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3,109 results for “Pathogens”
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>
Pathogenic Leptospira isolated from rodents in New Orleans, Louisiana USA, and associated site information
<p>Land use change can elevate disease risk by creating conditions beneficial to species that carry zoonotic pathogens. Observations of concordant global trends in pathogen prevalence and disease incidence have engendered concerns that urbanization could increase transmission risk of some pathogens. Yet host-pathogen relationships underlying transmission risk have not been well characterized within cities, even where contact between humans and species capable of transmitting pathogens of concern occur. We addressed this deficit by testing the hypothesis that areas in cities experiencing greater population loss and infrastructure decline (i.e., counter-urbanization) can support a greater diversity of host species and a larger and more diverse pool of pathogens. We did so by characterizing pathogenic <em>Leptospira</em> infection relative to rodent host richness and abundance across a mosaic of abandonment in post-Katrina New Orleans (Louisiana, USA). We found that <em>Leptospira</em> infection loads were highest in areas that harbored higher rodent species richness. Areas with greater host co-occurrence also harbored a greater number of hosts, including the most competent hosts, indicating that <em>Leptospira </em>infection is amplified by increases in overall and relative host abundance. Evidence of shared infection among rodent hosts indicates that cross-species transmission of <em>Leptospira </em>likely increases infection at sites with greater host syntopy. Additionally, evidence that rodent co-occurrence and abundance and <em>Leptospira</em> infection load parallel abandonment suggests that counter-urbanization can elevate zoonotic disease risk within cities, particularly in underserved communities that are burdened with disproportionate concentrations of derelict properties.</p>
The Genome Sequence of Citrus Melanose Pathogen Diaporthe citri and Two Citrus related Diaporthe species
<p>The melanose diseases is one the most widespread and economically important fungal diseases of citrus worldwide. The causative agent is filamentous fungus <em>Diaporthe citri</em> Wolf (syn. <em>Phomopsis citri</em> H.S. Fawc.). Here, we report genome assemblies of three strains of <em>D. citri</em>, namely strains ZJUD2, ZJUD14 and Q7, generated using a combination of PacBio Sequel long-read and Illumina paired-end sequencing data. The assembled genomes of <em>D. citri</em> ranged 53.97 Mb to 63.64 Mb in genome size, containing 15,977 ~ 16,622 protein-coding genes. In addition, we sequenced and annotated the genome sequences of two Citrus related <em>Diaporthe </em>species, including <em>D. citriasiana</em> and <em>D. citrichinensis</em>. The described genome sequences and annotations can provide a useful resource in the study of fungal biology, pathogen-host interaction, molecular diagnostic marker development, and population genomic analyses of Citrus-related <em>Diaporthe</em> species.</p>
Population genomics reveals molecular determinants of specialization to tomato in the polyphagous fungal pathogen Botrytis cinerea
<p>Single nucleotide polymorphisms detected in Illumina-sequenced isolates of B. cinerea collected from tomato, grape, hydrangea and bramble in France.</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>
Phage selection drives resistance-virulence trade-offs in Ralstonia solanacearum plant pathogenic bacterium irrespective of the growth temperature
<p><span>While temperature has been shown to affect the survival and growth of bacteria and their phage parasites, it is unclear if trade-offs between phage resistance and other bacterial traits depend on the temperature. Here, we experimentally compared the evolution of phage resistance-virulence trade-offs and underlying molecular mechanisms in phytopathogenic <em>Ralstonia</em> <em>solanacearum</em> bacterium at 25 °C and 35 °C temperature environments. We found that experimental growth conditions selected for small colony variants (SCVs) with increased growth rate and mutations in the quorum-sensing (QS) signalling receptor gene, <em>phcS</em>. Interestingly, SCVs were also phage-resistant and reached higher frequencies in the presence of phages in both temperature environments. Evolving phage resistance was costly in terms of reduced carrying capacity, biofilm formation and reduced virulence i<em>n planta</em> possibly due to loss of QS-mediated expression of key virulence genes. We also observed mucoid phage-resistant colonies that showed loss of virulence and reduced twitching motility likely due to parallel mutations in prepilin peptidase gene pilD. Moreover, phage-resistant SCVs from 35 °C-phage treatment had parallel mutations in genes encoding type II secretion system (T2SS) genes (<em>gspE</em> and <em>gspF</em>), indicating that defects in pseudopilus made bacterium resistant to the phage. Additional transcriptomic analysis revealed upregulation of CBASS and type Ⅰ restriction-modification phage defence systems in response to phage exposure, which coincided with reduced expression of motility and virulence-associated genes, including <em>pilD</em> and type II and III secretion systems. Together, these results suggest that phage resistance-virulence trade-offs are not affected by the growth temperature but can be mediated through both pre- and post-infection phage resistance mechanisms.</span></p>
SUPPLEMENTARY (For MD) An integrative pan-genome and subtractive proteomics approach for the identification of potential novel therapeutic drug target against antibiotic resistant honeybee pathogen Paenibacillus larvae
<p><strong>Parameters</strong></p><p>Force field: AMBER ff19SB</p><p>Water type: TIP3P</p><p>Ions: NaCl </p><p>Ligand topology force field: GAFF2</p><p>Temperature: 298k</p><p>Pressure: 1 bar</p><p>minimization step: 20000 on 5 nanoseconds</p><p>initial velocity is changed by changing "ntx" and "ig"</p><p>C2: ntx = 5 , ig = 8</p><p>C3: ntx = 2 , ig = 5</p><p> </p><p><strong>Uploads</strong>- </p><p>1. Zip file of all 3 main files</p><p>2. Unzip file of C1 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>3. Zip file of C1</p><p>4. Unzip file of C2 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>5. Zip file of C2</p><p>6. Unzip file of C3 (Trajectory, PDB complex after each 10 ns run, and Mp4 video of Complex)</p><p>7. Zip file of C3</p><p>8. Zip and unzip file of <strong>Initial</strong> PDB of complex prior to MD simulation with <strong>Post</strong> MD PDB (C1, C2, C3)</p><p>9. Zip file of <strong>topology</strong> files for C1, C2, and C3</p>
Agricultural soil legacy influences multitrophic interactions between crops, their pathogens, and pollinators
<p>Soil legacy influences plant interactions with antagonists and below-ground mutualists. Plant-antagonist interactions can jeopardize, while soil mutualists can enhance, plant-pollinator interactions. This suggests that soil legacy, either directly or mediated through plant symbionts, affects pollinators. However, despite the importance of pollinators to natural and managed ecosystems, there is almost no information on how soil legacy affects plant-pollinator interactions. We assessed effects of soil management legacy (organic vs. conventional) on floral rewards and plant interactions with wild pollinators, herbivores, beneficial fungi, and pathogens. We used an observational dataset and structural equation models to evaluate hypothesized relationships between soil and pollinators, then tested observed correlations in a manipulative experiment. Organic legacy increased mycorrhizal fungal colonization and improved resistance to powdery mildew, which promoted pollinator visitation. Further, soil legacy and powdery mildew independently and interactively impacted plant traits important to pollinators, including floral traits and floral reward nutrients. Our results indicate that pollination could be an overlooked consequence of soil legacy and suggests opportunity to develop long-term soil management plans that benefit pollinators and pollination.</p>
Figs 1–6 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Figs 1–6. Light micrographs of the microsporidian pathogen infecting P. brassicae. 1 – intestine which is heavily infected with microsporidian spores; 2–3 – microsporidian spores in fresh smears, note that meront and sporoblast stages are easily seen and marked by arrows; 4 – tetranucleate spherical meront (schizont); 5 – binucleate oval meront; 6 – diplokaryotic sporoblast. Scale bars: 30 µm (1), 15–10 µm (2–3), 3 μm (4), 2 μm (5), 4 μm (4).
Fig. 11 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Fig. 11. The phylogenetic analysis was carried out by Maximum Likelihood (ML) using an HKY85 substitution model of PAUP 4.0b10 software. The topology of the consensus tree was constructed and evaluated by 1000 bootstrap replications. The branches with lower than 50% confidence values were ignored.
Figs 7–10 in Nosema pieriae sp. n. (Microsporida, Nosematidae): A New Microsporidian Pathogen of the Cabbage Butterfly Pieris brassicae L. (Lepidoptera: Pieridae)
Figs 7–10. Transmission electron micrographs of microsporidian spores infecting P. brassicae. 7 – longitudinal (a) and transversal (b) sections of diplokaryotic spores, polar filament (pf), posterior vacuole (pv) and nuclei (n) are easily seen; 8 – spherical nuclei (n); 9 – polaroplast (pp) and anchoring disc (ad) structures; pp thin lamellar type polaroplast, pp thick lamellar type polaroplast; 10 – cross section of 1, 2, polar filaments; exospore (ex), endospore (en), plasmalemma (p) and polar filament (pf). Scale bars: 800 nm (7), 250 nm (8), 200 nm (9, 10).
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>
Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi
<p>The putative benefits to seeds in myrmecochory (ant-mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harbored different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant-handled seeds and seeds with manually-removed elaiosomes were less dissimilar. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction of the seed coat pathogenic community, which may be driven by elaiosome removal or as a byproduct of ant cleaning behaviors and chemical secretions. </p>
Regional Centromere Configuration in the Fungal Pathogens of Pneumocystis Genus
<p>Supplementary material </p>
Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
<p><span>The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen <em>Verticillium dahliae</em>,<em> </em>known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for <em>V. dahliae </em>are also present in other <em>Verticillium</em> species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the <em>Verticillium</em> genus.</span></p>
R scripts, input and output data for: Season of death, pathogen persistence and wildlife behaviour alter number of anthrax secondary infections from environmental reservoirs
<p>An important part of infectious disease management is predicting factors that influence disease outbreaks, such as <em>R</em>, the number of secondary infections arising from an infected individual. Estimating <em>R</em> is particularly challenging for environmentally transmitted pathogens given time lags between cases and subsequent infections. Here, we calculated <em>R</em> for <em>Bacillus anthracis</em> infections arising from anthrax carcass sites in Etosha National Park, Namibia. Combining host behavioural data, pathogen concentrations, and simulation models, we show that <em>R</em> is spatially and temporally variable, driven by spore concentrations at death, host visitation rates and early preference for foraging at infectious sites. While spores were detected up to a decade after death, most secondary infections occurred within two years. Transmission simulations under scenarios combining site infectiousness and host exposure risk under different environmental conditions led to dramatically different outbreak dynamics, from pathogen extinction (<em>R</em><1) to explosive outbreaks (<em>R</em>>10). These transmission heterogeneities may explain variation in anthrax outbreak dynamics observed globally, and more generally, the critical importance of environmental variation underlying host-pathogens interactions. Notably, our approach allowed us to estimate the lethal dose of a highly virulent pathogen non-invasively from observational studies and epidemiological data, useful when experiments on wildlife are undesirable or impractical.</p>
Fig. 1 in Cryptosporidium viatorum from the native Australian swamp rat Rattus lutreolus - An emerging zoonotic pathogen?
Fig. 1. Phylogenetic relationships of small subunit of nuclear ribosomal RNA (SSU) gene nucleotide sequence data (aligned over 563 bp) of selected Cryptosporidium taxa in relation to the novel C. viatorum genotype using the neighbor joining distance method. Individual GenBank accession numbers precede species name, followed by host common name and locality descriptors. Bootstrap support values (based on 2000 iterations) are indicated next to supported branches. Cryptosporidium baileyi was chosen as the outgroup. The novel genotype from this study is in bold-type. Scale bar indicates the number of nucleotide substitutions per site.
Invasibility of a North American soil ecosystem to amphibian-killing fungal pathogens
<p>North American salamanders are threatened by the intercontinental spread of chytridiomycosis, a deadly disease caused by the fungal pathogen <em>Batrachochytrium salamandrivorans</em> (<em>Bsal</em>). To predict the potential dispersal of <em>Bsal</em> spores to salamander habitats, we evaluated the capacity of soil microbial communities to resist invasion. We determined the degree of habitat invasibility using soils from five locations throughout the Great Smoky Mountains National Park, a region with a high abundance of susceptible hosts. Our experimental design consisted of replicate soil microcosms exposed to different propagule pressures of the non-native pathogen, <em>Bsal</em>, and an introduced but endemic pathogen, <em>B. dendrobatidis</em> (<em>Bd</em>). To compare growth and competitive interactions, we used quantitative PCR, live/dead cell viability assays, and 16S rRNA amplicon sequencing. We found that soil microcosms with intact bacterial communities inhibited both <em>Bsal</em> and <em>Bd</em> growth, but inhibitory capacity diminished with increased propagule pressure. <em>Bsal</em> showed greater persistence than <em>Bd</em>. Linear discriminant analysis (LDA) identified the family Burkolderiaceae as increasing in relative abundance with the decline of both pathogens. Although our findings provide evidence of environmental filtering in soils, such barriers weakened in response to pathogen type and propagule pressure, showing that habitats vary their invasibility based on the properties of their local microbial communities.</p>
Annotation files related to the Telomere-to-Telomere genome assembly of the clubroot pathogen Plasmodiophora brassicae (GCA_036867785.1)
<p>This repository contains annotation files related to the T2T genome aseembly of <em>Plasmodiophora brassicae</em>. Link to the NCBI genome submission- https://www.ncbi.nlm.nih.gov/bioproject/1071157</p> <p><strong>Description of the files :</strong></p> <p><strong>GCA_036867785.1_ULAVAL_Pb3A_genomic.fna</strong> - Soft-masked genome sequence FASTA file representing 20 chromosomes.</p> <p><strong>sequence_report.jsonl</strong> - Detailed information about individual chromosome seqeunce.</p> <p><strong>PBTT_annotation.gtf</strong> - GTF file corresponding to the genomic FASTA file.The GTF file was generated by BRAKER3 and contains information about all possible transcripts.</p> <p><strong>PBTT_CDS_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the CDS of only the longest isoform of the gene models.</p> <p><strong>PBTT_protein_longest_isoform.fasta</strong> - Contains 10521 FASTA sequences representing the amino acid sequences of only the longest isoform of the gene models.</p>
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.