ArticleGenomics, proteomics & bioinformatics2019
Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates.
Article in Genomics, proteomics & bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
8 citing papers in PubMed.
- Investigating Combination Therapy as a Means to Enhance Activity and Repurpose Antimicrobials.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples.Antibiotics (Basel, Switzerland) · 2023Article
- A Metagenomic Approach for Characterizing Antibiotic Resistance Genes in Specific Bacterial Populations: Demonstration with Escherichia coli in Cattle Manure.Applied and environmental microbiology · 2022Article
- Antimicrobial Peptides: From Design to Clinical Application.Antibiotics (Basel, Switzerland) · 2022Review
- One Day in Denmark: Comparison of Phenotypic and Genotypic Antimicrobial Susceptibility Testing in Bacterial Isolates From Clinical Settings.Frontiers in microbiology · 2022Article
- Species Identification and Antibiotic Resistance Prediction by Analysis of Whole-Genome Sequence Data by Use of ARESdb: an Analysis of Isolates from the Unyvero Lower Respiratory Tract Infection Trial.Journal of clinical microbiology · 2020Article
- Innovative and rapid antimicrobial susceptibility testing systems.Nature reviews. Microbiology · 2020Review
- Clinical Resistome Screening of 1,110Frontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.