Dataset Information

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

ABSTRACT: In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

SUBMITTER: Shefchek KA

PROVIDER: S-EPMC7056945 | biostudies-literature | 2020 Jan

REPOSITORIES: biostudies-literature

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The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Shefchek Kent A KA Harris Nomi L NL Gargano Michael M Matentzoglu Nicolas N Unni Deepak D Brush Matthew M Keith Daniel D Conlin Tom T Vasilevsky Nicole N Zhang Xingmin Aaron XA Balhoff James P JP Babb Larry L Bello Susan M SM Blau Hannah H Bradford Yvonne Y Carbon Seth S Carmody Leigh L Chan Lauren E LE Cipriani Valentina V Cuzick Alayne A Della Rocca Maria M Dunn Nathan N Essaid Shahim S Fey Petra P Grove Chris C Gourdine Jean-Phillipe JP Hamosh Ada A Harris Midori M Helbig Ingo I Hoatlin Maureen M Joachimiak Marcin M Jupp Simon S Lett Kenneth B KB Lewis Suzanna E SE McNamara Craig C Pendlington Zoë M ZM Pilgrim Clare C Putman Tim T Ravanmehr Vida V Reese Justin J Riggs Erin E Robb Sofia S Roncaglia Paola P Seager James J Segerdell Erik E Similuk Morgan M Storm Andrea L AL Thaxon Courtney C Thessen Anne A Jacobsen Julius O B JOB McMurry Julie A JA Groza Tudor T Köhler Sebastian S Smedley Damian D Robinson Peter N PN Mungall Christopher J CJ Haendel Melissa A MA Munoz-Torres Monica C MC Osumi-Sutherland David D

Nucleic acids research 20200101 D1

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Init ...[more]

PMID: 31701156

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Project description:AimThis report presents phenotypic and genetic data on the prevalence and characteristics of extended-spectrum β-lactamases (ESBLs) and representative carbapenemases-producing Gram-negative species in Mexico.Material and methodsA total of 52 centers participated, 43 hospital-based laboratories and 9 external laboratories. The distribution of antimicrobial resistance data for Escherichia coli, Klebsiella pneumoniae, Enterobacter cloacae complex, Acinetobacter baumannii complex, and Pseudomonas aeruginosa in selected clinical specimens from January 1 to March 31, 2020 was analyzed using the WHONET 5.6 platform. The following clinical isolates recovered from selected specimens were included: carbapenem-resistant Enterobacteriaceae, ESBL or carbapenem-resistant E. coli, and K. pneumoniae, carbapenem-resistant A. baumannii complex, and P. aeruginosa. Strains were genotyped to detect ESBL and/or carbapenemase-encoding genes.ResultsAmong blood isolates, A. baumannii complex showed more than 68% resistance for all antibiotics tested, and among Enterobacteria, E. cloacae complex showed higher resistance to carbapenems. A. baumannii complex showed a higher resistance pattern for respiratory specimens, with only amikacin having a resistance lower than 70%. Among K. pneumoniae isolates, blaTEM, blaSHV, and blaCTX were detected in 68.79%, 72.3%, and 91.9% of isolates, respectively. Among E. coli isolates, blaTEM, blaSHV, and blaCTX were detected in 20.8%, 4.53%, and 85.7% isolates, respectively. For both species, the most frequent genotype was blaCTX-M-15. Among Enterobacteriaceae, the most frequently detected carbapenemase-encoding gene was blaNDM-1 (81.5%), followed by blaOXA-232 (14.8%) and blaoxa-181(7.4%), in A. baumannii was blaOXA-24 (76%) and in P. aeruginosa, was blaIMP (25.3%), followed by blaGES and blaVIM (13.1% each).ConclusionOur study reports that NDM-1 is the most frequent carbapenemase-encoding gene in Mexico in Enterobacteriaceae with the circulation of the oxacillinase genes 181 and 232. KPC, in contrast to other countries in Latin America and the USA, is a rare occurrence. Additionally, a high circulation of ESBL blaCTX-M-15 exists in both E. coli and K. pneumoniae.

Dataset Information

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Publications

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

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