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429 results for “Bacterial infection”
Dataset - A lung-on-chip model reveals an essential role for alveolar epithelial cells in controlling bacterial growth during early M. tuberculosis infection
<p>Description of the sub-folders<br> Name, type of data, corresponding Figure in the manuscript<br> 3D view of the LoC model - .tiff image stack, Figure 1.</p> <p>Bacterial Growth Rate Data - .tiff image stacks, .csv files and MATLAB code to extract the fluorescence intensity over time, Figure 2, Figure 2 - figure supplement 2, Figure 2 - figure supplement 4, Figure 3, Figure 3 - figure supplement 2, Figure 4.</p> <p>AT Characterization - .tiff image stacks and MATLAB code to extract the number and volume of lamellar bodies from the stack of confocal images, Figure 1, Figure 1 - figure supplement 1, Figue 1 - figure supplement 2.</p> <p>AT Infection in LoC model - .tiff image stacks, Figure 2 - figure supplement 1.</p> <p>AT Infection in vivo - .tiff image stacks, Figure 1 - figure supplement 3.</p> <p>Simulations of in vivo infections - .dat files of growth rates in macrophages for the WT and ESX-1 deficient populations and MATLAB code to simulate an infection from this data, Figure 4.</p> <p> </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>
When does antimicrobial resistance increase bacterial fitness? Effects of dosing, social interactions and frequency dependence on the benefits of AmpC β-lactamases in broth, biofilms and a gut infection model.
<p><span>One of the longstanding puzzles of antimicrobial resistance is why the frequency of resistance persists at intermediate levels.<span> </span>Theoretical explanations for the lack of fixation of resistance include cryptic costs of resistance or negative frequency-dependence but are seldom explored experimentally. <span> </span><em>β</em>-lactamases, which detoxify penicillin-related antibiotics, have well-characterized frequency-dependent dynamics driven by cheating and cooperation.<span> </span>However, bacterial physiology determines whether <em>β</em>-lactamases are cooperative and we know little about the sociality or fitness of <em>β</em>-lactamase producers in infections.<span> </span>Moreover, media-based experiments constrain how we measure fitness, and ignore important parameters such as infectivity and transmission among hosts.<span> </span>Here, we investigated the fitness effects of broad-spectrum AmpC <em>β</em>-lactamases in <em>Enterobacter cloacae</em> in broth, biofilms and gut infections in a model insect. <span> </span>We quantified frequency- and dose-dependent fitness using cefotaxime, a third-generation cephalosporin.<span> </span>We predicted that infection dynamics would be similar to those observed in biofilms, with social protection extending over a wide dose range.<span> </span>We found evidence for the sociality of <em>β</em>-lactamases in all contexts with negative frequency-dependent selection ensuring the persistence of wild-type bacteria although cooperation was less prevalent in biofilms, contrary to predictions.<span> </span>While competitive fitness in gut infections and broth had similar dynamics, incorporating infectivity into measurements of fitness in infections<em> </em>significantly affected conclusions. <span> </span>Resistant bacteria had reduced infectivity which limited the fitness benefits of resistance to infections challenged with low antibiotic doses and having low initial frequencies of resistance. <span> </span>The fitness of resistant bacteria in more physiologically tolerant states (in biofilms, in infections) could be constrained by the presence of wild-type bacteria, high antibiotic doses and limited availability of <em>β</em>-lactamases.<span> </span>One conclusion is that increased tolerance of <em>β</em> -lactams does not necessarily increase selection pressure for resistance.<span> </span>Overall, both cryptic fitness costs and frequency-dependence curtailed the fitness benefits of resistance in this study.<span> </span></span></p> <p><span> </span></p>
Figure 5 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 5. Phylogenetic tree based on 16S rRNA sequences of Cardinium, constructed by a neighbor-joining procedure. Cardinium strains are depicted by the host name. The accession numbers are shown after the host name. Numbers on the nodes indicate bootstrap percent confidence values.
Figure 2 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 2. Neighbor-joining tree of COI sequences of the Erythraeidae mites of the present study and the Genbank sequence data. Numbers above/below nodes represent bootstrap values.
Figure 1 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 1. Erythraeus (Erythraeus) pistacicus Haitlinger, Mehrnejad & Šundić, 2016 larva (Black arrow)inside the gall, feeding on the aphid, Forda hirsuta Mordvilko, 1928, on pistachio trees. June 2022, Mashhad, Northeast of Iran.
Figure 7 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 7. Phylogenetic relationship of Planomicrobium symbiont identified from Erythraeus (Erythraeus) pistacicus with related sequences retrieved from GenBank. The tree was constructed using neighbor-joining procedure. The sequence obtained from E. (E.) pistacicus in this study is in red box. Sequence from Bacillus subtilis was used as an
High-content high-resolution microscopy and deep learning assisted analysis reveals host and bacterial heterogeneity during Shigella infection
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A bacterial effector manipulates host lysosomal protease activity-dependent plasticity in cell death modalities to facilitate infection
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Data from: Prior heat waves improve survival of field but not domesticated populations of tobacco hornworm exposed to repeated bacterial infections
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Nano MOFs as targeted drug delivery agents to combat antibiotic resistant bacterial infections
<p>The drug resistance of bacteria is a significant threat to human civilization while the action of antibiotics against drug-resistant bacteria is severely limited due to the hydrophobic nature of drug molecules, which unquestionably inhibit its permanency for clinical applications. The antibacterial action of nanomaterials offers major modalities to combat drug resistance of bacteria. The current work reports, the use of nano MOFs encapsulating drug molecules to enhance its antibacterial activity against model drug-resistant free living bacteria and biofilm of the bacteria. We have attached rifampicin (RF), a well-documented antituberculosis drug with tremendous pharmacological significance, into the pore surface of zeolitic imidazolate framework 8 (ZIF8) by a <span><span>simple synthetic procedure</span></span><span>.</span> The synthesized ZIF8 has been characterized using X-ray diffraction (XRD) method before and after drug encapsulation. The electron microscopic strategies such as scanning electron microscope (SEM) and transmission electron microscope (TEM) methods was performed to characterize the binding between ZIF8 and RF. We have also performed picosecond resolved fluorescence spectroscopy to validate the formation of the ZIF8-RF nanohybrids (NHs). The drug release profile experiment demonstrates that ZIF8-RF depicts pH-responsive drug delivery and ideal for targeting bacterial disease corresponding to its inherent acidic nature. Most remarkably, ZIF8-RF gives enhanced antibacterial activity against methicillin-resistant <i>S. aureus</i> (MRSA) bacteria and also prompts entire damage of structurally robust bacterial biofilms. Overall, the present study depicts a detailed physical insight for manufactured antibiotic-encapsulated NHs presenting tremendous antimicrobial activity that can be beneficial for manifold practical applications.</p>
Data from: Strong effects of lab-to-field environmental transitions on the bacterial intestinal microbiota of Mus musculus are modulated by Trichuris muris infection
<p>Studies of controlled lab animals and natural populations represent two insightful extremes of microbiota research. We bridged these two approaches by transferring lab-bred female C57BL/6 mice from a conventional mouse facility to an acclimation room and then to an outdoor enclosure, to investigate how the gut microbiota changes with environment. Mice residing under constant conditions served as controls. Using 16S rRNA sequencing of fecal samples, we found that the shift in temperature and humidity, as well as exposure to a natural environment, increased microbiota diversity and altered community composition. Community composition in mice exposed to high temperatures and humidity diverged as much from the microbiota of mice housed outdoors as from the microbiota of control mice. Additionally, infection with the nematode <i>Trichuris muris</i> modulated how the microbiota responded to environmental transitions: The dynamics of several families were buffered by the nematodes, while invasion rates of two taxa acquired outdoors were magnified. These findings suggest that gut bacterial communities respond dynamically and simultaneously to changes within the host's body (e.g., the presence of nematodes) and to changes in the wider environment of the host.</p>
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.
Host biomarkers and combinatorial scores for the detection of serious and invasive bacterial infection in pediatric patients with fever without source
<h3><span>Background </span></h3> <p><span>Improved tools are required to detect bacterial infection in children with fever without source (FWS), especially when younger than 3 years old. The aim of the present study was to investigate the diagnostic accuracy of a host signature combining for the first time two viral-induced biomarkers, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and interferon </span><span>γ</span><span>-induced protein-10 (IP-10), with a bacterial-induced one, C-reactive protein (CRP), to reliably predict bacterial infection in children with fever without source (FWS) and to compare its performance to routine individual biomarkers (CRP, procalcitonin (PCT), white blood cell and absolute neutrophil counts, TRAIL, and IP-10) and to the Labscore.</span></p> <h3><span>Methods</span></h3> <p><span>This was a prospective diagnostic accuracy study conducted in a single tertiary center in children aged less than 3 years old presenting with FWS. Reference standard etiology (bacterial or viral) was assigned by a panel of three independent experts. Diagnostic accuracy (AUC, sensitivity, specificity) of host individual biomarkers and combinatorial scores was evaluated in comparison to reference standard outcomes (expert panel adjudication and microbiological diagnosis). </span></p> <h3><span>Results </span></h3> <p><span>241 patients were included. 68 of them (28%) were diagnosed with a bacterial infection and 5 (2%) with invasive bacterial infection (IBI). Labscore, ImmunoXpert, and CRP attained the highest AUC values for the detection of bacterial infection, respectively 0.854 (0.804–0.905), 0.827 (0.764–0.890), and 0.807 (0.744–0.869). Labscore and ImmunoXpert outperformed the other single biomarkers with higher sensitivity and/or specificity and showed comparable performance to one another although slightly reduced sensitivity in children < 90 days of age.</span></p> <h3><span>Conclusion </span></h3> <p><span>Labscore and ImmunoXpert demonstrate high diagnostic accuracy for safely discriminating bacterial infection in children with FWS aged under and over 90 days, </span><span>supporting their adoption in the assessment of febrile patients. </span></p>
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>
Increasing adult density compromises survival following bacterial infections in Drosophila melanogaster
<p>The density-dependent prophylaxis hypothesis predicts that risk of pathogen transmission increases with increase in population density, and in response to this, organisms mount a prophylactic immune response when exposed to high density. This prophylactic response is expected to help organisms improve their chances of survival when exposed to pathogens. Alternatively, organisms living at high densities can exhibit compromised defense against pathogens due to lack of resources and density associated physiological stress; the crowding stress hypothesis. We housed adult Drosophila melanogaster flies at different densities and measured the effect this has on their post-infection survival and resistance to starvation. We find that flies housed at higher densities show greater mortality after being infected with bacterial pathogens, while also exhibiting increased resistance to starvation. Our results are more in line with the density-stress hypothesis that postulates a compromised immune system when hosts are subjected to high densities.</p>
Figure 6 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 6. Haplotype network of Cardinium endosymbionts based on 16S rDNA sequences.
Figure 4 in New host detection of the parasitic mite, Erythraeus pistacicus (Trombidiformes: Erythraeidae) from Iran and indication of possible infection with bacterial symbionts
Figure 4. Haplotype network of Wolbachia endosymbionts based on wsp gene.
Dataset - Dynamic persistence of intracellular bacterial communities of uropathogenic Escherichia coli in a human bladder-chip model of urinary tract infections
<p>Dataset for manuscript posted at biorxiv: https://doi.org/10.1101/2021.01.03.42483 and in revision for eLife. Data corresponding to each main figure and its associated figure supplements are in seperate .zip folders.</p>
Negative regulation of IMD contributes to disease tolerance during systemic bacterial infection in Drosophila
<p>Data and R code for <strong>Negative regulation of IMD contributes to disease tolerance during systemic bacterial infection in <em>Drosophila</em></strong></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.
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DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
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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.
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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.