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primary topic: Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes

Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes
type: AcademicArticle
type: Article
abstract: Introduction: Antimicrobial susceptibility testing (AST) is used to determine the susceptibility of an organism to antibiotics. The determination of susceptibility is based on MIC breakpoints and is provided by EUCAST and CLSI. Likewise, phenotypic classification criteria developed by CDC/ECDC are used for the classification of pathogens into susceptible, multidrug-resistant, extremely drug-resistant, or totally drug-resistant categories. Whole-genome sequencing (WGS)-based diagnosis is now supplementing existing gold-standard microbiology methods for rapid and more precise AST, and therefore, EUCAST recommended quality criteria to assess whole-genome sequence for reporting the same. In this study, these three global standards, MIC breakpoints, phenotypic classification, and genome quality, are applied to the largest publicly available data for Acinetobacter baumannii (AB), the most critical priority pathogen identified by WHO. Materials and Methods: The drug sensitivity profile and genomes for isolates of AB were obtained from PATRIC and evaluated with respect to AST standards (CLSI and EUCAST). Whole genome quality assessment and antimicrobial resistance mapping is performed with QUAST and ABRicate, respectively. Four in-house methods are developed for mapping standards and are integrated into a Galaxy workflow based system, Galaxy-ASIST. Analysis of the extent of agreement between CLSI 2022 and EUCAST 2022 for antibiotics was carried out using Cohen's kappa statistics. Results and Discussion: An automated pipeline, Galaxy-ASIST, is designed and developed for the characterization of clinical isolates based on these standards. Evaluation of over 6,500 AB strains using Galaxy-ASIST indicated that only 10% of the publicly available datasets have metadata to implement these standards. Furthermore, given that CLSI and EUCAST have different MIC breakpoints, discrepancies are observed in the classification of resistant and susceptible isolates following these standards. …
date: 2023-01-27
volume: 13
status: peerReviewed
status: published
author list: authors
type: EPrint
type: ArticleEPrint
is part of: repository
subject: QR Microbiology

Frontiers Media SA
type: Organization

Front. Microbiol.
type: Collection

Rakesh Kumar
type: Person
given name: Rakesh
family name: Kumar

Anshu Bhardwaj
type: Person
given name: Anshu
family name: Bhardwaj

Jasmeer Singh Kalra
type: Person
given name: Jasmeer Singh
family name: Kalra

Shreya Singh
type: Person
given name: Shreya
family name: Singh

Tina Sharma
type: Person
given name: Tina
family name: Sharma

Gurpreet Singh Bhalla
type: Person
given name: Gurpreet Singh
family name: Bhalla

HTML Summary of #3391 Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes
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primary topic: Galaxy ASIST: A web-based platform for mapping and assessment of global standards of antimicrobial susceptibility: A case study in Acinetobacter baumannii genomes

QR Microbiology
type: Concept