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 Análise genotípica do Helicobacter pylori pelo método Multiple-Locus Variable-Number Tandem-Repeats no sul do Brasil

2016 ◽  
Vol 6 (4) ◽  
Author(s):  
Priscila Cristina Bartolomeu Halicki ◽  
Ivy Bastos Ramis ◽  
Júlia Silveira Vianna ◽  
Thaísa Bozzetti Gautério ◽  
Andrea von Groll ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
In Silico ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Locus ◽  
H Pylori ◽  
Variable Number Tandem Repeats

Justificativa e objetivos: Apesar de ser utilizado como um método de genotipagem para diferentes microrganismos, poucos estudos relatam a utilização de Multiple-Locus Variable Number of Tandem Repeats Analysis (MLVA) para análise da diversidade clonal do Helicobacter pylori. O objetivo deste estudo foi determinar a variabilidade genética de cepas de H. pylori pelo MLVA no sul do Brasil. Métodos: 95 amostras de DNA de H. pylori foram obtidas a partir de biópsias gástricas de pacientes H. pylori-positivos provenientes de duas cidades do sul do Brasil e a diversidade genética das cepas foi avaliada pelo método MLVA utilizando eletroforese em gel de agarose. Para a seleção dos loci a serem analisados neste estudo, foi realizada uma análise in silico de 12 loci previamente descritos na literatura. Resultados: A partir da análise in silico, apenas quatro loci foram considerados viáveis para a análise genotípica das cepas, resultando em 90 cepas distribuídas em oito grupos diferentes e cinco cepas órfãs. Conclusões: Apesar de o método MLVA permitir fazer inferências acerca da diversidade genética de uma população, nossos resultados mostraram que os métodos de genotipagem do H. pylori devem ser criticamente avaliados antes de serem utilizados nessa região do Brasil.

scholarly journals Evaluation of multiple-locus variable-number tandem repeat analysis (MLVA) for genotyping of Escherichia coli isolated from Karaj River

2017 ◽  
Vol 18 (1) ◽  
pp. 160-166
Author(s):  
Reza Ranjbar ◽  
Samaneh Shokouhi Mostafavi ◽  
Hamed Memariani
Keyword(s):  
Escherichia Coli ◽  
Water Quality ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Coliform Bacteria ◽  
Vntr Locus ◽  
Multiple Locus ◽  
E Coli ◽  
Genotyping Method

Abstract Most microbiological water quality regulations rely upon the detection of indicators of fecal pollution, such as coliform bacteria, or more specifically Escherichia coli. In order to further understand the source, fate, and implications for water quality regulation, environmental E. coli isolates should be assessed genetically to observe various levels of genotypic diversity. Multiple-locus variable-number tandem repeat (VNTR) analysis (MLVA) is a novel, simple and inexpensive polymerase chain reaction (PCR) based genotyping method which relies on the detection of different copy numbers inside each VNTR locus. In this study, we evaluated MLVA as a tool for the genotyping of E. coli strains of water samples collected from the Karaj River, Iran. Overall, high genetic diversity was observed among environmental E. coli isolates. We also proved the feasibility of MLVA as a complementary or even future replacement genotyping method for the average routine laboratory.

Multilocus variable-number tandem-repeat analysis of Neisseria meningitidis serogroup C in China

2015 ◽  
Vol 143 (14) ◽  
pp. 3001-3010
Author(s):  
X. Y. SHAN ◽  
H. J. ZHOU ◽  
J. ZHANG ◽  
B. Q. ZHU ◽  
L. XU ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Neisseria Meningitidis ◽  
Tandem Repeat ◽  
Genetic Relatedness ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Sequence Type ◽  
Repeat Analysis ◽  
Vntr Analysis ◽  
Epidemiological Information

SUMMARYThis study characterized Neisseria meningitidis serogroup C strains in China in order to establish their genetic relatedness and describe the use of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) to provide useful epidemiological information. A total of 215 N. meningitidis serogroup C strains, obtained from 2003 to 2012 in China, were characterized by MLVA with different published schemes as well as multilocus sequence typing. (i) Based on the MLVA scheme with a combination of five highly variable loci, 203 genotypes were identified; this level of discrimination supports its use for resolving closely related isolates. (ii) Based on a combination of ten low variable loci, clear phylogenetic relationships were established within sequence type complexes. In addition, there was evidence of microevolution of VNTR loci over the decade as strain lineages spread from Anhui to other provinces, the more distant the provinces from Anhui, the higher the genetic variation.

A Comparative Multiple-Locus Variable-Number Tandem Repeat Analysis of Helicobacter pylori Isolates from Southern Russia

2021 ◽  
pp. 55-61
Author(s):  
Vladimir Mihajlovich Sorokin ◽  
Ruslan Vjacheslavovich Pisanov ◽  
Elena Vadimovna Golubkina ◽  
Elena Aleksandrovna Bereznyak ◽  
Lubov Aleksandrovna Prozorova
Keyword(s):  
Helicobacter Pylori ◽  
Tandem Repeat ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Multiple Locus ◽  
Repeat Analysis ◽  
Southern Russia

scholarly journals Simultaneous carriage of multiple genotypes of Staphylococcus aureus in children

2011 ◽  
Vol 60 (3) ◽  
pp. 317-322 ◽  
Author(s):  
Kanokporn Mongkolrattanothai ◽  
Barry M. Gray ◽  
Peggy Mankin ◽  
Amy B. Stanfill ◽  
Richard H. Pearl ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Tandem Repeat ◽  
Genetic Relatedness ◽  
Elective Surgery ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Multiple Locus

The co-existence of multiple genotypes in colonization by Staphylococcus aureus has not been fully investigated. The aim of this study was to evaluate the heterogeneity of S. aureus carriage in children. We evaluated 125 nasal and perianal swab samples that were positive for S. aureus from 76 children scheduled for elective surgery. For each sample, at least four colonies with the same or different morphotypes were selected for analysis. Multiple-locus variable-number tandem-repeat fingerprinting was used to determine the genetic relatedness and to characterize the clonality of the S. aureus strains. Of the 125 swabs, 91 (73 %) contained meticillin-sensitive S. aureus (MSSA), 8 (6 %) contained meticillin-resistant S. aureus (MRSA), and 26 (21 %) contained MSSA and MRSA simultaneously. A total of 738 S. aureus strains were evaluated with a mean of 6 colonies (range 4–15) picked from each culture. Of the 125 swabs, 32 (26 %) samples contained two genetically distinct S. aureus strains and 6 (5 %) contained three different genotypes. Multiple S. aureus strains simultaneously carried by individual children were genetically unrelated to each other. We concluded that the co-existence of multiple genotypes of S. aureus was common. The significance of multiple carriage is yet to be determined, but this intraspecies interplay could be important to pathogenicity and virulence in S. aureus.

Sign in / Sign up

Export Citation Format

Share Document