{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T06:04:31Z","timestamp":1790834671919,"version":"4.1.0"},"reference-count":100,"publisher":"Wiley","issue":"2","license":[{"start":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T00:00:00Z","timestamp":1697241600000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T00:00:00Z","timestamp":1697241600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","award":["FT200100732"],"award-info":[{"award-number":["FT200100732"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Molecular Ecology Resources"],"published-print":{"date-parts":[[2024,2]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Apicomplexan haemoparasites generate significant morbidity and mortality in humans and other animals, particularly in many low\u2010to\u2010middle income countries. Malaria caused by <jats:italic>Plasmodium<\/jats:italic> remains responsible for some of the highest numbers of annual deaths of any human pathogen, whilst piroplasmids, such as <jats:italic>Babesia<\/jats:italic> and <jats:italic>Theileria<\/jats:italic> can have immense negative economic effects through livestock loss. Diagnosing haemoparasites via traditional methods like microscopy is challenging due to low\u2010level and transient parasitaemia. PCR\u2010based diagnostics overcome these limitations by being both highly sensitive and specific, but they may be unable to accurately detect coinfections or identify novel species. In contrast, next\u2010generation sequencing (NGS)\u2010based methods can characterize all pathogens from a group of interest concurrently, although, the short\u2010read platforms previously used have been limited in the taxonomic resolution achievable. Here, we used Oxford Nanopore Technologies' (ONT) long\u2010read MinION\u2122 sequencer to conduct apicomplexan haemoparasite metabarcoding via sequencing the near full\u2010length 18S ribosomal RNA gene, demonstrating its ability to detect <jats:italic>Babesia<\/jats:italic>, <jats:italic>Hepatozoon<\/jats:italic>, <jats:italic>Neospora<\/jats:italic>, <jats:italic>Plasmodium<\/jats:italic>, <jats:italic>Theileria<\/jats:italic> and <jats:italic>Toxoplasma<\/jats:italic> species. This method was tested on blood\u2010extracted DNA from 100 dogs and the results benchmarked against qPCR and Illumina\u2010based metabarcoding. For two common haemoparasites, nanopore sequencing performed as well as qPCR (kappa agreement statistics\u2009&gt;\u20090.98), whilst also detecting one pathogen, <jats:italic>Hepatozoon felis<\/jats:italic>, missed by the other techniques. The long\u2010reads obtained by nanopore sequencing provide an improved species\u2010level taxonomic resolution whilst the method's broad applicability mean it can be used to explore apicomplexan communities from diverse mammalian hosts, on a portable sequencer that easily permits adaptation to field use.<\/jats:p>","DOI":"10.1111\/1755-0998.13878","type":"journal-article","created":{"date-parts":[[2023,10,14]],"date-time":"2023-10-14T11:39:43Z","timestamp":1697283583000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Metabarcoding using nanopore long\u2010read sequencing for the unbiased characterization of apicomplexan haemoparasites"],"prefix":"10.1111","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1384-2886","authenticated-orcid":false,"given":"Lucas G.","family":"Huggins","sequence":"first","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4903-1479","authenticated-orcid":false,"given":"Vito","family":"Colella","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8756-229X","authenticated-orcid":false,"given":"Neil D.","family":"Young","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rebecca J.","family":"Traub","sequence":"additional","affiliation":[{"name":"Melbourne Veterinary School, Faculty of Science University of Melbourne  Parkville Victoria Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2023,10,14]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1080\/10635150701494127"},{"key":"e_1_2_12_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetpar.2015.02.015"},{"key":"e_1_2_12_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s00436-013-3403-6"},{"key":"e_1_2_12_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_12_6_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00399-18"},{"key":"e_1_2_12_7_1","first-page":"389","article-title":"Preventing PCR amplification carryover contamination in a clinical laboratory","volume":"34","author":"Aslanzadeh J.","year":"2004","journal-title":"Annals of Clinical and Laboratory Science"},{"key":"e_1_2_12_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cvsm.2022.06.011"},{"key":"e_1_2_12_9_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-019-3385-z"},{"key":"e_1_2_12_10_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-015-0830-5"},{"key":"e_1_2_12_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1471-4922(02)00016-8"},{"key":"e_1_2_12_12_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0181279"},{"key":"e_1_2_12_13_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.tree.2019.07.012"},{"key":"e_1_2_12_14_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mib.2017.10.008"},{"key":"e_1_2_12_15_1","doi-asserted-by":"publisher","DOI":"10.1007\/s12639-017-0902-x"},{"key":"e_1_2_12_16_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0031182003004748"},{"key":"e_1_2_12_17_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10096-019-03520-3"},{"key":"e_1_2_12_18_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-019-0209-9"},{"key":"e_1_2_12_19_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3869"},{"key":"e_1_2_12_20_1","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2012.8"},{"key":"e_1_2_12_21_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1550-7408.1999.tb05128.x"},{"key":"e_1_2_12_22_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0013042"},{"key":"e_1_2_12_23_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2019.101276"},{"key":"e_1_2_12_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty560"},{"key":"e_1_2_12_25_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.csbj.2021.02.020"},{"key":"e_1_2_12_26_1","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.14645"},{"key":"e_1_2_12_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/0020-7519(92)90139-C"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.1556\/avet.2015.017"},{"key":"e_1_2_12_29_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetpar.2017.02.023"},{"key":"e_1_2_12_30_1","doi-asserted-by":"publisher","DOI":"10.1111\/jvim.15233"},{"key":"e_1_2_12_31_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0257521"},{"key":"e_1_2_12_32_1","first-page":"99","article-title":"Babesiosis in an Egyptian boy acquired from pet dog, and a general review","volume":"41","author":"El\u2010Bahnasawy M. M.","year":"2011","journal-title":"Journal of the Egyptian Society of Parasitology"},{"key":"e_1_2_12_33_1","doi-asserted-by":"publisher","DOI":"10.1128\/9781555816018"},{"key":"e_1_2_12_34_1","doi-asserted-by":"publisher","DOI":"10.1186\/1756-3305-3-33"},{"key":"e_1_2_12_35_1","first-page":"1","article-title":"Targeted next\u2010generation sequencing and informatics as an effective tool to establish the composition of bovine piroplasm populations in endemic regions","volume":"9","author":"Ghafar A.","year":"2021","journal-title":"Microorganisms"},{"key":"e_1_2_12_36_1","doi-asserted-by":"publisher","DOI":"10.4172\/2157-7579.1000261"},{"key":"e_1_2_12_37_1","doi-asserted-by":"publisher","DOI":"10.1002\/ece3.5758"},{"key":"e_1_2_12_38_1","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.03088-22"},{"key":"e_1_2_12_39_1","doi-asserted-by":"publisher","DOI":"10.1111\/tbed.14180"},{"key":"e_1_2_12_40_1","first-page":"1","article-title":"Advanced approaches for the diagnosis and chemoprevention of canine vector\u2010borne pathogens and parasites\u2014Implications for the Asia\u2010Pacific region and beyond","volume":"118","author":"Huggins L. G.","year":"2023","journal-title":"Advances in Parasitology"},{"key":"e_1_2_12_41_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-49118-9"},{"key":"e_1_2_12_42_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-019-3651-0"},{"key":"e_1_2_12_43_1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens9040258"},{"key":"e_1_2_12_44_1","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms9051092"},{"key":"e_1_2_12_45_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-018-07641-9"},{"key":"e_1_2_12_46_1","first-page":"1","article-title":"Molecular evidence of Hepatozoon felis infection in wild captured royal Bengal tiger cub (Panthera tigris tigris)","volume":"1","author":"Journal I.","year":"2022","journal-title":"Indian Journal of Animal Research"},{"key":"e_1_2_12_47_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2014.01.004"},{"key":"e_1_2_12_48_1","doi-asserted-by":"publisher","DOI":"10.1002\/2211-5463.12590"},{"key":"e_1_2_12_49_1","doi-asserted-by":"publisher","DOI":"10.3390\/ani12060739"},{"key":"e_1_2_12_50_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-017-0267-5"},{"key":"e_1_2_12_51_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41579-018-0029-9"},{"key":"e_1_2_12_52_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.215087.116"},{"key":"e_1_2_12_53_1","doi-asserted-by":"publisher","DOI":"10.1007\/s11686-022-00625-2"},{"key":"e_1_2_12_54_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-08183-3"},{"key":"e_1_2_12_55_1","doi-asserted-by":"publisher","DOI":"10.1093\/jxb\/erx289"},{"key":"e_1_2_12_56_1","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2018.02868"},{"key":"e_1_2_12_57_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijppaw.2014.12.006"},{"key":"e_1_2_12_58_1","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_2_12_59_1","doi-asserted-by":"publisher","DOI":"10.11613\/BM.2012.031"},{"key":"e_1_2_12_60_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00205"},{"key":"e_1_2_12_61_1","doi-asserted-by":"publisher","DOI":"10.21105\/joss.00861"},{"key":"e_1_2_12_62_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.micinf.2012.04.007"},{"key":"e_1_2_12_63_1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10030351"},{"key":"e_1_2_12_64_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2410.180234"},{"key":"e_1_2_12_65_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.1865-1682.2010.01113.x"},{"key":"e_1_2_12_66_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(12)60034-8"},{"key":"e_1_2_12_67_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-021-01059-0"},{"key":"e_1_2_12_68_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.pt.2014.09.003"},{"key":"e_1_2_12_69_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-020-04325-6"},{"key":"e_1_2_12_70_1","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens9121041"},{"key":"e_1_2_12_71_1","first-page":"2825","article-title":"Scikit\u2010learn: Machine learning in Python","volume":"12","author":"Pedregosa F.","year":"2011","journal-title":"Journal of Machine Learning Research"},{"key":"e_1_2_12_72_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-020-04062-w"},{"key":"e_1_2_12_73_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2020.105985"},{"key":"e_1_2_12_74_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2020.105985"},{"key":"e_1_2_12_75_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-020-6557-5"},{"key":"e_1_2_12_76_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa900"},{"key":"e_1_2_12_77_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2021.806476"},{"key":"e_1_2_12_78_1","doi-asserted-by":"publisher","DOI":"10.14202\/vetworld.2019.700-705"},{"key":"e_1_2_12_79_1","doi-asserted-by":"publisher","DOI":"10.1292\/jvms.11-0210"},{"key":"e_1_2_12_80_1","doi-asserted-by":"publisher","DOI":"10.5897\/JVMAH2014.0345"},{"key":"e_1_2_12_81_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40101-020-00251-9"},{"key":"e_1_2_12_82_1","doi-asserted-by":"publisher","DOI":"10.3201\/eid2809.220248"},{"key":"e_1_2_12_83_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-016-1596-0"},{"key":"e_1_2_12_84_1","doi-asserted-by":"publisher","DOI":"10.1186\/s13071-020-04475-7"},{"key":"e_1_2_12_85_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetpar.2011.05.032"},{"key":"e_1_2_12_86_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.05848-11"},{"key":"e_1_2_12_87_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2015.06.082"},{"key":"e_1_2_12_88_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ttbdis.2018.12.004"},{"key":"e_1_2_12_89_1","doi-asserted-by":"publisher","DOI":"10.1101\/gr.214270.116"},{"key":"e_1_2_12_90_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2020.104305"},{"key":"e_1_2_12_91_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.vetpar.2018.02.028"},{"key":"e_1_2_12_92_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-021-01108-x"},{"key":"e_1_2_12_93_1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2018.02225"},{"key":"e_1_2_12_94_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijppaw.2012.11.003"},{"key":"e_1_2_12_95_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2022.114664"},{"key":"e_1_2_12_96_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0226781","article-title":"Zoonotic Babesia: A scoping review of the global evidence","volume":"4","author":"Youngid K. M.","year":"2019","journal-title":"PLoS One"},{"key":"e_1_2_12_97_1","doi-asserted-by":"publisher","DOI":"10.1007\/s004360050445"},{"key":"e_1_2_12_98_1","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbv001"},{"key":"e_1_2_12_99_1","first-page":"1572","article-title":"Rapid detection of bacterial pathogens and antimicrobial resistance genes in clinical urine samples with urinary tract infection by metagenomic nanopore sequencing","volume":"13","author":"Zhang L.","year":"2022","journal-title":"Frontiers in Microbiology"},{"key":"e_1_2_12_100_1","first-page":"1","article-title":"Human babesiosis, an emerging tick\u2010borne disease in the People's Republic of China","volume":"7","author":"Zhou X.","year":"2014","journal-title":"Parasites and Vectors"},{"key":"e_1_2_12_101_1","doi-asserted-by":"publisher","DOI":"10.1155\/2020\/6675206"}],"container-title":["Molecular Ecology Resources"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13878","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/1755-0998.13878","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,1,21]],"date-time":"2024-01-21T14:20:44Z","timestamp":1705846844000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/1755-0998.13878"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,14]]},"references-count":100,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2]]}},"alternative-id":["10.1111\/1755-0998.13878"],"URL":"https:\/\/doi.org\/10.1111\/1755-0998.13878","archive":["Portico"],"relation":{},"ISSN":["1755-098X","1755-0998"],"issn-type":[{"value":"1755-098X","type":"print"},{"value":"1755-0998","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,10,14]]},"assertion":[{"value":"2023-05-04","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-09-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2023-10-14","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e13878"}}