Use of quantitative molecular diagnostic methods to assess the aetiology, burden, and clinical characteristics of diarrhoea in children in low-resource settings: a reanalysis of the MAL-ED cohort study

Abstract

SummaryBackgroundOptimum management of childhood diarrhoea in low-resource settings has been hampered by insufficient data on aetiology, burden, and associated clinical characteristics. We used quantitative diagnostic methods to reassess and refine estimates of diarrhoea aetiology from the Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development (MAL-ED) cohort study.MethodsWe re-analysed stool specimens from the multisite MAL-ED cohort study of children aged 0–2 years done at eight locations (Dhaka, Bangladesh; Vellore, India; Bhaktapur, Nepal; Naushero Feroze, Pakistan; Venda, South Africa; Haydom, Tanzania; Fortaleza, Brazil; and Loreto, Peru), which included active surveillance for diarrhoea and routine non-diarrhoeal stool collection. We used quantitative PCR to test for 29 enteropathogens, calculated population-level pathogen-specific attributable burdens, derived stringent quantitative cutoffs to identify aetiology for individual episodes, and created aetiology prediction scores using clinical characteristics.FindingsWe analysed 6625 diarrhoeal and 30 968 non-diarrhoeal surveillance stools from 1715 children. Overall, 64·9% of diarrhoea episodes (95% CI 62·6–71·2) could be attributed to an aetiology by quantitative PCR compared with 32·8% (30·8–38·7) using the original study microbiology. Viral diarrhoea (36·4% of overall incidence, 95% CI 33·6–39·5) was more common than bacterial (25·0%, 23·4–28·4) and parasitic diarrhoea (3·5%, 3·0–5·2). Ten pathogens accounted for 95·7% of attributable diarrhoea: Shigella (26·1 attributable episodes per 100 child-years, 95% CI 23·8–29·9), sapovirus (22·8, 18·9–27·5), rotavirus (20·7, 18·8–23·0), adenovirus 40/41 (19·0, 16·8–23·0), enterotoxigenic Escherichia coli (18·8, 16·5–23·8), norovirus (15·4, 13·5–20·1), astrovirus (15·0, 12·0–19·5), Campylobacter jejuni or C coli (12·1, 8·5–17·2), Cryptosporidium (5·8, 4·3–8·3), and typical enteropathogenic E coli (5·4, 2·8–9·3). 86·2% of the attributable incidence for Shigella was non-dysenteric. A prediction score for shigellosis was more accurate (sensitivity 50·4% [95% CI 46·7–54·1], specificity 84·0% [83·0–84·9]) than current guidelines, which recommend treatment only of bloody diarrhoea to cover Shigella (sensitivity 14·5% [95% CI 12·1–17·3], specificity 96·5% [96·0–97·0]).InterpretationQuantitative molecular diagnostics improved estimates of pathogen-specific burdens of childhood diarrhoea in the community setting. Viral causes predominated, including a substantial burden of sapovirus; however, Shigella had the highest overall burden with a high incidence in the second year of life. These data could improve the management of diarrhoea in these low-resource settings.FundingBill & Melinda Gates Foundation.

Enteropathogen seroepidemiology among children in low-resource settings

“…The relative intensity of pathogen transmission based on serological measures in this analysis aligns with relative differences in infection from large-scale molecular testing in stool. For example, rapid rises in IgG levels, seroprevalence, and force of infection for ETEC and Campylobacter beginning very early in life is consistent with their prominence in molecular testing of stool specimens in the MAL-ED studies [3,39] . Higher force of infection for norovirus GII.4 compared with norovirus GI.4 in Haiti is consistent with the relative prominence of circulating genogroups [40,41] .…”

“…We excluded cholera β toxin antibody responses from remaining analyses because of the difficulty of interpreting its epidemiologic measures in light of high levels of cross-reactivity with ETEC LT β subunit. Heat labile toxin-producing ETEC is very common among children in low-resource settings [3] , and there was no documented transmission of cholera in the study populations during measurement periods.…”

“…A broad set of viral, bacterial, and parasitic enteropathogens are leading causes of the global infectious disease burden, with the highest burden among young children living in lower income countries [1] . Infections that result in acute diarrhea and related child deaths drive disease burden estimates attributed to enteropathogens, but asymptomatic infections are extremely common and the full scope of sequelae is only partially understood [2,3] . Much of what we know about enteropathogen transmission is based on passive clinical surveillance, which reflects a small fraction of all infections.…”

“…Stool-based, high-throughput PCR assays have helped solve the logistical difficulties of single-pathogen testing for enterics and have provided new insights into pathogen-specific infections and disease burden [2,3] . Yet, stool is not routinely collected in population-based surveys, and infection with many globally important enteric pathogens can be sufficiently rare and relatively short-lived to require designs with almost continuous surveillance [3,9] . At the same time, large-scale serological surveillance platforms create new opportunities for expanded enteropathogen surveillance alongside other infectious diseases [10,11] .…”

“…Compared with permanently immunizing infections such as measles, transient immunity adds a layer of complexity to seroepidemiologic inference and methods. To our knowledge, there has been no detailed study of enteropathogen seroepidemiology among children in low-resource settings where transmission is intense beginning early in life [3] . Such studies are needed to determine if serology is a viable approach to measure enteropathogen transmission in low-resource settings.…”