scholarly journals Comparison of Four Polymerase Chain Reaction Methods for the Rapid Detection of Human Fecal Pollution in Marine and Inland Waters

2010 ◽  
Vol 2010 ◽  
pp. 1-7 ◽  
Author(s):  
Dave S. Bachoon ◽  
Cortney M. Miller ◽  
Christen P. Green ◽  
Ernesto Otero
Keyword(s):  
Puerto Rico ◽  
Environmental Samples ◽  
Fecal Pollution ◽  
Chain Reaction ◽  
Bifidobacterium Adolescentis ◽  
Fecal Samples ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Positive Results ◽  
Human Specific

We compared the effectiveness of three PCR protocols for the detection ofBifidobacterium adolescentisand one PCR protocol for detectingBacteroidalesas indicators of human fecal pollution in environmental samples. Quantitative PCR indicated that a higher concentration ofB. adolescentisDNA was recovered from sewage samples on the 0.2 μm filters compared to the 0.45 μm filters, and there was no evidence of qPCR inhibitors in the DNA extracts. With the Matsuki method (1999),B. adolescentiswas detected only in undiluted sewage samples. The King method (2007) performed well and detectedB. adolescentisin all of the sewage dilutions (from undiluted to10−4). In contrast, the Bonjoch approach (2004) was effective at detectingB. adolescentisat lower dilutions (10−3) of sewage samples and it gave false positive results with some (3/8) pig fecal samples. Human-specificBacteroidales(HuBacs) were detected in the lower diluents of sewage samples but was positive in pig (6/8) and cattle fecal samples. PCR detection ofB. adolescentisin marine samples from Puerto Rico and freshwater samples from Georgia indicated that the PCR method of King et al. (2007) and the modified Layton method for HuBac were in agreement in detecting human fecal pollution in most sites.

Identification of Bacteroides forsythus in Subgingival Dental Plaque with the Aid of a Rapid PCR Method

1997 ◽  
Vol 76 (7) ◽  
pp. 1376-1380 ◽  
Author(s):  
J.H. Meurman ◽  
J. Wahlfors ◽  
A. Korhonen ◽  
P. Alakuijala ◽  
P. Väisänen ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Subgingival Plaque ◽  
Chain Reaction ◽  
Rapid Pcr ◽  
Microbiological Methods ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Pre Treatment ◽  
Culture Positive ◽  
Positive Results

Bacteroides forsythus has been shown to be prevalent among patients with periodontitis. Conventional microbiological methods used to identify this bacterium, however, are laborious and time-consuming and are therefore not well-suited for screening purposes. We have developed a polymerase chain-reaction (PCR) method which is rapid, specific, and simple to perform and does not require other sample pre-treatment except a brief centrifugation. This method was applied to the detection of B. forsythus in subgingival plaque of 58 periodontitis patients. When compared with the results of conventional culturing, the PCR method always confirmed the culture-positive results, while none of the PCR negative samples was shown to be culture-positive. The PCR method appeared to give more than double the number of samples positive for B. forsythus than culturing (89.7% vs. 37.9%). The analysis requires less than 4 hrs to perform, and is specific only to B. forsythus and sensitive enough to detect fewer than 5 bacteria.

scholarly journals Diversity ofLeptospiraspp. in Rats and Environment from Urban Areas of Sarawak, Malaysia

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Chai Fung Pui ◽  
Lesley Maurice Bilung ◽  
Kasing Apun ◽  
Lela Su’ut
Keyword(s):  
Polymerase Chain Reaction ◽  
Water Samples ◽  
Urban Areas ◽  
Environmental Samples ◽  
Soil Samples ◽  
Chain Reaction ◽  
Prevalence Studies ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Soil And Water

Various prevalence studies onLeptospirain animals and humans, as well as environmental samples, had been conducted worldwide, including Malaysia. However, limited studies have been documented on the presence of pathogenic, intermediate, and saprophyticLeptospirain selected animals and environments. This study was therefore conducted to detectLeptospiraspp. in rats, soil, and water from urban areas of Sarawak using the polymerase chain reaction (PCR) method. A total of 107 rats, 292 soil samples, and 324 water samples were collected from April 2014 to February 2015. PathogenicLeptospirawas present in 5.6% (6/107) of rats, 11.6% (34/292) of soil samples, and 1.9% (6/324) of water samples. IntermediateLeptospirawas present in 2.7% (8/292) of soil samples and 1.9% (6/324) of water samples. SaprophyticLeptospirawas present in 10.3% (11/107) of rats, 1.4% (4/292) of soil samples, and 0.3% (1/324) of water samples. From this study, 76Leptospiraspp. were isolated. Based on DNA sequencing, the dominantLeptospiraspp. circulating in urban areas of Sarawak are pathogenicLeptospira noguchii, intermediateLeptospira wolffiiserovar Khorat, and saprophyticLeptospira meyeri, respectively. Overall, this study provided important surveillance data on the prevalence ofLeptospiraspp. from rats and the environment, with dominant local serovars in urban areas of Sarawak.

scholarly journals Current quantitative polymerase chain reaction to detect severe acute respiratory syndrome coronavirus 2 may give positive results for other described coronavirus

2021 ◽  
Author(s):  
Antonio Martínez-Murcia ◽  
Adrián García-Sirera ◽  
Aaron Navarro ◽  
Patricia Ros-Tárraga ◽  
Laura Pérez
Keyword(s):  
Experimental Data ◽  
Polymerase Chain Reaction ◽  
Severe Acute Respiratory Syndrome ◽  
Environmental Samples ◽  
Quantitative Polymerase Chain Reaction ◽  
Epidemiological Surveillance ◽  
Chain Reaction ◽  
Polymerase Chain ◽  
Positive Results

SUMMARYSome weeks after the first CoVID-19 outbreak, the WHO published some qPCR protocol assays developed by different institutions worldwide. These qPCR designs are being used to detect the presence of SARS-CoV-2 in the population, which allow us to monitore the prevalence of the virus during the pandemic. Moreover, the use of these designs is wide spreading and nowadays they are used to detect SARS-CoV-2 in environmental samples to act as epidemiological surveillance tool. However, at the time of designing the published RT-qPCR assays, a lack of SARS-CoV-2 genomes available may explain a low exclusivity in some cases. In this study, we are reporting experimental data which demonstrate that some of the current qPCR used to detect SARS-CoV-2 may give positive results for other described coronavirus different from SARS-CoV-2.

Optimization of a PCR method for the detection of astrovirus type 1 in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 359-362 ◽  
Author(s):  
F. E. Marx ◽  
M. B. Taylor ◽  
W. O. K. Grabow
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Chain Reaction ◽  
Environmental Waters ◽  
Serotype 1 ◽  
Human Astrovirus ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Improved Technique

An improved technique is described that uses the polymerase chain reaction in the detection of astroviruses with much greater sensitivity than existing methods. It is demonstrated to detect human astrovirus serotype 1 in environmental waters from the Pretoria area.

scholarly journals Toxic cyanobacteria in reservoirs in northeastern Brazil: detection using a molecular method

2010 ◽  
Vol 70 (4) ◽  
pp. 1005-1010 ◽  
Author(s):  
MC. Bittencourt-Oliveira ◽  
DMS. Santos ◽  
NA. Moura
Keyword(s):  
Environmental Samples ◽  
Public Health Problem ◽  
Northeastern Brazil ◽  
Cyanobacterial Blooms ◽  
Molecular Method ◽  
Chain Reaction ◽  
Toxic Cyanobacteria ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Brazilian Populations

Cyanobacterial blooms are a frequent occurrence in northeastern Brazil and constitute a serious public health problem. Using the polymerase chain reaction (PCR) method, eleven environmental samples with cyanobacteria from seven reservoirs were used to determine the presence of the gene involved in microcystin biosynthesis (mcyB). Two sets of oligonucleotide primers were designed from the sequencing of Brazilian populations of microcystin producing cyanobacteria (mcyB-F/R and mcyB-F/R-A). The presence of the mcyB gene involved in microcystin biosynthesis was found in all samples, indicating the potential of this gene for producing the toxin. The PCR method proved sensitive and appropriate for the detection of potential producers of microcystins in environmental samples. Its ability to reveal potentially toxic cyanobacteria demonstrates that it can be a valuable tool in the monitoring of blooms.

scholarly journals Cost-effectiveness of diagnostic strategies to identify Mycobacterium avium subspecies paratuberculosis super-shedder cows in a large dairy herd using antibody enzyme-linked immunosorbent assays, quantitative real-time polymerase chain reaction, and bacterial culture

2012 ◽  
Vol 24 (5) ◽  
pp. 821-832 ◽  
Author(s):  
Sharif S. Aly ◽  
Randall J. Anderson ◽  
Robert H. Whitlock ◽  
Terry L. Fyock ◽  
Susan C. McAdams ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Cost Effectiveness ◽  
Mycobacterium Avium ◽  
Environmental Samples ◽  
Dairy Herd ◽  
Chain Reaction ◽  
Fecal Samples ◽  
Diagnostic Strategies ◽  
Polymerase Chain ◽  
The Cost

Diagnostic strategies to detect Mycobacterium avium subsp. paratuberculosis (MAP) super-shedder cows in dairy herds have been minimally studied. The objective of the current study was to compare the cost-effectiveness of strategies for identification of MAP super-shedders on a California dairy herd of 3,577 cows housed in free-stall pens. Eleven strategies that included serum or milk enzyme-linked immunosorbent assay (ELISA), quantitative real-time polymerase chain reaction (qPCR) or culture of environmental samples, pooled or individual cow fecal samples, or combinations thereof were compared. Nineteen super-shedders (0.5%) were identified by qPCR and confirmed by culture as cows shedding ≥10,000 colony forming units (CFU)/g feces (median of 30,000 CFU/g feces). A stratified random sample of the study herd based on qPCR results of fecal pools was the most sensitive (74%) strategy and had the highest cost ($5,398/super-shedder). The reference strategy with the lowest cost ($1,230/super-shedder) and sensitivity (47%) included qPCR testing of fecal samples from ELISA-positive lactating (milk) and nonlactating (serum) cows housed in pens with the highest MAP bioburden. The most cost-effective alternative to the reference was to perform qPCR testing of fecal samples from ELISA-positive cows (milk and serum for milking and dry cows, respectively) for a sensitivity of 68% and cost of $2,226/super-shedder. In conclusion, diagnostic strategies varied in their cost-effectiveness depending on the tests, specimen type, and labor costs. Initial qPCR testing of environmental samples from free-stall pens to target cows in pens with the highest MAP bioburden for further testing can improve the cost-effectiveness of strategies for super-shedder identification.

Prevalence of SHV-extended spectrum β-lactamase producing carbapenem –resistantKlebsiellapneumoniae among patients with lower respiratory tractinfections in Babylon Province-Iraq.

2018 ◽  
Vol 9 (SPL1) ◽  
Author(s):  
Fatima Moeen Abbas
Keyword(s):  
Resistance Rate ◽  
Combination Method ◽  
Diffusion Method ◽  
Disk Diffusion Method ◽  
Carbapenem Resistant ◽  
Extended Spectrum ◽  
Pcr Method ◽  
Polymerase Chain ◽  
Tract Infections ◽  
Positive Results

This study was carried out to screen the prevalence of Klebsiella pneumoniae isolated from patients with lower respiratory tract infections in Babylon province.From December,2015 to the end of March,2016,a total of 100 sputum samples were collected from patients visited or hospitalized Merjan Teaching Hospital and Al- Hashimya General Hospital. Fifteenth (65%) isolates were identified as Klebsiellapneumoniae. All bacterial isolates were evaluated for extended spectrum β-lactamase (ESBL) production phenotypically using disk combination method. Eleven (73.3%) isolates were detected as ESBL-producers. Kirby-Bauer disk diffusion method was employed to determine resistance profile of ESBLs-positive isolates. Higher rates of resistance were observed for ampicillin and piperacillin antibiotics with (81.8%) and (72.7%) resistance rate, respectively, while the lowest rate was noticed for imipenem antibiotic (14.28%). Carbapenem-resistant isolates were investigated for blaSHV gene by Polymerase Chain Reaction (PCR) method, 2 (100%) isolates gave positive results.

Polymerase chain reaction amplification and typing of rotavirus in environmental samples

1995 ◽  
Vol 31 (5-6) ◽  
pp. 371-374 ◽  
Author(s):  
R. Gajardo ◽  
R. M. Pintó ◽  
A. Bosch
Keyword(s):  
Polymerase Chain Reaction ◽  
Environmental Samples ◽  
Polymerase Chain Reaction Amplification ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Group A ◽  
Reaction Amplification ◽  
Stool Specimens ◽  
Polymerase Chain

A reverse transcription polymerase chain reaction (RT-PCR) assay is described that has been developed for the detection and serotyping of group A rotavirus in stool specimens and concentrated and non-concentrated sewage specimens.

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