Strain differentiation of Trichophyton rubrum by randomly amplified polymorphic DNA and analysis of rDNA nontranscribed spacer

Trichophyton rubrum is the most common pathogen causing dermatophytosis. Molecular strain-typing methods have recently been developed to tackle epidemiological questions and the problem of relapse following treatment. A total of 67 strains of T. rubrum were screened for genetic variation by randomly amplified polymorphic DNA (RAPD) analysis, with two primers, 5′-d[GGTGCGGGAA]-3′ and 5′-d[CCCGTCAGCA]-3′, as well as by subrepeat element analysis of the nontranscribed spacer of rDNA, using the repetitive subelements TRS-1 and TRS-2. A total of 12 individual patterns were recognized with the first primer and 11 with the second. Phylogenetic analysis of the RAPD products showed a high degree of similarity (>90 %) among the epidemiologically related clinical isolates, while the other strains possessed 60 % similarity. Specific amplification of TRS-1 produced three strain-characteristic banding patterns (PCR types); simple patterns representing one copy of TRS-1 and two copies of TRS-2 accounted for around 85 % of all isolates. It is concluded that molecular analysis has important implications for epidemiological studies, and RAPD analysis is especially suitable for molecular typing in T. rubrum.

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Strain Identification of Trichophyton rubrum by Specific Amplification of Subrepeat Elements in the Ribosomal DNA Nontranscribed Spacer

Journal of Clinical Microbiology ◽

10.1128/jcm.38.12.4527-4534.2000 ◽

2000 ◽

Vol 38 (12) ◽

pp. 4527-4534 ◽

Cited By ~ 68

Author(s):

Colin J. Jackson ◽

Richard C. Barton ◽

Steven L. Kelly ◽

E. Glyn V. Evans

Keyword(s):

Ribosomal Dna ◽

Trichophyton Rubrum ◽

Strain Identification ◽

Clear Correlation ◽

Strain Characteristic ◽

Nontranscribed Spacer ◽

Trichophyton Soudanense ◽

Specific Amplification ◽

Characteristic Banding

Trichophyton rubrum is the commonest cause of dermatophytosis of skin and nail tissue. Molecular characterization of the T. rubrum ribosomal DNA nontranscribed-spacer region revealed two novel tandemly repetitive subelements (TRSs): TRS-1, containing a 27-bp palindromic sequence, and TRS-2. Specific amplification of TRS-1 produced strain-characteristic banding patterns (PCR types), with 21 TRS-1 PCR types recognized from 101 clinical isolates. Four simple patterns representing 1 to 4 copies of TRS-1 accounted for 75 (75%) of all 101 strains, whereas more complex patterns were observed for 21 (20%) of the 101 isolates. The copy number of TRS-2 was 0 to 3 repeats per cistron, with a majority of isolates having two copies of this element. Eleven isolates were polymorphic for TRS-2, and in combination, 23 separate PCR types were recognized by amplification of both TRS-1 and TRS-2. The PCR patterns from both elements were stable and reproducible. Elements with homology to TRS-1 were present in three phylogenetically related species,Trichophyton violaceum, Trichophyton gourvilii, and Trichophyton soudanense, but these elements were not identified in other dermatophyte taxa. There was no clear correlation of PCR type with specimen (skin or nail tissue), but certain PCR types appeared to show a bias in geographic distribution. This new method of typing T. rubrum will enable important questions about pathogenesis and epidemiology of this fungus to be addressed.

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Strain differentiation of Trichophyton rubrum by random amplification of polymorphic DNA (RAPD)

Revista do Instituto de Medicina Tropical de São Paulo ◽

10.1590/s0036-46652004000600008 ◽

2004 ◽

Vol 46 (6) ◽

pp. 339-341 ◽

Cited By ~ 13

Author(s):

Lilian Cristiane Baeza ◽

Maria José Soares Mendes Giannini

Keyword(s):

Trichophyton Rubrum ◽

Rapd Analysis ◽

Epidemiological Studies ◽

Strain Typing ◽

Strain Differentiation ◽

Random Amplification ◽

Typing Methods

Trichophyton rubrum is an important cause of dermatomycoses. Molecular strain typing methods have recently been developed to address questions about epidemiology and source of relapse following treatment. This report describes the application of RAPD for molecular strain differentiation of this fungus utilizing the primers 1- (5'-d[GGTGCGGGAA]-3') and 6- (5'-d[CCCGTCAGCA]-3'). A total of five RAPD patterns were observed among 10 strains of T. rubrum, with each of the primers used. We conclude that RAPD analysis using primers 1 and 6 can be used in epidemiological studies.

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Characterization of Alstroemeria Species using Random Amplified Polymorphic DNA (RAPD) Analysis

HortScience ◽

10.21273/hortsci.32.3.482f ◽

1997 ◽

Vol 32 (3) ◽

pp. 482F-482 ◽

Cited By ~ 2

Author(s):

Deric D. Picton ◽

Harrison G. Hughes

Keyword(s):

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Randomly Amplified Polymorphic Dna ◽

Banding Patterns ◽

Extraction Buffer ◽

Rapd Pcr ◽

High Degree ◽

Species Hybrids ◽

Color Variants

In this study, 11 species, hybrids, and color variants were characterized using randomly amplified polymorphic DNA (RAPD) analysis. Total genomic DNA was extracted using a 2% CTAB extraction buffer using fresh or frozen leaf material. The DNA was amplified using standard RAPD-PCR protocols utilizing 10-mer primers. All primers utilized exhibited a high degree of polymorphism in their banding patterns among the species and hybrids studied. The primers used produced ≈40 reproducible bands. It was possible to identify and uniquely distinguish all species and hybrids investigated using these bands.

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Geographic Discrimination of Paracoccidioides brasiliensis Strains by Randomly Amplified Polymorphic DNA Analysis

Journal of Clinical Microbiology ◽

10.1128/jcm.36.6.1733-1736.1998 ◽

1998 ◽

Vol 36 (6) ◽

pp. 1733-1736 ◽

Cited By ~ 40

Author(s):

Ana María Calcagno ◽

Gustavo Niño-Vega ◽

Felipe San-Blas ◽

Gioconda San-Blas

Keyword(s):

Dna Analysis ◽

Paracoccidioides Brasiliensis ◽

Epidemiological Studies ◽

Randomly Amplified Polymorphic Dna ◽

Group V ◽

Group Iii ◽

Group I ◽

Geographical Regions ◽

High Degree ◽

Discriminatory Index

Randomly amplified polymorphic DNA (RAPD) analysis of 33Paracoccidioides brasiliensis strains from Argentina, Brazil, Colombia, Peru, and Venezuela produced reproducible amplification products which were sufficiently polymorphic to allow differentiation of the strains. Types generated with five primers (OPG 03, OPG 05, OPG 14, OPG 16, and OPG 18) resulted in a high discriminatory index (0.956). The discriminatory index was slightly reduced (0.940) when only two primers (OPG 3 and OPG 14) were used. A dendrogram based on these results showed a high degree of similarity among the strains, and genetic differences were expressed in clusters related to geographical regions but not to pathological features of the disease. With a few exceptions, strains were sorted into five groups by geographical origin as follows: group I, Venezuelan strains; group II, Brazilian strains; group III, Peruvian strains; group IV, Colombian strains; and group V, Argentinian strains. The group containing the most disparate strains was group V (discriminatory index, 0.633); the discriminatory index for the other four groups was 0.824. The use of primer OPG 18 by itself was sufficient to discriminate species specificity, and the use of primer OPG 14 by itself was sufficient to discriminate among the geographical locations of the strains in the sample. This method may be helpful for epidemiological studies ofP. brasiliensis.

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Performance of Phenotypic and Genotypic Methods To Determine the Clinical Relevance of Serial Blood Isolates ofStaphylococcus epidermidis in Patients with Septicemia

Journal of Clinical Microbiology ◽

10.1128/jcm.38.7.2488-2493.2000 ◽

2000 ◽

Vol 38 (7) ◽

pp. 2488-2493 ◽

Cited By ~ 20

Author(s):

J. H. Sloos ◽

L. Dijkshoorn ◽

L. Vogel ◽

C. P. A. van Boven

Keyword(s):

Blood Culture ◽

Staphylococcus Epidermidis ◽

Fragment Length Polymorphism ◽

Rapd Analysis ◽

Pulsed Field Gel Electrophoresis ◽

Performance Criteria ◽

Polymorphism Analysis ◽

Randomly Amplified Polymorphic Dna ◽

Different Types ◽

Typing Methods

Five typing methods, including biotyping (API ID32; BioMérieux, Marcy l'Etoile, France), quantitative antibiogram typing based on actual zone sizes, plasmid typing, randomly amplified polymorphic DNA (RAPD) analysis (with primer M13 and primer set ERIC-2–1026), and pulsed-field gel electrophoresis (PFGE), were compared with a previously performed method of DNA fingerprinting by AFLP (amplified fragment length polymorphism analysis) for their performance in the typing of blood isolates of Staphylococcus epidermidis. Sixteen epidemiologically unrelated strains and 11 sets of four blood culture isolates from 11 patients with septicemia were used. The stabilities and reproducibilities of the patterns, the discriminatory capacities of the methods, and the ability to apply the methods to blood culture isolates were used as performance criteria. All strains tested were typeable by each method, and the patterns were stable and reproducible. The numbers of different types within the collection of 16 epidemiologically different isolates were 5 by biotyping, 14 by antibiogram typing, 4 by plasmid typing, 9 by the RAPD assay (combination of results with primer M13 and primer set ERIC-2–1026), and 16 by PFGE. Within the 11 sets of four blood culture isolates the types found by quantitative antibiogram typing, plasmid typing, and PFGE were unique for each set, whereas by biotyping and RAPD analysis some types were observed in more than one set. The results of biotyping did not correspond with the results of the other methods or the results of AFLP. For 6 of the 11 sets, the results of all methods except those of biotyping corresponded completely. Quantitative antibiogram typing, PFGE, and AFLP proved to be the most accurate of the six typing methods tested.

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RAPD analysis of grapevine hybrids and cultivars

International Journal of Horticultural Science ◽

10.31421/ijhs/10/4/515 ◽

2004 ◽

Vol 10 (4) ◽

Cited By ~ 2

Author(s):

J. Halász ◽

J. Korbuly ◽

T. Deák ◽

Gy. D. Bisztray

Keyword(s):

Vitis Vinifera ◽

Plant Breeding ◽

Genetic Similarity ◽

Rapd Analysis ◽

Phenotypic Selection ◽

Randomly Amplified Polymorphic Dna ◽

Morphologic Characteristics ◽

Two Generations ◽

Identical Number ◽

High Degree

Utilization of the Randomly Amplified Polymorphic DNA (RAPD) technique as a molecular marker was tested to investigate the relationships between some representative grapevine cultivars and hybrids established at the Department of Genetics and Plant Breeding (CUB), to distinguish clones as well as to characterize various hybrids between species or cultivars and their parents. Vitis vinifera cultivars were easily and successfully distinguished by the RAPD technique and they were grouped according to the traditional taxonomic classification. RAPD patterns of the examined Pinot gris clones proved to be completely identical. Number of generations was reflected by the value of genetic distance of the examined hybrids. Genetic identity of parents and their offsprings was influenced by the selection applied in the process of plant breeding. Parental phenotypic and morphologic characteristics showed high degree of segregation in hybrids, but RAPD analysis revealed that their genetic similarity is considerable. The three Vitis anntrensis clones were properly discriminated from every cultivar and hybrid of Vitis vinifera, i.e. hybrids are much closer to the cultivated grapevine than to V. anzurensis due to the phenotypic selection carried out during the life-cycle of one or two generations.

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Nationwide Temporal and Geographical Distribution of Tick Populations and Phylogenetic Analysis of Severe Fever with Thrombocytopenia Syndrome Virus in Ticks in Korea, 2020

Microorganisms ◽

10.3390/microorganisms9081630 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1630

Author(s):

Min-Goo Seo ◽

Byung-Eon Noh ◽

Hak Seon Lee ◽

Tae-Kyu Kim ◽

Bong-Goo Song ◽

...

Keyword(s):

Tick Species ◽

Temporal Distribution ◽

Epidemiological Studies ◽

Haemaphysalis Longicornis ◽

Geographical Regions ◽

Control And Prevention ◽

Amblyomma Testudinarium ◽

High Degree ◽

Severe Fever ◽

Minimum Infection Rate

Since 2010, the Korea Disease Control and Prevention Agency has established centers at 16 locations to monitor disease vectors and pathogens. Here, we examined tick populations to understand the geographical and temporal distribution of severe fever with thrombocytopenia syndrome virus (SFTSV) vectors in 2020. From April to November, 63,376 ticks were collected from traps to monitor tick populations, with a trap index of 41.3. Tick incidence varied from April to October, with population peaks observed for nymphs in May, adults in July, and larvae in September. The predominant tick species were Haemaphysalis longicornis, Haemaphysalis spp., H. flava, Ixodes spp., Amblyomma testudinarium, and Ixodes nipponensis. Approximately 50% of the collected ticks were pooled into 2973 groups to detect the rate of SFTSV infection in ticks. The minimum infection rate (MIR) of SFTSV was 0.2%, and Andong had the highest MIR for SFTSV (4.0%). The B3 genotype was the most prevalent (52.2%) followed by B2 (28.6%), B5 (15.9%), B4 (1.6%), and B6 (1.6%). We identified widely distributed tick species and a high degree of diversity in SFTSV strains in ticks from different geographical regions. The results may provide a basis for future epidemiological studies and risk assessments for tick-borne diseases.

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Random amplified polymorphic DNA (RAPD) finger prints evidencing high genetic variability among marine angiosperms of India

Journal of the Marine Biological Association of the United Kingdom ◽

10.1017/s0025315416000631 ◽

2016 ◽

Vol 97 (6) ◽

pp. 1307-1315 ◽

Cited By ~ 3

Author(s):

Elangovan Dilipan ◽

Jutta Papenbrock ◽

Thirunavakkarasu Thangaradjou

Keyword(s):

Genetic Variability ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Rapd Marker ◽

Seagrass Species ◽

Complex Species ◽

Marine Angiosperms ◽

Different Populations ◽

High Degree ◽

Identification Tool

In India 14 seagrass species can be found with monospecific genera (Enhalus, ThalassiaandSyringodium),Cymodoceawith two species andHalophilaandHalodulerepresented by more than two taxonomically complex species. Considering this, the present study was made to understand the level and pattern of genetic variability among these species collected from Tamilnadu coast, India. Random amplified polymorphic DNA (RAPD) analysis was used to evaluate the level of polymorphism existing between the species. Out of the 12 primers tested, 10 primers amplified 415 DNA fragments with an average of 41.5 fragments per primer. Of the total 415 amplified fragments only 123 (29.7%) were monomorphic and the remaining 292 (70.3%) were polymorphic for Indian seagrass species. Among the 10 primers used four are identified as the key primers capable of distinguishing all the Indian seagrasses with a high degree of polymorphism and bringing representative polymorphic alleles in all the tested seagrasses. From the present investigation, this study shows that the RAPD marker technique can be used not only as a tool to analyse genetic diversity but also to resolve the taxonomic uncertainties existing in the Indian seagrasses. The efficiency of these primers in bringing out the genetic polymorphism or homogeneity among different populations of theHalophilaandHalodulecomplex still has to be tested before recommending these primers as an identification tool for Indian seagrasses.

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Molecular characterization of Anaplasma phagocytophilum infection in the cervids and feeding ticks from Lithuania

Biologija ◽

10.6001/biologija.v66i3.4308 ◽

2020 ◽

Vol 66 (3) ◽

Author(s):

Jana Radzijevskaja ◽

Justina Snegiriovaitė ◽

Artūras Kibiša ◽

Irma Ražanskė ◽

Algimantas Paulauskas

Keyword(s):

Sequence Analysis ◽

Anaplasma Phagocytophilum ◽

Red Deer ◽

Roe Deer ◽

Bacterial Pathogen ◽

Epidemiological Studies ◽

Msp4 Gene ◽

Ixodes Ticks ◽

High Degree ◽

Sequence Types

Anaplasma phagocytophilum is a bacterial pathogen, which is a major cause of zoonotic disease, anaplasmosis. The main vectors of A. phagocytophilum are ticks of the Ixodes ricinus complex. A. phagocytophilum has a broad geographic distribution and a high degree of biological and clinical diversity. Epidemiological studies in multiple countries have shown that the prevalence of A. phagocytophilum highly depends on the density of ticks and their potential hosts such as the cervids, which are one of the main sources of nutrition for Ixodes ticks. In Lithuania, the cervids are important game animals but their contribution as reservoirs for A. phagocytophilum remains unknown. The objectives of the study were to investigate the prevalence of A. phagocytophilum infections in the cervids and feeding ticks and to characterize the A. phagocytophilum strains obtained from the cervids and ticks based on sequence analysis of msp4 gene. A total of 187 ticks were collected from 44 cervids (roe deer, red deer, and moose) harvested by professional hunters during the hunting seasons of 2010–2013 and 2016–2017 in Lithuania. Blood and spleen samples were collected from 29 animals (27 roe deer and two red deer). A. phagocytophilum DNA was identified in ten (37.04%) of the 27 roe deer. The overall prevalence of A. phagocytophilum in I. ricinus and D. reticulatus ticks was 39.3% (70/178) and 22.2% (2/9) respectively. The sequence analysis of the msp4 gene of A. phagocytophilum revealed nine different sequence types: five msp4 sequence types were detected in ticks and seven in roe deer.

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Genetic variability within isolates of Colletotrichum lindemuthianum belonging to race 65 from the state of Minas Gerais, Brazil

Biologia ◽

10.2478/s11756-008-0039-6 ◽

2008 ◽

Vol 63 (2) ◽

Cited By ~ 12

Author(s):

Francine Ishikawa ◽

Elaine Souza ◽

Livia Davide

Keyword(s):

Rapd Analysis ◽

Anastomosis Group ◽

Minas Gerais ◽

Great Variability ◽

The State ◽

Colletotrichum Lindemuthianum ◽

Randomly Amplified Polymorphic Dna ◽

Dice Coefficient ◽

The Common ◽

Pathogenic Variability

AbstractColletotrichum lindemuthianum, the causal agent of anthracnose in the common bean (Phaseolus vulgaris), presents a wide genetic and pathogenic variability that gives rise to complications in the development of resistant bean cultivars. The aim of this study was to identify the variability within race 65 of C. lindemuthianum, the race most commonly encountered in Brazil, through randomly amplified polymorphic DNA (RAPD) and anastomosis analyses. Thirteen isolates of race 65, collected in different years and from various host cultivars located in diverse areas of the state of Minas Gerais, Brazil, were investigated. Twenty-four RAPD primers were employed and 83 polymorphic bands amplified. Genetic similarities were estimated from the Sorensen-Dice coefficient and ranged from 0.54 to 0.82. The dendrogram obtained by cluster analysis classified the isolates into 11 separate groups. For the purposes of the analysis of anastomosis, isolates were considered to be compatible when the fusion of hyphae from different isolates could be observed. The proportion of compatible reactions for each isolate was estimated and similarity estimates, based on the Russel & Rao coefficient, ranged from 0.28 to 0.85. Isolates were classified into 11 anastomosis groups, 10 of which were formed by only one isolate. Although isolates LV61, LV73 and LV58 were classified in the same anastomosis group, they were genetically distinct according to RAPD analysis. Results from both RAPD and anastomosis analyses revealed great variability within C. lindemuthianum race 65.

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