lunes, 7 de diciembre de 2015

Advanced Molecular Detection Clips || Public Health Genomics Knowledge Base (v1.0)

Public Health Genomics Knowledge Base (v1.0)

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Advanced Molecular Detection Clips

Public Health Genomics Knowledge Base

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The utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks. A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.




EVENTS / TRAINING / WEB RESOURCES

METHODS / TOOLS

EVOLUTION / ECOLOGY / POPULATIONS

PATHOGENICITY / ANTIMICROBIAL RESISTANCE

DETECTION / DIAGNOSIS

EPIDEMIOLOGY / OUTBREAKS / TRANSMISSION

ANTIMICROBIALS / VACCINES / INTERVENTIONS

Public Health Genomics Knowledge Base (v1.0)

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