scholarly journals Genotyping of Chlamydia Abortus Using Multiple Loci Variable Number of Tandem Repeats Analysis Technique

2021 ◽  
Author(s):  
Sara Barati ◽  
Naghmeh Moori Bakhtiari ◽  
Leili Shokoohizadeh ◽  
Masoud Gorbanpoor ◽  
Hassan Momtaz
Keyword(s):  
Tandem Repeats ◽  
L929 Cell ◽  
Variable Number ◽  
Bacterial Strains ◽  
Chlamydia Abortus ◽  
Multiple Loci ◽  
Analysis Technique ◽  
The Difference ◽  
Mlva Typing ◽  
L929 Cell Line

Abstract Background: The correlation between various factors (geographical region, clinical incidence, and host type) and the genomic heterogeneity has been shown in several bacterial strains including Chlamydia abortus. Methods: The aim of this study was to survey the predominant types of C. abortus strains isolated from ruminants in Iran by the multiple loci variable number of tandem repeats (VNTR) analysis (MLVA) method. C. abortus infection was evaluated in a total of 117 aborted fetuses by real-time PCR. The isolation was done via the inoculation of the positive samples in chicken embryo and the L929 cell line. Genotyping was carried out by MLVA typing technique. Results: Forty samples (34.2%) were detected with C. abortus infection; however, chlamydial infection in ruminants of Charmahal/Bakhtiari (3 bovines and 35 sheep) was higher than that of Khuzestan (2 sheep). All MLVA types (MT1-MT8) were detected in the collected samples from Charmahal/Bakhtiari but only 2 types (MT1 and MT3) were reported in samples from Khuzestan. The main MT type was MT1 (32% of samples). Although in this study only 9 cow samples were investigated, they possessed similar clusters to those obtained from sheep (MT1 and MT6).Variation of type in sheep samples (MT1 to MT8) was more than that of bovine samples (MT1, and MT6); this can be attributed to the fact that more samples of sheep were studied as against the bovine samples. Conclusion: Although the difference between the detected same MT types in several animal species or between 2 geographic areas is significant, comprehensive studies are still needed. In Iran, due to traditional intercourse between animals of different provinces, the spread of other types is typically highly probable.

scholarly journals Whole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden

2019 ◽  
Vol 7 (10) ◽  
pp. 398 ◽  
Author(s):  
Sacchini ◽  
Wahab ◽  
Di Giannatale ◽  
Zilli ◽  
Abass ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Geographic Origin ◽  
Variable Number ◽  
Human Brucellosis ◽  
Whole Genome ◽  
Multiple Loci ◽  
Imported Cases

Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.

scholarly journals A variable number of tandem repeats locus within the human complement C2 gene is associated with a retroposon derived from a human endogenous retrovirus.

1992 ◽  
Vol 175 (6) ◽  
pp. 1783-1787 ◽  
Author(s):  
Z B Zhu ◽  
S L Hsieh ◽  
D R Bentley ◽  
R D Campbell ◽  
J E Volanakis
Keyword(s):  
Tandem Repeats ◽  
Average Length ◽  
Endogenous Retrovirus ◽  
Variable Number ◽  
Human Endogenous Retrovirus ◽  
Vntr Locus ◽  
Length Polymorphisms ◽  
Mouse Mammary Tumor ◽  
Tumor Virus ◽  
The Difference

We have previously described multiallelic restriction fragment length polymorphisms of the C2 gene, suggesting the presence of a variable number of tandem repeats (VNTR) locus. We report here the cloning and sequencing of the polymorphic fragments from the two most common alleles of the gene, a and b. The results confirm the presence of a VNTR locus consisting of a nucleotide sequence, 41 bp in average length, repeated tandemly 23 and 17 times in alleles a and b, respectively. The difference in the number of repeats between the two alleles is due to the deletion/insertion of two noncontiguous segments, 143 and 118 bp long, of allele a, and of a 40-bp segment of allele b. The VNTR region is associated with a SINE (short interspersed sequence)-type retroposon, SINE-R.C2, located within the third intron of the C2 gene. SINE-R.C2 is a member of a previously described large retroposon family of the human genome, apparently derived from the human endogenous retrovirus, (HERV) K10, which is homologous to the mouse mammary tumor virus.

scholarly journals Development of a Multiple Loci Variable Number of Tandem Repeats Analysis (MLVA) to Unravel the Intra-Pathovar Structure of Pseudomonas syringae pv. actinidiae Populations Worldwide

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0135310 ◽  
Author(s):  
Serena Ciarroni ◽  
Lorenzo Gallipoli ◽  
Maria C. Taratufolo ◽  
Margi I. Butler ◽  
Russell T. M. Poulter ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Loci

scholarly journals Polymorphism of Variable-Number Tandem Repeats at Multiple Loci in Mycobacterium tuberculosis

2005 ◽  
Vol 43 (10) ◽  
pp. 5034-5043 ◽  
Author(s):  
N. Smittipat ◽  
P. Billamas ◽  
M. Palittapongarnpim ◽  
A. Thong-On ◽  
M. M. Temu ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Loci ◽  
Variable Number Tandem Repeats

Epigenetic differences between male and female bovine blastocysts produced in vitro

2008 ◽  
Vol 32 (2) ◽  
pp. 264-272 ◽  
Author(s):  
P. Bermejo-Álvarez ◽  
D. Rizos ◽  
D. Rath ◽  
P. Lonergan ◽  
A. Gutierrez-Adan
Keyword(s):  
Tandem Repeats ◽  
Dna Methyltransferases ◽  
Blastocyst Stage ◽  
Variable Number ◽  
Mtdna Copy Number ◽  
Male And Female ◽  
Epigenetic Events ◽  
Binding Factor ◽  
The Difference

Epigenetic differences between male and female bovine blastocysts provide a plausible link between physiological and gene transcription differences observed between male and female embryos. The aim of this study was to examine sex-related epigenetic differences in bovine blastocysts produced in vitro. Oocytes were matured in vitro and inseminated with frozen-thawed sex-sorted (X or Y) and unsorted (control) bull sperm. Zygotes were cultured to blastocyst stage and were analyzed for embryo sexing, mtDNA content, telomere lengths, methylation analysis, and quantification of mRNA transcripts of DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) HMT1 hnRNP methyltransferase-like 2 (Hmt1), and interleukin enhancer binding factor 3 (Ilf3). There was a difference ( P < 0.05) in the mean mtDNA copy number between male (410,000 ± 23,000) and female (360,000 ± 21,000) blastocysts. Telomere length was shorter in male blastocysts ( P < 0.01). The level of methylation in a sequence near a variable number of tandem repeats minisatellite region [variable number of tandem repeats (VNTR)] in males (39.8% ± 4.8) was higher than in females (23.7% ± 3.1) ( P < 0.05); however, no differences were found in other regions analyzed. Moreover, transcription differences between sexes were observed for Dnmt3a, Dnmt3b, Hmt1, and Ilf3. These results provide evidence of epigenetic differences between male and female bovine in vitro produced embryos and suggest that before initiation of gonadal differentiation, epigenetic events may modulate the difference between speed of development, metabolism, and transcription observed during preimplantation development between male and female embryos.

scholarly journals A regional outbreak of S. Typhimurium in Denmark and identification of the source using MLVA typing

2006 ◽  
Vol 11 (5) ◽  
pp. 5-6 ◽  
Author(s):  
M Torpdahl ◽  
G Sørensen ◽  
S Ethelberg ◽  
G Sandø ◽  
K Gammelgard ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
National Laboratory ◽  
Geographic Region ◽  
Variable Number ◽  
Phage Types ◽  
Routine Surveillance ◽  
Outbreak Investigations ◽  
Enteric Infections ◽  
Human Infections ◽  
Mlva Typing

In Denmark, as part of the national laboratory-based surveillance system of human enteric infections, all S. Typhimurium isolates are currently sub-typed using phage typing, antibiogram typing, and pulsed-field gel electrophoresis (PFGE). However, the discriminatory ability of PFGE is not always high enough to discriminate within certain phage types, and it is not always possible to separate unrelated and related isolates. We have therefore applied multiple locus variable number of tandem repeats analysis (MLVA) for surveillance typing of S. Typhimurium since 2004. In May and June 2005, an outbreak with 26 cases of S. Typhimurium infection was identified by MLVA. The isolates were fully sensitive and had one of the most frequently occurring Danish phage types (DT12) and PFGE types. S. Typhimurium DT12 isolates from routine surveillance of animals and food were typed using MLVA and PFGE for comparison with the human isolates. The typing results revealed that an isolate from a pig herd and its corresponding slaughterhouse located in the same geographic region as the outbreak had the same PFGE and MLVA type as the human isolates. In contrast, all other DT12 isolates investigated, which had the same PFGE profile, had different MLVA types. The conclusion that the pig herd was the source of the human infections was supported by patient information, and pork from the herd stopped entering the market on 29 June. MLVA may contribute significantly to both surveillance and outbreak investigations of S. Typhimurium, as without MLVA typing this outbreak would not have been found nor its origin traced.

scholarly journals Genome Sequences of Brucella Melitensis Strains QH2019001 and QH2019005 Provides Insight Into Different Evolutionary Origins Within Qinghai Province, China

2020 ◽  
Author(s):  
Zhijun Zhao ◽  
Jiquan Li ◽  
Li Ma ◽  
Hongmei Xue ◽  
Xuxin Yang ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Brucella Melitensis ◽  
Eastern Mediterranean ◽  
Draft Genome ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Whole Genome ◽  
Qinghai Province ◽  
Evolutionary Origins ◽  
Multiple Loci

Abstract Background Brucellosis, which is cause by Brucella, is one of the most important zoonoses and is considered a “forgotten, neglected zoonosis” by the WHO. Methods Blood samples were isolated from two brucellosis males that were confirmed B. melitensis positive following multiple loci variable-number tandem repeat analysis (MLVA) and strains QH2019001 and QH2019005 were identified. Genomic DNA was extracted from these samples and whole genome sequencing (WGS) was performed. Next, SNP-based phylogenetic analysis was performed to compare the two strains to 94 B. melitensis strains (complete genome and draft genome) retrieved from online databases. Results The QH2019001 and QH2019005 strains were found to have differences in their variable-number tandem repeats. Phylogenetic examination of the 96 strains assigned them to 5 genotype groups, with QH2019001 and QH2019005 assigned to the same group, but to different subgroups; with the QH2019005 strain assigned to a new subgenotype, IIj. These findings were then combined to determine strain origin. Conclusions Utilizing a whole genome SNP-based approach highlights the diversity between B. melitensis strains, and it can facilitate the elucidation of different evolutionary histories. This approach also revealed that the QH2019005 is part of a new subgenotype with an ancient origin in the eastern Mediterranean Sea.

scholarly journals Backward compatibility of whole genome sequencing data with MLVA typing using a newMLVAtypeshiny application: the example ofVibrio cholerae

2019 ◽  
Author(s):  
Jérôme Ambroise ◽  
Léonid M. Irenge ◽  
Jean-François Durant ◽  
Bertrand Bearzatto ◽  
Godfrey Bwire ◽  
...  
Keyword(s):  
Vibrio Cholerae ◽  
Genome Sequencing ◽  
Genome Assembly ◽  
Sanger Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Whole Genome ◽  
Backward Compatibility ◽  
Typing Methods ◽  
Mlva Typing

AbstractMultiple-Locus Variable Number of Tandem Repeats (VNTR) Analysis (MLVA) is widely used by laboratory-based surveillance networks for subtyping pathogens causing foodborne and water-borne disease outbreaks. However, Whole Genome Sequencing (WGS) has recently emerged as the new more powerful reference for pathogen subtyping, making a data conversion method necessary which enables the users to compare the MLVA identified by either method. TheMLVATypeshiny application was designed to extract MLVA profiles from WGS data while ensuring backward compatibility with traditional MLVA typing methods.To test and validate theMLVATypealgorithm, WGS-derived MLVA profiles of nineteenVibrio choleraeisolates from Democratic Republic of the Congo (n=9) and Uganda (n=10) were compared to MLVA profiles generated by microchip electrophoresis (Bioanalyzer Agilent 2100), GeneScan analysis, and Sanger sequencing as the reference method. Unlike amplicon-size derived MLVA profiles, results obtained by Sanger sequencing and WGS were totally concordant. However, the latter were affected by censored estimations whose percentage was inversely proportional to the k-mer parameter used during genome assembly. With a k-mer of 127, less than 15% estimation ofV. choleraeVNTR was censored. Preventing censored estimation was only achievable when using a longer k-mer size (i.e. 175), which is not proposed in the SPAdes v.3.13.0 software.In silicoanalysis showed that this limitation does not apply to other microbial species (e.g. Mycobacterium, Streptococcus, Staphylococcus, andPseudomonas) characterized by smaller lengths of motif repeats. As NGS read lengths and qualities tend to increase with time, one may expect the increase of k-mer size in a near future. UsingMLVATypeapplication with a longer k-mer size will then efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation irrespective of the microbial species.Author summaryNext Generation Sequencing (NGS) has emerged as a powerful high throughput genomic approach enabling the Whole Genome Sequence (WGS) of pathogens to be assembled in a relatively short time. A major advantage of WGS, compared to traditional genotypic identification and typing methods, is its ability to generate data that can be exploitedin silicofor multiple bacterial tests including accurate subtyping, determination of genetic relatedness, and characterization of virulence and antimicrobial resistance determinants. Accordingly, WGS is now rapidly replacing traditional methods like Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA) that has long been used in the public health sector for laboratory-based surveillance of pathogens and outbreak response. While these missions require maintenance of data comparability within networks, the lack of backward compatibility between WGS-derived and traditional MLVA methods is a well-recognized issue. As illustrated here withVibrio choleraeisolates from DRC and Uganda, theMLVATypesoftware application analyzes WGS data to generate MLVA profiles that are identical to those determined with traditional typing. Interestingly, this tool has also the potential to extract MLVA profiles from any bacterial genome that are characterized by a small number of tandem repeats,e.g. Streptococcus, Staphylococcus, Pseudomonas, andMycobacteriumspecies. This restriction can be lifted if subsequences of length k, called k-mers, are longer than what is currently proposed by genome assembly algorithm like SPAdes v.3.13.0.

scholarly journals Multilocus VNTR analysis of Mycobacterium ulcerans strains isolated in Côte d’Ivoire

2010 ◽  
Vol 5 (01) ◽  
pp. 059-063 ◽  
Author(s):  
Grossmann Marie-David Coulibaly-N´Golo ◽  
Euloge Ekaza ◽  
Bakary Coulibaly ◽  
N’guetta Aka ◽  
Raymond Kouassi N’Guessan ◽  
...  
Keyword(s):  
Cote D'ivoire ◽  
Tandem Repeats ◽  
Côte D’Ivoire ◽  
Buruli Ulcer ◽  
Variable Number ◽  
Mycobacterium Ulcerans ◽  
Clinical Samples ◽  
Bacterial Strains ◽  
Cote D’Ivoire ◽  
Côte D'ivoire

Introduction: Buruli ulcer, caused by Mycobacterium ulcerans, is endemic in more than 30 countries worldwide, with Côte d'Ivoire being among the most affected countries. Methodology: We used seven variable number of tandem repeats (VNTR) markers and analyzed 114 samples from 11 Ivorian localities consisting of 33 bacterial strains and 81 clinical samples. Complete data sets at loci 1, 6, 9 and 33 were obtained for 18 of these strains (n = 15) and samples (n = 3) collected in each of the localities. Results: All the strains had allelic profile [3113], corresponding to the previously described Atlantic Africa genotype. Conclusion: Sequencing of PCR products at all loci showed no variation in sequence or repeat number, underlining the genetic monomorphism of M. ulcerans in Côte d'Ivoire.

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