Interlaboratory accuracy and precision among results of three sewage-associated marker genes in urban environmental estuarine waters and freshwater streams

Ahmed, Warish; Payyappat, Sudhi; Cassidy, Michele; Harrison, Nathan; Besley, C.H.

doi:10.1016/j.scitotenv.2020.140071

Cited by 10 publications

(5 citation statements)

References 32 publications

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“…The validation of a protocol is a challenge because several variables should be considered and many factors could affect the goodness of the results and cause a systematic bias or the increase in several forms of variabilities ( Ahmed et al, 2020 ). There are at least two strong factors to control, that are, intra- and inter-laboratories variability ( Ahmed et al, 2020 ); both variabilities could strongly affect the quality of results.…”

Section: Resultsmentioning

confidence: 99%

“…Two-way joining suggests a low intra-laboratory variability within each RU. Intra-laboratory variability is linked to several factors and generally could not be controlled because it is a strong source of error and is responsible of failing of some protocols ( Ahmed et al, 2020 ). In this research, the clustering of the replicates from each RU in the same region of y -axis suggests that the protocol had a low intra-laboratory variability, probably due to the application of standardized conditions and a common flowsheet, as detailed in the section “Materials and Methods”.…”

Section: Resultsmentioning

confidence: 99%

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Validation of a Standard Protocol to Assess the Fermentative and Chemical Properties of Saccharomyces cerevisiae Wine Strains

et al. 2022

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This paper reports on a common experiment performed by 17 Research Units of the Italian Group of Microbiology of Vine and Wine (GMVV), which belongs to the Scientific Society SIMTREA, with the aim to validate a protocol for the characterization of wine strains of Saccharomyces cerevisiae. For this purpose, two commercial S. cerevisiae strains (EC 1118 and AWRI796) were used to carry out inter-laboratory-scale comparative fermentations using both synthetic medium and grape musts and applying the same protocol to obtain reproducible, replicable, and statistically valid results. Ethanol yield, production of acetic acid, glycerol, higher alcohols, and other volatile compounds were assessed. Moreover, the Fourier transform infrared spectroscopy was also applied to define the metabolomic fingerprint of yeast cells from each experimental trial. Data were standardized as unit of compounds or yield per gram of sugar (glucose and fructose) consumed throughout fermentation, and analyzed through parametric and non-parametric tests, and multivariate approaches (cluster analysis, two-way joining, and principal component analysis). The results of experiments carried out by using synthetic must showed that it was possible to gain comparable results from three different laboratories by using the same strains. Then, the use of the standardized protocol on different grape musts allowed pointing out the goodness and the reproducibility of the method; it showed the main traits of the two yeast strains and allowed reducing variability amongst independent batches (biological replicates) to acceptable levels. In conclusion, the findings of this collaborative study contributed to the validation of a protocol in a specific synthetic medium and in grape must and showed how data should be treated to gain reproducible and robust results, which could allow direct comparison of the experimental data obtained during the characterization of wine yeasts carried out by different research laboratories.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Validation of a Standard Protocol to Assess the Fermentative and Chemical Properties of Saccharomyces cerevisiae Wine Strains

et al. 2022

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“…In recent years, digital PCR (dPCR) has gained attention as a novel approach to detect and quantify nucleic acids [ 24 , 25 ]. The major benefit of dPCR over qPCR is the direct absolute quantification of virus genome copy numbers in a sample without the necessity of external calibration.…”

Section: Direct Virus Concentration and Detection Methods- Pcr Basedmentioning

confidence: 99%

Wastewater-Based Epidemiology to monitor COVID-19 outbreak: Present and future diagnostic methods to be in your radar

Barceló

2020

Case Studies in Chemical and Environmental Engineering

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The WHO has declared the COVID-19 epidemic on January 31, 2020. This virus has infected millions of people worldwide in just a few months. Shortly afterwards, the National Medical Products Administration (NMPA) announced nucleic acid testing as the gold standard for virus detection. Antibody testing is used as well as a supplementary test for suspected cases where nucleic acid detection was negative. In short, nucleic acid–based polymerase chain reaction (PCR) is the mainstream detection method for clinical samples as well as for the detection of SARS-CoV-2 in wastewaters. First data collected around the globe were reported in the last few months being part of the so-called Wastewater-Based Epidemiology (WBE) approach. Selection of concentration methods and primers, laboratory inter-comparison and various modalities of PCR detection of the virus in complex wastewater matrices were flagged up as main bullets that require urgent improvement. Novel approaches to enhance sensitivity, speed and automate streamlined virus detection will be discussed here as well. This list comprises devices mainly used for clinical purposes like Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), Digital PCR, Lab-on-a-chip (LOC) and related platforms as well as Biosensors. The last part will be devoted to the identification of biomolecules to target Covid-19 outbreak based on inflammatory response biomarkers among others. To this end this opinion paper brings for discussion the issue of PCR detection and its limitations as well as new diagnostic methods in WBE.

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“…When expanding the use of quantitative wastewater-based epidemiology to other viruses such as SARS-CoV-2, it is necessary to determine the analytic uncertainty at each of the following stages: (1) virus shedding into sewers; (2) sample collection; (3) transportation and storage; (4) concentration; (5) quantitative analysis of the virus concentration in wastewater (including determinations of linearity of response, absolute limits of detection (LOD) and quantitation (LOQ), and inter-experiment repeatability over the dynamic range); and (6) normalization and interpretation, including inferring of numbers of infected individuals [ 58 , 59 , 60 , 61 ]. Standardized protocols, laboratory equipment, sample processing strategies, appropriate quality controls, methods for preparing standard curves, and performance limits need to be established for each new pathogen in order to enable inter-laboratory comparisons [ 62 , 63 ]. As for poliovirus surveillance [ 10 ], it is essential to develop explicit performance standards and proficiency testing panels to validate the methods selected to enhance the ability to compare findings between laboratories [ 64 ].…”

Section: Discussionmentioning

confidence: 99%

Inferring Numbers of Wild Poliovirus Excretors Using Quantitative Environmental Surveillance

et al. 2021

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Response to and monitoring of viral outbreaks can be efficiently focused when rapid, quantitative, kinetic information provides the location and the number of infected individuals. Environmental surveillance traditionally provides information on location of populations with contagious, infected individuals since infectious poliovirus is excreted whether infections are asymptomatic or symptomatic. Here, we describe development of rapid (1 week turnaround time, TAT), quantitative RT-PCR of poliovirus RNA extracted directly from concentrated environmental surveillance samples to infer the number of infected individuals excreting poliovirus. The quantitation method was validated using data from vaccination with bivalent oral polio vaccine (bOPV). The method was then applied to infer the weekly number of excreters in a large, sustained, asymptomatic outbreak of wild type 1 poliovirus in Israel (2013) in a population where >90% of the individuals received three doses of inactivated polio vaccine (IPV). Evidence-based intervention strategies were based on the short TAT for direct quantitative detection. Furthermore, a TAT shorter than the duration of poliovirus excretion allowed resampling of infected individuals. Finally, the method documented absence of infections after successful intervention of the asymptomatic outbreak. The methodologies described here can be applied to outbreaks of other excreted viruses such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), where there are (1) significant numbers of asymptomatic infections; (2) long incubation times during which infectious virus is excreted; and (3) limited resources, facilities, and manpower that restrict the number of individuals who can be tested and re-tested.

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Interlaboratory accuracy and precision among results of three sewage-associated marker genes in urban environmental estuarine waters and freshwater streams

Cited by 10 publications

References 32 publications

Validation of a Standard Protocol to Assess the Fermentative and Chemical Properties of Saccharomyces cerevisiae Wine Strains

Validation of a Standard Protocol to Assess the Fermentative and Chemical Properties of Saccharomyces cerevisiae Wine Strains

Wastewater-Based Epidemiology to monitor COVID-19 outbreak: Present and future diagnostic methods to be in your radar

Inferring Numbers of Wild Poliovirus Excretors Using Quantitative Environmental Surveillance

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