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SATICIOĞLU IB, DUMAN M, ALTUN S. Gökkuşağı Alabalıklarından Izole Edilen Chryseobacterium sp. C-204 Suşunun Fenotipik ve Genom Özelliklerinin Belirlenmesi. ACTA ACUST UNITED AC 2020. [DOI: 10.32707/ercivet.828829] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Cooper AL, Low AJ, Koziol AG, Thomas MC, Leclair D, Tamber S, Wong A, Blais BW, Carrillo CD. Systematic Evaluation of Whole Genome Sequence-Based Predictions of Salmonella Serotype and Antimicrobial Resistance. Front Microbiol 2020; 11:549. [PMID: 32318038 PMCID: PMC7147080 DOI: 10.3389/fmicb.2020.00549] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/13/2020] [Indexed: 01/21/2023] Open
Abstract
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.
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Affiliation(s)
- Ashley L Cooper
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Andrew J Low
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Adam G Koziol
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
| | - Matthew C Thomas
- Microbial Contaminants, Canadian Food Inspection Agency, Calgary, AB, Canada
| | - Daniel Leclair
- Ecotoxicology and Wildlife Health Division, Environment and Climate Change Canada, Ottawa, ON, Canada
| | - Sandeep Tamber
- Microbiology Research Division, Bureau of Microbial Hazards, Health Canada, Ottawa, ON, Canada
| | - Alex Wong
- Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Burton W Blais
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada.,Department of Biology, Carleton University, Ottawa, ON, Canada
| | - Catherine D Carrillo
- Research and Development, Ottawa Laboratory (Carling), Canadian Food Inspection Agency, Ottawa, ON, Canada
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