.2016 Sep 24;388(10051):1291-301.

doi: 10.1016/S0140-6736(16)31529-X.

Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

Jie Liu¹, James A Platts-Mills¹, Jane Juma², Furqan Kabir³, Joseph Nkeze⁴, Catherine Okoi⁵, Darwin J Operario¹, Jashim Uddin⁶, Shahnawaz Ahmed⁶, Pedro L Alonso⁷, Martin Antonio⁵, Stephen M Becker¹, William C Blackwelder⁴, Robert F Breiman⁸, Abu S G Faruque⁶, Barry Fields⁸, Jean Gratz¹, Rashidul Haque⁶, Anowar Hossain⁶, M Jahangir Hossain⁵, Sheikh Jarju⁵, Farah Qamar³, Najeeha Talat Iqbal³, Brenda Kwambana⁵, Inacio Mandomando⁹, Timothy L McMurry¹⁰, Caroline Ochieng², John B Ochieng², Melvin Ochieng², Clayton Onyango⁸, Sandra Panchalingam¹¹, Adil Kalam³, Fatima Aziz³, Shahida Qureshi³, Thandavarayan Ramamurthy¹², James H Roberts¹⁰, Debasish Saha⁵, Samba O Sow¹³, Suzanne E Stroup¹, Dipika Sur¹², Boubou Tamboura¹³, Mami Taniuchi¹, Sharon M Tennant⁴, Deanna Toema⁴, Yukun Wu⁴, Anita Zaidi³, James P Nataro¹⁴, Karen L Kotloff¹⁵, Myron M Levine¹⁶, Eric R Houpt¹⁷

Affiliations

¹ Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
² Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
³ Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
⁴ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
⁵ Medical Research Council Unit, Banjul, The Gambia.
⁶ International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh.
⁷ Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain.
⁸ Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya.
⁹ Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique.
¹⁰ Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
¹¹ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
¹² National Institute of Cholera and Enteric Diseases, Kolkata, India.
¹³ Centre pour le Développement des Vaccins, Bamako, Mali.
¹⁴ Department of Pediatrics, University of Virginia, Charlottesville, VA, USA.
¹⁵ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA.
¹⁶ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
¹⁷ Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA. Electronic address: erh6k@virginia.edu.

PMID:27673470
PMCID: PMC5471845
DOI: 10.1016/S0140-6736(16)31529-X

Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

Jie Liu et al. Lancet.2016.

.2016 Sep 24;388(10051):1291-301.

doi: 10.1016/S0140-6736(16)31529-X.

Authors

Affiliations

¹ Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
² Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya.
³ Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan.
⁴ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
⁵ Medical Research Council Unit, Banjul, The Gambia.
⁶ International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh.
⁷ Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain.
⁸ Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya.
⁹ Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique.
¹⁰ Public Health Sciences, University of Virginia, Charlottesville, VA, USA.
¹¹ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
¹² National Institute of Cholera and Enteric Diseases, Kolkata, India.
¹³ Centre pour le Développement des Vaccins, Bamako, Mali.
¹⁴ Department of Pediatrics, University of Virginia, Charlottesville, VA, USA.
¹⁵ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA.
¹⁶ Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.
¹⁷ Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA. Electronic address: erh6k@virginia.edu.

PMID:27673470
PMCID: PMC5471845
DOI: 10.1016/S0140-6736(16)31529-X

Abstract

Background: Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS).

Methods: GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children.

Findings: We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections.

Interpretation: A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised.

Funding: Bill & Melinda Gates Foundation.

PubMed Disclaimer

Conflict of interest statement

Declaration of interests: We declare no competing interests.

Figures

**Figure 1. Relation between pathogen quantity and diarrhoea**
Pathogens are ordered from top to bottom and left to right by prevalence in cases. Data are numbers of dectections (vertical bars) in cases (dark grey) and controls (light grey) with odds ratios (red lines) and 95% CIs (bands). The model-derived cutoffs used for identification of diarrhoea-associated pathogens in individuals (overlaid in blue) are defined as all detections above the point at which the 95% CI no longer includes 1. EAEC=enteroaggregativeE coli. EIEC=enteroinvasiveE coli. EPEC=enteropathogenicE coli. LT-ETEC=heat-labile enterotoxin-producingE coli. ST-ETEC=STh-producing enterotoxigenicE coli. STEC=Shiga toxin producingE coli.

**Figure 2. Attributable incidence of pathogen-specific moderate to severe diarrhoea per 100 child-years, by age stratum, across study sites, in this and the original GEMS**
For each age stratum, any pathogens significantly associated with diarrhoea by one or both diagnostic approaches are shown. GEMS=Global Enteric Multicenter Study. EAEC=enteroaggregativeE coli. EIEC=enteroinvasiveE coli. tEPEC=typical enteropathogenicE coli. ST-ETEC=STh-producing enterotoxigenicE coli. qPCR=quantitative realtime PCR. *Indicates the microbiology in the original GEMS did not test forH pylori orC cayetanensis.

**Figure 3. Relative attribution of watery diarrhoea and dysentery to each pathogen**
Data are overall adjusted attributable fractions (vertical bars) with 95% CIs. Pathogens are ordered by the proportion of total attributable cases that were watery diarrhoea (dotted line). All pathogens significantly associated with either dysentery or watery diarrhoea are shown. ST-ETEC=STh-producing enterotoxigenicE coli. tEPEC=typical enteropathogenicE coli. EIEC=enteroinvasiveE coli.

**Figure 4. Detection of co-infections in diarrhoeal cases**
(A) Numbers of pathogens at diarrhoea-associated quantities and any quantity in individual cases of diarrhoea. (B) Distribution of pathogens, alone and in co-infections, by quantity and association with diarrhoea. The quantification cycle cutoff used to identify diarrhoea-associated detections is shown in parentheses after each pathogen name. Cq=quantification cycle. EIEC=enteroinvasiveE coli. ST-ETEC=STh-producing enterotoxigenicEscherichia coli. tEPEC=typical enterpathogenicE coli.

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Comment in

GEMS extend understanding of childhood diarrhoea.
Keddy KH, Smith AM, Page NA.Keddy KH, et al.Lancet. 2016 Sep 24;388(10051):1252-4. doi: 10.1016/S0140-6736(16)31664-6.Lancet. 2016.PMID:27673454No abstract available.

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References

1. GBD 2013 DALYs and HALE Collaborators. Global, regional, and national disability-adjusted life years (DALYs) for 306 diseases and injuries and healthy life expectancy (HALE) for 188 countries, 1990–2013: quantifying the epidemiological transition. Lancet. 2015;386:2145–91. - PMC - PubMed
1. Liu L, Johnson HL, Cousens S, et al. Global, regional, and national causes of child mortality: an updated systematic analysis for 2010 with time trends since 2000. Lancet. 2012;379:2151–61. - PubMed
1. GBD 2013 Mortality and Causes of Death Collaborators. Global, regional, and national age-sex specific all-cause and cause-specific mortality for 240 causes of death, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013. Lancet. 2015;385:117–71. - PMC - PubMed
1. Lanata CF, Fischer-Walker CL, Olascoaga AC, et al. Global causes of diarrheal disease mortality in children <5 years of age: a systematic review. PLoS One. 2013;8:e72788. - PMC - PubMed
1. Huilan S, Zhen LG, Mathan MM, et al. Etiology of acute diarrhoea among children in developing countries: a multicentre study in five countries. Bull World Health Organ. 1991;69:549–55. - PMC - PubMed

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Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

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Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study

Authors

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Abstract

Conflict of interest statement

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