scholarly journals Three transmission events of Vibrio cholerae O1 into Lusaka, Zambia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
John Mwaba ◽  
Amanda K. Debes ◽  
Kelsey N. Murt ◽  
Patrick Shea ◽  
Michelo Simuyandi ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Genetic Lineage ◽  
Single Nucleotide Variants ◽  
East African ◽  
African Countries ◽  
Random Mutation ◽  
Vibrio Cholerae O1

Abstract Background Cholera has been present and recurring in Zambia since 1977. However, there is a paucity of data on genetic relatedness and diversity of the Vibrio cholerae isolates responsible for these outbreaks. Understanding whether the outbreaks are seeded from existing local isolates or if the outbreaks represent separate transmission events can inform public health decisions. Results Seventy-two V. cholerae isolates from outbreaks in 2009/2010, 2016, and 2017/2018 in Zambia were characterized using multilocus variable number tandem repeat analysis (MLVA) and whole genome sequencing (WGS). The isolates had eight distinct MLVA genotypes that clustered into three MLVA clonal complexes (CCs). Each CC contained isolates from only one outbreak. The results from WGS revealed both clustered and dispersed single nucleotide variants. The genetic relatedness of isolates based on WGS was consistent with the MLVA, each CC was a distinct genetic lineage and had nearest neighbors from other East African countries. In Lusaka, isolates from the same outbreak were more closely related to themselves and isolates from other countries than to isolates from other outbreaks in other years. Conclusions Our observations are consistent with i) the presence of random mutation and alternative mechanisms of nucleotide variation, and ii) three separate transmission events of V. cholerae into Lusaka, Zambia. We suggest that locally, case-area targeted invention strategies and regionally, well-coordinated plans be in place to effectively control future cholera outbreaks.

scholarly journals Relatedness of Vibrio cholerae O1/O139 Isolates from Patients and Their Household Contacts, Determined by Multilocus Variable-Number Tandem-Repeat Analysis

2010 ◽  
Vol 192 (17) ◽  
pp. 4367-4376 ◽  
Author(s):  
Emily A. Kendall ◽  
Fahima Chowdhury ◽  
Yasmin Begum ◽  
Ashraful I. Khan ◽  
Shan Li ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Index Patient ◽  
Variable Number ◽  
Repeat Analysis ◽  
Household Contacts ◽  
Vibrio Cholerae O1

ABSTRACT The genetic relatedness of Vibrio cholerae O1/O139 isolates obtained from 100 patients and 146 of their household contacts in Dhaka, Bangladesh, between 2002 and 2005 was assessed by multilocus variable-number tandem-repeat analysis. Isolate genotypes were analyzed at five loci containing tandem repeats. Across the population, as well as within households, isolates with identical genotypes were clustered in time. Isolates from individuals within the same household were more likely to have similar or identical genotypes than were isolates from different households, but even within a household, isolates from different individuals often had different genotypes. When household contacts were sampled regularly for 3 weeks after the illness of the household index patient, isolates with genotypes related to the index patient appeared in contacts, on average, ∼3 days after the index patient, while isolates with unrelated genotypes appeared in contacts ∼6 days after. Limited data revealed that multiple isolates from the same individual collected within days of each other or even from a single stool sample may have identical, similar, or unrelated genotypes as well. Our results demonstrate that genetically related V. cholerae strains cluster in local outbreaks but also suggest that multiple distinct strains of V. cholerae O1 may circulate simultaneously within a household.

scholarly journals Molecular epidemiology of Vibrio cholerae O1 in northern Vietnam (2007–2009), using multilocus variable-number tandem repeat analysis

2016 ◽  
Vol 65 (9) ◽  
pp. 1007-1012 ◽  
Author(s):  
Dong Tu Nguyen ◽  
Tuan Cuong Ngo ◽  
Thanh Huong Le ◽  
Hoai Thu Nguyen ◽  
Masatomo Morita ◽  
...  
Keyword(s):  
Molecular Epidemiology ◽  
Vibrio Cholerae ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Northern Vietnam ◽  
Repeat Analysis ◽  
Vibrio Cholerae O1

Vibrio cholerae O1 El Tor from southern Vietnam in 2010 was molecularly distinct from that present from 1999 to 2004

2015 ◽  
Vol 144 (6) ◽  
pp. 1241-1247 ◽  
Author(s):  
V. H. NGUYEN ◽  
H. T. PHAM ◽  
T. T. DIEP ◽  
C. D. H. PHAN ◽  
T. Q. NGUYEN ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Gel Electrophoresis ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Pulsed Field Gel Electrophoresis ◽  
Environmental Isolates ◽  
Southern Vietnam ◽  
Large Outbreak ◽  
Vibrio Cholerae O1 ◽  
El Tor

SUMMARYThe Vibrio cholerae O1 (VCO1) El Tor biotype appeared during the seventh cholera pandemic starting in 1961, and new variants of this biotype have been identified since the early 1990s. This pandemic has affected Vietnam, and a large outbreak was reported in southern Vietnam in 2010. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem-repeat analyses (MLVA) were used to screen 34 VCO1 isolates from the southern Vietnam 2010 outbreak (23 patients, five contact persons, and six environmental isolates) to determine if it was genetically distinct from 18 isolates from outbreaks in southern Vietnam from 1999 to 2004, and two isolates from northern Vietnam (2008). Twenty-seven MLVA types and seven PFGE patterns were identified. Both analyses showed that the 2008 and 2010 isolates were distinctly clustered and separated from the 1999–2004 isolates.

scholarly journals Can 15-Locus Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Analysis Provide Insight into the Evolution of Mycobacterium tuberculosis?

2005 ◽  
Vol 71 (12) ◽  
pp. 8207-8213 ◽  
Author(s):  
Andrea Gibson ◽  
Timothy Brown ◽  
Lucy Baker ◽  
Francis Drobniewski
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number Tandem Repeat ◽  
Epidemiological Studies ◽  
Variable Number ◽  
Molecular Techniques ◽  
Nucleotide Polymorphisms ◽  
East African ◽  
Phylogeny And Evolution ◽  
Phylogenetic Lineages

ABSTRACT The phylogeny and evolution of the bacterium Mycobacterium tuberculosis is still poorly understood despite the application of a variety of molecular techniques. We analyzed 469 M. tuberculosis and 49 Mycobacterium bovis isolates to evaluate if the mycobacterial interspersed repetitive units-variable-number tandem repeats (MIRU-VNTR) commonly used for epidemiological studies can define the phylogeny of the M. tuberculosis complex. This population was characterized by previously identified silent single-nucleotide polymorphisms (sSNPs) or by a macroarray based on these sSNPs that was developed in this study. MIRU-VNTR phylogenetic codes capable of differentiating between phylogenetic lineages were identified. Overall, there was 90.9% concordance between the lineages of isolates as defined by the MIRU-VNTR and sSNP analyses. The MIRU-VNTR phylogenetic code was unique to M. bovis and was not observed in any M. tuberculosis isolates. The codes were able to differentiate between different M. tuberculosis strain families such as Beijing, Delhi, and East African-Indian. Discrepant isolates with similar but not identical MIRU-VNTR codes often displayed a stepwise trend suggestive of bidirectional evolution. A lineage-specific panel of MIRU-VNTR can be used to subdivide each lineage for epidemiological purposes. MIRU-VNTR is a valuable tool for phylogenetic studies and could define an evolutionarily uncharacterized population of M. tuberculosis complex organisms.

scholarly journals Multilocus variable-number tandem repeat analysis of Vibrio cholerae O1 El Tor strains harbouring classical toxin B

2010 ◽  
Vol 59 (7) ◽  
pp. 763-769 ◽  
Author(s):  
Seon Young Choi ◽  
Je Hee Lee ◽  
Yoon-Seong Jeon ◽  
Hye Ri Lee ◽  
Eun Jin Kim ◽  
...  
Keyword(s):  
Cholera Toxin ◽  
Vibrio Cholerae ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Group Iii ◽  
Repeat Analysis ◽  
Group I ◽  
Ctx Prophage ◽  
El Tor

Atypical Vibrio cholerae O1 strains – hybrid strains (strains that cannot be classified either as El Tor or classical biotype) and altered strains (El Tor biotype strains that produce classical cholera toxin) – are currently prevalent in Asia and Africa. A total of 74 hybrid and altered strains that harboured classical cholera toxin were investigated by multilocus variable-number tandem repeat analysis (MLVA). The results showed that the hybrid/altered strains could be categorized into three groups and that they were distant from the El Tor strain responsible for the seventh cholera pandemic. Hybrid/altered strains with a tandem repeat of the classical CTX prophage on the small chromosome were divided into two MLVA groups (group I: Mozambique/Bangladesh group; group III: Vietnam group), and altered strains with the RS1–CTX prophage containing the El Tor type rstR and classical ctxB on the large chromosome were placed in two MLVA groups (group II: India/Bangladesh group; group III: India/Vietnam group).

scholarly journals Development of a Multiple-Locus Variable-Number Tandem-Repeat Typing Scheme for Genetic Fingerprinting of Burkholderia cenocepacia and Application to Nationwide Epidemiological Analysis

2014 ◽  
Vol 53 (2) ◽  
pp. 398-409 ◽  
Author(s):  
Christine Segonds ◽  
Michelle Thouverez ◽  
Antoine Barthe ◽  
Nadège Bossuet-Greif ◽  
Lenka Tisseyre ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Burkholderia Cepacia ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Cost Effective ◽  
Variable Number ◽  
Discriminatory Power ◽  
Burkholderia Cenocepacia ◽  
Content Type ◽  
Burkholderia Multivorans

Organisms of theBurkholderia cepaciacomplex are especially important pathogens in cystic fibrosis (CF), with a propensity for patient-to-patient spread and long-term respiratory colonization.B. cenocepaciaandBurkholderia multivoransaccount for the majority of infections in CF, and major epidemic clones have been recognized throughout the world. The aim of the present study was to develop and evaluate a multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) scheme forB. cenocepacia. Potential VNTR loci were identified upon analysis of the annotated genome sequences ofB. cenocepaciastrains AU1054, J2315, and MCO-3, and 10 of them were selected on the basis of polymorphisms and size. A collection of 100B. cenocepaciastrains, including epidemiologically related and unrelated strains, as well as representatives of the major epidemic lineages, was used to evaluate typeability, epidemiological concordance, and the discriminatory power of MLVA-10 compared with those of pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Longitudinal stability was assessed by testing 39 successive isolates from 14 patients. Typeability ranged from 0.91 to 1, except for that of one marker, which was not amplified in 53% of theB. cenocepaciaIIIA strains. The MLVA types were shown to be stable in chronically colonized patients and within outbreak-related strains, with excellent epidemiological concordance. Epidemic and/or globally distributed lineages (epidemic Edinburgh-Toronto electrophoretic type 12 [ET-12], sequence type 32 [ST-32], ST-122, ST-234, and ST-241) were successfully identified. Conversely, the discriminatory power of MLVA was lower than that of PFGE or MLST, although PFGE variations within the epidemic lineages sometimes masked their genetic relatedness. In conclusion, MLVA represents a promising cost-effective first-line tool inB. cenocepaciasurveillance.

scholarly journals Improvement of Multiple-Locus VNTR Analysis Typing Scheme for Helicobacter pylori

2019 ◽  
pp. 1-7
Author(s):  
Vladimir M. Sorokin ◽  
Ruslan V. Pisanov ◽  
Aleksej S. Vodop'janov
Keyword(s):  
Helicobacter Pylori ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Genome Database ◽  
Vntr Locus ◽  
Multiple Locus ◽  
H Pylori ◽  
Mlva Typing ◽  
Vntr Analysis

Aims: To improve a multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) assay for Helicobacter pylori typing. Materials and Methods: Polymorphic VNTRs were searched by Gene Expert. The distribution and polymorphism of each VNTR locus were analyzed in 18 H. pylori genomes from the NCBI genome database by BLAST and were compared with a collection of 15 clinical H. pylori strains. The MLVA assay was compared with MLST-typing for discriminating H. pylori isolates. Results: Twelve VNTR loci were identified by bioinformatic screening of H. pylori genomes, and five of them were highly polymorphic. Therefore, an MLVA assay composed of five VNTR loci was developed with greatest discriminatory power. Conclusion: MLVA typing is a faster and more standardized method for studying the genetic relatedness of H. pylori isolates. At preliminary stage it is sufficient to use only 3 VNTR loci for the differentiation of H. pylori strains.

scholarly journals Multi-locus variable number tandem repeat analysis of 7th pandemic Vibrio cholerae

2012 ◽  
Vol 12 (1) ◽  
pp. 82 ◽  
Author(s):  
Connie Lam ◽  
Sophie Octavia ◽  
Peter R Reeves ◽  
Ruiting Lan
Keyword(s):  
Vibrio Cholerae ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Repeat Analysis

scholarly journals Molecular epidemiology of tuberculosis in northeastern Ethiopia

2021 ◽  
Author(s):  
Fikru Gashaw ◽  
Aboma Zewde ◽  
Endalkachew Tedla ◽  
Biniam Wondale ◽  
Yalemtsehay Mekonnen ◽  
...  
Keyword(s):  
Statistical Significance ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
East African ◽  
Chain Reaction ◽  
Culture Positivity ◽  
Smear Positive Pulmonary Tuberculosis ◽  
Polymerase Chain ◽  
Culture Positive ◽  
Descriptive Statistical Analysis

Abstract Background: Tuberculosis (TB) is a major public health threat causing the highest morbidity and mortality in Ethiopia. However, there is shortage of information on the species and strains of mycobacteria that cause TB in Ethiopia. The objective of this study is to investigate the diversity of Mycobacterium tuberculosis (M. tb) isolated from TB patients in northeastern Ethiopia. Methods: A total of 384 smear positive pulmonary and extra-pulmonary TB cases were recruited on the basis of clinical examination and ZiehlNeelsen staining for further investigation. Mycobacterial culturing, region of difference (RD) 9-based polymerase chain reaction (PCR), spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing were used for the identification the species and strains. Descriptive statistical analysis was used for the expression of the results while proportions were compared using c2 test. Statistical significance was considered when p<0.05.Results: Smear positive pulmonary tuberculosis accounted for 74.5% (286/384). The disease proportion was highest in age group of 18–37 years. Culture positivity was confirmed only in 29.2% (112/384). Speciation of the culture positive isolates using RD9 indicated that 77.7% (87/112) were M. tuberculosis. Further identification of the isolates using spoligotyping indicated 92.9% (104/112) interpretable spoligotyping patterns of which 20.2% (21/104) were grouped under 10 clustered patterns. Further grouping of the spoligotypes indicated that 86.5% (90/104) of the isolates as orphan types. Grouping of the isolates into the major lineages showed 52.9%, 27.9% and 19.2% of the isolates as Euroamerican, Indio-oceanic and East African Indian lineages, respectively. Typing of 69 isolates using 24-loci MIRU-VNTR typing gave interpretable results for 56 isolates each of them having distinct MIRU-VNTR profile and were considered as 56 different genotypes (strains).Conclusion: M. tuberculosis was identified as the main cause of TB in northeastern Ethiopia and its strains were highly diversified.

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