ArticlePloS one2018
Impact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg.
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Seamless, rapid, and accurate analyses of outbreak genomic data using splitGenome research · 2024Article
- Combining analytical epidemiology and genomic surveillance to identify risk factors associated with the spread of antimicrobial resistance inMicrobial genomics · 2022Article
- A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires' Disease.Journal of clinical microbiology · 2021Article
- One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.PLoS computational biology · 2021Article
- Cereulide Synthetase Acquisition and Loss Events within the Evolutionary History of Group IIImBio · 2020Article
- Ceftiofur-resistantEpidemiology and infection · 2019Review
- Characterization of Emetic and DiarrhealFrontiers in microbiology · 2019Article
Corrections and comments
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Authors and funding
10 authors.
Funding
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Abstract
Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. The core genome single nucleotide variant pipeline (cgSNV) is one of several whole genome based sequence typing methods used for the laboratory investigation of foodborne pathogens. SNV detection using this method requires a reference genome. The purpose of this study was to investigate the impact of the choice of the reference genome on the cgSNV-informed phylogenetic clustering and inferred isolate relationships. We found that using a draft or closed genome of S. Heidelberg as reference did not impact the ability of the cgSNV methodology to differentiate among 145 S. Heidelberg isolates involved in foodborne outbreaks. We also found that using a distantly related genome such as S. Dublin as choice of reference led to a loss in resolution since some sporadic isolates were found to cluster together with outbreak isolates. In addition, the genetic distances between outbreak isolates as well as between outbreak and sporadic isolates were overall reduced when S. Dublin was used as the reference genome as opposed to S. Heidelberg.
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Registered trials
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