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In Portugal, knowledge on their occurrence and genetic diversity remains fragmented. This study integrates new molecular results from multiple animal groups with a comprehensive review of published national data to establish an updated baseline for these parasites within a One Health framework.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      A total of 805 faecal samples from 91 animal species were analysed, including domestic (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009192 samples), captive (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009283) and wild (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u2009330) hosts. Detection was performed by modified Ziehl\u2013Neelsen and direct immunofluorescence assays; samples that were positive or doubtful after microscopic screening were further subjected to nested PCR and sequencing targeting\n                      <jats:italic>SSU rRNA<\/jats:italic>\n                      ,\n                      <jats:italic>gp60<\/jats:italic>\n                      (for\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>C. parvum<\/jats:italic>\n                      <\/jats:styled-content>\n                      ), and\n                      <jats:italic>gdh<\/jats:italic>\n                      ,\n                      <jats:italic>bg<\/jats:italic>\n                      and\n                      <jats:italic>tpi<\/jats:italic>\n                      (for\n                      <jats:italic>G. duodenalis<\/jats:italic>\n                      ). Newly generated sequences were compared to GenBank references and compiled with data from 29 Portuguese studies published between 2001 and 2025.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Overall,\n                      <jats:italic>Cryptosporidium<\/jats:italic>\n                      spp. were detected in 11\/805 samples (1.4%) and\n                      <jats:italic>G. duodenalis<\/jats:italic>\n                      in 101\/805 (12.5%). Detection rates of\n                      <jats:italic>Cryptosporidium<\/jats:italic>\n                      spp. were 3.6% (7\/192) in domestic, 0.0% in captive, and 1.2% (4\/330) in wild animals, while\n                      <jats:italic>Giardia<\/jats:italic>\n                      spp. occurred in 18.8% (36\/192), 8.5% (24\/283), and 12.4% (41\/330), respectively. Molecular analysis revealed\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>C. parvum<\/jats:italic>\n                      <\/jats:styled-content>\n                      (IIaA19G2R1 in Iberian wolf, and IIcA5G3 in hedgehogs),\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>C. canis<\/jats:italic>\n                      <\/jats:styled-content>\n                      , and\n                      <jats:styled-content style=\"fixed-case\">\n                        <jats:italic>C. cuniculus<\/jats:italic>\n                      <\/jats:styled-content>\n                      . Moreover,\n                      <jats:italic>G. duodenalis<\/jats:italic>\n                      assemblages were diverse, including assemblage E in ruminants, D in canids and felids, B in rabbits, lemurs, cheetahs and suricates, F in lions, and E and B co\u2010occurring in suricates and raccoons. The compiled dataset from available Portuguese studies included 3741 animals tested for\n                      <jats:italic>Cryptosporidium<\/jats:italic>\n                      spp. and 3353 for\n                      <jats:italic>Giardia<\/jats:italic>\n                      spp., providing a descriptive overview of host and genotype diversity across the country.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      This study provides the first integrated overview of\n                      <jats:italic>Cryptosporidium<\/jats:italic>\n                      spp. and\n                      <jats:italic>G.\u2009duodenalis<\/jats:italic>\n                      occurrences in animals across the Portuguese territory. The findings demonstrate that livestock, pets, zoo animals, and free\u2010ranging wildlife can contribute to the circulation of these protozoan parasites, emphasizing the importance of harmonized molecular surveillance and integrated One Health strategies for early detection and control.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/zph.70077","type":"journal-article","created":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T05:42:54Z","timestamp":1784266974000},"page":"563-583","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Occurrence and Diversity of\n                    <i>Cryptosporidium<\/i>\n                    spp. and\n                    <i>Giardia duodenalis<\/i>\n                    in Animals in Portugal: Novel Data and Public Health Implications"],"prefix":"10.1111","volume":"73","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5668-745X","authenticated-orcid":false,"given":"Mariana","family":"Louro","sequence":"first","affiliation":[{"name":"Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon  Lisbon Portugal"},{"name":"Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS)  Portugal"},{"name":"Instituto Nacional de Investiga\u00e7\u00e3o Agr\u00e1ria e Veterin\u00e1ria (INIAV)  Oeiras Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5390-6998","authenticated-orcid":false,"given":"Jo\u00e3o","family":"Lozano","sequence":"additional","affiliation":[{"name":"Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon  Lisbon Portugal"},{"name":"Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS)  Portugal"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9962-2170","authenticated-orcid":false,"given":"Patr\u00edcia","family":"Lopes","sequence":"additional","affiliation":[{"name":"Instituto Nacional de Investiga\u00e7\u00e3o Agr\u00e1ria e Veterin\u00e1ria (INIAV)  Oeiras Portugal"},{"name":"Center for Ecology, Evolution and Environmental Changes (cE3c) &amp; 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