Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks Bacteriology

Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We performed a prospective pilot study to evaluate the analysis of methicillin-resistant Staphylococcus aureus (MRSA) genomes using the Next Gen Diagnostics (NGD) automated bioinformatics system. Seventeen unselected MRSA-positive patients were identified in a clinical microbiology laboratory in England over a period of 2 weeks in 2018, and 1 MRSA isolate per case was sequenced on the Illumina MiniSeq instrument. The NGD system automatically activated after sequencing and processed fastq folders to determine species, multilocus sequence type, the presence of a mec gene, antibiotic susceptibility predictions, and genetic relatedness based on mapping to a reference MRSA genome and detection of pairwise core genome single-nucleotide polymorphisms. The NGD system required 90 s per sample to automatically analyze data from each run, the results of which were automatically displayed. The same data were independently analyzed using a research-based approach. There was full concordance between the two analysis methods regarding species (S. aureus), detection of mecA, sequence type assignment, and detection of genetic determinants of resistance. Both analysis methods identified two MRSA clusters based on relatedness, one of which contained 3 cases that were i...
Source: Journal of Clinical Microbiology - Category: Microbiology Authors: Tags: Bacteriology Source Type: research

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Source: Expert Review of Anti-Infective Therapy - Category: Infectious Diseases Tags: Expert Rev Anti Infect Ther Source Type: research
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Source: New Zealand Medical Journal - Category: General Medicine Tags: N Z Med J Source Type: research
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Source: Expert Opinion on Pharmacotherapy - Category: Drugs & Pharmacology Tags: Expert Opin Pharmacother Source Type: research
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Source: Journal of Functional Foods - Category: Nutrition Source Type: research
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Source: Daily Express - Health - Category: Consumer Health News Source Type: news
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Source: Journal of Clinical Neurology - Category: Neurology Tags: J Clin Neurol Source Type: research
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Source: World Journal of Hepatology - Category: Gastroenterology Tags: World J Hepatol Source Type: research
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Source: Annals of Hepatology - Category: Gastroenterology Tags: Ann Hepatol Source Type: research
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Source: The Journal of Allergy and Clinical Immunology: In Practice - Category: Allergy & Immunology Source Type: research
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Source: Expert Review of Endocrinology and Metabolism - Category: Endocrinology Tags: Expert Rev Endocrinol Metab Source Type: research
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