathogens in Germany – has the situation changed after a decade?"
<p>The dataset supplements the journal article "Prevalence of tick-borne bacterial pathogens in Germany – has the situation changed after a decade?" published by Katja Mertens-Scholz, Bernd Hoffmann, Jörn M. Gethmann, Hanka Brangsch, Mathias W. Pletz and Christine Klaus in the journal mdpi microorganisms (DOI: <a href="https://doi.org/10.3389/fcimb.2024.1429667">https://doi.org/10.3389/fcimb.2024.1429667 </a><a>)</a></p> <p>The file "Tick samples" contains all data regarding time, location and detected pathogens". The files "Rickettsia sequences" and Borrelia sequences" contains all sequence information of positive samples. The file "Rickettsia reference genes" contains information of used reference genes for phylogenetic analysis.</p>
BacSPaD: A robust bacterial strains' pathogenicity resource based on integrated and curated genomic metadata
<p>The vast array of omics data in microbiology presents significant opportunities for studying bacterial pathogenesis and creating computational tools for predicting pathogenic potential. However, the field lacks a comprehensive, curated resource that catalogs bacterial strains and their ability to cause human infections. Current methods for identifying pathogenicity determinants often introduce biases and miss critical aspects of bacterial pathogenesis.<br>In response to this gap, we introduce BacSPaD (Bacterial Strains’ Pathogenicity Database), a thoroughly curated database focusing on pathogenicity annotations for a wide range of high-quality, complete bacterial genomes. Our rule-based annotation workflow combines metadata from trusted sources with automated keyword matching, extensive manual curation, and detailed literature review. Our analysis classified 5,502 genomes as pathogenic to humans (HP) and 490 as non-pathogenic to humans (NHP), encompassing 532 species, 193 genera, and 96 families. Statistical analysis demonstrated a significant but moderate correlation between virulence factors and HP classification, highlighting the complexity of bacterial pathogenicity and the need for ongoing research. This resource is poised to enhance our understanding of bacterial pathogenicity mechanisms and aid in the development of predictive models. To improve accessibility and provide key visualization statistics, we developed a user-friendly web interface, accessible at<a href="https://bacspad.altrabio.com/"> </a><a href="https://bacspad.altrabio.com/"><u>https://bacspad.altrabio.com</u></a>.</p>
WorldCOM Deliverable 1: Prevalence of ESBL subtypes in bacterial pathogens and a sequence database of selected alleles
<p><strong>OHEJP Project: WorldCOM, Deliverable 1, Work Package 1.</strong></p> <p>This dataset is connected to Work Package 1, Task1 of the WorldCOM consortium grant within the One Health EJP group. The aim was to analyse publicly available sequences for antimicrobial resistance genes associated with <em>Salmonella</em>, <em>Campylobacter</em> and <em>E. coli</em>. For the initial phase of this work package, we have focused on ESBL-related AMR genes. As these genes are absent from <em>Campylobacter</em>, we have not included this bacterium in these analyses, and have used the important pathogens <em>Klebsiella</em> and <em>Acinetobacter</em>. All types and subtypes of Extended Spectrum β-Lactamases (ESBLs) and plasmid-mediated colistin resistance genes have been analysed for frequency among reported and extracted sequences. High frequency resistant genes subtypes have been highlighted for further sequence analysis to illustrate geographic distribution and geographic-specific single nucleotide polymorphisms (SNPs). The data shown are work in progress. </p>
In vitro antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance
<p>Supplemental material to the publication "<i>In vitro</i> antibacterial activity of microbial natural products against bacterial pathogens of veterinary and zoonotic relevance"</p>
Bacterial pathogens dynamic during multi-species infections
<p>Illumina gapA sequences of synthetic communities of plant bacterial pathogens: Pectobacterium and Dickeya genus. Sequencing was performed after growth on TSB synthetic medium (2 days post inoculation) or growth on potato tubers (5 days post infection).</p> <p> </p> <p>The following files are available:</p> <p>PT_table.txt: description of the potato tubers samples</p> <p>TSB_table.txt: description of samples in synthetic medium (TSB)</p> <p>gapA_PT.fasta.gz: Illumina fasta sequences after potato tubers infection (35,000 reads)</p> <p>gapA_TSB.fasta.gz: Illumina fasta sequences after synthetic medium inoculation (35,000 reads)</p> <p>gapA_without_primers.fasta: gapA sequences (without primers) of Pectobacterium and Dickeya strains used in this study (27 strains)</p> <p>species.txt: list of bacterial species used in this study (9 species)</p> <p>strains.txt: list of bacterial strains used in this study (27 strains)</p> <p>count.py: python3 script used to analyse the output of blastn</p> <p>R_script_FigureS1.R: R script for statistical analysis</p> <p>R_script_Figure2b.R: R script for statistical analysis</p> <p>R_script_Figure2a.R: R script for statistical analysis</p> <p> </p> <p>Method (examplified with the gapA_TSB sequences at the species level):</p> <p>• gapA sequences were blasted (blastn) against gapA sequences of Pectobacterium and Dickeya strains used in this study:</p> <p>makeblastdb -in gapA_without_primers.fasta -dbtype nucl -out dbblastn</p> <p>blastn -db dbblastn -query gapA_TSB.fasta -outfmt 6 -out blast.blastn -num_threads 12 -evalue 0.00001 -num_alignments 1</p> <p>• Reads count. Reads matching (100% identity) with gapA sequences of Pectobacterium and Dickeya strains used in this study were counted using the count.py python script. The output is a tab-separated values (.tsv) file:</p> <p>python3 count.py species.txt blast.blastn</p>
Dataset from the analysis of biological activity of endophytic strain Serratia quinivorans KP32, the expression of biocontrol-related genes and the activity of antioxidant enzymes in bacterial cells treated with pathogenic fungi filtrates
<p>This dataset contains the data from the analyses published in the article entitled "Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain <i>Serratia quinivorans</i> KP32 to Fungal Phytopathogens" in the International Journal of Molecular Sciences (https://doi.org/10.3390/ijms232415561). The data consist of results collected for studies on the antifungal activity of KP32 strain towards four fungal phytopathogens, results of primer efficiency determination and studies on the expression of genes potentially involved in biocontrol after treatment of KP32 strain with the fungal phytopathogens filtrates. Additionally, absorbances from activity tests for catalase (CAT) and superoxide dismutase (SOD) in the strain treated with fungal pathogens are included.</p>
The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen
<p>Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels by using an opportunistic pathogen, the bacterium <em>Serratia marcescens</em>, that harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the bacterial outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on <em>S. marcescens</em> and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.</p>
High virulence is associated with pathogen spreadability in a songbird-bacterial system
<p>How directly-transmitted pathogens benefit from harming hosts is key to understanding virulence evolution. It is recognized that pathogens benefit from high within-host loads, often associated with virulence. However, high virulence may also directly augment spread of a given amount of pathogen, here termed "spreadability". We used house finches and the conjunctival pathogen <em>Mycoplasma gallisepticum</em> to test whether two components of virulence– the severity of conjunctival inflammation and behavioral morbidity produced– predict pathogen spreadability. We applied ultraviolet powder around the conjunctiva of finches that were inoculated with<em> </em>pathogen<em> </em>treatments of distinct virulence and measured within-flock powder spread, our proxy for "spreadability". When compared to uninfected controls, birds infected with a high-virulence, but not low-virulence, pathogen strain, spread significantly more powder to flockmates. Relative to controls, high-virulence treatment birds both had more severe conjunctival inflammation– which potentially facilitated powder shedding– and longer bouts on feeders, which serve as fomites. However, food peck rates and displacements with flockmates were lowest in the high-virulence treatment relative to controls, suggesting inflammatory rather than behavioral mechanisms likely drive augmented spreadability at high virulence. Our results suggest that inflammation associated with virulence can facilitate pathogen spread to conspecifics, potentially favoring virulence evolution in this system and others.</p>
Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes and invertebrates
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Microbiome diversity and zoonotic bacterial pathogen prevalence in Peromyscus mice from agricultural landscapes and synanthropic habitat
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High virulence is associated with pathogen spreadability in a songbird-bacterial system
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The effect of a temperature‐sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen
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Core symbionts, age at inoculation, and diet affect colonization of the bumble bee gut by a common bacterial pathogen
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Data from: Reduced skin bacterial diversity correlates with increased pathogen infection intensity in an endangered amphibian host
The fungal pathogen Batrachochytrium dendrobatidis (Bd) infects the skin of amphibians, and has caused severe declines and extinctions of amphibians globally. In this study, we investigate the interaction between Bd and the bacterial skin microbiome of the endangered Sierra Nevada yellow-legged frog, Rana sierrae, using both culture-dependent and culture-independent methods. Samples were collected from two populations of R. sierrae that likely underwent Bd epizootics in the past, but that continue to persist with Bd in an enzootic disease state, and we address the hypothesis that such "persistent" populations are aided by mutualistic skin microbes. Our 16S rRNA metabarcoding data reveal that the skin microbiome of highly infected juvenile frogs is characterized by significantly reduced species richness and evenness, and by strikingly lower variation between individuals, compared to juveniles and adults with lower infection levels. Over 90% of DNA sequences from the skin microbiome of highly infected frogs were derived from bacteria in a single order, Burkholderiales, compared to just 54% in frogs with lower infection levels. In a culture-dependent Bd-inhibition assay, the bacterial metabolites we evaluated all inhibited the growth of Bd. Together, these results illustrate the disruptive effects of Bd infection on host skin microbial community structure and dynamics, and suggest possible avenues for the development of anti-Bd probiotic treatments.
Data from: Transmission pathways and spillover of an erythrocytic bacterial pathogen from domestic cats to wild felids
Many pathogens infect multiple hosts, and spillover from domestic to wild species poses a significant risk for spread of diseases that threaten wildlife and humans. Documentation of cross-species transmission, and unravelling the mechanisms that drive it, remains a challenge. Focusing on co-occurring domestic and wild felids, we evaluate possible transmission mechanisms and evidence of spillover of 'Candidatus Mycoplasma haemominutum' (CMhm), an erythrocytic bacterial parasite of cats. We examine transmission and possibility of spillover by analysing CMhm prevalence, modeling possible transmission pathways, deducing genotypes of CMhm pathogens infecting felid hosts based on sequences of the bacterial 16S rRNA gene, and conducting phylogenetic analyses with ancestral state reconstruction to identify likely cross-species transmission events. Model selection analyses suggest both indirect (i.e., spread via vectors) and direct (i.e., via inter-specific predation) pathways may play a role in CMhm transmission. Phylogenetic analyses indicate that transmission of CMhm appears to predominate within host species, with occasional spillover, at unknown frequency, between species. These analyses are consistent with transmission by predation of smaller cats by larger species, with subsequent within-species persistence after spillover. Our results implicate domestic cats as a source of global dispersal and spillover to wild felids via predation. We contribute to the emerging documentation of predation as a common means of pathogen spillover from domestic to wild cats, including pathogens of global conservation significance. These findings suggest risks for top predators as bioaccumulators of pathogens from subordinate species.
Data from: Pharmaceutical pollution alters the cost of bacterial infection and its relationship to pathogen load
<p><span>The relationship between pathogen proliferation and the cost of infection experienced by a host drives the ecology and evolution of host-pathogen dynamics. While environmental factors can shape this relationship, there is currently limited knowledge on the consequences of emerging contaminants, such as pharmaceutical pollutants, for the commonly observed trade-off between a pathogen's growth within the host and the damage it causes, termed its virulence. Here, we investigated how exposure to fluoxetine (Prozac), a commonly detected psychoactive pollutant, could alter this key relationship using the water flea <em>Daphnia magna</em> and its bacterial pathogen <em>Pasteuria ramosa </em>as a model system. Across a variety of fluoxetine concentrations, we found that fluoxetine shaped the damage a pathogen caused, such as the reduction in fecundity or intrinsic growth experienced by infected individuals, but with minimal change in average pathogen spore loads. Instead, fluoxetine modified the relationship between the degree of pathogen proliferation and its virulence, with both the strength of this trade-off and the component of host fitness most affected varying by fluoxetine concentration and host genotype. Our study underscores the potential for pharmaceutical pollution to modify the virulence of an invading pathogen, as well as the fundamental trade-off between host and pathogen fitness, even at the trace amounts increasingly found in natural waterways. </span></p>
Bacterial predation of a fungal wheat pathogen: Prelude to experimental evolution of enhanced biocontrol agents
<p><span>Research to identify appropriate biological agents for controlling pathogens might exploit experimental evolution to select for enhanced antagonism against pathogens. We report development of an experimental regime facilitating this approach featuring the broad-spectrum bacterial predator <em>Myxococcus</em> <em>xanthus</em> and the fungal wheat pathogen <em>Zymoseptoria</em> <em>tritici</em>. We demonstrate that <em>Z. tritici</em>, a major cause of crop loss and fungicide use worldwide, both fuels growth of and is killed by <em>M. xanthus</em> on wheat straw, a likely source of vernal seedling infection. <em>M. xanthus</em> is first found capable of density-dependent growth on moistened straw alone, unaided by <em>Z. tritici</em> as prey, growth that also depends on how long straw was moistened before <em>M. xanthus</em> inoculation. Such growth of non-cellulolytic myxobacteria on plant detritus may have implications for understanding their roles in nutrient cycling. However, straw with <em>Z. tritici </em>is found to fuel greater <em>M. xanthus </em>growth than straw alone under many conditions. After shorter moistening, growth by low-density <em>M. xanthus</em> populations is found to be fully dependent on <em>Z. tritici</em>. Such pathogen-dependent <em>M. xanthus</em> populations could be sustained with population replacement over five one-week growth cycles, indicating feasibility of conducting long-term experimental evolution with this system. Further, <em>M. xanthus</em> is found to kill majorities of <em>Z. tritici</em> populations on both buffered agar and straw. Our results suggest that myxobacteria may serve as effective biocontrol agents of <em>Z. tritici</em> and are amenable to long-term experimental selection for enhanced killing of this pathogen, an approach broadly applicable to many potential biocontrol agents and target pathogens.</span></p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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.