Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates.
Antibiotic resistance
Bacteria
Pan-genome
Whole-genome sequencing
Journal
Genomics, proteomics & bioinformatics
ISSN: 2210-3244
Titre abrégé: Genomics Proteomics Bioinformatics
Pays: China
ID NLM: 101197608
Informations de publication
Date de publication:
04 2019
04 2019
Historique:
received:
04
06
2018
revised:
09
10
2018
accepted:
07
11
2018
pubmed:
18
5
2019
medline:
18
10
2019
entrez:
18
5
2019
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 31100356
pii: S1672-0229(19)30092-0
doi: 10.1016/j.gpb.2018.11.002
pmc: PMC6624217
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
169-182Informations de copyright
Copyright © 2019 The Authors. Production and hosting by Elsevier B.V. All rights reserved.
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