Gastrointestinal pathogens in paediatric patients with diarrhoea during the COVID-19 pandemic in Spain: a multicentre molecular-based prospective study

Gastroenteritis is a major cause of morbidity in young children worldwide. A prospective multicentre study was conducted from September 2020 to September 2021 in three tertiary hospitals in Spain to assess the burden of the gastrointestinal pathogens causing paediatric gastroenteritis in different Spanish regions, to understand the impact of COVID-19 pandemic in their incidence, and to assess potential risk factors for infection. Stool samples from children aged 0-59 months with acute or chronic diarrhoea were analysed by PCR to detect and characterise gastrointestinal bacteria, parasites, and viruses. Whole-genome sequencing was carried out on enteroaggregative Escherichia coli isolates. Epidemiological and clinical data were analysed using univariable and multivariable logistic regression models. A total of 1114 children were included (median age, 16 months; 57.3% male). The most prevalent bacteria were enteropathogenic E. coli (16.0%) and Campylobacter spp. (15.0%). Giardia duodenalis (9.8%) and Cryptosporidium parvum (1.8%) were the most common parasites, while norovirus (5.5%) predominated among viruses. Molecular analyses revealed substantial genetic diversity across all pathogens. Campylobacter infection increased with age and was associated with fever and bloody diarrhoea, while norovirus infection decreased with age and was associated with vomiting.Conclusion COVID-19 countermeasures substantially altered the transmission of faecal-orally transmitted gastrointestinal pathogens in children, particularly reducing person-to-person spread of human-adapted pathogens such as C. hominis and endemic enteroaggregative E. coli subtypes. Zoonotic pathogens were largely unaffected, highlighting the selective impact of non-pharmaceutical interventions on anthroponotic transmission. What is Known: • Paediatric gastroenteritis is caused by faecal-orally transmitted viral, bacterial, and parasitic agents. • COVID-19 countermeasures contributed to the significant reduction of person-to-person transmitted gastrointestinal pathogens. What is New: • COVID-19 countermeasures drastically interrupted the person-to-person transmission of human-adapted Cryptosporidium hominis and endemic enteroaggregative Escherichia coli subtypes in Spanish children. • Cryptosporidium parvum and other zoonotically transmitted gastrointestinal pathogens were largely unaffected.