A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of theRalstonia solanacearumspecies complex

Background.Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of theRalstonia solanacearumspecies complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III.Methods.We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used.Results and Discussion.Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.

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Clostridioides difficile Ribotype 027 (RT027) Outbreak Investigation Due to the Emergence of Rifampicin Resistance Using Multilocus Variable-Number Tandem Repeat Analysis (MLVA)

Infection and Drug Resistance ◽

10.2147/idr.s324745 ◽

2021 ◽

Vol Volume 14 ◽

pp. 3247-3254

Author(s):

Monika Kabała ◽

Zygmunt Gofron ◽

Małgorzata Aptekorz ◽

Krzysztof Sacha ◽

Celine Harmanus ◽

...

Keyword(s):

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Outbreak Investigation ◽

Rifampicin Resistance ◽

Repeat Analysis ◽

Ribotype 027 ◽

Clostridioides Difficile

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Defining criteria to interpret multilocus variable-number tandem repeat analysis to aid Clostridium difficile outbreak investigation

Journal of Medical Microbiology ◽

10.1099/jmm.0.029819-0 ◽

2011 ◽

Vol 60 (8) ◽

pp. 1095-1100 ◽

Cited By ~ 13

Author(s):

George Broukhanski ◽

Andrew Simor ◽

Dylan R. Pillai

Keyword(s):

Clostridium Difficile ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Outbreak Investigation ◽

Repeat Analysis

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Comparison of Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Investigation of Clostridium difficile Transmission

Journal of Clinical Microbiology ◽

10.1128/jcm.01095-13 ◽

2013 ◽

Vol 51 (12) ◽

pp. 4141-4149 ◽

Cited By ~ 48

Author(s):

D. W. Eyre ◽

W. N. Fawley ◽

E. L. Best ◽

D. Griffiths ◽

N. E. Stoesser ◽

...

Keyword(s):

Clostridium Difficile ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Whole Genome ◽

Repeat Analysis

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Evaluating the Use of Multilocus Variable Number Tandem Repeat Analysis of Shiga Toxin-Producing Escherichia coli O157 as a Routine Public Health Tool in England

PLoS ONE ◽

10.1371/journal.pone.0085901 ◽

2014 ◽

Vol 9 (1) ◽

pp. e85901 ◽

Cited By ~ 17

Author(s):

Lisa Byrne ◽

Richard Elson ◽

Timothy J. Dallman ◽

Neil Perry ◽

Philip Ashton ◽

...

Keyword(s):

Public Health ◽

Escherichia Coli ◽

Tandem Repeat ◽

Shiga Toxin ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Escherichia Coli O157 ◽

Repeat Analysis

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Multilocus Variable-Number Tandem-Repeat Analysis, Pulsed-Field Gel Electrophoresis, and Antimicrobial Susceptibility Patterns in Discrimination of Sporadic and Outbreak-Related Strains of Yersinia enterocolitica

BMC Microbiology ◽

10.1186/1471-2180-11-42 ◽

2011 ◽

Vol 11 (1) ◽

pp. 42 ◽

Cited By ~ 30

Author(s):

Leila M Sihvonen ◽

Susanna Toivonen ◽

Kaisa Haukka ◽

Markku Kuusi ◽

Mikael Skurnik ◽

...

Keyword(s):

Yersinia Enterocolitica ◽

Tandem Repeat ◽

Antimicrobial Susceptibility ◽

Gel Electrophoresis ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Pulsed Field Gel Electrophoresis ◽

Pulsed Field ◽

Repeat Analysis ◽

Susceptibility Patterns

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Evaluation of Multiple-Locus Variable-Number Tandem-Repeat Analysis for Typing a Polyclonal Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Population in an Area Where Such Infections Are Endemic

Journal of Clinical Microbiology ◽

10.1128/jcm.02220-09 ◽

2010 ◽

Vol 48 (8) ◽

pp. 2991-2994 ◽

Cited By ~ 8

Author(s):

B. Rivero-Perez ◽

E. Perez-Roth ◽

S. Mendez-Alvarez

Keyword(s):

Staphylococcus Aureus ◽

Tandem Repeat ◽

Methicillin Resistant Staphylococcus Aureus ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Methicillin Resistant ◽

Multiple Locus ◽

Repeat Analysis ◽

Hospital Acquired

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Multiple-Locus Variable-Number Tandem Repeat Analysis of Dutch Bordetella pertussis Strains Reveals Rapid Genetic Changes with Clonal Expansion during the Late 1990s

Journal of Bacteriology ◽

10.1128/jb.186.16.5496-5505.2004 ◽

2004 ◽

Vol 186 (16) ◽

pp. 5496-5505 ◽

Cited By ~ 99

Author(s):

Leo M. Schouls ◽

Han G. J. van der Heide ◽

Luc Vauterin ◽

Paul Vauterin ◽

Frits R. Mooi

Keyword(s):

The Netherlands ◽

Tandem Repeat ◽

Bordetella Pertussis ◽

Minimum Spanning Tree ◽

Whooping Cough ◽

Variable Number Tandem Repeat ◽

Clonal Expansion ◽

Variable Number ◽

Multiple Locus ◽

Repeat Analysis

ABSTRACT Bordetella pertussis, the causative agent of whooping cough, has remained endemic in The Netherlands despite extensive nationwide vaccination since 1953. In the 1990s, several epidemic periods have resulted in many cases of pertussis. We have proposed that strain variation has played a major role in the upsurges of this disease in The Netherlands. Therefore, molecular characterization of strains is important in identifying the causes of pertussis epidemiology. For this reason, we have developed a multiple-locus variable-number tandem repeat analysis (MLVA) typing system for B. pertussis. By combining the MLVA profile with the allelic profile based on multiple-antigen sequence typing, we were able to further differentiate strains. The relationships between the various genotypes were visualized by constructing a minimum spanning tree. MLVA of Dutch strains of B. pertussis revealed that the genotypes of the strains isolated in the prevaccination period were diverse and clearly distinct from the strains isolated in the 1990s. Furthermore, there was a decrease in diversity in the strains from the late 1990s, with a remarkable clonal expansion that coincided with the epidemic periods. Using this genotyping, we have been able to show that B. pertussis is much more dynamic than expected.

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