57 datasets

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1. NCL Data2026 · Genome sequencing

   <p>Delamanid (DLM) and pretomanid (Pa) minimum inhibitory concentrations (MICs), genomic variants, lineage, and clinical characteristics of 17 <i>Mycobacterium tuberculosis</i> isolates included in the study.</p>

   <p>Delamanid (DLM) and pretomanid (Pa) minimum inhibitory concentrations (MICs), genomic variants, lineage, and clinical characteristics of 17 <i>Mycobacterium tuberculosis</i> isolates included in the study.</p>

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2. Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Genome sequencing

   MRSP WGS-AST boundary benchmark: reproducibility package (revision version)

   MRSP WGS-AST boundary benchmark: reproducibility package (revision version). Reproducibility package for the Microbial Genomics manuscript MGEN-D-26-00487 (de Souza and Santoro): Staphylococcus pseudintermedius whole-genome sequencing antimicrobial susceptibility boundary benchmark with a training-only-dictionary pangenome projection, restricted-shell model inputs, frozen prediction chains and out

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3. figshare + Loughborough Research Repository + GRANTS Data + UP Research Data Repository2026 · Genome sequencing

   Data Sheet 1_Comparative genomic analysis of Staphylococcus spp. and Mammaliicoccus sciuri suggests potential sharing between dogs and their owners.pdf

   Introduction<p>Staphylococci are a diverse group of bacteria commonly found on the skin and mucosal surfaces of humans and animals. Members of the genus can transition from commensalism to opportunistic pathogenicity. The extent to which close contact facilitates transmission of staphylococci remains misunderstood, particularly at the genomic level. In this context, the present study aimed to inve

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4. ZivaHub + Deakin Research Online + DMU Figshare2026 · Genome sequencing

   A study of the bacterial ecology of a chocolate ingredient production environment and characterisation of Salmonella species a zoonotic food-borne bacteria of importance to this food industry

   The safe production of chocolate is a critical issue to both the consumer and the brand, requiring the application of Hazard Analysis Critical Control Points (HACCP) system across the production process. These production environments are challenged on occasion with different hazards of importance to food safety. Control of bacterial hazards as exemplified by pathogenic bacteria like Salmonella is

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5. ZivaHub + Deakin Research Online + DMU Figshare2026 · Genome sequencing · unknown

   Bovine TB: reconstructing the molecular evolution of Mycobacterium bovis

   Bovine tuberculosis (bTB), caused by Mycobacterium bovis, remains a significant challenge in Ireland, affecting cattle, wildlife, and agricultural trade despite decades of control measures. This thesis employs genomic tools to enhance our understanding of M. bovis evolution and epidemiology, with the goal of refining bTB surveillance and management strategies. By integrating whole-genome sequence

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   Genome sequencing · mapped from keyword“WGS”

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6. ZivaHub + Deakin Research Online + DMU Figshare2026 · Genome sequencing

   Levofloxacin: reducing the risk of Pseudomonas aeruginosa resistance

   <i>Pseudomonas aeruginosa</i> (<i>P. aeruginosa</i>) is a common cause of airway infections in people with cystic fibrosis (pwCF). Nebulised levofloxacin is the latest inhaled antibiotic available to manage chronic <i>P. aeruginosa</i> infections in pwCF. Little data is currently available on how this therapy is practically used in CF clinics or how <i>P. aeruginosa</i> isolates respond to levoflo

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7. HKU DataHub + figshare + Loughborough Research Repository + UP Research Data Repository2026 · Genome sequencing

   Table 1_Genomic characteristics of a carbapenem-resistant NDM-1-producing Aeromonas caviae isolate from extraintestinal infection.xlsx

   Objective<p>This study aims to clarify the drug resistance characteristics and genomic background of bile-derived NDM-1-producing Aeromonas caviae (A. caviae) isolate from extraintestinal infection, providing a theoretical basis for the prevention and control of clinical infections.</p>Methods<p>A bile-derived LHL25108073-A. caviae isolate (NCBI accession number: JBSUSV000000000) was chosen as the

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8. HKU DataHub + figshare + Loughborough Research Repository + UP Research Data Repository2026 · Genome sequencing

   Table 2_Genomic characteristics of a carbapenem-resistant NDM-1-producing Aeromonas caviae isolate from extraintestinal infection.xlsx

   Objective<p>This study aims to clarify the drug resistance characteristics and genomic background of bile-derived NDM-1-producing Aeromonas caviae (A. caviae) isolate from extraintestinal infection, providing a theoretical basis for the prevention and control of clinical infections.</p>Methods<p>A bile-derived LHL25108073-A. caviae isolate (NCBI accession number: JBSUSV000000000) was chosen as the

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9. HKU DataHub + figshare + Loughborough Research Repository + UP Research Data Repository2026 · Genome sequencing

   Table 3_Genomic characteristics of a carbapenem-resistant NDM-1-producing Aeromonas caviae isolate from extraintestinal infection.xlsx

   Objective<p>This study aims to clarify the drug resistance characteristics and genomic background of bile-derived NDM-1-producing Aeromonas caviae (A. caviae) isolate from extraintestinal infection, providing a theoretical basis for the prevention and control of clinical infections.</p>Methods<p>A bile-derived LHL25108073-A. caviae isolate (NCBI accession number: JBSUSV000000000) was chosen as the

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10. HKU DataHub + figshare + Loughborough Research Repository2026 · Genome sequencing

    Supplementary file 1_Genomic insight into the antibiotic-resistant determinants of Escherichia coli from small ruminants and manure in North West Province, South Africa.docx

    Introduction<p>Livestock-associated Escherichia coli are important reservoirs of antimicrobial resistance and virulence determinants, yet comprehensive genomic data describing their genomic diversity and antibiotic resistance in South African small-ruminant production systems remain limited.</p>Objective<p>Whole-genome sequencing was performed on 19 E. coli isolates recovered from sheep, goats, an

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11. ZivaHub + HKU DataHub + figshare + Loughborough Research Repository + UP Research Data Repository2026 · Genome sequencing

    RefSeq viral genomes database for mashID - RefSeq release 237 (2026-09-28)

    <p dir="ltr">Mash sketch database of all viral genomes in NCBI RefSeq release 237 for virus identification and prophage or viral contamination detection with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- refseq_viral_r237_2026-09-28.msh: Mash 2.3 sketches, k-mer size 21, sketch size 2000, 19,625 RefSeq viral records (complete genomes and genome segments;

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12. HKU DataHub + figshare + Loughborough Research Repository2026 · Genome sequencing

    Supporting data for genome sequence and phenotypic datasets for three calf-associated Parabacteroides isolates

    <p dir="ltr">This dataset contains supporting data files for the Data note entitled “Genome sequence and phenotypic datasets for three calf-associated <i>Parabacteroides </i>isolates.” The files provide processed genomic, comparative genomic, antimicrobial resistance screening, visualization, and methodology resources for <i>Parabacteroides </i>sp. KHUB-01, KHUB-02, and KHUB-03, which were recover

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13. figshare + Loughborough Research Repository2026 · Genome sequencing

    Table 1_Genomic and phenotypic characterization of a multidrug-resistant Pseudomonas putida strain associated with skin ulceration disease in farmed sea cucumbers (Apostichopus japonicus).xlsx

    <p>Skin ulceration disease (SUD) increasingly threatens sea cucumber (Apostichopus japonicus) aquaculture. In this study, we isolated and characterized the associated pathogen from diseased sea cucumbers using phenotypic and whole-genome analyses. Naturally infected individuals exhibited white ulcer spots, evisceration, and tissue disintegration. Multiple strains were isolated and identified as Ps

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14. figshare + Loughborough Research Repository2026 · Genome sequencing

    Supplementary file 1_Genomic and phenotypic characterization of a multidrug-resistant Pseudomonas putida strain associated with skin ulceration disease in farmed sea cucumbers (Apostichopus japonicus).docx

    <p>Skin ulceration disease (SUD) increasingly threatens sea cucumber (Apostichopus japonicus) aquaculture. In this study, we isolated and characterized the associated pathogen from diseased sea cucumbers using phenotypic and whole-genome analyses. Naturally infected individuals exhibited white ulcer spots, evisceration, and tissue disintegration. Multiple strains were isolated and identified as Ps

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15. figshare + Loughborough Research Repository2026 · Genome sequencing

    Escherichia and Shigella database for mashID - 2026-09-22

    <p dir="ltr">Mash sketch database of the genera Escherichia (NCBI taxon 561) and Shigella (taxon 620) for species-level identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- escherichia_shigella_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 4503 reference genomes: Escherichia coli (3316), E. albertii, E. fergusonii, E. m

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16. figshare + Loughborough Research Repository2026 · Genome sequencing

    Brucella database for mashID - 2026-09-22

    <p dir="ltr">Mash sketch database of the genus Brucella (NCBI taxon 234), including the species formerly classified as Ochrobactrum, for species-level identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- brucella_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 387 reference genomes covering 29 Brucella species (31 MB). MD

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17. figshare + Loughborough Research Repository2026 · Genome sequencing

    BAG_WGS SummaryData

    <p dir="ltr">Genome-wide association summary statistics for organ-specific biological aging phenotypes across 17 human organs, derived from whole-genome sequencing data in the UK Biobank.</p>

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18. figshare + Loughborough Research Repository2026 · Genome sequencing

    proGenomes 4 representative genomes database for mashID - 2026-09-22

    <p dir="ltr">Mash sketch database of the proGenomes 4 representative genomes (https://progenomes.embl.de) for species-level identification of bacteria and archaea with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- progenomes4_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 2000, 32,887 representative genomes, one per proGenomes species clust

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19. figshare + Loughborough Research Repository2026 · Genome sequencing

    Salmonella database for mashID - 2026-09-22

    <p dir="ltr">Mash sketch database of the genus Salmonella (NCBI taxon 590) for species- and subspecies-level identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- salmonella_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 1442 reference genomes covering Salmonella bongori and all six subspecies of Salmonella enterica (116

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20. figshare + Loughborough Research Repository2026 · Genome sequencing

    Mycobacteriaceae database for mashID - 2026-09-22 update

    <p dir="ltr">Mash sketch database of the family Mycobacteriaceae (NCBI taxon 1762) for species identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- mycobacteriaceae_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 3534 reference genomes (284 MB). MD5: cc73df8b8b5f7257849c6039430f2a43</p><p dir="ltr">- mycobacteriaceae_2026

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21. figshare + Loughborough Research Repository2026 · Genome sequencing

    Listeria database for mashID - 2026-09-22 update

    <p dir="ltr">Mash sketch database of the genus Listeria (NCBI taxon 1637) for species identification with mashID (https://github.com/duceppemo/mashID).</p><p dir="ltr">Contents</p><p dir="ltr">- listeria_2026-09-22.msh: Mash 2.3 sketches, k-mer size 21, sketch size 10000, 1441 reference genomes covering 42 Listeria species and subspecies (116 MB). MD5: 4d0f8f53d71dbcea526508f1b246ab2f</p><p dir="l

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22. figshare2026 · Genome sequencing

    Table 1_Survey-based risk factors and genomic characterization of oral and oropharyngeal Enterobacterales carriage in humans and companion animals: a One Health study.docx

    <p>Antimicrobial-resistant (AMR) Enterobacterales, including extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing organisms, represent an important One Health concern involving humans, animals, and shared environments. This cross-sectional study evaluated survey-based risk factors for oral and oropharyngeal Enterobacterales carriage in humans and companion animals and characterized

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23. figshare2026 · Genome sequencing

    Table 1_The endophyte Fusarium oxysporum 3RR genome analysis identifies bioactive compounds targeting biofilm formation.docx

    Introduction<p>The rising global challenge of antimicrobial resistance and biofilm-associated infections necessitates the discovery of novel bioactive compounds. Endophytic fungi, recognized for their metabolic versatility and ecological adaptability, represent a promising, yet underexplored, source of such molecules. This study aimed to comprehensively characterize the biosynthetic potential of F

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24. figshare2026 · Genome sequencing

    Genetic findings and clinical features of extreme refractive errors in Thai children using whole genome sequencing

    <p>Extreme refractive errors in children may indicate underlying genetic or syndromic conditions. This study investigated the genetic basis of high refractive errors in Thai children and compared clinical characteristics between high myopia and high hyperopia, and identified clinical predictors of a positive genetic result.</p> <p>Ninety-eight children (<18 years) with high refractive errors were

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25. figshare2026 · Genome sequencing

    <p>A spreadsheet in CSV format (file downloadable separately), providing the raw data for the experimental measurements of each of 123 sequences generated using genomic data from <i>E. coli.</i></p>

    <p>The sheet provides the measured fluorescence from each sequence when a plasmid containing the sequence was transformed into <i>E. coli</i> and when the same plasmid was transformed into <i>L. reuteri.</i></p> <p>(CSV)</p>

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    Genome sequencing · mapped from keyword“genomic data”