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Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters

Overview of attention for article published in Journal of Microbiological Methods, April 2016
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  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (80th percentile)
  • High Attention Score compared to outputs of the same age and source (95th percentile)

Mentioned by

blogs
1 blog
policy
1 policy source

Citations

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16 Dimensions

Readers on

mendeley
28 Mendeley
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Title
Multi-laboratory survey of qPCR enterococci analysis method performance in U.S. coastal and inland surface waters
Published in
Journal of Microbiological Methods, April 2016
DOI 10.1016/j.mimet.2016.01.017
Pubmed ID
Authors

Richard A. Haugland, Shawn Siefring, Manju Varma, Kevin H. Oshima, Mano Sivaganesan, Yiping Cao, Meredith Raith, John Griffith, Stephen B. Weisberg, Rachel T. Noble, A. Denene Blackwood, Julie Kinzelman, Tamara Anan’eva, Rebecca N. Bushon, Erin A. Stelzer, Valarie J. Harwood, Katrina V. Gordon, Christopher Sinigalliano

Abstract

Quantitative polymerase chain reaction (qPCR) has become a frequently used technique for quantifying enterococci in recreational surface waters, but there are several methodological options. Here we evaluated how three method permutations, type of mastermix, sample extract dilution and use of controls in results calculation, affect method reliability among multiple laboratories with respect to sample interference. Multiple samples from each of 22 sites representing an array of habitat types were analyzed using EPA Method 1611 and 1609 reagents with full strength and five-fold diluted extracts. The presence of interference was assessed three ways: using sample processing and PCR amplifications controls; consistency of results across extract dilutions; and relative recovery of target genes from spiked enterococci in water sample compared to control matrices with acceptable recovery defined as 50 to 200%. Method 1609, which is based on an environmental mastermix, was found to be superior to Method 1611, which is based on a universal mastermix. Method 1611 had over a 40% control assay failure rate with undiluted extracts and a 6% failure rate with diluted extracts. Method 1609 failed in only 11% and 3% of undiluted and diluted extracts analyses. Use of sample processing control assay results in the delta-delta Ct method for calculating relative target gene recoveries increased the number of acceptable recovery results. Delta-delta tended to bias recoveries from apparent partially inhibitory samples on the high side which could help in avoiding potential underestimates of enterococci - an important consideration in a public health context. Control assay and delta-delta recovery results were largely consistent across the range of habitats sampled, and among laboratories. The methodological option that best balanced acceptable estimated target gene recoveries with method sensitivity and avoidance of underestimated enterococci densities was Method 1609 without extract dilution and using the delta-delta calculation method. The applicability of this method can be extended by the analysis of diluted extracts to sites where interference is indicated but, particularly in these instances, should be confirmed by augmenting the control assays with analyses for target gene recoveries from spiked target organisms.

Mendeley readers

The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 28 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 8 29%
Student > Master 6 21%
Student > Ph. D. Student 5 18%
Other 3 11%
Student > Bachelor 3 11%
Other 2 7%
Unknown 1 4%
Readers by discipline Count As %
Environmental Science 9 32%
Biochemistry, Genetics and Molecular Biology 4 14%
Engineering 3 11%
Agricultural and Biological Sciences 2 7%
Immunology and Microbiology 2 7%
Other 1 4%
Unknown 7 25%

Attention Score in Context

This research output has an Altmetric Attention Score of 9. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 01 January 2021.
All research outputs
#3,205,725
of 19,862,278 outputs
Outputs from Journal of Microbiological Methods
#201
of 2,220 outputs
Outputs of similar age
#53,646
of 277,526 outputs
Outputs of similar age from Journal of Microbiological Methods
#2
of 20 outputs
Altmetric has tracked 19,862,278 research outputs across all sources so far. Compared to these this one has done well and is in the 83rd percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,220 research outputs from this source. They receive a mean Attention Score of 3.5. This one has done particularly well, scoring higher than 90% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 277,526 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 80% of its contemporaries.
We're also able to compare this research output to 20 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 95% of its contemporaries.