دورية أكاديمية

Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance

التفاصيل البيبلوغرافية
العنوان: Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance
المؤلفون: Ashley L. Cooper, Andrew J. Low, Adam G. Koziol, Matthew C. Thomas, Daniel Leclair, Sandeep Tamber, Alex Wong, Burton W. Blais, Catherine D. Carrillo
المصدر: Frontiers in Microbiology, Vol 11 (2020)
بيانات النشر: Frontiers Media S.A., 2020.
سنة النشر: 2020
المجموعة: LCC:Microbiology
مصطلحات موضوعية: Salmonella, antimicrobial resistance, serotyping, whole-genome sequence, nuoF, phenotype, Microbiology, QR1-502
الوصف: Whole-genome sequencing (WGS) is used increasingly in public-health laboratories for typing and characterizing foodborne pathogens. To evaluate the performance of existing bioinformatic tools for in silico prediction of antimicrobial resistance (AMR) and serotypes of Salmonella enterica, WGS-based genotype predictions were compared with the results of traditional phenotyping assays. A total of 111 S. enterica isolates recovered from a Canadian baseline study on broiler chicken conducted in 2012-2013 were selected based on phenotypic resistance to 15 different antibiotics and isolates were subjected to WGS. Both SeqSero2 and SISTR accurately determined S. enterica serotypes, with full matches to laboratory results for 87.4 and 89.2% of isolates, respectively, and partial matches for the remaining isolates. Antimicrobial resistance genes (ARGs) were identified using several bioinformatics tools including the Comprehensive Antibiotic Resistance Database – Resistance Gene Identifier (CARD-RGI), Center for Genomic Epidemiology (CGE) ResFinder web tool, Short Read Sequence Typing for Bacterial Pathogens (SRST2 v 0.2.0), and k-mer alignment method (KMA v 1.17). All ARG identification tools had ≥ 99% accuracy for predicting resistance to all antibiotics tested except streptomycin (accuracy 94.6%). Evaluation of ARG detection in assembled versus raw-read WGS data found minimal observable differences that were gene- and coverage- dependent. Where initial phenotypic results indicated isolates were sensitive, yet ARGs were detected, repeat AMR testing corrected discrepancies. All tools failed to find resistance-determining genes for one gentamicin- and two streptomycin-resistant isolates. Further investigation found a single nucleotide polymorphism (SNP) in the nuoF coding region of one of the isolates which may be responsible for the observed streptomycin-resistant phenotype. Overall, WGS-based predictions of AMR and serotype were highly concordant with phenotype determination regardless of computational approach used.
نوع الوثيقة: article
وصف الملف: electronic resource
اللغة: English
تدمد: 1664-302X
Relation: https://www.frontiersin.org/article/10.3389/fmicb.2020.00549/full; https://doaj.org/toc/1664-302X
DOI: 10.3389/fmicb.2020.00549
URL الوصول: https://doaj.org/article/13f9084bb9c149cea8a60f7e25643ced
رقم الأكسشن: edsdoj.13f9084bb9c149cea8a60f7e25643ced
قاعدة البيانات: Directory of Open Access Journals
الوصف
تدمد:1664302X
DOI:10.3389/fmicb.2020.00549