ArticleJournal of bacteriology2014
Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons.
Article in Journal of bacteriology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Controlled Experimental Infection in Pigs with a Strain of Yersinia enterocolitica Harboring Genetic Markers for Human Pathogenicity: Colonization and Stability.Infection and immunity · 2023Article
- Invasive non-typhoidalFrontiers in microbiology · 2023Article
- Intestinal carriage of invasive non-typhoidalFrontiers in microbiology · 2023Article
- Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo.PLoS neglected tropical diseases · 2022Article
- High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo.PLoS neglected tropical diseases · 2020Article
- Non-typhoidal Salmonella intestinal carriage in a Schistosoma mansoni endemic community in a rural area of the Democratic Republic of Congo.PLoS neglected tropical diseases · 2020Article
- Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso.PLoS neglected tropical diseases · 2019Article
- In vivo passage of Salmonella Typhimurium results in minor mutations in the bacterial genome and increases in vitro invasiveness.Veterinary research · 2019Article
- Rise and fall of outbreak-specific clone inside endemic pulsotype ofEuro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2018Article
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- Phenotypic and Genotypic Eligible Methods forFrontiers in microbiology · 2017Review
- Whole genome sequencing of Salmonella Typhimurium illuminates distinct outbreaks caused by an endemic multi-locus variable number tandem repeat analysis type in Australia, 2014.BMC microbiology · 2016Article
- Evolution of Variable Number Tandem Repeats and Its Relationship with Genomic Diversity inFrontiers in microbiology · 2016Article
- Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage.Journal of clinical microbiology · 2015Article
- Multilocus variable-number tandem-repeat analysis of Neisseria meningitidis serogroup C in China.Epidemiology and infection · 2015Article
- A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium.Applied microbiology and biotechnology · 2015Article
- PCR melting profile as a tool for outbreak studies of Salmonella enterica in chickens.BMC veterinary research · 2015Article
- Studying Bordetella pertussis populations by use of SNPeX, a simple high-throughput single nucleotide polymorphism typing method.Journal of clinical microbiology · 2015Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Variable-number tandem repeats (VNTRs) mutate rapidly and can be useful markers for genotyping. While multilocus VNTR analysis (MLVA) is increasingly used in the detection and investigation of food-borne outbreaks caused by Salmonella enterica serovar Typhimurium (S. Typhimurium) and other bacterial pathogens, MLVA data analysis usually relies on simple clustering approaches that may lead to incorrect interpretations. Here, we estimated the rates of copy number change at each of the five loci commonly used for S. Typhimurium MLVA, during in vitro and in vivo passage. We found that loci STTR5, STTR6, and STTR10 changed during passage but STTR3 and STTR9 did not. Relative rates of change were consistent across in vitro and in vivo growth and could be accurately estimated from diversity measures of natural variation observed during large outbreaks. Using a set of 203 isolates from a series of linked outbreaks and whole-genome sequencing of 12 representative isolates, we assessed the accuracy and utility of several alternative methods for analyzing and interpreting S. Typhimurium MLVA data. We show that eBURST analysis was accurate and informative. For construction of MLVA-based trees, a novel distance metric, based on the geometric model of VNTR evolution coupled with locus-specific weights, performed better than the commonly used simple or categorical distance metrics. The data suggest that, for the purpose of identifying potential transmission clusters for further investigation, isolates whose profiles differ at one of the rapidly changing STTR5, STTR6, and STTR10 loci should be collapsed into the same cluster.
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