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21 results for “Genomic Epidemiology”
Genomic Epidemiology Dataset for Important Nosocomial Pathogenic Bacteria Acinetobacter baumannii
<p>The<strong> </strong>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 comprehensive genomic epidemiology analysis of 17,546 genomes of a dangerous bacterial pathogen <i>Acinetobacter baumannii</i>. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), intrinsic<i> blaOXA-51-like</i> gene variants, capsular (KL) and oligosaccharide (OCL) types, CRISPR-Cas systems, and cgMLST profiles are presented, as well as the assignment of particular isolates to nine known international clones of high risk. The presence of antimicrobial resistance genes within the genomes is also reported. </p><p>These data will be useful for researchers in the field of <i>A. baumannii</i> genomic epidemiology, resistance analysis and prevention measure development.</p>
Supplementary dataset to publication: "Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany"
<p>Supplementary dataset to publication: "Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany" by Abdel-Glil Mostafa Y., Hotzel Helmut, Tomaso Herbert, Didelot Xavier, Brandt Christian, Seyboldt Christian, Linde Jörg, Schwarz Stefan, Neubauer Heinrich, El-Adawy Hosny. Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany. Frontiers in Veterinary Science. volume 9 (https://www.frontiersin.org/articles/10.3389/fvets.2022.1069062) <br> </p>
The genomic and epidemiological virulence patterns of Salmonella enterica serovars in the United States
<p>The serovars of <i>Salmonella enterica </i>display dramatic differences in pathogenesis and host preferences. We developed a process (patent pending) for grouping <i>Salmonella</i> isolates and serovars by their public health risk. We collated a curated set of 12,337 <i>S. enterica</i> isolate genomes from human, beef, and bovine sources in the US. After annotating a virulence gene catalog for each isolate, we used unsupervised random forest methods to estimate the proximity (similarity) between isolates based upon the genomic presentation of putative virulence traits We then grouped isolates (virulence clusters) using hierarchical clustering (Ward's method), used non-parametric bootstrapping to assess cluster stability, and externally validated the clusters against epidemiological virulence measures from FoodNet, the National Outbreak Reporting System (NORS), and US federal sampling of beef products. We identified five stable virulence clusters of <i>S. enterica</i> serovars. Cluster 1 (higher virulence) serovars yielded an annual incidence rate of domestically acquired sporadic cases roughly one and a half times higher than the other four clusters combined (Clusters 2-5, lower virulence). Compared to other clusters, cluster 1 also had a higher proportion of infections leading to hospitalization and was implicated in more foodborne and beef-associated outbreaks, despite being isolated at a similar frequency from beef products as other clusters. We also identified subpopulations within 11 serovars. Remarkably, we found <i>S.</i> Infantis and<i> S.</i> Typhimurium subpopulations that significantly differed in genome length and clinical case presentation. Further, we found that the presence of the pESI plasmid accounted for the genome length differences between the <i>S. </i>Infantis subpopulations. Our results show that <i>S. enterica</i> strains associated with highest incidence of human infections share a common virulence repertoire. This work could be updated regularly and used in combination with foodborne surveillance information to prioritize serovars of public health concern. </p><p>Files contained in this repository will reproduce elements of figures 3,4,6, and 7 of the accompanying PLOS One manuscript. </p><p> </p>
BTyperDB: a community-curated, global atlas of Bacillus cereus sensu lato genomes for epidemiological surveillance
<p>The ability to cause foodborne illness, anthrax, and other infections has been attributed to numerous lineages within <em>Bacillus cereus sensu lato</em> (<em>s.l.</em>). However, existing pathogen surveillance databases facilitate dangerous pathogen misidentifications when applied to <em>B. cereus s.l.</em>, potentially hindering outbreak or bioterrorism attack response efforts. To address this, we developed BTyperDB (<a href="http://www.btyper.app/">www.btyper.app</a>), an atlas of <em>B. cereus s.l.</em> genomes with standardized, community-curated metadata. BTyperDB aggregates all publicly available <em>B. cereus s.l.</em> genomes (including >2,600 previously unassembled genomes) with novel genomes donated by laboratories around the world, nearly doubling the number of publicly available <em>B. cereus s.l.</em> genomes. To showcase its utility for pathogen surveillance, we use BTyperDB to identify emerging anthrax toxin- and capsule-harboring lineages. Overall, our study provides insight into the epidemiology of an under-studied group of emerging pathogens and highlights the benefits of inclusive, community-driven metadata FAIRification efforts.</p>
Supplementary Data for "Combining genomics and epidemiology to track mumps virus transmission in the United States"
<p>Supplementary data and scripts used to produce figures for "Combining genomics and epidemiology to track mumps virus transmission in the United States."</p> <p>Files are divided into "code" and "data" directories and a README is provided for each.</p>
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil
<p>Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated <em>Aedes aegypti</em> was able to capture the seasonality of reported human infections. Spatial modelling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centres in the Southeast. Phylodynamic analysis unravelled the circulation of three distinct YFV lineages, and provided proof of the directionality of a known spatial corridor of viral spread that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology in a One Health framework can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.</p>
Data from: How Bank Vole-PUUV Interactions Influence the Eco-Evolutionary Processes Driving Nephropathia Epidemica Epidemiology—An Experimental and Genomic Approach
<p><strong>Abstract: </strong>In Europe, Puumala virus (PUUV) is responsible for nephropathia epidemica (NE), a mild form of hemorrhagic fever with renal syndrome (HFRS). Despite the presence of its reservoir, the bank vole, on most of French territory, the geographic distribution of NE cases is heterogeneous and NE endemic and non-endemic areas have been reported. In this study we analyzed whether bank vole-PUUV interactions could partly shape these epidemiological differences. We performed crossed-experimental infections using wild bank voles from French endemic (Ardennes) and non-endemic (Loiret) areas and two French PUUV strains isolated from these areas. The serological response and dynamics of PUUV infection were compared between the four cross-infection combinations. Due to logistical constraints, this study was based on a small number of animals. Based on this experimental design, we saw a stronger serological response and presence of PUUV in excretory organs (bladder) in bank voles infected with the PUUV endemic strain. Moreover, the within-host viral diversity in excretory organs seemed to be higher than in other non-excretory organs for the NE endemic cross-infection but not for the NE non-endemic cross-infection. Despite the small number of rodents included, our results showed that genetically different PUUV strains and in a lesser extent their interaction with sympatric bank voles, could affect virus replication and diversity. This could impact PUUV excretion/transmission between rodents and to humans and in turn at least partly shape NE epidemiology in France.</p>
Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya
<p><strong><span>Background</span></strong></p> <p><span>Livestock systems have been proposed as a reservoir for antimicrobial-resistant (AMR) bacteria and AMR genetic determinants that may infect or colonise humans, yet quantitative evidence regarding their epidemiological role remains lacking. Here we used a combination of genomics, epidemiology and ecology to investigate patterns of AMR gene carriage in <em>Escherichia</em> <em>coli</em>, regarded as a sentinel organism.</span></p> <p><strong><span>Methods</span></strong></p> <p><span>We conducted a structured epidemiological survey of 99 households across Nairobi, Kenya, and whole genome sequenced <em>E</em>. <em>coli</em> isolates from 311 human, 606 livestock, and 399 wildlife faecal samples. We used statistical models to investigate the prevalence of AMR carriage and characterise AMR gene diversity and structure of AMR genes in different host populations across the city. We also investigated house-hold level risk factors for exchange of AMR genes between sympatric humans and livestock.</span></p> <p><strong><span>Findings</span></strong></p> <p><span>We detected 56 unique acquired genes along with 13 point mutations present in variable proportions in human and animal isolates, known to confer resistance to nine antibiotic classes. We find that AMR gene community composition is not associated with host species, but AMR genes were frequently co-located, potentially enabling the acquisition and dispersal of multi-drug resistance in a single step. We find that whilst keeping livestock had no influence on human AMR gene carriage, the potential for AMR transmission across human-livestock interfaces is greatest when manure is poorly disposed of and in larger households.</span></p> <p><strong><span>Conclusions</span></strong></p> <p><span>Findings of widespread carriage of AMR bacteria in human and animal populations, including in long-distance wildlife species, in community settings, highlight the value of evidence-based surveillance to address antimicrobial resistance on a global scale. Our genomic analysis provided in-depth understanding of AMR determinants at the interfaces of One-Health sectors that will inform AMR prevention and control.</span></p>
Genomic epidemiology of Escherichia coli: antimicrobial resistance through a One Health lens in sympatric humans, livestock and peri-domestic wildlife in Nairobi, Kenya
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Data from: Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae
Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity.
Genomic epidemiology of SARS-CoV-2 in Mozambique
<p><strong>Abstract: </strong>Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020. Since then, the virus has spread to all provinces in the country. Here we set out to perform a retrospective molecular epidemiological analysis of the first 25 months of the epidemic in Mozambique. In total, 1 146 whole genome sequences from Mozambique were phylogenetically analyzed against a globally representative set of references to put the epidemic in the country into context. The domestic pandemic was marked by four successive waves of infection, with the first wave associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for the majority of cases and death during the second, third, and fourth waves. Viral exchanges between Mozambique and the outside world mimicked pandemic waves, with most exchanges occurring during the second, third, and forth waves and most imports and exports being attributed to South Africa. Due to a health system already under constraint and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.</p>
Data from: Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae
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Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats
<p><span>In the largest DNA-based study of domestic cat to date, 11,036 individuals (10,419 pedigreed cats from 91 breeds and breed types and 617 non-pedigreed cats) were genotyped via commercial panel testing, </span><span>elucidating the distribution and frequency of known genetic variants associated with blood type, disease and physical traits across cat breeds. </span><span>Blood group determining variants, which are relevant clinically and in cat breeding, were genotyped to assess the across breed distribution of blood types A, B and AB.</span> <span>Extensive panel testing identified 13 disease-associated variants in 48 breeds or breed types for which the variant had not previously been observed, strengthening the argument for panel testing across populations. The study also indicates that multiple breed clubs have effectively used DNA testing to reduce disease-associated genetic variants within certain pedigreed cat populations. Appearance-associated genetic variation in all cats is also discussed. Additionally, we combined genotypic data with phenotype information and clinical documentation</span><span>, actively conducted owner and veterinarian interviews, and recruited cats for clinical examination</span><span> to investigate the causality of a number of</span><span> tested variants across different breed backgrounds</span><span>. Lastly, genome-wide informative SNP heterozygosity levels were calculated to obtain a comparable measure of the genetic diversity in different cat breeds.</span></p> <p><span>This study represents the first comprehensive exploration of informative Mendelian variants in felines by screening over 10,000 domestic cats. The results qualitatively contribute to the understanding of feline variant heritage and genetic diversity and demonstrate the clinical utility and importance of such information in supporting breeding programs and the research community. The work also highlights the crucial commitment of pedigreed cat breeders and registries in supporting the establishment of large genomic databases that when combined with phenotype information can advance scientific understanding and provide insights that can be applied to improve the health and welfare of cats.</span></p>
Data for "Genomic Epidemiology of Gonococcal Resistance to Extended-Spectrum Cephalosporins, Macrolides, and Fluoroquinolones in the United States, 2000-2013"
<p>Assemblies from https://www.ncbi.nlm.nih.gov/pubmed/27638945.</p>
Epidemiology and Genomic Surveillance of Staphylococcus Aureus in ICU Neonatology
ClinicalTrials.gov study NCT06267352. IPD Sharing: NO. Countries: 0. Publications: 1.
Genetic epidemiology of blood type, disease and trait variants, and genome-wide genetic diversity in over 11,000 domestic cats
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Data from: Genome-wide identification of host-segregating epidemiological markers for source attribution in Campylobacter jejuni
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Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the US.
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Genomics-based molecular epidemiology of human clinical and feedlot cattle C. jejuni isolates in Alberta, Canada
GEO Series GSE13228. Campylobacter jejuni; Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819. 119 samples. Type: Genome variation profiling by array.
Neonatal Enterovirus Infections in Italy: Virological Characterization, Genomic and Clinical-epidemiological Insights on Echovirus 11
ClinicalTrials.gov study NCT07356583. IPD Sharing: NO. Countries: 1. Publications: 0.
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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
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