ArticlePloS one2016
Optimization of Quantitative PCR Methods for Enteropathogen Detection.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 145 papers.
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Who cites it
145 citing papers in PubMed, 187 citations in OpenAlex.
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- Effect of Non-Rotavirus Enteric Infections on Vaccine Efficacy in a ROTASIIL Clinical Trial.The American journal of tropical medicine and hygiene · 2024Trial
- Azithromycin for Bacterial Watery Diarrhea: A Reanalysis of the AntiBiotics for Children With Severe Diarrhea (ABCD) Trial Incorporating Molecular Diagnostics.The Journal of infectious diseases · 2024Trial
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- Impact of Biannual Mass Azithromycin Treatment on Enteropathogen Carriage in Children <5 Years Old in Niger.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Trial
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- Etiology of severe invasive infections in young infants in rural settings in sub-Saharan Africa.PloS one · 2022Trial
- Etiology and Incidence of Moderate-to-Severe Diarrhea in Young Children in Niger.Journal of the Pediatric Infectious Diseases Society · 2021Trial
- Oral rotavirus vaccine shedding as a marker of mucosal immunity.Scientific reports · 2021Trial
- Prevalence and diversity of enteric pathogens among cholera treatment centre patients with acute diarrhea in Uvira, Democratic Republic of Congo.BMC infectious diseases · 2020Trial
- Impact of Low-Cost Point-of-Use Water Treatment Technologies on Enteric Infections and Growth among Children in Limpopo, South Africa.The American journal of tropical medicine and hygiene · 2020Trial
- Impact of Water Quality, Sanitation, Handwashing, and Nutritional Interventions on Enteric Infections in Rural Zimbabwe: The Sanitation Hygiene Infant Nutrition Efficacy (SHINE) Trial.The Journal of infectious diseases · 2020Trial
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- Enteropathogens and Rotavirus Vaccine Immunogenicity in a Cluster Randomized Trial of Improved Water, Sanitation and Hygiene in Rural Zimbabwe.The Pediatric infectious disease journal · 2019Trial
- Histo-Blood Group Antigen Phenotype Determines Susceptibility to Genotype-Specific Rotavirus Infections and Impacts Measures of Rotavirus Vaccine Efficacy.The Journal of infectious diseases · 2018Trial
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- Community transmission of type 2 poliovirus after cessation of trivalent oral polio vaccine in Bangladesh: an open-label cluster-randomised trial and modelling study.The Lancet. Infectious diseases · 2017Trial
- 5-Year effectiveness of an oral cholera vaccine in a cholera outbreak in rural Haiti: a case-control study.Lancet regional health. Americas · 2026Article
- Measles Without Rash During Acute Febrile Illness Surveillance in Tanzania, 2023-2024.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Adenovirus 40 and 41 Antibodies Associated With Protection From Infection in a Bangladeshi Birth Cohort.The Journal of infectious diseases · 2026Article
85 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
22 authors at 7 institutions in 6 countries.
Funding
Abstract
Detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. Here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. First, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized with diarrhea in Tanzania. Swabs generally yielded a higher quantification cycle (Cq) (average 29.7, standard deviation 3.5 vs. 25.3 ± 2.9 from stool, P<0.001) but were still able to detect 80% of pathogens with a Cq < 30 in stool. Second, a simplified total nucleic acid (TNA) extraction procedure was compared to separate DNA and RNA extractions and showed 92% (318/344) sensitivity and 98% (951/968) specificity, with no difference in Cq value for the positive results (ΔCq(DNA+RNA-TNA) = -0.01 ± 1.17, P = 0.972, N = 318). Third, we devised a quantification scheme that adjusts pathogen quantity to the specimen's extraction and amplification efficiency, and show that this better estimates the quantity of spiked specimens than the raw target Cq. In sum, these methods for enteropathogen quantification, stool sample collection, and nucleic acid extraction will be useful for laboratories studying enteric disease.
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Registered trials
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