ArticleJournal of clinical microbiology2016
Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations.
Article in Journal of clinical microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Article
- Genomic analysis of Salmonella Heidelberg isolated from the Brazilian poultry farms.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Outbreak detection in Harar town and Kersa district, Ethiopia using phylogenetic analysis and source attribution.BMC infectious diseases · 2024Article
- DODGE: automated point source bacterial outbreak detection using cumulative long term genomic surveillance.Bioinformatics (Oxford, England) · 2024Article
- Application of Next-Generation Sequencing to Enterobacter Hormaechei Subspecies Analysis during a Neonatal Intensive Care Unit Outbreak.Children (Basel, Switzerland) · 2023Article
- Oxford nanopore technologies-a valuable tool to generate whole-genome sequencing data forFrontiers in veterinary science · 2023Article
- Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance inMicrobial genomics · 2022Article
- Whole-genome sequence analysis of Clostridium chauvoei isolated from clinical case of black quarter (BQ) from India.Archives of microbiology · 2022Article
- Evaluation of whole-genome sequencing-based subtyping methods for the surveillance ofMicrobial genomics · 2021Article
- Article
- Enhancing genomics-based outbreak detection of endemicMicrobial genomics · 2021Article
- ProspectiveEpidemiology and infection · 2020Article
- Source Tracking Based on Core Genome SNV and CRISPR Typing ofFrontiers in microbiology · 2020Article
- Ceftiofur-resistantEpidemiology and infection · 2019Review
- Multidrug-ResistantJournal of food protection · 2019Article
- Status and potential of bacterial genomics for public health practice: a scoping review.Implementation science : IS · 2019Article
- A core genome approach that enables prospective and dynamic monitoring of infectious outbreaks.Scientific reports · 2019Article
- Article
- Shared genome analyses of notable listeriosis outbreaks, highlighting the critical importance of epidemiological evidence, input datasets and interpretation criteria.Microbial genomics · 2019Article
- Whole genome sequencing ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2019Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Salmonella enterica serovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for common Salmonella serovars, such as S. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonal S. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.
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