دورية أكاديمية
أعرض في EDS

Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae.

التفاصيل البيبلوغرافية
العنوان: Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae.
المؤلفون: Vieira AA; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil., Piccoli BC; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil., Y Castro TR; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil., Casarin BC; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil., Tessele LF; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil., Martins RCR; Laboratório de Parasitologia Médica (LIM-46), Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical da Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, 01246-903, Brazil., Schwarzbold AV; Departamento de Clínica Médica, Universidade Federal de Santa Maria, Rio Grande do Sul, Brazil., Trindade PA; Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil. priscila.trindade@ufsm.br.
المصدر: Scientific reports [Sci Rep] 2023 Sep 14; Vol. 13 (1), pp. 15189. Date of Electronic Publication: 2023 Sep 14.
نوع المنشور: Journal Article; Research Support, Non-U.S. Gov't
اللغة: English
بيانات الدورية: Publisher: Nature Publishing Group Country of Publication: England NLM ID: 101563288 Publication Model: Electronic Cited Medium: Internet ISSN: 2045-2322 (Electronic) Linking ISSN: 20452322 NLM ISO Abbreviation: Sci Rep Subsets: MEDLINE
أسماء مطبوعة: Original Publication: London : Nature Publishing Group, copyright 2011-
مواضيع طبية MeSH: Klebsiella pneumoniae*/genetics , Carbapenem-Resistant Enterobacteriaceae*/genetics, Reproducibility of Results ; Benchmarking ; Carbapenems/pharmacology
مستخلص: Antimicrobial-resistant Klebsiella pneumoniae is a global threat to healthcare and an important cause of nosocomial infections. Antimicrobial resistance causes prolonged treatment periods, high mortality rates, and economic impacts. Whole Genome Sequencing (WGS) has been used in laboratory diagnosis, but there is limited evidence about pipeline validation to parse generated data. Thus, the present study aimed to validate a bioinformatics pipeline for the identification of antimicrobial resistance genes from carbapenem-resistant K. pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome, and annotated. Contigs were submitted to different tools for bacterial (Kraken2 and SpeciesFinder) and antimicrobial resistance gene identification (ResFinder and ABRicate). We analyzed 201 K. pneumoniae genomes. In the bacterial identification by Kraken2, all samples were correctly identified, and in SpeciesFinder, 92.54% were correctly identified as K. pneumoniae, 6.96% erroneously as Pseudomonas aeruginosa, and 0.5% erroneously as Citrobacter freundii. ResFinder found a greater number of antimicrobial resistance genes than ABRicate; however, many were identified more than once in the same sample. All tools presented 100% repeatability and reproducibility and > 75% performance in other metrics. Kraken2 was more assertive in recognizing bacterial species, and SpeciesFinder may need improvements.
(© 2023. Springer Nature Limited.)
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المشرفين على المادة: 0 (Carbapenems)
تواريخ الأحداث: Date Created: 20230914 Date Completed: 20230918 Latest Revision: 20231121
رمز التحديث: 20231215
مُعرف محوري في PubMed: PMC10502106
DOI: 10.1038/s41598-023-42154-6
PMID: 37709838
قاعدة البيانات: MEDLINE
الوصف
تدمد:2045-2322
DOI:10.1038/s41598-023-42154-6