Molecular Characterization ofStreptococcus PyogenesIsolates to investigate an outbreak of Puerperal Sepsis

AbstractObjective:To describe microbiological characteristics and epidemiologic features of an outbreak of postpartum endometritis.Methods:Various markers were investigated in five patients and three throat carriage isolates ofStreptococcus pyogenesobtained during an outbreak of endometritis occurring in a 13-week period. Molecular characterization included biotyping, T-serotyping,emmgene sequence and restriction, pulsed-field gel electrophoresis (PFGE), and random amplified polymorphic DNA (RAPD) analysis.Results:Biotype, T-serotype, and genotypic data (emmanalysis, PFGE, and RAPD analysis) revealed a close relationship among the isolates from three patients, suggesting that cross-contamination had occurred. These isolates were biotype 1, T type 28, andemmtype 28. The isolates from one patient and one carrier differed from those of the index patient by minor variations of theemmamplicon restriction pattern, PFGE pattern, or RAPD pattern. The remaining isolates were phenotypically and genetically different.Conclusion:Identification of different isolates demonstrated that different strains may circulate simultaneously during a true outbreak and that the predominant strain might persist for several months.

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Transport of escherichia coli through soil to groundwater traced by randomly amplified polymorphic DNA (RAPD)

Water Science & Technology ◽

10.2166/wst.1997.0758 ◽

1997 ◽

Vol 35 (11-12) ◽

pp. 351-357 ◽

Cited By ~ 2

Author(s):

R. Rothmaier ◽

A. Weidenmann ◽

K. Botzenhart

Keyword(s):

Negative Impact ◽

Random Amplified Polymorphic Dna ◽

Coli Strain ◽

Soil Samples ◽

Test Field ◽

Liquid Manure ◽

E Coli ◽

Rapd Pattern ◽

Geological Situation ◽

Different Strains

Isolates (50) of E. coli obtained from liquid manure (20 bovine, 20 porcine) were genotyped using random amplified polymorphic DNA (RAPD). Typing revealed 9 and 14 different strains in bovine and porcine liquid manure respectively with no strains in common. One porcine strain, showing a simple RAPD pattern, was subcultured and spread on a test field (1.5l/m2 at 1010 cfu/l) in a drinking water protection zone with loamy to sandy sediments in the Donauried area, Baden-Wurttemberg. Soil samples and groundwaters were collected at monthly intervals October 1994 – June 1995 during which 114 E. coli isolates were recovered. The first occurrence and maximum concentration of E. coli in soil samples taken from more than 20cm depth was in January 1995, declining rapidly with depth and time. All isolates from soil and only one from groundwater showed the RAPD pattern of the spread E. coli strain. The results could not demonstrate a severe negative impact of the spreading of liquid manure on the bacteriological quality of the groundwater in the given geological situation. The distinct strain patterns found in different kinds of liquid manure suggest that genotyping of E. coli by RAPD may be an adequate tool for tracing sources of faecal contamination.

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Approach to molecular characterization of different strains of Fasciola hepatica using random amplified polymorphic DNA polymerase chain reaction

Parasitology Research ◽

10.1007/s00436-015-4310-9 ◽

2015 ◽

Vol 114 (4) ◽

pp. 1341-1345 ◽

Cited By ~ 1

Author(s):

S. Scarcella ◽

E. Miranda-Miranda ◽

M. V. Solana ◽

H. Solana

Keyword(s):

Polymerase Chain Reaction ◽

Molecular Characterization ◽

Dna Polymerase ◽

Fasciola Hepatica ◽

Random Amplified Polymorphic Dna ◽

Chain Reaction ◽

Polymerase Chain ◽

Different Strains

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Molecular typing of the Legionella pneumophila population isolated from several locations in a contaminated water network

Water Science & Technology ◽

10.2166/wst.2004.0068 ◽

2004 ◽

Vol 50 (1) ◽

pp. 281-285 ◽

Cited By ~ 2

Author(s):

A.-S. Lepeuple ◽

M. Jovic ◽

M.-R. de Roubin

Keyword(s):

Legionella Pneumophila ◽

Molecular Typing ◽

Random Amplified Polymorphic Dna ◽

Hot Water ◽

Water Network ◽

Rapd Pattern ◽

Different Populations ◽

Definition Of ◽

Different Strains ◽

Key Steps

The RAPD (random amplified polymorphic DNA) technique has been developed for the molecular typing of Legionella in order to characterise the populations of hot water systems. During this study, 22 primers were tested and the four most informative ones were selected. The optimisation of the PCR conditions allowed the setting up of a powerful discriminative genotyping method. Moreover, the definition of a quality management method allowed definition of the key steps and the number of replicates to ensure reproducibility of the RAPD pattern. The RAPD was used to study the hot water network of a building. Legionella colonies (91) were isolated from seven locations and genotyped. The diversity of the population in one sample could vary from one to seven different strains. The study of the traceability showed that, in most of the cases, different populations could be present at different locations of the same network.

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Random amplified polymorphic DNA (RAPD) analysis of Ornithobacterium rhinotracheale strains isolated from chickens in Turkey

Veterinární Medicína ◽

10.17221/5660-vetmed ◽

2012 ◽

Vol 50 (No. 12) ◽

pp. 526-530 ◽

Cited By ~ 4

Author(s):

G. Ozbey ◽

Ertas HB ◽

A. Muz

Keyword(s):

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Random Primer ◽

Serotype A ◽

Dna Assay ◽

Rapd Profile ◽

Rapd Pattern ◽

Serotype B ◽

Dna Profiles ◽

Ornithobacterium Rhinotracheale

Six field strains of Ornithobacterium rhinotracheale isolated from chickens in Elazig province located in the East of Turkey were typed by serotyping and random amplified polymorphic DNA assay using a random primer (OPG-11). Using the AGP test used for serotyping, serotype A was found to be the predominant serotype, only one strain was serotyped as serotype B. By RAPD assay, the tested ORT strains were found to have different RAPD profiles. In addition, the RAPD assay showed almost similar DNA profiles among the tested strains of the serotypes A, B, D and E. The strain of serotype C did give a different RAPD profile. Within strains of the same serotype (A), different profiles were found but the strain of serotype (B) had an identical profile as strains of serotype A. This study suggests that more genotypes of ORT strains are present within the same serotype and thus that no relationship exists between the RAPD pattern of ORT and their serotype.

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Echinococcus granulosus from Mexican pigs is the same strain as that in Polish pigs

Journal of Helminthology ◽

10.1017/s0022149x07787564 ◽

2007 ◽

Vol 81 (3) ◽

pp. 287-292 ◽

Cited By ~ 17

Author(s):

A. Cruz-Reyes ◽

C.C. Constantine ◽

A.C. Boxell ◽

R.P. Hobbs ◽

R.C.A. Thompson

Keyword(s):

Echinococcus Granulosus ◽

Fragment Length Polymorphism ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Taxonomic Status ◽

Distinct Strain ◽

Close Relationship ◽

Sequencing Part ◽

Polymerase Chain ◽

Relationship Of

AbstractSamples of Echinococcus granulosus from seven pigs from Mexico were compared with isolates of the parasite from pigs in Poland and representative strains and species of Echinococcus. Isolates from pigs in Mexico were found to be genetically identical to E. granulosus from Polish pigs and distinct from other major genotypes by sequencing part of the mitochondrial cytochrome c oxidase I (COI) mtDNA locus, restriction fragment length polymorphism (RFLP) of the polymerase chain reaction (PCR) amplified rDNA internal transcribed spacer (ITS) 1 using five different enzymes, and random amplified polymorphic DNA (RAPD) analysis. These results were complemented by data on hook morphology and together strengthen the view that Echinococcus maintained in a cycle involving pigs and dogs is a distinct strain that is conserved genetically in different geographical areas. The present study supports the close relationship of the cervid, camel and pig strains and raises the question of their taxonomic status.

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Pulsed-Field Gel Electrophoresis Is More Efficient than Ribotyping and Random Amplified Polymorphic DNA Analysis in Discrimination of Pasteurella haemolytica Strains

Journal of Clinical Microbiology ◽

10.1128/jcm.37.2.380-385.1999 ◽

1999 ◽

Vol 37 (2) ◽

pp. 380-385 ◽

Cited By ~ 19

Author(s):

Angeli Kodjo ◽

Laurence Villard ◽

Chantal Bizet ◽

Jean-Louis Martel ◽

Richard Sanchis ◽

...

Keyword(s):

Gel Electrophoresis ◽

Dna Analysis ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Geographic Origin ◽

Pulsed Field Gel Electrophoresis ◽

Pasteurella Haemolytica ◽

Pulsed Field ◽

Rapd Pattern ◽

Almost All

One hundred thirty-three strains of Pasteurella haemolytica of both biotypes (90 and 43 strains of biotypes A and T, respectively) and almost all the serotypes were subjected to ribotyping, random amplified polymorphic DNA (RAPD) analysis, and pulsed-field gel electrophoresis (PFGE) analysis for epidemiological purposes. A total of 15 patterns recorded as ribotypes HA to HO were found for the P. haemolytica biotype A strains, with ribotypes HA, HC, and HD being encountered most often (66 strains [74%]); and 20 ribotypes, designated HA′ to HT′, that were clearly distinct from those observed for biotype A strains were observed for strains of biotype T. RAPD analysis generated a total of 44 (designated Rp1 to Rp44) and 15 (designated Rp1′ to Rp 15′) unique RAPD patterns for biogroup A and biogroup T, respectively. Analysis of the data indicated that a given combined ribotype-RAPD pattern could be observed for biotype A strains of different serotypes, whatever the zoological or geographic origin, whereas this was not the case for biotype T strains. PFGE appeared to be more efficient in strain discrimination since selected strains from various zoological or geographical origins harboring the same ribotype-RAPD group were further separated into unique entities.

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Genetic Characterization by RAPD Analysis of Isolates of Fusarium oxysporum f. sp. erythroxyli Associated with an Emerging Epidemic in Peru

Phytopathology ◽

10.1094/phyto.1997.87.12.1220 ◽

1997 ◽

Vol 87 (12) ◽

pp. 1220-1225 ◽

Cited By ~ 26

Author(s):

Amy J. Nelson ◽

Karol S. Elias ◽

E. Arévalo G. ◽

Lee C. Darlington ◽

Bryan A. Bailey

Keyword(s):

Fusarium Oxysporum ◽

Dna Fingerprinting ◽

Genetic Characterization ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Dna Fingerprint ◽

Pathogenicity Test ◽

Vascular Wilt ◽

Genetic Complexity ◽

Rapd Pattern

An epidemic of vascular wilt caused by Fusarium oxysporum f. sp. erythroxyli is currently occurring on Erythroxylum coca var. coca in the coca-growing regions of the Huallaga Valley in Peru. Random amplified polymorphic DNA (RAPD) analysis of isolates of the pathogen was undertaken to elucidate its genetic complexity, as well as to identify a specific DNA fingerprint for the pathogen. Two hundred isolates of Fusarium were collected from 10 coca-growing regions in Peru. Of these, 187 were confirmed to be F. oxysporum, and 143 of the F. oxysporum were shown to be pathogens of coca by a root-dip pathogenicity test. The pathogens could be grouped into two subpopulations based on RAPD analysis, and no polymorphism in RAPD pattern was observed among isolates of either subpopulation. Both subpopulations were present in the central Huallaga Valley, where earliest reports of the epidemic occurred. RAPD analysis could easily distinguish the isolates of F. oxysporum f. sp. erythroxyli from the nonpathogenic isolates of F. oxysporum from E. coca var. coca, indicating its utility in DNA fingerprinting.

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Molecular Characterization of Five Medicinally Important Species of Typhonium (Araceae) through Random Amplified Polymorphic DNA (RAPD)

Zeitschrift für Naturforschung C ◽

10.1515/znc-2005-7-815 ◽

2005 ◽

Vol 60 (7-8) ◽

pp. 600-604 ◽

Cited By ~ 5

Author(s):

Laxmikanta Acharya ◽

Arup Kumar Mukherjee ◽

Pratap Chandra Panda ◽

Premananda Das

Keyword(s):

Molecular Characterization ◽

Genetic Similarity ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Similarity Index ◽

The Other ◽

Important Species ◽

Species Specific ◽

Maximum Similarity

The interrelationship of five medicinally important species of Typhonium (Araceae) including T. venosum, which was previously placed under the genus Sauromatum, was inferred by analysis of random amplified polymorphic DNA (RAPD). DNA from pooled leaf samples was isolated and RAPD analysis was performed using 20 decamer oligonucleotide primers. Out of a total of 245 bands amplified, 12 were found to be monomorphic while 233 bands were polymorphic including 86 species-specific bands. The genetic similarities were analyzed from the dendrogram constructed by the pooled RAPD data using a similarity index. The dendrogram showed two distinct clades, one containing T. roxburghii, T. trilobatum and T. venosum and the other containing the remainder two species, i.e. T. diversifolium and T. flagelliforme. Both the clusters shared a common node approx. at 23.7% level of similarity. The maximum similarity of 31.2% was observed between T. venosum and T. trilobatum. In view of its close genetic similarity with other members of Typhonium, transfer of Sauromatum venosum to the genus Typhonium and merger of the two genera was supported.

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SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum

Microorganisms ◽

10.3390/microorganisms7010012 ◽

2019 ◽

Vol 7 (1) ◽

pp. 12 ◽

Cited By ~ 2

Author(s):

O-Chul Kwon ◽

Chang-Soo Lee ◽

Young-Jin Park

Keyword(s):

Ganoderma Lucidum ◽

Gene Sequence ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Morphological Characteristics ◽

Pcr Analysis ◽

Scar Markers ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Specific Fragment

In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.

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