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576 results for “salmonella”
Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
<p>Pigs infected with <em><span>Salmonella</span></em> may excrete large amounts of <em><span>Salmonella</span></em>, increasing the risk of spread of this pathogen in the food chain. Identifying <em><span>Salmonella</span></em> high shedder pigs is therefore required to mitigate this risk. We analyzed immune-associated markers and composition of the gut microbiota in specific-pathogen-free pigs presenting different shedding levels after an oral infection with <span>Salmonella</span>. Immune response was studied through total blood cell counts, production of anti-<em><span>Salmonella</span></em> antibodies and cytokines, and gene expression quantification. Total <em><span>Salmonella</span></em> shedding for each pig was estimated and hierarchical clustering was used to cluster pigs into high, intermediate, and low shedders. Gut microbiota compositions were assessed using 16S rRNA microbial community profiling. Comparisons were made between control and inoculated pigs, then between high and low shedders pigs. Prior to infection, high shedders had similar immunological profiles compared to low shedders. As soon as 1 day postinoculation (dpi), significant differences in the cytokine production level and on the expression level of several host genes related to a proinflammatory response were observed between high and low shedders. Infection with <em><span>Salmonella</span></em> induced an early and profound remodeling of the immune response in all pigs, but the intensity of the response was stronger in high shedders. In contrast, low shedders seroconverted earlier than high shedders. Just after induction of the proinflammatory response (at 2 dpi), some taxa of the fecal microbiota were specific to the shedding phenotypes. This was related to the enrichment of several functional pathways related to anaerobic respiration in high shedders. In conclusion, our data show that the immune response to <em><span>Salmonella</span></em> modifies the fecal microbiota and subsequently could be responsible for shedding phenotypes. Influencing the gut microbiota and reducing intestinal inflammation could be a strategy for preventing <em><span>Salmonella</span></em> high shedding in livestock.</p>
Safety and Immunogenicity of a Novel Conjugate Vaccine Against Salmonella Typhi and Salmonella Paratyphi A in Healthy Adults
ClinicalTrials.gov study NCT05613205. IPD Sharing: YES. Countries: 1. Publications: 1.
A temporary cholesterol-rich diet and bacterial extracellular matrix factors favor Salmonella spp. biofilm formation in the cecum
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Data from: Mucus-derived glycans are inhibitory signals for <em>Salmonella</em> Typhimurium SPI-1-mediated invasion
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Inflammatory responses induced by the monophasic variant of Salmonella typhimurium in pigs play a role in the high shedder phenotype and fecal microbiota composition
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Salmonella enterica serovar Enteritidis EN1660 proteome spectral data
<p>H-NS is a nucleoid structuring protein and global repressor of virulence and horizontally-acquired genes in bacteria. H-NS can interact with itself or with homologous proteins, but protein family diversity and regulatory network overlap remain poorly defined. Here we present a comprehensive phylogenetic analysis that revealed deep-branching clades, dispelling the presumption that H-NS is the progenitor of varied molecular backups. With few exceptions, clades are either entirely chromosomal or entirely plasmid-encoded proteins. On chromosomes, StpA and newly discovered HlpP are core genes in specific genera, whereas Hfp and newly discovered HlpC are sporadically distributed. Six clades of <u>H</u>-NS <u>p</u>lasmid <u>p</u>roteins (Hpp) exhibit ancient and dedicated associations with plasmids, including three clades with fidelity for plasmid incompatibility groups H, F, or X. A proliferation of H-NS homologs in Erwiniaceae includes the first observation of potentially co-dependent H-NS forms. Conversely, the observed diversification of oligomerization domains may facilitate stable co-existence of divergent homologs in a genome. Transcriptomic and proteomic analysis of regulatory crosstalk in <i>Salmonella </i>revealed networked and hierarchical control of H-NS homologs. We also discovered that H-NS is both a repressor and activator of <i>Salmonella</i> Pathogenicity Island 1 gene expression, and both modes are restored by Sfh (HppH) in the absence of H-NS.</p>
Extended Data: Population structure of Salmonella serotype Mbandaka
<p>This project contains supplementary figures associated with the project.</p>
Data from: Hotspot mutations and ColE1 plasmids contribute to the fitness of Salmonella Heidelberg in poultry litter
Salmonella enterica subsp. enterica serovar Heidelberg (S. Heidelberg) is a clinically-important serovar linked to food-borne illness, and commonly isolated from poultry. Investigations of a large, multistate outbreak in the USA in 2013 identified poultry litter (PL) as an important extra-intestinal environment that may have selected for specific S. Heidelberg strains. Poultry litter is a mixture of bedding materials and chicken excreta that contains chicken gastrointestinal (GI) bacteria, undigested feed, feathers, and other materials of chicken origin. In this study, we performed a series of controlled laboratory experiments which assessed the microevolution of two S. Heidelberg strains (SH-2813 and SH-116) in PL previously used to raise 3 flocks of broiler chickens. The strains are closely related at the chromosome level, differing from the reference genome by 109 and 89 single nucleotide polymorphisms/InDels, respectively. Whole genome sequencing was performed on 86 isolates recovered after 0, 1, 7 and 14 days of microevolution in PL. Only strains carrying an IncX1 (37kb), 2 ColE1 (4 and 6kb) and 1 ColpVC (2kb) plasmids survived more than 7 days in PL. Competition experiments showed that carriage of these plasmids was associated with increased fitness. This increased fitness was associated with an increased copy number of IncX1 and ColE1 plasmids. Further, all Col plasmid-bearing strains had hotspot mutations in 37 loci on the chromosome and in 3 loci on the IncX1 plasmid. Additionally, we observed a decrease in susceptibility to tobramycin, kanamycin, gentamicin, neomycin and fosfomycin for Col plasmid-bearing strains. Our study demonstrates how positive selection from poultry litter can change the evolutionary path of S. Heidelberg.
Horizontal gene transfer is the main driver of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg
<p>Overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg (SH), a model food pathogen, to test if chicks raised antibiotic-free harbor transferable AR. We challenged chicks with an antibiotic susceptible SH strain using various routes of inoculation and determined if SH isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole genome sequencing (WGS) to show that chicks grown without antibiotics harbored antimicrobial resistant SH population 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing we found that SH infection perturbed the microbiota of broiler chicks and used metagenomics and WGS to confirm commensal Escherichia coli population as the main reservoir of IncI1 plasmid acquired by SH. The carriage of this IncI1 plasmid posed no fitness cost to SH but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of SH and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella.</p>
Salmonella In Silico Typing Resource (SISTR) commandline tool database version 1.1.3 used by SISTR release version 1.1.3 and up
<h3><strong>Context</strong></h3> <p>Salmonella In Silico Typing Resource (SISTR) commandline tool enables the identification of the Salmonella serovar and cgMLST types of Salmonella from whole genome sequencing (WGS) data tby using a large database (10,000+) of Salmonella genomes and cgMLST profiles based on the 330 alleles. This database is the central part of the SISTR tool and contains both metadata on 2660 serovars and the corresponding antigenic formula, 84463 genomes to serovar mappings, sequences of the O, H1 and H2 antigens, 139729 cgMLST sequences and 38240 profiles with pairwise distances, MASH sketch of the 15465 genomes used for species and serovar identification.</p> <p>For more information and citation please refer to the following publication and official repository at <a href="https://github.com/phac-nml/sistr_cmd/tree/master">https://github.com/phac-nml/sistr_cmd/tree/master</a> </p> <p>Note: This database was used by SISTR tool up to version 1.1.2 inclusive. From SISTR release 1.1.3 onwards the slightly modified version of this database will be used onwards with changes detailed in <a href="https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md">https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md</a></p> <h3><strong>Citation</strong></h3> <p><em>The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101. <a title="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101" href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101</a></em></p> <p> </p> <h3><strong>Version changes from v2 to v3</strong></h3> <p>In<em> </em><code><strong>genomes-to-serovar.txt</strong></code><em> </em>following serovar changes were made to increase serovar prediction accuracy</p> <table> <tbody> <tr> <th>genome accession</th> <th>serovar previous</th> <th>serovar current</th> </tr> <tr> <td><strong>SRR3048937</strong></td> <td>Ibadan</td> <td>Mississippi</td> </tr> </tbody> </table>
Chromatin accessibility QTL lead variants in macrophages stimulated with IFNg and Salmonella
<p>Lead caQTL variants from RASQUAL and FastQTL analyses.</p>
CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING
<p><strong><span>Table S1.</span></strong><span> </span><span>Metadata for the 21 <em>Salmonella</em> <em>enterica</em> genomes used to perform phylogenetic analysis.</span></p> <p><strong><span>Table S2.</span></strong><span> Comprehensive overview of sequences of targeted serovars present in the genomic database by prescribed selection criteria. </span></p>
CARACTERIZAÇÃO GENÉTICA DE SOROVARES DE Salmonella spp. ISOLADOS NA AVICULTURA POR WHOLE GENOME SEQUENCING
<p><strong><span>Table S1:</span></strong><span> Metadata for the 317 <em>Salmonella</em> Heidelberg genomes retrieved from the Enterobase database to perform genomic analysis in this study.</span></p>
Challenge tests Salmonella in BSF larvae rearing
Open the record for dataset details and reuse information.
Processed gene expression read counts from the AcLDL and IFNg+Salmonella studies
<p>Raw and normalised read count matrices together with metadata.</p>
Salmonella In Silico Typing Resource (SISTR) commandline tool database version 1.1 used by SISTR tool up to release version 1.1.2 inclusive
<h3>Context</h3> <p>Salmonella In Silico Typing Resource (<a href="https://github.com/phac-nml/sistr_cmd/tree/master">SISTR</a>) commandline tool enables the identification of the Salmonella serovar and cgMLST types of <em>Salmonella</em> from whole genome sequencing (WGS) data tby using a large database (10,000+) of <em>Salmonella</em> genomes and cgMLST profiles based on the 330 alleles. This database is the central part of the SISTR tool and contains both metadata on 2672 serovars and the corresponding antigenic formula, 84464 genomes to serovar mappings, sequences of the O, H1 and H2 antigens, 139729 cgMLST sequences and 38240 profiles with pairwise distances, MASH sketch of the 15465 genomes used for species and serovar identification.</p> <p>For more information and citation please refer to the following publication and official repository at <a href="https://github.com/phac-nml/sistr_cmd/tree/master">https://github.com/phac-nml/sistr_cmd/tree/master </a></p> <p>Note: This database was used by SISTR tool up to version 1.1.2 inclusive. From SISTR release 1.1.3 onwards the slightly modified version of this database will be used onwards with changes detailed in <a href="https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md">https://github.com/phac-nml/sistr_cmd/blob/master/CHANGELOG.md</a></p> <h3>Citation</h3> <p><em>The Salmonella In Silico Typing Resource (SISTR): an open web-accessible tool for rapidly typing and subtyping draft Salmonella genome assemblies. Catherine Yoshida, Peter Kruczkiewicz, Chad R. Laing, Erika J. Lingohr, Victor P.J. Gannon, John H.E. Nash, Eduardo N. Taboada. PLoS ONE 11(1): e0147101. doi: 10.1371/journal.pone.0147101. <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101" rel="nofollow">http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0147101</a></em></p> <p> </p> <p> </p>
Source data sets_Figure 1, 2, 6_Salmonella cancer therapy metabolically disrupts tumours at the collateral cost of T cell immunity
<p>Flow cytometry data files associated with Copland <em>et al., </em><strong><em><span>Salmonella </span></em></strong><strong><span>cancer therapy metabolically disrupts tumours at the collateral cost of T cell immunity.</span></strong></p> <p><span>Data associated to Figures 1, 2 and 6. <br></span></p>
Novel insight into the effects of CPXR on Salmonella enteritidis cells during the chlorhexidine treatment and non-stressful growing conditions
<p>The emergence and spread of antimicrobial resistance is a significant global challenge. To solve this emerging problem, the discovery of novel bacterial cellular targets and the critical pathways associated with antimicrobial resistance is urgently needed. In this study, we investigated the role of the two most critical extracytoplasmic stress response regulators, RpoE and CpxR, on the physiology and susceptibility of growing <i>Salmonella</i> <i>enterica</i> serovar Enteritidis cells using the polycationic antimicrobial agent, chlorhexidine (CHX). We showed that deletion of the <i>cpxR</i> gene significantly increased the susceptibility of this organism, whereas deletion of the <i>rpoE</i> gene had no effect on the pathogen's susceptibility to the drug. It has been shown that a lack of the CpxR regulator induces multifaceted stress responses not only in the envelope but also in the cytosol, further affecting the key biomolecules, including DNA, RNA, and proteins. We showed that alterations in cellular trafficking and most of the stress responses are associated with a dysfunctional CpxR regulator during non-stressful (exponential growth phase) conditions, indicating that these physiological changes are intrinsically associated with the lack of the CpxR regulator. In contrast, induction of type II toxin-antitoxin systems and decrease of abundances of enzymes and proteins associated with the recycling of muropeptides and resistance to polymixin and cationic antimicrobial peptides were specific responses of the ∆<i>cpxR</i> mutant to the CHX treatment. Overall, our study provides insight into the effects of CpxR on the physiology of S. Enteritidis cells during the exponential growth phase and drug treatment, which may point to potential cellular targets for the development of an effective antimicrobial agent. </p>
data for Pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella
<p>Contains the results of the MCMC sampling (i.e. fluxes) as well as the simulated MS measurements.</p> <p> </p>
Survival of Salmonella enterica serovar Heidelberg in pine shavings used as broiler litter
<p>Wood shavings is the most common bedding material used around the world to raise broiler. Therefore, wood shavings can be a vehicle for the transmission of pathogens to live birds. In this study, we performed an in-depth genomic characterization of three <em>Salmonella enterica </em>serovar Heidelberg (<em>S</em>. Heidelberg) strains recovered after their inoculation into fresh pine shaving. The three strains used for the microcosm study were previously isolated from broiler feces (SH-AAFC), broiler carcass (SH-ARS) and chicken thigh (SH-FSIS) and differed one from another by 46 - 94 single nucleotide variants. The SH-AAFC strain harbored an antimicrobial resistant gene (ARG) (<em>bla</em><sub>CMY-2</sub>) on an IncI1 plasmid while the SH-FSIS strain harbored multiple ARGs (<em>floR, cmlA1, tet(A), bla</em><sub>TEM-1B</sub><em>, ant(2'')-Ia, aph(6)-Id, aph(3'')-Ib </em>and<em> sul2</em>) on an IncC plasmid. The SH-ARS isolate was pan susceptible to several antibiotics evaluated. We determined the abundance of <em>Salmonella </em>at days 0, 1, 7, 14 and 21 and performed antibiotic susceptibility testing and whole genome sequencing (on 77 randomly selected <em>S</em>. Heidelberg isolates. After 21 days of incubation, <em>Salmonella </em>abundance decreased by 4.4 logs. <em>Salmonella</em> with high minimum inhibitory concentrations (MICs) against ampicillin showed a significantly higher abundance and survival rate compared to <em>Salmonella</em> with high MIC against gentamicin (<em>P</em>< 0.05). Clonal SH-AAFC was the most prevalent strain in the microcosms (48/77), followed by the strain SH-ARS (25/77). Only 4/77 isolates were determined to be clones of SH-FSIS. We identified recombination events and plasmid copy number changes that were associated with the fitness of <em>S</em>. Heidelberg strain carrying IncI1 and Col plasmids. Lastly, we found that litter physicochemical variables including water activity could explain up to 85% of the variability in our data.</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.