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

Alejandro Dashti1, Carolina Hernández-Castro1,2, Jin-Min Yuan3

  • 1Parasitology Reference and Research Laboratory, National Centre for Microbiology, Health Institute Carlos III, 28820, Majadahonda, Spain.

European Journal of Pediatrics
|July 2, 2026
PubMed

Insights

COVID-19 measures significantly reduced human-adapted gastrointestinal pathogen transmission in Spanish children. Zoonotic pathogens like Cryptosporidium parvum were largely unaffected, showing a selective impact on disease spread.

Area of Science:

  • Pediatric Infectious Diseases
  • Epidemiology
  • Microbiology

Background:

  • Gastroenteritis is a significant cause of illness in young children globally.
  • Faecal-orally transmitted pathogens, including viruses, bacteria, and parasites, are primary causes of pediatric gastroenteritis.
  • The COVID-19 pandemic prompted non-pharmaceutical interventions (NPIs) that may have impacted pathogen transmission dynamics.

Purpose of the Study:

  • To assess the burden of gastrointestinal pathogens causing pediatric gastroenteritis in Spain.
  • To evaluate the impact of COVID-19 pandemic countermeasures on pathogen incidence.
  • To identify potential risk factors associated with pediatric gastrointestinal infections.

Main Methods:

  • A prospective, multicenter study involving 1114 children aged 0-59 months with diarrhea in Spain (September 2020-September 2021).
  • Stool sample analysis using PCR for bacteria, parasites, and viruses; whole-genome sequencing for enteroaggregative Escherichia coli.
  • Univariable and multivariable logistic regression for epidemiological and clinical data analysis.

Main Results:

  • Enteropathogenic E. coli (16.0%) and Campylobacter spp. (15.0%) were the most common bacteria; Giardia duodenalis (9.8%) and Cryptosporidium parvum (1.8%) the most frequent parasites; norovirus (5.5%) predominated among viruses.
  • Campylobacter infections increased with age and were linked to fever and bloody diarrhea; norovirus decreased with age and was associated with vomiting.
  • COVID-19 countermeasures significantly reduced the transmission of human-adapted pathogens like Cryptosporidium hominis and endemic enteroaggregative E. coli subtypes.

Conclusions:

  • COVID-19 NPIs substantially altered the transmission patterns of faecal-orally transmitted pathogens in children.
  • The impact was selective, drastically reducing person-to-person spread of anthroponotic pathogens while largely sparing zoonotic pathogens.
  • This highlights the differential effect of NPIs on human-adapted versus zoonotic gastrointestinal infections in pediatric populations.

Keywords:
ChildrenGastroenteritisGastrointestinal pathogensGenotypingMolecular detectionRisk factors

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