Genetic diversity of Mycoplasma hyopneumoniae isolates from conventional farrow-to-finish pig farms in Serbia

2010 ◽  
Vol 58 (3) ◽  
pp. 297-308 ◽  
Author(s):  
Bozidar Savic ◽  
Vojin Ivetic ◽  
Vesna Milicevic ◽  
Ivan Pavlovic ◽  
Milenko Zutic ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Genetic Relatedness ◽  
Pcr Amplification ◽  
Mycoplasma Hyopneumoniae ◽  
Variable Number ◽  
Repeat Motif ◽  
Typing Method ◽  
Pig Farms ◽  
Different Ages ◽  
Swine Population

Mycoplasma hyopneumoniaeis a primary agent associated with mycoplasma pneumonia and the porcine respiratory disease complex (PRDC). Various reports have indicated that different strains ofM. hyopneumoniaeare circulating in the swine population. Lysates from lung swabs from naturally infected pigs of different ages were tested according to a new variable number of tandem repeats (VNTR) genetic typing method based on the polyserine repeat motif of the P146 lipoproteoadhesin, which can be applied directly on clinical material without isolation ofM. hyopneumoniae. The aim was to determine the diversity ofM. hyopneumoniaeisolates from conventional farrow-to-finish pig farms located in different geographical areas of Serbia. PCR amplification was carried out usingM. hyopneumoniae-specific designed, conserved primers (p146MH — L and p146MH — R) flanking the region encoding the repeat motif, followed by sequencing and cluster analysis. Five groups ofM. hyopneumoniaewith thirteen to twenty-four serine repeats were observed. Analysis of three samples from each farm indicated that the specific isolate is ubiquitous in pigs of different ages. Furthermore, seven clusters were observed within 27 tested samples. The results indicated a considerable diversity amongM. hyopneumoniaefield isolates in the swine population from conventional farrow-to-finish farms in Serbia and suggest close genetic relatedness of the corresponding isolates.

scholarly journals Slipped-Strand Mispairing at Noncontiguous Repeats in Poecilia reticulata: A Model for Minisatellite Birth

Genetics ◽  
2000 ◽  
Vol 155 (3) ◽  
pp. 1313-1320 ◽  
Author(s):  
John S Taylor ◽  
Felix Breden
Keyword(s):  
Tandem Repeat ◽  
Poecilia Reticulata ◽  
Tandem Repeats ◽  
Phylogenetic Reconstruction ◽  
Variable Number ◽  
Repeat Motif ◽  
Raw Material ◽  
Direct Repeats ◽  
Mt Dna ◽  
Variable Number Tandem Repeats

Abstract The standard slipped-strand mispairing (SSM) model for the formation of variable number tandem repeats (VNTRs) proposes that a few tandem repeats, produced by chance mutations, provide the “raw material” for VNTR expansion. However, this model is unlikely to explain the formation of VNTRs with long motifs (e.g., minisatellites), because the likelihood of a tandem repeat forming by chance decreases rapidly as the length of the repeat motif increases. Phylogenetic reconstruction of the birth of a mitochondrial (mt) DNA minisatellite in guppies suggests that VNTRs with long motifs can form as a consequence of SSM at noncontiguous repeats. VNTRs formed in this manner have motifs longer than the noncontiguous repeat originally formed by chance and are flanked by one unit of the original, noncontiguous repeat. SSM at noncontiguous repeats can therefore explain the birth of VNTRs with long motifs and the “imperfect” or “short direct” repeats frequently observed adjacent to both mtDNA and nuclear VNTRs.

scholarly journals Genotyping of ClinicalMycobacterium tuberculosisIsolates Based on IS6110and MIRU-VNTR Polymorphisms

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Anna Żaczek ◽  
Anna Brzostek ◽  
Arkadiusz Wojtasik ◽  
Jarosław Dziadek ◽  
Anna Sajduda
Keyword(s):  
Polyacrylamide Gel Electrophoresis ◽  
Variable Number Tandem Repeat ◽  
Pcr Amplification ◽  
Detailed Comparison ◽  
Variable Number ◽  
Apparent Difference ◽  
Typing Method ◽  
Banding Patterns ◽  
Typing Technique ◽  
Discriminatory Index

In this study, 155 clinicalMycobacterium tuberculosisisolates were subject to genotyping with fast ligation-mediated PCR (FLiP). This typing method is a modified mixed-linker PCR, a rapid approach based on the PCR amplification ofHhaI restriction fragments of genomic DNA containing the 3′ end of IS6110and resolving the amplicons by polyacrylamide gel electrophoresis. The results were compared with previous data of the more commonly used methods, 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing and, to verify combined FLiP/MIRU-VNTR clusters, the reference IS6110restriction fragment length polymorphism (RFLP). FLiP banding patterns were highly reproducible and polymorphic. This method differentiated 119 types among the study set compared to 108 distinct MIRU-VNTR profiles. The discriminatory power of FLiP was slightly higher than that of MIRU-VNTR analysis (Hunter-Gaston Discriminatory Index = 0.991 and 0.990, resp.). Detailed comparison of the clusters defined by each of the methods revealed, however, a more apparent difference in the discriminatory abilities that favored FLiP. Clustering of strains by using combined results of these two PCR-based methods correlated well with IS6110RFLP-defined clusters, further confirming high discriminatory potential of FLiP typing. These results indicate that FLiP could be an attractive and valuable secondary typing technique for verification of MIRU-VNTR clusters ofM. tuberculosisstrains.

Introduction of Infected Animals to Herds Is an Important Route for the Spread of Yersinia enterocolitica Infection between Pig Farms

2014 ◽  
Vol 77 (1) ◽  
pp. 116-121 ◽  
Author(s):  
S. VIRTANEN ◽  
S. NIKUNEN ◽  
H. KORKEALA
Keyword(s):  
Yersinia Enterocolitica ◽  
Tandem Repeats ◽  
Variable Number ◽  
Multiple Locus ◽  
Pig Farms ◽  
Sources Of Infection ◽  
Enterocolitica Infection ◽  
Variable Number Tandem Repeats ◽  
Pathogenic Yersinia

Altogether, 369 pathogenic Yersinia enterocolitica isolates from 1,118 fecal samples collected from 22 pig farms of different production types were characterized by biotyping, serotyping, and genotyping using multiple-locus variable-number tandem repeats analysis. We investigated the distribution of the different genotypes at the farm level and their association with different farm conditions. Pigs were found to carry and transmit Y. enterocolitica between farms, because the same genotypes were found on farms that had previously transported the pigs between them. The purchase of new animals for the farms associated significantly with the number of different multiple-locus variable-number tandem repeats analysis types of Y. enterocolitica found within a farm. Some genotypes seemed to persist on farms for years. The results of this study show that pigs purchased from infected herds transmit Y. enterocolitica infection between farms. Certain pig farms may act as long-term sources of infection.

scholarly journals Development of a Variable Number of Tandem Repeats Typing Scheme for the Bacterial Rice Pathogen Xanthomonas oryzae pv. oryzicola

2012 ◽  
Vol 102 (10) ◽  
pp. 948-956 ◽  
Author(s):  
Shuai Zhao ◽  
Lucie Poulin ◽  
Luis M. Rodriguez-R ◽  
Natalia Forero Serna ◽  
Shu-Yan Liu ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
Bacterial Pathogen ◽  
Pcr Amplification ◽  
Cost Effective ◽  
Variable Number ◽  
Xanthomonas Oryzae ◽  
Chinese Strain ◽  
Epidemiological Monitoring ◽  
Population Structures ◽  
Polymerase Chain

Xanthomonas oryzae pv. oryzicola is an important bacterial pathogen responsible for outbreaks of bacterial leaf streak (BLS) on rice, mostly occurring in Asia and parts of Africa. To better monitor epidemics and assess population structures, efficient tools that allow the precise identification and diagnosis of pathogenic populations are needed. In this study, we explored variable numbers of tandem repeats (VNTR) as a fast, reliable, and cost-effective molecular typing tool. Screening of three X. oryzae pv. oryzicola genome sequences (Philippine strain BLS256, Chinese strain GX01, and Malian strain MAI10) predicted 28 candidate VNTR loci. Primer pairs for polymerase chain reaction (PCR) amplification of all 28 loci were designed and applied to a panel of 20 X. oryzae pv. oryzicola strains originating from Asia and Africa. Sequencing of PCR amplicons revealed 25 robust and polymorphic VNTR loci that are shared among Asian and African X. oryzae pv. oryzicola strains. A dendrogram constructed from 25 VNTR loci indicated that most Asian strains are clearly discriminated from African strains. However, in agreement with previous reports, one strain from Mali is related to Asian strains, pointing to a possible introduction of Asian strains to the African continent. The new VNTR-based tool described here is useful for studies of population structures and epidemiological monitoring of X. oryzae pv. oryzicola.

Tuberculosis in swine co-infected withMycobacterium aviumsubsp.hominissuisandMycobacterium bovisin a cluster from Argentina

2014 ◽  
Vol 143 (5) ◽  
pp. 966-974 ◽  
Author(s):  
S. BARANDIARAN ◽  
A. M. PÉREZ ◽  
A. K. GIOFFRÉ ◽  
M. MARTÍNEZ VIVOT ◽  
A. A. CATALDI ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Null Hypothesis ◽  
Tandem Repeats ◽  
Spatial Clustering ◽  
Variable Number ◽  
Molecular Tools ◽  
Chain Reaction ◽  
Analysis Techniques ◽  
Swine Population ◽  
Polymerase Chain

SUMMARYIn Argentina little is known about the epidemiology of tuberculosis (TB) infection in swine. We characterized the epidemiological dynamics ofMycobacterium aviumcomplex (MAC) infection in a swine population of Argentina using molecular tools and spatial analysis techniques. Isolates (n = 196) obtained from TB-like lesions (n = 200) were characterized by polymerase chain reaction. The isolates were positive to eitherM. bovis(IS6110) (n = 160) orM. avium(IS1245) (n= 16) while the remaining 20 (10·2%) isolates were positive to bothM. bovisandM. avium. The detection of both bacteria together suggests co-infection at the animal level. In addition, MAC-positive isolates (n = 36) were classified asM. aviumsubsp.avium(MAA) (n = 30) andM. aviumsubsp.hominissuis(MAH) (n = 6), which resulted in five genotypes when they were typed using mycobacterial interspersed repetitive unit, variable number of tandem repeats (MIRU-VNTR). One significant (P = 0·017) spatial clustering of genotypes was detected, in which the proportion of MAH isolates was larger than expected under the null hypothesis of even distribution of genotypes. These results show that in Argentina the proportion of TB cases in pigs caused byM. aviumis larger than that reported in earlier studies. The proportion ofM. bovis–MAC co-infections was also higher than in previous reports. These results provide valuable information on the epidemiology of MAC infection in swine in Argentina.

scholarly journals First Molecular Characterisation of Clinical Strains of Mycobacterium ulcerans in Togo (West Africa)

2019 ◽  
pp. 1-14
Author(s):  
Menssah Teko ◽  
Mounerou Salou ◽  
Solange E. Kakou Ngazoa ◽  
Issaka Maman ◽  
Kodjovi Agbodeka ◽  
...  
Keyword(s):  
West Africa ◽  
Tandem Repeats ◽  
Buruli Ulcer ◽  
Variable Number ◽  
Mycobacterium Ulcerans ◽  
Clinical Samples ◽  
Molecular Technique ◽  
Endemic Region ◽  
Typing Method ◽  
Genetic Strains

Background: Buruli ulcer is the third most common mycobacterial disease worldwide. Cases most occur in 30 countries but severe cases occur in West Africa countries such as Benin, Cote d’Ivoire and Togo mainly in rural regions. Early diagnosis may prevent severe disability. The molecular technique seems the best solution and new Mycobacterial Interspersed Repetitive Units (MIRU) and variable number tandem repeats (VNTR) typing method are themost reproducible in this regard. They propose geographical, inter and intraspecies differentiation and can be used as a diagnosis tool. Objective: The objective of this study was to investigate the molecular diversity by using MIRUVNTR typing in clinical samples of BU patients in Togo. Study Design: 64 DNA extracts from clinical samples were collected from BU patients in the two principal endemics districts in Togo (Yoto and Zio) with three less endemic districts (Bas Mono, Lacs and Vo). First, IS2404 and KR real-time PCR plus IS2606 conventional PCR were performed. In a second step, the strains were analysed by PCR typing for five specific and sensitive markers MIRU1, VNTR6, ST1, VNTR19 and VNTR9. Results and Conclusion: 71.11% were positive for IS2404, 3.13% were positives for PCR-KR and 31.11% for IS 2606. By MIRU-VNTR typing, 48.86% positive result was found for MIRU1 and 25.00%, 20.31%, 18.75% and 14.06% for VNTR6, ST1, VNTR19 and VNTR9 respectively. One of the samples was negative for all genotyping markers. Two different genetic profiles were identified by MIRU1, ST1 and VNTR loci by gel-analysed of the amplified products. The VNTR profile B (3,1,1,2) corresponding of 3 copies MIRU1, 1 copy VNTR6, 1 copy ST-1 and two copies of VNTR19 was detected in 15.63% of samples and the VNTR profile A (1,1,1,2) corresponding of 1 copy MIRU1, 1 copy VNTR6, 1 copy ST-1 and 2 copies of VNTR19 was detected in 3.13% of samples and confirms the West African genotype (3,1,1) in Togo. Different genetic strains of Mycobacterium ulcerans (M. ulcerans) were co-circulated in the same endemic region in the country. This study has described first the circulating of different genetic strains of M. ulcerans in Togo.

scholarly journals Molecular Characterization of Mycobacterium tuberculosis H37Rv/Ra Variants: Distinguishing the Mycobacterial Laboratory Strain †

2000 ◽  
Vol 38 (9) ◽  
pp. 3200-3204 ◽  
Author(s):  
P. Bifani ◽  
S. Moghazeh ◽  
B. Shopsin ◽  
J. Driscoll ◽  
A. Ravikovitch ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Tandem Repeats ◽  
Pcr Amplification ◽  
Laboratory Strain ◽  
Variable Number ◽  
Culture Collection ◽  
Molecular Techniques ◽  
Clinical Isolates ◽  
Mycobacterium Tuberculosis H37rv

The Mycobacterium tuberculosis strains H37Rv and H37Ra are the most commonly used controls for M. tuberculosis identification in the clinical and research laboratory setting. To reduce the likelihood of misidentification and possible cross-contamination with this laboratory neotype, it is important to be able to distinguish H37 from clinical isolates. To provide a reference for identifying H37, we used multiple molecular techniques to characterize H37 strains, including 18 of the most frequently used variants available through the American Type Culture Collection. Isolates were genotyped using gene probes to IS6110 and IS1085. In addition, we performed polymorphic GC-rich sequence typing (PGRS), spoligotyping, determination of variable number of tandem repeats (VNTR), and PCR amplification of the mtp40, msx4, andmpp8 polymorphic regions. Southern hybridization with IS6110 provided the most discrimination, differentiating the 18 H37 isolates into 10 discrete patterns made up of 9 H37Rv variants and 1 H37Ra variant. PGRS, IS1085,mpp8, and spoligotyping were not able to distinguish any H37 variants, while VNTR and msx4 discriminated two. Only IS6110 and spoligotyping could distinguish the H37 strain from clinical isolates. In summary, spoligotyping and IS6110 provide a rapid and accurate way to identify H37 contamination, though IS6110 can, in addition, classify many of the H37 variants that would otherwise require phenotypic segregation.

Discrimination of Mycobacterium tuberculosis complex bacteria using novel VNTR-PCR targets

Microbiology ◽  
2002 ◽  
Vol 148 (2) ◽  
pp. 519-528 ◽  
Author(s):  
Robin A Skuce ◽  
Thomas P McCorry ◽  
Julie F McCarroll ◽  
Solvig M. M Roring ◽  
Alistair N Scott ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Molecular Epidemiology ◽  
Tandem Repeats ◽  
Antigenic Variation ◽  
Variable Number ◽  
Strain Typing ◽  
The Novel ◽  
Typing Method ◽  
Intergenic Regions ◽  
Typing Methods

The lack of a convenient high-resolution strain-typing method has hampered the application of molecular epidemiology to the surveillance of bacteria of the Mycobacterium tuberculosis complex, particularly the monitoring of strains of Mycobacterium bovis. With the recent availability of genome sequences for strains of the M. tuberculosis complex, novel PCR-based M. tuberculosis-typing methods have been developed, which target the variable-number tandem repeats (VNTRs) of minisatellite-like mycobacterial interspersed repetitive units (MIRUs), or exact tandem repeats (ETRs). This paper describes the identification of seven VNTR loci in M. tuberculosis H37Rv, the copy number of which varies in other strains of the M. tuberculosis complex. Six of these VNTRs were applied to a panel of 100 different M. bovis isolates, and their discrimination and correlation with spoligotyping and an established set of ETRs were assessed. The number of alleles varied from three to seven at the novel VNTR loci, which differed markedly in their discrimination index. There was positive correlation between spoligotyping, ETR- and VNTR-typing. VNTR-PCR discriminates well between M. bovis strains. Thirty-three allele profiles were identified by the novel VNTRs, 22 for the ETRs and 29 for spoligotyping. When VNTR- and ETR-typing results were combined, a total of 51 different profiles were identified. Digital nomenclature and databasing were intuitive. VNTRs were located both in intergenic regions and annotated ORFs, including PPE (novel glycine-asparigine-rich) proteins, a proposed source of antigenic variation, where VNTRs potentially code repeating amino acid motifs. VNTR-PCR is a valuable tool for strain typing and for the study of the global molecular epidemiology of the M. tuberculosis complex. The novel VNTR targets identified in this study should additionally increase the power of this approach.

scholarly journals Multilocus Variable Number of Tandem Repeat Analysis for molecular typing of uropathogenic Escherichia coli

2020 ◽  
Author(s):  
Reza Ranjbar ◽  
Farhad Safarpoor Dehkordi ◽  
Morteza Mashhouri ◽  
Omid Farahani
Keyword(s):  
Escherichia Coli ◽  
Tandem Repeat ◽  
Tandem Repeats ◽  
Genetic Relationships ◽  
Variable Number Tandem Repeat ◽  
Pcr Amplification ◽  
Variable Number ◽  
E Coli ◽  
Repeat Analysis

Abstract Background: The aim of this study was genotyping of Uropathogenic Escherichia coli (UPEC) based on Variable Number of Tandem Repeats (VNTRs) sequences. Methods: E. coli strains isolated from urine samples were included in this study. Seven VNTR loci were subjected to Multilocus variable-number tandem repeat analysis (MLVA) based on PCR amplification. Then data was analyzed via online mlvaplus software and the information was displayed in the form of MST analysis. Results: A total of 100 E. coli strains were isolated and subjected to the study. MLVA was able to differentiate 56 different genotypes. Also, the technique could classify E. coli isolates in 5 clonal complexes. Based on UPGMA dendrograms, E. coli isolates were classified into 4 clusters (clusters A to D). The strains associated with Complex No. 1 appeared to be dominant pathogens of UPEC in Tehran's patients. The present study provides valuable insights into the genetic relationships of E. coli isolates recovered from clinical cases in a major hospital in Iran. Conclusions: The analysis of MLVA profiles using the MST algorithm showed the usefulness of the MLVA method in the classification of uropathogenic E. coli collected in different periods. We evaluated MLVA in a laboratory equipped with simple molecular equipment. Based on these results, it has been assumed that the E. coli strains were derived from a limited number of clones that have undergo a small genetic change during this period.

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