Prevalence of diarrhoeal pathogens among children under five years of age with and without diarrhoea in Guinea-Bissau

Background Childhood diarrhoea, a major cause of morbidity and mortality in low-income regions, remains scarcely studied in many countries, such as Guinea-Bissau. Stool sample drying enables later qPCR analyses of pathogens without concern about electricity shortages. Methods Dried stool samples of children under five years treated at the Bandim Health Centre in Bissau, Guinea-Bissau were screened by qPCR for nine enteric bacteria, five viruses, and four parasites. The findings of children having and not having diarrhoea were compared in age groups 0-11 and 12-59 months. Results Of the 429 children- 228 with and 201 without diarrhoea- 96.9% and 93.5% had bacterial, 62.7% and 44.3% viral, and 52.6% and 48.3% parasitic pathogen findings, respectively. Enteroaggregarive Escherichia coli (EAEC; 60.5% versus 66.7%), enteropathogenic E. coli (EPEC; 61.4% versus 62.7%), Campylobacter (53.2% versus 51.8%), and enterotoxigenic E. coli (ETEC; 54.4% versus 44.3%) were the most common bacterial pathogens. Diarrhoea was associated with enteroinvasive E. coli (EIEC)/Shigella (63.3%), astrovirus (75.0%), norovirus GII (72.6%) and Cryptosporidium (71.2%). The only pathogen associated with severe diarrhoea was EIEC/Shigella (p Conclusions Stool pathogens proved common among all the children regardless of them having diarrhoea or not. Author summary Diarrhoeal diseases rank second as cause of childhood mortality and morbidity in low-income countries, yet prospective cohort studies in children with and without diarrhea covering the large variety of diarrhoeal pathogens are limited. While some studies have been conducted among Guinea-Bissauan children, many of them were from the 1990s, when the coverage of the various pathogens was less extensive and the diagnostic methods less sensitive than the modern qPCR methods. We conducted an observational study with a large cohort and covered concomitantly the various bacterial, viral and parasitic agents, and analyzed their associations with the presence/absence of diarrhoeal symptoms and age groups. Importantly, the assay performed well with dried stool samples and, therefore, appears applicable for epidemiological studies in resource-poor regions. A pathogen finding was recorded for almost all (98%) children: bacteria in 97%, viruses in 59% and parasites in 51%. Ongoing diarrhoea was associated with findings of enteroninvasive Escherichia coli/Shigella, astrovirus, norovirus GII and Cryptosporidium. Differences were seen between age groups, infants and young children. The only pathogen associated with severe diarrhoea was enteroninvasive Escherichia coli/Shigella.Peer reviewe