Evaluation of CrAssphage Marker for Tracking Fecal Contamination in River Water in Nepal

Ward, Lauren; Shrestha, Rajani Ghaju; Tandukar, Sarmila; Sherchand, Jeevan Bahadur; Haramoto, Eiji; Sherchan, Samendra P.

doi:10.1007/s11270-020-04648-1

Cited by 14 publications

(5 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…According to previous studies that explored crAssphage identification and prevalence, a trend exists between the detection rates of Western and Eastern human fecal samples. The detection rates in Western regions such as Australia ( Ahmed et al, 2018 ), the United States ( Park et al, 2020 ), and Spain ( García-Aljaro et al, 2017 ) are relatively higher than that in Eastern regions such as South Korea ( Nam et al, 2022 ), China ( Liang et al, 2018 ; Li et al, 2021 ), Nepal ( Ward et al, 2020 ), and Thailand ( Kongprajug et al, 2019 ). For instance, in a detection experiment using the combination CrAssBP, crAssphage was detected in 45 of 68 American fecal samples (66.2%) ( Park et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Improvement of crAssphage detection/quantification method and its extensive application for food safety

2023

View full text Add to dashboard Cite

Water-borne diseases are usually caused by the fecal–oral transmission of human fecal pathogens. Traditionally, coliforms and enterococci are widely used as indicator bacteria, but they do not allow to differentiate between human and animal fecal contamination. Owing to its presence only in the human gut environment, crAssphage has been suggested as an alternative indicator of human fecal contamination to overcome the above challenges. In this study, 139 human and 89 animal fecal samples (e.g., chicken, cow, dog, pig, pigeon, and mouse) were collected. For the rapid detection of human crAssphage in fecal samples, quantitative real-time PCR (qPCR) was performed using five different oligonucleotide primer/probe combinations. These included three previously reported oligonucleotide primer/probe combinations (RQ, CPQ056, and CrAssBP) and two newly developed combinations (ORF00018-targeting CrAssPFL1 and ORF00044-targeting CrAssPFL2). The detection rate (crAssphage-positive rate) in human fecal samples were 23.0, 30.2, 28.8, 20.1, and 30.9%, respectively, suggesting CrAssPFL2 showed the highest detection rate. Furthermore, the lowest copy numbers (436.16 copy numbers) could be detected using the CrAssPFL2 combination. Interestingly, no difference in crAssphage detection rates was found between healthy people and intestinal inflammatory patients. As expected, no crAssphage was detected in any animal fecal samples, indicating its human specificity. Furthermore, qPCR analysis of sewage samples collected from five different sewage treatment plants revealed that they were all contaminated with 105.71 copy numbers/mL of crAssphage on average. The simulation test of crAssphage-contaminated food samples also confirmed that the detection limit was from 107.55 copy numbers of crAssphage in foods. Therefore, the newly developed and optimized qPCR would be useful for the sensitive detection of crAssphage while identifying the source of human fecal contamination.

show abstract

Section: Discussionmentioning

confidence: 99%

Improvement of crAssphage detection/quantification method and its extensive application for food safety

2023

View full text Add to dashboard Cite

show abstract

“…Another study in the UK represented two to six orders of crAssphage CPQ_056 and up to three orders of HPyVs (JC) in freshwater, with moderate correlation (Spearman correlation coefficient of 0.49) (Farkas et al, 2019, 2018). A river in Nepal was monitored for crAssphage (CPQ_056) at four to seven orders, expressed as copies/100 mL, and HPyVs (JC and BK) of up to six orders; moderate correlation (Spearman’s rank-order correlation coefficient of 0.47) was found between crAssphage and BK, while no correlation was found between crAssphage and JC (Tandukar et al, 2018; Ward et al, 2020). However, although HPyVs were lower in abundance than crAssphage, they exhibited a higher positive rate in freshwater samples and, thus, presented higher benefits for water quality monitoring, indicating human pollution.…”

Section: Discussionmentioning

confidence: 99%

Superior performance of human wastewater-associated viral markers compared to bacterial markers in tropical environments

Sangkaew

Kongprajug

Chyerochana

et al. 2020

Preprint

View full text Add to dashboard Cite

Identifying human sewage contamination via microbial source tracking (MST) marker genes has proven useful for effective water quality management worldwide; however, performance evaluations for these genes in tropical areas are limited. Therefore, this research assessed four human-associated MST marker genes in aquatic environments of Central Thailand: human polyomaviruses (JC and BK viruses [HPyVs]), bacteriophage crAssphage (CPQ_056), Lachnospiraceae Lachno3, and Bacteroides BacV6-21. HPyV and crAssphage assays were highly sensitive and specific to sewage (n = 19), with no cross-detection in 120 swine, cattle, chicken, duck, goat, sheep, and buffalo composite fecal samples. Lachno3 and BacV6-21 demonstrated high sensitivity but moderate specificity; however, using both markers could improve specificity to >0.80 (max value of 1.00). The most abundant markers in sewage were Lachno3 and BacV6-21 (5.42-8.02 and non-detected-8.05 log10 copies/100 mL), crAssphage (5.28-7.38 log10 copies/100 mL), and HPyVs (3.66-6.53 log10 copies/100 mL), respectively. HPyVs showed higher levels (up to 4.33 log10 copies/100 mL) and higher detection rates (92.7%) in two coastal beaches (n = 41) than crAssphage (up to 3.51 log10 copies/100 mL and 56.1%). HPyVs were also found at slightly lower levels (up to 5.10 log10 copies/100 mL), but at higher detection rates (92.6%), in a freshwater canal (n = 27) than crAssphage (up to 5.21 log10 copies/100 mL and 88.9%). Overall, both HPyVs and crAssphage are suggested as human sewage-associated MST markers in aquatic environments of Central Thailand. This study underlines the importance of characterizing and validating MST markers in host groups and environmental waters before including them in a water quality management toolbox.

show abstract

“…1A ). Based on previous studies ( 36 , 37 , 40 , 49 ), we predict that crAssphage in contaminated sites will be more abundant and diverse. We selected three conserved capsid and genome-packaging proteins (terminase large subunit, portal proteins, and major capsid proteins) as markers for detecting crAss-like phages in samples collected from both pristine and contaminated sites.…”

Section: Introductionmentioning

confidence: 86%

“…However, several studies have also demonstrated that crAssphage may not occur exclusively in the human gut, but may be present in the guts of animals and feces, albeit at lower concentrations ( 36 , 47 , 48 ). Nevertheless, there is an urgent need to investigate the suitability of using crAssphage as a biomarker of fecal contamination in underrepresented and understudied geographic locations such as Africa, to assess the feasibility of using the virus as a universal marker ( 48 – 50 ).…”

Section: Introductionmentioning

confidence: 99%

CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

et al. 2023

View full text Add to dashboard Cite

show abstract

Evaluation of CrAssphage Marker for Tracking Fecal Contamination in River Water in Nepal

Cited by 14 publications

References 31 publications

Improvement of crAssphage detection/quantification method and its extensive application for food safety

Improvement of crAssphage detection/quantification method and its extensive application for food safety

Superior performance of human wastewater-associated viral markers compared to bacterial markers in tropical environments

CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water

Contact Info

Product

Resources

About