Use of multilocus variable-number tandem repeat analysis in molecular subtyping of Salmonella enterica serovar Typhi isolates

Tien, Yung-Yen; Ushijima, Hiroshi; Mizuguchi, Masashi; Liang, Shiu-Yun; Chiou, Chien-Shun

doi:10.1099/jmm.0.037291-0

Cited by 14 publications

(17 citation statements)

References 31 publications

(28 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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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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“…PFGE has been adopted as the standard subtyping tool in the PulseNet food-borne disease surveillance network (7,8). The MLVA typing scheme based on rapidly evolving VNTR loci is more discriminatory than PFGE in discerning very closely related strains of S. Typhi and other bacterial organisms (3,5,6,9). However, both methods seem to be too discriminatory for S. Typhi in these 3 outbreaks; the use of PFGE and MLVA data alone would exclude the epidemiological association of the cases from the corresponding outbreak.…”

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Salmonella enterica Serovar Typhi Variants in Long-Term Carriers

Chiou

Wei²,

Mu³

et al. 2013

J Clin Microbiol

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“…Clonal relationships among isolates. The genetic relatedness among the S. Typhi isolates was assessed based on PFGE patterns and MLVA5 profiles resulting from an analysis of 5 less-variable VNTRs (Sty2, Sty3, Sty20, Sty39, and Sty42) (22). The dendrogram in Fig.…”

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“…PFGE images were recorded digitally in tiff file format, using a Gel Logic 212 Pro imaging system (Carestream Health Inc., Rochester, NY). A previously described multilocus variable-number tandem-repeat analysis (MLVA) protocol (22) was used to characterize the S. Typhi isolates. To investigate the phylogenetic relationships among the 19 S. Typhi strains described by Holt et al (23) and the prevalent MDR strains from Bangladesh and Vietnam, two MDR strains from Bangladesh, Bd1380 (antibiogram type A11) and Bd1980 (type A2), were subjected to whole-genome sequencing using the Ion Torrent platform, which was performed by a local biotechnology company.…”

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Antimicrobial Resistance in Salmonella enterica Serovar Typhi Isolates from Bangladesh, Indonesia, Taiwan, and Vietnam

Chiou

Lauderdale

Phung

et al. 2014

Antimicrob Agents Chemother

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We characterized Salmonella enterica serovar Typhi isolates from Bangladesh, Indonesia, Taiwan, and Vietnam to investigate their genetic relatedness and antimicrobial resistance. The isolates from Bangladesh and Vietnam were genetically closely related but were distant from those from Indonesia and Taiwan. All but a few isolates from Indonesia and Taiwan were susceptible to all antimicrobials tested. The majority of isolates from Bangladesh and Vietnam were multidrug resistant (MDR) and belonged to the widespread haplotype H58 clone. IncHI1 plasmids were detected in all MDR S. Typhi isolates from Vietnam but in only 15% of MDR isolates from Bangladesh. Resistance genes in the majority of MDR S. Typhi isolates from Bangladesh should reside in the chromosome. Among the isolates from Bangladesh, 82% and 40% were resistant to various concentrations of nalidixic acid and ciprofloxacin, respectively. Several resistance mechanisms, including alterations in gyrase A, the presence of QnrS, and enhanced efflux pumps, were involved in the reduced susceptibility and resistance to fluoroquinolones. Intensive surveillance is necessary to monitor the spread of chromosome-mediated MDR and fluoroquinolone-resistant S. Typhi emerging in Bangladesh.

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Use of multilocus variable-number tandem repeat analysis in molecular subtyping of Salmonella enterica serovar Typhi isolates

Cited by 14 publications

References 31 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

Salmonella enterica Serovar Typhi Variants in Long-Term Carriers

Antimicrobial Resistance in Salmonella enterica Serovar Typhi Isolates from Bangladesh, Indonesia, Taiwan, and Vietnam

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