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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\u201359\u00a0months 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\n                    <jats:italic>Escherichia coli<\/jats:italic>\n                    isolates. Epidemiological and clinical data were analysed using univariable and multivariable logistic regression models. A total of 1114 children were included (median age, 16\u00a0months; 57.3% male). The most prevalent bacteria were enteropathogenic\n                    <jats:italic>E. coli<\/jats:italic>\n                    (16.0%) and\n                    <jats:italic>Campylobacter<\/jats:italic>\n                    spp. (15.0%).\n                    <jats:italic>Giardia duodenalis<\/jats:italic>\n                    (9.8%) and\n                    <jats:italic>Cryptosporidium parvum<\/jats:italic>\n                    (1.8%) were the most common parasites, while norovirus (5.5%) predominated among viruses. Molecular analyses revealed substantial genetic diversity across all pathogens.\n                    <jats:italic>Campylobacter<\/jats:italic>\n                    infection increased with age and was associated with fever and bloody diarrhoea, while norovirus infection decreased with age and was associated with vomiting.\n                  <\/jats:p>\n                  <jats:p>\n                    <jats:italic>Conclusion<\/jats:italic>\n                    COVID-19 countermeasures substantially altered the transmission of faecal\u2013orally transmitted gastrointestinal pathogens in children, particularly reducing person-to-person spread of human-adapted pathogens such as\n                    <jats:italic>C. hominis<\/jats:italic>\n                    and endemic enteroaggregative\n                    <jats:italic>E. coli<\/jats:italic>\n                    subtypes. Zoonotic pathogens were largely unaffected, highlighting the selective impact of non-pharmaceutical interventions on anthroponotic transmission.\n                    <jats:table-wrap>\n                      <jats:table>\n                        <jats:tbody>\n                          <jats:tr>\n                            <jats:td colspan=\"2\">\n                              <jats:bold>What is Known:<\/jats:bold>\n                              \u2022 Paediatric gastroenteritis is caused by faecal\u2013orally transmitted viral, bacterial, and parasitic agents.\u2022 COVID-19 countermeasures contributed to the significant reduction of person-to-person transmitted gastrointestinal pathogens.\n                            <\/jats:td>\n                          <\/jats:tr>\n                          <jats:tr>\n                            <jats:td colspan=\"2\">\n                              <jats:bold>What is New:<\/jats:bold>\n                              \u2022 COVID-19 countermeasures drastically interrupted the person-to-person transmission of human-adapted\n                              <jats:italic>Cryptosporidium hominis<\/jats:italic>\n                              and endemic enteroaggregative\n                              <jats:italic>Escherichia coli<\/jats:italic>\n                              subtypes in Spanish children.\u2022\n                              <jats:italic>Cryptosporidium parvum<\/jats:italic>\n                              and other zoonotically transmitted gastrointestinal pathogens were largely unaffected.\n                            <\/jats:td>\n                          <\/jats:tr>\n                        <\/jats:tbody>\n                      <\/jats:table>\n                    <\/jats:table-wrap>\n                  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All study procedures were approved by the Ethics Committee of the Health Institute Carlos III (Date: April 4, 2019\/CEI PI 11_2019-v2). As the study was conducted within the framework of routine diagnostic practice, additional approval from participating hospital ethics committees was not required.","order":1,"name":"Ethics","label":"Ethics approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"As the study was conducted within the framework of routine diagnostic practice, individual informed consents were not required.","order":2,"name":"Ethics","label":"Consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":3,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":4,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"545"}}