Evidence map›Paper›PMID 33964239›Full record

ArticleThe Lancet. Planetary health2021

Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study.

Rachael Lappan, Rebekah Henry, Steven L Chown, Stephen P Luby, Ellen E Higginson, Lamiya Bata, Thanavit Jirapanjawat, Christelle Schang, John J Openshaw, Joanne O'Toole and 9 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in The Lancet. Planetary health, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
35citing papers in PubMed, 2 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

35 citing papers in PubMed, 2 syntheses or guidelines pooled it.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

19 authors.

Rachael LappanDepartment of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; School of Biological Sciences, Monash University, Clayton, VIC, Australia.
Rebekah HenryDepartment of Civil Engineering, Monash University, Clayton, VIC, Australia.
Steven L ChownSchool of Biological Sciences, Monash University, Clayton, VIC, Australia.
Stephen P LubyDivision of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Ellen E HigginsonCambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK.
Lamiya BataDepartment of Civil Engineering, Monash University, Clayton, VIC, Australia.
Thanavit JirapanjawatDepartment of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; School of Biological Sciences, Monash University, Clayton, VIC, Australia.
Christelle SchangDepartment of Civil Engineering, Monash University, Clayton, VIC, Australia. Electronic address: chris.greening@monash.edu.
John J OpenshawDivision of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA.
Joanne O'TooleSchool of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia.
Audrie LinDivision of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, CA, USA.
Autiko TelaSchool of Public Health, Fiji National University, Suva, Fiji.
Amelia TuragabeciSchool of Public Health, Fiji National University, Suva, Fiji.
Tony H F WongWater Sensitive Cities Institute, Monash University, Clayton, VIC, Australia.
Matthew A FrenchMonash Sustainable Development Institute, Monash University, Clayton, VIC, Australia.
Rebekah R BrownMonash Sustainable Development Institute, Monash University, Clayton, VIC, Australia.
Karin LederSchool of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia.
Chris GreeningDepartment of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia; School of Biological Sciences, Monash University, Clayton, VIC, Australia.
David McCarthyDepartment of Civil Engineering, Monash University, Clayton, VIC, Australia. Electronic address: david.mccarthy@monash.edu.

Funding

Wellcome TrustWellcome Trust 205222/Z/16/Z
6 · The paper itself

Abstract

backgroundMultiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples.

methodsIn this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR.

findingsBoth methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R

interpretationThe two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load.

fundingWellcome Trust Our Planet, Our Health programme.

Indexed as

BacteriaAustraliaFijiHumansReal-Time Polymerase Chain ReactionSensitivity and Specificity

Identifiers

PMID33964239
PMCPMC8116308

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.