An Evaluation of Microbial Contamination in Ontario Beach Waters: qPCR Vercus Culture for Enterococcus

2018 ◽  
Author(s):  
Ashlee Rachel Woolfson
Keyword(s):  
Membrane Filtration ◽  
Microbial Contamination ◽  
Genetic Material ◽  
Sample Collection ◽  
Chain Reaction ◽  
Fecal Indicator ◽  
Testing Method ◽  
Unit Value ◽  
Recreational Beach ◽  
Polymerase Chain

Contamination in recreational beach water is currently assessed using culture-based measurements of fecal indicator bacteria, a process that requires eighteen to twenty-four hours, from the time of sample collection until results can be released (Converse 2012). Due to the fluctuating nature of microbial contamination, data obtained twenty-four hours later are barely pertinent, and decisions regarding beach closure must be made on outdated information. To avoid this lag, real time polymerase chain reaction (qPCR) has been suggested as an alternate testing method, since it directly measures the genetic material in a sample, and thus can reduce lag time to about three to four hours (Ferretti 2010). The major concern of using qPCR is that the value obtained is a measure of DNA in a sample, and, even though the value can be compared to the amount of DNA in one cell, there may be DNA in the sample that should not be counted towards the total, such as DNA from dead organisms (Haugland 2005). This paper focuses on samples collected during the summer of 2012 from Outlet Beach and Bath Filtration Plant in Kingston, Ontario. DNA was extracted from the samples and subjected to qPCR. The amount of DNA was then compared to a known amount of DNA in calibrator cells. This calculated calibrator cell equivalent value can then be compared to the colony forming unit value, as determined by membrane filtration. Through statistical analysis, a relationship can then be found between the two related values.

scholarly journals Accuracy of quantitative polymerase chain reaction in samples of frozen and paraffin-embedded healthy skin for the diagnosis of canine visceral leishmaniasis

2017 ◽  
Vol 69 (6) ◽  
pp. 1443-1450 ◽  
Author(s):  
M.P. Campos ◽  
M.F. Madeira ◽  
D.A. Silva ◽  
M.S. Solcà ◽  
O.M. Espíndola ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Quantitative Polymerase Chain Reaction ◽  
Healthy Skin ◽  
Sample Collection ◽  
Chain Reaction ◽  
Dna Recovery ◽  
Ffpe Samples ◽  
Fresh Frozen ◽  
Polymerase Chain ◽  
Commercial Kits

ABSTRACT The purpose of the present work was to evaluate the accuracy of quantitative polymerase chain reaction (qPCR) performed on samples of fresh frozen tissue (FT) and formalin-fixed, paraffin-embedded (FFPE) healthy skin. This is a validation study conducted with samples from 46 dogs from an endemic area in Brazil. After sample collection, DNA extractions were conducted using commercial kits and qPCR was oriented to kinetoplast DNA (kDNA) targets of the Leishmania infantum species. The results obtained for the FFPE samples showed 63.6% sensitivity and 77.1% specificity, whereas those obtained for the FT samples showed 100% and 48.6%, respectively. Poor agreement was observed for the results of the qPCR technique with FT and FFPE samples. Our results suggest freezing as the most suitable conservation method for the formation of sample databases considering DNA recovery

scholarly journals Psittacine beak and feather disease virus in budgerigars and ring-neck parakeets in South Africa

2004 ◽  
Vol 71 (1) ◽  
Author(s):  
J. Albertyn ◽  
K.M. Tajbhai ◽  
R.R. Bragg
Keyword(s):  
South Africa ◽  
Polymerase Chain Reaction ◽  
Genetic Variation ◽  
Disease Virus ◽  
Common Disease ◽  
Sample Collection ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Feather Disease Virus ◽  
Viral Isolates

Psittacine beak and feather disease (PBFD) is a common disease of the psittacine species and is caused by the psittacine beak and feather disease virus (PBFDV). In this study the occurrence of the disease in ring-neck parakeets and budgerigars in South Africa suffering from feathering problems, using polymerase chain reaction as a diagnostic test was investigated. The genetic variation between viral isolates was also studied. Results indicate that PBFDV can be attributed to being the cause of feathering problems in some of the ring-neck parakeets and budgerigars in South Africa. Genetic variation of isolates occurs between species and individuals. A cheap and easy to use method of blood sample collection on filter paper for diagnostic purposes was also evaluated. It proved to be less stressful to the birds and did not inhibit further processes.

scholarly journals Simplified Method of Detection of Dialister invisus and Olsenella uli in Oral Cavity Samples by Polymerase Chain Reaction

2017 ◽  
Vol 8 (1-2) ◽  
pp. 47-52 ◽  
Author(s):  
Manohar S. Kugaji ◽  
Kishore G. Bhat ◽  
Vinayak M. Joshi ◽  
Madhu Pujar ◽  
Pratik T. Mavani
Keyword(s):  
Polymerase Chain Reaction ◽  
Bacterial Species ◽  
Universal Primers ◽  
Sample Collection ◽  
Chain Reaction ◽  
Infection Group ◽  
Endodontic Infection ◽  
Predominant Component ◽  
Endodontic Infections ◽  
Polymerase Chain

Aims and Objectives: The oral microbial flora is highly complex and diverse with obligate anaerobic bacteria as the predominant component. Most of these are not yet cultivated/difficult to cultivate due to technical limitations. In this study, we aim to detect two novel oral bacterial species Dialister invisus and Olsenella uli by simplified and economical procedure of polymerase chain reaction (PCR) and study their association with primary and persistent endodontic infections. Material and Methods: The study involved 60 patients that included 30 patients of primary endodontic infections and 30 with persistent endodontic infections. The sample collection from the root canal was performed by universally accepted protocol by using sterile paper points. The deoxyribonucleic acid (DNA) extraction was done, followed by PCR with species specific primers. We made several changes to the protocol mentioned by original authors. We adopted a one-step protocol for amplification of bacterial DNA, omitting the 16SrDNA amplification step with universal primers. Results: It was seen that 7 (23.3 %) samples in primary endodontic infection group and 24 (80 %) samples in persistent endodontic infection group were positive for D. invisus. On the other hand, 11 (36.6 %) patients of primary endodontic infection showed positivity for O. uli in comparison to 9 (30 %) of persistent endodontic infection. Conclusion: The results from the present study showed efficient amplification of both O. uli and D. invisus in a single-step PCR. Hence, we conclude that the modified protocol used here with taq polymerase enzyme offers a faster and cheaper alternative to nested PCR without compromising the quality of amplification process.

scholarly journals Antimony-resistant Leishmania donovani in eastern Sudan: incidence and in vitro correlation

2003 ◽  
Vol 9 (4) ◽  
pp. 837-843 ◽  
Author(s):  
M. G. Abdo ◽  
W. M. El Amin ◽  
E. A. G. Khalil ◽  
M. M. Mukhtar
Keyword(s):  
Leishmania Donovani ◽  
Pcr Amplification ◽  
Sodium Stibogluconate ◽  
Chain Reaction ◽  
Endemic Region ◽  
Testing Method ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Eastern Sudan

A longitudinal study was done in a leishmaniasis -endemic region in eastern Sudan during the period November 2001-February 2003 to determine the incidence of failure of sodium stibogluconate treatment. We studied 820 confirmed visceral leishmaniasis patients. All were treated with sodium stibogluconate, 20 mg/kg body weight for at least 28 days. Parasites were isolated from lymph node aspirates from 22 participants identified as relapsed patients. All isolates were typed as Leishmania donovani based on polymerase chain reaction [PCR] amplification of parasite kDNA. Six parasites showed in vitro resistance to sodium stibogluconate using murine J774 macrophage amastigote testing method. The resistant isolates showed different restriction profiles when the amplified kDNA PCR products were digested with ALU1 restriction enzyme, indicating that resistance was mediated by different parasite clones

scholarly journals Epidemiology of epizootic lymphangitis of carthorses in northern Ethiopia using conventional diagnostic methods and nested polymerase chain reaction

2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Birhanu Hadush ◽  
Molla Michaelay ◽  
Habtamu Taddele Menghistu ◽  
Nigus Abebe ◽  
Abreha Tesfaye Genzebu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Clinical Examination ◽  
Nested Pcr ◽  
Control Measure ◽  
Genetic Material ◽  
Diagnostic Methods ◽  
Northern Ethiopia ◽  
Chain Reaction ◽  
Nested Polymerase Chain Reaction ◽  
Polymerase Chain

Abstract Background Epizootic lymphangitis (EL), caused by Histoplasma capsulatum variety farciminosum (HCF) is a contagious, chronic disease of equines, characterized by development of nodular lesions in the lymph nodes, lymphatic vessels and skin. It is one of the most important diseases of equines in Ethiopia, causing significant economic loss, particularly in the livelihood of carthorse owners. To date there is neither effective diagnostic nor control measure implemented in the country. Furthermore, there is a shortage of data on the epidemiology of the disease in different regions of this country. The aim of this study was to investigate epidemiology of EL in northern Ethiopia, using the conventional methods as well as nested polymerase chain reaction (PCR). Results The presence of HCF genetic material was confirmed in 44% (84/191) of the carthorses. Subclinical infection was observed in 18.2% (22/121) of the apparently healthy carthorses. Considering the nested PCR as a gold standard, sensitivity and specificity of clinical examination were 74% and 92.5%, respectively, while the area under the ROC curve (AUR) was 0.83 (95% confidence interval, 0.77, 0.896). Moreover, a moderate (k = 0.675) agreement observed between the nested PCR and clinical examination. Conclusions This study demonstrated widespread occurrence of EL in northern Ethiopia, and the advantage of the nested PCR in detecting infection of HCF, even before the clinical symptoms became apparent.

scholarly journals Molecular Identification and Analysis of Multi-Drug Resistant Klebsiella pneumonia

2018 ◽  
Vol 6 (3) ◽  
pp. 279-284
Author(s):  
Rajeswari Ramasamy ◽  
Subha Ashley Thanga Subramanian ◽  
R. Abinaya Rajagopal ◽  
Karthikadevi Muthusamy ◽  
Jesteena Johney ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Bacterial Infections ◽  
Genetic Material ◽  
Multidrug Resistant ◽  
Klebsiella Pneumonia ◽  
Drug Resistant ◽  
Remedial Measures ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Susceptibility Tests

Multidrug resistant Klebsiella pneumoniae was resistant to various antibiotics which are commonly used to treat   against the bacterial infections, and is now emerged as a great risk.  Antibiotic susceptibility tests were performed to determine the scope of drug resistance of the bacteria. Further studies regarding the responsible genetic material were performed by Polymerase Chain Reaction and RFLP techniques. The remedial measures for treating these bacteria were studied with the help of metabolites obtained from various strains.Int. J. Appl. Sci. Biotechnol. Vol 6(3): 279-284

Sign in / Sign up

Export Citation Format

Share Document