Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters

Zimmer‐Faust, Amity G.; Thulsiraj, Vanessa; Madi, Tania; Hanley, Kaitlyn T.; Ebentier, Darcy L.; Byappanahalli, Muruleedhara N.; Layton, Blythe A.; Raith, Meredith R.; Boehm, Alexandria B.; Griffith, John F.; Holden, Patricia A.; Shanks, Orin C.; Weisberg, Stephen B.; Jay, Jennifer A.

doi:10.1016/j.jenvman.2014.01.029

Cited by 20 publications

(18 citation statements)

References 29 publications

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“…Moreover, qPCR usually requires lower concentrations of target genomic DNA (< 1000X) 14 , 35 . In addition, environmental samples may harbor several kinds of substances that partially inhibit the amplification; the use of qPCR may result in a lower incidence of false negatives and a higher reliability of results 31 . Regarding costs, when reagents and kits are considered, some studies show that there is an equivalence in costs between conventional PCR and qPCR (using…”

Section: Introductionmentioning

confidence: 99%

Quantitative vs. Conventional PCR for Detection of Human Adenoviruses in Water and Sediment Samples

Staggemeier

Bortoluzzi

Heck

et al. 2015

Rev. Inst. Med. trop. S. Paulo

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SUMMARYHuman Adenoviruses (HAdV) are notably resistant in the environment. These agents may serve as effective indicators of fecal contamination, and may act as causative agents of a number of different diseases in human beings. Conventional polymerase chain reaction (PCR) and, more recently, quantitative PCR (qPCR) are widely used for detection of viral agents in environmental matrices. In the present study PCR and SYBR(r)Green qPCR assays were compared for detection of HAdV in water (55) and sediments (20) samples of spring and artesian wells, ponds and streams, collected from dairy farms. By the quantitative methodology HAdV were detected in 87.3% of the water samples and 80% of the sediments, while by the conventional PCR 47.3% and 35% were detected in water samples and sediments, respectively.

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Section: Introductionmentioning

confidence: 99%

Quantitative vs. Conventional PCR for Detection of Human Adenoviruses in Water and Sediment Samples

Staggemeier

Bortoluzzi

Heck

et al. 2015

Rev. Inst. Med. trop. S. Paulo

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“…The two human-associated assays consisted of: 1) Taq HF183, which has been shown to be associated with the species Bacteroides dorei (Haugland et al 2010) and 2) HumM2 (Shanks et al 2009). The gull/pelican fecal marker assay used in this study detects Catellicoccus marimammalium , a bacterial species found in feces of gulls and pelicans (Lu et al 2008; Riedel et al 2014; Sinigalliano et al 2013). Sand samples from the microcosms were also analyzed by qPCR for enterococci and for the GenBac species, which detects many of the Bacteroidales subgroups (US EPA Method B.…”

Section: Methodsmentioning

confidence: 99%

Sources and Persistence of Fecal Indicator Bacteria and Bacteroidales in Sand as Measured by Culture-Based and Culture-Independent Methods: a Case Study at Santa Monica Pier, California

Mika

Chavarria

Imamura

et al. 2017

Water Air Soil Pollut

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This study investigated causes of persistent fecal indicator bacteria (FIB) in beach sand under the pier in Santa Monica, CA. FIB levels were up to 1,000 times higher in sand underneath the pier than that collected from adjacent to the pier, with the highest concentrations under the pier in spring and fall. Escherichia coli (EC) and enterococci (ENT) under the pier were significantly positively correlated with moisture (ρ = 0.61, p < 0.001, n = 59; ρ = 0.43, p < 0.001, n = 59, respectively), and ENT levels measured by qPCR (qENT) were much higher than those measured by membrane filtration (cENT). Microcosm experiments tested the ability of EC, qENT, cENT, and general Bacteroidales (GenBac) to persist under in-situ moisture conditions (10% and 0.1%). Decay rates of qENT, cENT, and GenBac were not significantly different from zero at either moisture level, while decay rates for EC were relatively rapid during the microcosm at 10% moisture (k = 0.7 days−1). Gull/pelican marker was detected at eight of 12 sites and no human-associated markers (TaqHF183 and HumM2) were detected at any site during a one-day site survey. Results from this study indicate that the high levels of FIB observed likely stem from environmental sources combined with high persistence of FIB under the pier.

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“…Technology transfer, analytical costs, and trained personnel needs are some of the important factors to consider in implementing advanced technologies, such as qPCR, in water quality monitoring programs (Riedel et al, 2014). For instance, high volume laboratories require more analytical time for processing samples to obtain results in a timely manner, which can only be achieved with high throughput capabilities or multiple thermal cyclers.…”

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confidence: 99%

“…For instance, high volume laboratories require more analytical time for processing samples to obtain results in a timely manner, which can only be achieved with high throughput capabilities or multiple thermal cyclers. While there are instances of successful implementation of qPCR technology in monitoring programs (Dorevitch et al, 2017; Ferretti et al, 2013), a broader application of this technology remains years away due, in part, to the cost of technology transfer (Riedel et al, 2014). This situation is particularly relevant to small agencies or local park districts that are directly responsible for running water quality monitoring programs.…”

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confidence: 99%

Real‐Time Water Quality Monitoring at a Great Lakes National Park

et al. 2018

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Quantitative polymerase chain reaction (qPCR) was used by the USEPA to establish new recreational water quality criteria in 2012 using the indicator bacteria enterococci. The application of this method has been limited, but resource managers are interested in more timely monitoring results. In this study, we evaluated the efficacy of qPCR as a rapid, alternative method to the time‐consuming membrane filtration (MF) method for monitoring water at select beaches and rivers of Sleeping Bear Dunes National Lakeshore in Empire, MI. Water samples were collected from four locations (Esch Road Beach, Otter Creek, Platte Point Bay, and Platte River outlet) in 2014 and analyzed for culture‐based (MF) and non‐culture‐based (i.e., qPCR) endpoints using Escherichia coli and enterococci bacteria. The MF and qPCR enterococci results were significantly, positively correlated overall (r = 0.686, p < 0.0001, n = 98) and at individual locations as well, except at the Platte River outlet location: Esch Road Beach (r = 0.441, p = 0.031, n = 24), Otter Creek (r = 0.592, p = 0.002, n = 24), and Platte Point Bay (r = 0.571, p = 0.004, n = 24). Similarly, E. coli MF and qPCR results were significantly, positively correlated (r = 0.469, p < 0.0001, n = 95), overall but not at individual locations. Water quality standard exceedances based on enterococci levels by qPCR were lower than by MF method: 3 and 16, respectively. Based on our findings, we conclude that qPCR may be a viable alternative to the culture‐based method for monitoring water quality on public lands. Rapid, same‐day results are achievable by the qPCR method, which greatly improves protection of the public from water‐related illnesses. Core Ideas Genomic methods are increasingly used in environmental monitoring programs. qPCR provides timely water quality results at a national park. Culture‐based and qPCR results were correlated. qPCR results (enterococci) yielded fewer beach advisories.

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Detection limits and cost comparisons of human- and gull-associated conventional and quantitative PCR assays in artificial and environmental waters

Cited by 20 publications

References 29 publications

Quantitative vs. Conventional PCR for Detection of Human Adenoviruses in Water and Sediment Samples

Quantitative vs. Conventional PCR for Detection of Human Adenoviruses in Water and Sediment Samples

Sources and Persistence of Fecal Indicator Bacteria and Bacteroidales in Sand as Measured by Culture-Based and Culture-Independent Methods: a Case Study at Santa Monica Pier, California

Real‐Time Water Quality Monitoring at a Great Lakes National Park

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