A method for correcting underestimation of enteric pathogen genome quantities in environmental samples

Liu, P; Amin, N; Miah, R; Foster, T; Raj, S; Corpuz, MJB; Rahman, M; Willetts, J; Moe, CL

A method for correcting underestimation of enteric pathogen genome quantities in environmental samples

Liu, P Amin, N Miah, R Foster, T

Raj, S Corpuz, MJB Rahman, M Willetts, J Moe, CL

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Publisher:: Elsevier BV
Publication Type:: Journal Article
Citation:: Journal of Microbiological Methods, 2021, 189, pp. 1-10
Issue Date:: 2021-09

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Field	Value	Language
dc.contributor.author	Liu, P
dc.contributor.author	Amin, N
dc.contributor.author	Miah, R
dc.contributor.author	Foster, T https://orcid.org/0000-0003-1738-3450
dc.contributor.author	Raj, S
dc.contributor.author	Corpuz, MJB
dc.contributor.author	Rahman, M
dc.contributor.author	Willetts, J
dc.contributor.author	Moe, CL
dc.date.accessioned	2021-10-31T02:31:09Z
dc.date.available	2021-10-31T02:31:09Z
dc.date.issued	2021-09
dc.identifier.citation	Journal of Microbiological Methods, 2021, 189, pp. 1-10
dc.identifier.issn	0167-7012
dc.identifier.issn	1872-8359
dc.identifier.uri	http://hdl.handle.net/10453/151281
dc.description.abstract	Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathogens (Shigella/EIEC, Salmonella Typhi, Vibrio cholera, Norovirus, and Giardia) in samples from open drains, canals, floodwater, septic tanks, and anaerobic baffled reactors (ABR) collected in Mirpur, Dhaka, Bangladesh from April to October 2019. Overall, the grab and sediment samples showed low inhibition but the ultrafiltration samples collected from open drain had significantly higher (P = 0.0049) degree of PCR inhibition (median Ct = 31.06) compared to the extraction controls (Ct = 28.54). We developed a two-step method to adjust underestimation of pathogen quantities due to PCR inhibition and non-optimum PCR efficiency. Compared to other sample types, ultrafiltration samples demonstrated a wide range of concentration increase (1.0%–182.5%) by pathogens after adjusting for PCR inhibition and non-optimum efficiencies. These quantitative qPCR assays are successful in quantifying multiple enteric pathogens in environmental samples, and the adjustment method would be useful for correcting underestimates of pathogen quantities due to partial PCR inhibition and non-optimum efficiency.
dc.language	en
dc.publisher	Elsevier BV
dc.relation	Water and Sanitation for the Urban Poor
dc.relation.ispartof	Journal of Microbiological Methods
dc.relation.isbasedon	10.1016/j.mimet.2021.106320
dc.rights	info:eu-repo/semantics/closedAccess
dc.subject	0605 Microbiology, 1108 Medical Microbiology
dc.subject.classification	Microbiology
dc.title	A method for correcting underestimation of enteric pathogen genome quantities in environmental samples
dc.type	Journal Article
utslib.citation.volume	189
utslib.for	0605 Microbiology
utslib.for	1108 Medical Microbiology
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/DVC (Research)
pubs.organisational-group	/University of Technology Sydney/DVC (Research)/Institute For Sustainable Futures
pubs.organisational-group	/University of Technology Sydney/Strength - ISF - Institute for Sustainable Futures
utslib.copyright.status	closed_access	*
pubs.consider-herdc	true
dc.date.updated	2021-10-31T02:31:08Z
pubs.publication-status	Published
pubs.volume	189

Abstract:

Exposure to enteric pathogens in the environment poses a serious risk for infection and disease. The accurate detection and quantification of enteric pathogens in environmental samples is critical for understanding pathogen transport and fate and developing risk assessment models. In this study, we successfully applied TaqMan real-time PCR assays to quantitatively detect five human-specific pathogens (Shigella/EIEC, Salmonella Typhi, Vibrio cholera, Norovirus, and Giardia) in samples from open drains, canals, floodwater, septic tanks, and anaerobic baffled reactors (ABR) collected in Mirpur, Dhaka, Bangladesh from April to October 2019. Overall, the grab and sediment samples showed low inhibition but the ultrafiltration samples collected from open drain had significantly higher (P = 0.0049) degree of PCR inhibition (median Ct = 31.06) compared to the extraction controls (Ct = 28.54). We developed a two-step method to adjust underestimation of pathogen quantities due to PCR inhibition and non-optimum PCR efficiency. Compared to other sample types, ultrafiltration samples demonstrated a wide range of concentration increase (1.0%–182.5%) by pathogens after adjusting for PCR inhibition and non-optimum efficiencies. These quantitative qPCR assays are successful in quantifying multiple enteric pathogens in environmental samples, and the adjustment method would be useful for correcting underestimates of pathogen quantities due to partial PCR inhibition and non-optimum efficiency.

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http://hdl.handle.net/10453/151281