Multilocus variable-number tandem-repeat analysis for subtypingSalmonella entericaserovar Gallinarum

Kang, Min; Kwon, Yong-Kuk; Oh, Jae Young; Call, Douglas R.; An, Byung-Ki; Song, Eun A; Kim, Jeong Y.; Shin, Eun G.; Kim, Mi J.; Kwon, Jun-Hun; Chung, Gab S.

doi:10.1080/03079457.2011.613915

Cited by 10 publications

(4 citation statements)

References 26 publications

(25 reference statements)

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“…Since repeat lengths in STTR3 can differ, this locus is sometimes expressed using allele codes as presented in reference 8 or as the total size in base pairs. Similar schemes are also in use or development for other S. enterica serovars, including Enteritidis, Gallinarum, Heidelberg, Dublin, and Typhi (12)(13)(14)(15)(16)(17)(18), and almost a hundred papers reported the use of MLVA for Salmonella analysis between 2004 and 2013 (see the supplemental material).…”

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confidence: 99%

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

et al. 2014

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c 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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confidence: 99%

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

et al. 2014

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“…This protein is considered essential; however, its gene length varies between serovars [25] and a VNTR (variable number tandem repeat, named STTR7) is located within the gene, which is used in MLVA schemes in several serovars but not in S. enterica Typhimurium [26, 27].…”

Section: Resultsmentioning

confidence: 99%

“…The second is a 195 bp in-frame deletion in the variable PQ repeat region found in the ftsK gene, which functions in cell division. This protein is considered essential; however, its gene length varies between serovars [25] and a VNTR (variable number tandem repeat, named STTR7) is located within the gene, which is used in MLVA schemes in several serovars but not in S. enterica Typhimurium [26,27].…”

Section: Utility Of Complete Sequencing In Genomic Surveillancementioning

confidence: 99%

Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds

et al. 2021

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Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These findings have general applicability to outbreak detection of bacterial pathogens.

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“…MLVA exhibited sufficient discriminatory power in both Brucella isolates from cattle and S. Gallinarum isolates from chickens in Korea [ 15 , 17 ]. However, by MLVA alone, Salmonella 4,[5],12:i:- cannot be distinguished from the S. Typhimurium cluster, because of the close genetic relationship between the two serovars.…”

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confidence: 99%

Characterization of Salmonella enterica serovar Typhimurium and Salmonella enterica serovar 4,[5],12:i:- isolates from pigs presenting with diarrhea in Korea

Lee

Choi³

et al. 2015

The Journal of Veterinary Medical Science

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Between 2011 and 2012, a total of 896 pig fecal samples were collected from nine provinces in Korea, and 50 salmonella enterica susp. enterica serovar Typhimurium (S. Typhimurium) was isolated. The characteristics of the 50 strains were analyzed, and 4 strains were identified as Salmonella enterica subsp. enterica serovar 4,[5],12:i:-. Salmonella 4,[5],12:i:- could not be distinguished from S. Typhimurium through phage typing, antimicrobial resistance testing or multiple-locus variable-number tandem repeat analysis (MLVA). However, among the four Salmonella 4,[5],12:i:- strains, one (KVCC-BA1400078) was identified as a Salmonella 4,[5],12:i:- clone isolated from humans in the United States, and another (KVCC-BA1400080) was identified as DT193, which has been primarily isolated from humans and animals in European countries. The presence of Salmonella 4,[5],12:i:- in Korea poses a significant threat of horizontal transfer between pigs and humans.

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Multilocus variable-number tandem-repeat analysis for subtypingSalmonella entericaserovar Gallinarum

Cited by 10 publications

References 26 publications

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

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

Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds

Characterization of <i>Salmonella enterica</i> serovar Typhimurium and <i>Salmonella enterica</i> serovar 4,[5],12:i:- isolates from pigs presenting with diarrhea in Korea

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