Please use this identifier to cite or link to this item:
doi:10.22028/D291-33737
Title: | Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates |
Author(s): | Galata, Valentina Laczny, Cédric C. Backes, Christina Hemmrich-Stanisak, Georg Schmolke, Susanne Franke, Andre Meese, Eckart Herrmann, Mathias von Müller, Lutz Plum, Achim Müller, Rolf Stähler, Cord Posch, Andreas E. Keller, Andreas |
Language: | English |
Title: | Genomics, Proteomics & Bioinformatics |
Volume: | 17 |
Issue: | 2 |
Pages: | 169-182 |
Publisher/Platform: | Elsevier |
Year of Publication: | 2019 |
Free key words: | Antibiotic resistance Whole-genome sequencing Bacteria Pan-genome |
DDC notations: | 500 Science 600 Technology |
Publikation type: | Journal Article |
Abstract: | Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com. |
DOI of the first publication: | 10.1016/j.gpb.2018.11.002 |
Link to this record: | urn:nbn:de:bsz:291--ds-337376 hdl:20.500.11880/31075 http://dx.doi.org/10.22028/D291-33737 |
ISSN: | 1672-0229 |
Date of registration: | 7-Apr-2021 |
Description of the related object: | Supplementary material |
Related object: | https://doi.org/10.1016/j.gpb.2018.11.002 |
Faculty: | M - Medizinische Fakultät NT - Naturwissenschaftlich- Technische Fakultät |
Department: | M - Humangenetik M - Medizinische Biometrie, Epidemiologie und medizinische Informatik NT - Pharmazie |
Professorship: | M - Prof. Dr. Eckhart Meese M - Univ.-Prof. Dr. Andreas Keller NT - Prof. Dr. Rolf Müller |
Collections: | SciDok - Der Wissenschaftsserver der Universität des Saarlandes |
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File | Description | Size | Format | |
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1-s2.0-S1672022919300920-main.pdf | 2,13 MB | Adobe PDF | View/Open |
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