Genetic relatedness analysis of Nocardia strains by random amplification polymorphic DNA: validation and applications

2000 ◽  
Vol 151 (4) ◽  
pp. 263-270 ◽  
Author(s):  
Frédéric Laurent ◽  
Frédérique Provost ◽  
Andrée Couble ◽  
Emmanuelle Casoli ◽  
Patrick Boiron
Keyword(s):  
Genetic Relatedness ◽  
Random Amplification ◽  
Relatedness Analysis

An Outbreak of ESBL-producing Klebsiella pneumoniae in an Iranian Referral Hospital: Epidemiology and Molecular Typing

2019 ◽  
Vol 19 (1) ◽  
pp. 46-54 ◽  
Author(s):  
Shima Mahmoudi ◽  
Babak Pourakbari ◽  
Aliakbar Rahbarimanesh ◽  
Mohammad Reza Abdosalehi ◽  
Keyghobad Ghadiri ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Nosocomial Infections ◽  
Molecular Typing ◽  
Genetic Relatedness ◽  
Referral Hospital ◽  
Limited Information ◽  
Hospital Epidemiology ◽  
Rapd Pcr ◽  
Published Report ◽  
Random Amplification

Introduction: Klebsiella pneumoniae is a common cause of nosocomial infections; however, there is limited information in Iran regarding nosocomial outbreaks due to extended-spectrum β–lactamase (ESBL) producing K pneumoniae strains, particularly using molecular methods. The present study focused on the molecular mechanism of ESBL resistance and genetic relatedness in K. pneumoniae isolates causing nosocomial infections in an Iranian referral hospital. Material and Methods: This study evaluated the antimicrobial resistance and molecular epidemiology of K. pneumoniae causing nosocomial infections in children between October 2013 and March 2014. The ESBL detection was carried out for all the isolates by the CLSI method and PCR was carried out for the detection of the blaSHV, blaTEM, and blaCTX-M genes among ESBL-producing K. pneumonia. Molecular typing of the K. pneumoniae was performed using random amplification of polymorphic DNA-polymerase chain reaction (RAPD-PCR). Results: A total of 30 isolates of K. pneumoniae were used for epidemiological analysis. High rates of resistance to cefotaxime (n=29, 97%), cefazolin (n=29, 97%), cefepime (n=25, 83%) and gentamicin (n=23, 77%) were observed. A total of 29 strains (97%) produced ESBLs. The frequency of blaSHV, blaCTX-M and blaTEM genes among these isolates was 83% (n=25), 70% (n=21) and 57% (n=17), respectively. Surprisingly 11 isolated (37%) carried blaSHV, blaCTX-M and blaTEM genes simultaneously. Moreover, the concurrent presence of “blaSHV and blaCTX-M” and “blaSHV and blaTEM” was seen in 8 (27%) and 4 (13%) isolates, respectively. RAPDPCR analyses revealed that K. pneumoniae isolates belonged to 2 RAPD-PCR types among which one cluster counted for 28 isolates. Conclusion: To our knowledge, this is the first published report of a nosocomial outbreak of ESBL-producing K. pneumoniae in children in Iran. Although the epidemiology of nosocomial infections with ESBL-producing organisms has not yet been explored in depth in Iran, our findings suggest that ESBL-producing organisms are already an established public health threat in our country.

scholarly journals Strain Typing of Trichosporon asahii Clinical Isolates by Random Amplification of Polymorphic DNA (RAPD) Analysis

2021 ◽  
Author(s):  
Thayanidhi Premamalini ◽  
Vijayaraman Rajyoganandh ◽  
Ramaraj Vijayakumar ◽  
Hemanth Veena ◽  
Anupma Jyoti Kindo ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Rapd Analysis ◽  
Clinical Isolates ◽  
Clinical Samples ◽  
Strain Typing ◽  
Trichosporon Asahii ◽  
Pcr Fingerprinting ◽  
Specific Pcr ◽  
Rapd Primer ◽  
Random Amplification

Abstract Objective The aim of this study was to identify and isolate Trichosporon asahii (T. asahii) from clinical samples and to assess the genetic relatedness of the most frequently isolated strains of T. asahii using random amplification of polymorphic DNA (RAPD) primers GAC-1 and M13. Methods All the clinical samples that grew Trichosporon species, identified and confirmed by polymerase chain reaction (PCR) using Trichosporon genus-specific primers, were considered for the study. Confirmation of the species T. asahii was carried out by T. asahii-specific PCR. Fingerprinting of the most frequently isolated T. asahii isolates was carried out by RAPD using random primers GAC-1 and M13. Results Among the 72 clinical isolates of Trichosporon sp. confirmed by Trichosporon-specific PCR, 65 were found to be T. asahii as identified by T. asahii-specific PCR. Fingerprinting of the 65 isolates confirmed as T. asahii using GAC-1 RAPD primer yielded 11 different patterns, whereas that of M13 primer produced only 5 patterns. The pattern I was found to be the most predominant type (29.2%) followed by pattern III (16.9%) by GAC-1 primer. Conclusions This study being the first of its kind in India on strain typing of T. asahii isolates by adopting RAPD analysis throws light on genetic diversity among the T. asahii isolates from clinical samples. Fingerprinting by RAPD primer GAC-1 identified more heterogeneity among the T. asahii isolates than M13.

The genetic relatedness analysis of male sterile and their maintainer lines of onion (Allium cepa L.) by using RAPD primers

2013 ◽  
Vol 16 (1) ◽  
pp. 29-33 ◽  
Author(s):  
Dhanya Shivnanajappa ◽  
Lakshmana Reddy Dhoranalapalli Chinnappareddy ◽  
Verre Gowda ◽  
Sreedhara Sindughatta Antharamiah ◽  
Aswath Chennareddy
Keyword(s):  
Allium Cepa ◽  
Genetic Relatedness ◽  
Male Sterile ◽  
Allium Cepa L ◽  
Relatedness Analysis

scholarly journals Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

2020 ◽  
Author(s):  
Rachel F. Daniels ◽  
Stephen F. Schaffner ◽  
Yakou Dieye ◽  
Gnagna Dieng ◽  
Michael Hainsworth ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Imported Malaria ◽  
Intervention Selection ◽  
Optimal Intervention ◽  
Relatedness Analysis ◽  
Molecular Barcode ◽  
Gates Foundation ◽  
Low Prevalence ◽  
Imported Infections ◽  
Local Transmission

Abstract Background: Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history.Methods: We applied a genetic strategy to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal.Results: Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travelers compared to travelers.Conclusions: These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement. This work was supported by the Bill & Melinda Gates Foundation, Grant Number OPP1156051

scholarly journals Polymorphism of Sakini Chicken Population From Different Locations/Altitudes of Nepal Using Randomly Amplified Polymorphic Dna Markers

2021 ◽  
Vol 18 (2) ◽  
pp. 115-124
Author(s):  
NA Gorkhali ◽  
R Dhakal ◽  
S Sapkota ◽  
P Koirala ◽  
BR Pokhrel ◽  
...  
Keyword(s):  
Genetic Polymorphism ◽  
Genetic Distance ◽  
Principle Component Analysis ◽  
Individual Variation ◽  
Dna Markers ◽  
Genetic Relatedness ◽  
Randomly Amplified Polymorphic Dna ◽  
Chicken Population ◽  
Random Amplification ◽  
Cluster Pattern

A study was conducted to evaluate genetic polymorphism in three Sakini chicken populations using random amplification of polymorphic DNA (RAPD) with seven highly polymorphic primers. All populations showed polymorphism with these primers that generates 59 different bands with an average of 8.4 bands per primer with 78.6% polymorphism nature. Primer OPA-16 produced the highest number of polymorphism bands 47 % and the lowest number of bands was produced by the OPA-05 primer 24 %. Differences for genetic distance (D) among populations were significant (P<0.05). A consensus dendogram was therefore developed to show the phylogenetic relationship among the populations. The cluster pattern is well supported by the principle component analysis that also separates all three populations of Sakini chicken into six major groups. The results provide evidence of the applicability of RAPD to determining genetic relatedness within and among different poultry populations and in developing reproducible markers useful in evaluating individual variation in poultry. SAARC J. Agri., 18(2): 115-124 (2020)

scholarly journals Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal

2020 ◽  
Author(s):  
Sarah K. Volkman ◽  
Oumar Sarr ◽  
Richard W. Steketee ◽  
Stephen F. Schaffner ◽  
Yakou Dieye ◽  
...  
Keyword(s):  
Genetic Relatedness ◽  
Imported Malaria ◽  
Travel History ◽  
Intervention Selection ◽  
Optimal Intervention ◽  
Relatedness Analysis ◽  
Molecular Barcode ◽  
Low Prevalence ◽  
Imported Infections ◽  
Local Transmission

Abstract Background Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. Methods A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. Results Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. Conclusions These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.

scholarly journals Genetic relatedness analysis reveals the cotransmission of genetically related Plasmodium falciparum parasites in Thiès, Senegal

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Wesley Wong ◽  
Allison D. Griggs ◽  
Rachel F. Daniels ◽  
Stephen F. Schaffner ◽  
Daouda Ndiaye ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Genetic Relatedness ◽  
Relatedness Analysis

scholarly journals Biodiversity ofClostridium botulinumType E Associated with a Large Outbreak of Botulism in Wildlife from Lake Erie and Lake Ontario

2010 ◽  
Vol 77 (3) ◽  
pp. 1061-1068 ◽  
Author(s):  
George E. Hannett ◽  
Ward B. Stone ◽  
Stephen W. Davis ◽  
Danielle Wroblewski
Keyword(s):  
Botulinum Toxin ◽  
Clostridium Botulinum ◽  
Lake Erie ◽  
Genetic Relatedness ◽  
Large Range ◽  
Lake Ontario ◽  
Mouse Bioassay ◽  
Sediment Samples ◽  
Random Amplification ◽  
Large Outbreak

ABSTRACTThe genetic relatedness ofClostridium botulinumtype E isolates associated with an outbreak of wildlife botulism was studied using random amplification of polymorphic DNA (RAPD). Specimens were collected from November 2000 to December 2008 during a large outbreak of botulism affecting birds and fish living in and around Lake Erie and Lake Ontario. In our present study, a total of 355 wildlife samples were tested for the presence of botulinum toxin and/or organisms. Type E botulinum toxin was detected in 110 samples from birds, 12 samples from fish, and 2 samples from mammals. Sediment samples from Lake Erie were also examined for the presence ofC. botulinum. Fifteen of 17 sediment samples were positive for the presence ofC. botulinumtype E. Eighty-oneC. botulinumisolates were obtained from plants, animals, and sediments; of these isolates, 44C. botulinumisolates produced type E toxin, as determined by mouse bioassay, while the remaining 37 isolates were not toxic for mice. All toxin-producing isolates were typed by RAPD; that analysis showed 12 different RAPD types and multiple subtypes. Our study thus demonstrates that multiple genetically distinct strains ofC. botulinumwere involved in the present outbreak of wildlife botulism. We found thatC. botulinumtype E is present in the sediments of Lake Erie and that a large range of bird and fish species is affected.

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