{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,3]],"date-time":"2026-11-03T08:35:20Z","timestamp":1793694920438,"version":"4.5.1"},"reference-count":79,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T00:00:00Z","timestamp":1735516800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T00:00:00Z","timestamp":1735516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100000265","name":"RCUK | Medical Research Council","doi-asserted-by":"publisher","award":["MRC IAA2129"],"award-info":[{"award-number":["MRC IAA2129"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"RCUK | Medical Research Council","doi-asserted-by":"publisher","award":["MR\/X005895\/1"],"award-info":[{"award-number":["MR\/X005895\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"RCUK | Medical Research Council","doi-asserted-by":"publisher","award":["MR\/M021157\/1"],"award-info":[{"award-number":["MR\/M021157\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"RCUK | Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/Y018842\/1"],"award-info":[{"award-number":["EP\/Y018842\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["214227\/Z\/18\/Z"],"award-info":[{"award-number":["214227\/Z\/18\/Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004440","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["225844_Z_22_Z"],"award-info":[{"award-number":["225844_Z_22_Z"]}],"id":[{"id":"10.13039\/100004440","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    <jats:italic>Plasmodium malariae<\/jats:italic>\n                    parasites are widely observed across the tropics and sub-tropics. This slow-growing species, known to maintain chronic asymptomatic infections, has been associated with reduced antimalarial susceptibility. We analyse 251\u2009\n                    <jats:italic>P. malariae<\/jats:italic>\n                    genomes from 28 countries, and leveraging 131,601 high-quality SNPs, demonstrate segregation of African and Asian isolates. Signals of recent evolutionary selection were identified in genes encoding putative surface proteins (\n                    <jats:italic>pmmsp1<\/jats:italic>\n                    ) and putative erythrocyte invasion proteins (\n                    <jats:italic>pmdpap3, pmrbp2, pmnif4<\/jats:italic>\n                    ). Amino acid substitutions were identified in orthologs of genes associated with antimalarial susceptibility including 2 amino acid substitutions in\n                    <jats:italic>pmdhfr<\/jats:italic>\n                    aligning with pyrimethamine resistance mutations in\n                    <jats:italic>P. falciparum<\/jats:italic>\n                    . Additionally, we characterise\n                    <jats:italic>pmdhfr<\/jats:italic>\n                    mutation F57L and demonstrate its involvement in reduced susceptibility to pyrimethamine in an in vitro parasite assay. We validate CRISPR-Cas9 mediated ortholog replacement in\n                    <jats:italic>P. knowlesi<\/jats:italic>\n                    parasites to determine the function of\n                    <jats:italic>pmdhfr<\/jats:italic>\n                    mutations and demonstrate that circulating\n                    <jats:italic>pmdhfr<\/jats:italic>\n                    genotypes are less susceptible to pyrimethamine.\n                  <\/jats:p>","DOI":"10.1038\/s41467-024-55102-3","type":"journal-article","created":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T12:21:35Z","timestamp":1735561295000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["Genome sequencing of Plasmodium malariae identifies continental segregation and mutations associated with reduced pyrimethamine susceptibility"],"prefix":"10.1038","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5155-7974","authenticated-orcid":false,"given":"Amy","family":"Ibrahim","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Franziska","family":"Mohring","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilia","family":"Manko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7375-3439","authenticated-orcid":false,"given":"Donelly A.","family":"van Schalkwyk","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8323-7019","authenticated-orcid":false,"given":"Jody E.","family":"Phelan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debbie","family":"Nolder","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steffen","family":"Borrmann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayola A.","family":"Adegnika","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8049-2014","authenticated-orcid":false,"given":"Silvia Maria","family":"Di Santi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8330-5499","authenticated-orcid":false,"given":"Mohammad Shafiul","family":"Alam","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dinesh","family":"Mondal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7951-0745","authenticated-orcid":false,"given":"Francois","family":"Nosten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1592-6407","authenticated-orcid":false,"given":"Colin J.","family":"Sutherland","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9070-4292","authenticated-orcid":false,"given":"Robert W.","family":"Moon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8985-9265","authenticated-orcid":false,"given":"Taane G.","family":"Clark","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1403-6138","authenticated-orcid":false,"given":"Susana","family":"Campino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,30]]},"reference":[{"key":"55102_CR1","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1056\/NEJM199802053380605","volume":"338","author":"JM Vinetz","year":"1998","unstructured":"Vinetz, J. M., Li, J., McCutchan, T. F. & Kaslow, D. C. Plasmodium malariae infection in an asymptomatic 74-year-old Greek woman with splenomegaly. N. Engl. J. Med. 338, 367\u2013371 (1998).","journal-title":"N. Engl. J. Med."},{"key":"55102_CR2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0004195","volume":"9","author":"S Langford","year":"2015","unstructured":"Langford, S. et al. Plasmodium malariae infection associated with a high burden of anemia: a hospital-based surveillance study. PLoS Negl. Trop. Dis. 9, e0004195 (2015).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"55102_CR3","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1128\/CMR.00027-07","volume":"20","author":"WE Collins","year":"2007","unstructured":"Collins, W. E. & Jeffery, G. M. Plasmodium malariae: parasite and disease. Clin. Microbiol. Rev. 20, 579\u2013592 (2007).","journal-title":"Clin. Microbiol. Rev."},{"key":"55102_CR4","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.ijpara.2021.06.003","volume":"52","author":"MA Abdulraheem","year":"2022","unstructured":"Abdulraheem, M. A. et al. High prevalence of Plasmodium malariae and Plasmodium ovale in co-infections with Plasmodium falciparum in asymptomatic malaria parasite carriers in southwestern Nigeria. Int. J. Parasitol. 52, 23\u201333 (2022).","journal-title":"Int. J. Parasitol."},{"key":"55102_CR5","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1038\/nature21038","volume":"542","author":"GG Rutledge","year":"2017","unstructured":"Rutledge, G. G. et al. Plasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution. Nature 542, 101\u2013104 (2017).","journal-title":"Nature"},{"key":"55102_CR6","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/j.actatropica.2003.11.002","volume":"90","author":"KKG Scopel","year":"2004","unstructured":"Scopel, K. K. G., Fontes, C. J. F., Nunes, A. C., Horta, M. F. & Braga, E. M. High prevalence of Plamodium malariae infections in a Brazilian Amazon endemic area (Apiac\u00e1s-Mato Grosso State) as detected by polymerase chain reaction. Acta Trop. 90, 61\u201364 (2004).","journal-title":"Acta Trop."},{"key":"55102_CR7","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-46194-9","volume":"9","author":"TG Woldearegai","year":"2019","unstructured":"Woldearegai, T. G. et al. Characterization of Plasmodium infections among inhabitants of rural areas in Gabon. Sci. Rep. 9, 9784 (2019).","journal-title":"Sci. Rep."},{"key":"55102_CR8","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1080\/20469047.2017.1378797","volume":"38","author":"S Islam","year":"2018","unstructured":"Islam, S. & Hai, F. Recrudescing Plasmodium malariae infection despite appropriate treatment in an immigrant toddler. Paediatr. Int. Child Health 38, 290\u2013293 (2018).","journal-title":"Paediatr. Int. Child Health"},{"key":"55102_CR9","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1016\/S0140-6736(02)09336-4","volume":"360","author":"JD Maguire","year":"2002","unstructured":"Maguire, J. D. et al. Chloroquine-resistant Plasmodium malariae in south Sumatra, Indonesia. Lancet Lond. Engl. 360, 58\u201360 (2002).","journal-title":"Lancet Lond. Engl."},{"key":"55102_CR10","doi-asserted-by":"publisher","first-page":"442","DOI":"10.4269\/ajtmh.2008.78.442","volume":"78","author":"JT Bousema","year":"2008","unstructured":"Bousema, J. T. et al. Increased Plasmodium falciparum gametocyte production in mixed infections with P. malariae. Am. J. Trop. Med. Hyg. 78, 442\u2013448 (2008).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"55102_CR11","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1016\/S0140-6736(94)90203-8","volume":"343","author":"J Black","year":"1994","unstructured":"Black, J., Hommel, M., Snounou, G. & Pinder, M. Mixed Infections with Plasmodium falciparum and P malariae and fever In malaria. Lancet 343, 1095 (1994).","journal-title":"Lancet"},{"key":"55102_CR12","doi-asserted-by":"publisher","first-page":"549","DOI":"10.1006\/jtbi.1999.0932","volume":"198","author":"DP Mason","year":"1999","unstructured":"Mason, D. P., McKenzie, F. E. & Bossert, W. H. The blood-stage dynamics of mixed Plasmodium malariae-Plasmodium falciparum infections. J. Theor. Biol. 198, 549\u2013566 (1999).","journal-title":"J. Theor. Biol."},{"key":"55102_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23422-3","volume":"12","author":"ED Benavente","year":"2021","unstructured":"Benavente, E. D. et al. Distinctive genetic structure and selection patterns in Plasmodium vivax from South Asia and East Africa. Nat. Commun. 12, 3160 (2021).","journal-title":"Nat. Commun."},{"key":"55102_CR14","doi-asserted-by":"publisher","first-page":"22","DOI":"10.12688\/wellcomeopenres.18681.1","volume":"8","author":"MalariaGEN","year":"2023","unstructured":"MalariaGEN et al. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res. 8, 22 (2023).","journal-title":"Wellcome Open Res."},{"key":"55102_CR15","doi-asserted-by":"publisher","first-page":"e0177134","DOI":"10.1371\/journal.pone.0177134","volume":"12","author":"E Diez Benavente","year":"2017","unstructured":"Diez Benavente, E. et al. Genomic variation in Plasmodium vivax malaria reveals regions under selective pressure. PloS One 12, e0177134 (2017).","journal-title":"PloS One"},{"key":"55102_CR16","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-67568-4","volume":"10","author":"A Ibrahim","year":"2020","unstructured":"Ibrahim, A. et al. Selective whole genome amplification of Plasmodium malariae DNA from clinical samples reveals insights into population structure. Sci. Rep. 10, 10832 (2020).","journal-title":"Sci. Rep."},{"key":"55102_CR17","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","volume":"26","author":"D Kim","year":"2016","unstructured":"Kim, D., Song, L., Breitwieser, F. P. & Salzberg, S. L. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. 26, 1721\u20131729 (2016).","journal-title":"Genome Res."},{"key":"55102_CR18","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-26625-w","volume":"12","author":"EC Oriero","year":"2022","unstructured":"Oriero, E. C. et al. Plasmodium malariae structure and genetic diversity in sub-Saharan Africa determined from microsatellite variants and linked SNPs in orthologues of antimalarial resistance genes. Sci. Rep. 12, 21881 (2022).","journal-title":"Sci. Rep."},{"key":"55102_CR19","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1073\/pnas.1119058109","volume":"109","author":"E Yalcindag","year":"2012","unstructured":"Yalcindag, E. et al. Multiple independent introductions of Plasmodium falciparum in South America. Proc. Natl Acad. Sci. Usa. 109, 511\u2013516 (2012).","journal-title":"Proc. Natl Acad. Sci. Usa."},{"key":"55102_CR20","doi-asserted-by":"publisher","first-page":"480","DOI":"10.1080\/21645515.2019.1669415","volume":"16","author":"MB Laurens","year":"2019","unstructured":"Laurens, M. B. RTS,S\/AS01 vaccine (MosquirixTM): an overview. Hum. Vaccines Immunother. 16, 480\u2013489 (2019).","journal-title":"Hum. Vaccines Immunother."},{"key":"55102_CR21","doi-asserted-by":"publisher","first-page":"13275","DOI":"10.1073\/pnas.1110303108","volume":"108","author":"P Srinivasan","year":"2011","unstructured":"Srinivasan, P. et al. Binding of Plasmodium merozoite proteins RON2 and AMA1 triggers commitment to invasion. Proc. Natl Acad. Sci. 108, 13275\u201313280 (2011).","journal-title":"Proc. Natl Acad. Sci."},{"key":"55102_CR22","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1038\/s41586-018-0779-6","volume":"565","author":"W Wong","year":"2019","unstructured":"Wong, W. et al. Structure of Plasmodium falciparum Rh5-CyRPA-Ripr invasion complex. Nature 565, 118\u2013121 (2019).","journal-title":"Nature"},{"key":"55102_CR23","doi-asserted-by":"publisher","first-page":"1466","DOI":"10.1111\/j.1462-5822.2006.00885.x","volume":"9","author":"J Thompson","year":"2007","unstructured":"Thompson, J. et al. Plasmodium cysteine repeat modular proteins 1-4: complex proteins with roles throughout the malaria parasite life cycle. Cell. Microbiol. 9, 1466\u20131480 (2007).","journal-title":"Cell. Microbiol."},{"key":"55102_CR24","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1038\/nature12920","volume":"507","author":"BFC Kafsack","year":"2014","unstructured":"Kafsack, B. F. C. et al. A transcriptional switch underlies commitment to sexual development in malaria parasites. Nature 507, 248\u2013252 (2014).","journal-title":"Nature"},{"key":"55102_CR25","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1038\/nature11174","volume":"487","author":"M Manske","year":"2012","unstructured":"Manske, M. et al. Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature 487, 375\u2013379 (2012).","journal-title":"Nature"},{"key":"55102_CR26","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1016\/j.chom.2015.05.009","volume":"17","author":"GA Josling","year":"2015","unstructured":"Josling, G. A. et al. A plasmodium falciparum bromodomain protein regulates invasion gene expression. Cell Host Microbe 17, 741\u2013751 (2015).","journal-title":"Cell Host Microbe"},{"key":"55102_CR27","doi-asserted-by":"publisher","first-page":"16166","DOI":"10.1038\/nmicrobiol.2016.166","volume":"1","author":"MY-X Lim","year":"2016","unstructured":"Lim, M. Y.-X. et al. UDP-galactose and acetyl-CoA transporters as Plasmodium multidrug resistance genes. Nat. Microbiol. 1, 16166 (2016).","journal-title":"Nat. Microbiol."},{"key":"55102_CR28","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1016\/j.ijpara.2020.10.011","volume":"51","author":"M Biddau","year":"2021","unstructured":"Biddau, M. et al. Plasmodium falciparum LipB mutants display altered redox and carbon metabolism in asexual stages and cannot complete sporogony in Anopheles mosquitoes. Int. J. Parasitol. 51, 441\u2013453 (2021).","journal-title":"Int. J. Parasitol."},{"key":"55102_CR29","doi-asserted-by":"publisher","first-page":"e231","DOI":"10.1038\/cddis.2011.118","volume":"2","author":"S Rathore","year":"2011","unstructured":"Rathore, S. et al. Disruption of a mitochondrial protease machinery in Plasmodium falciparum is an intrinsic signal for parasite cell death. Cell Death Dis. 2, e231\u2013e231 (2011).","journal-title":"Cell Death Dis."},{"key":"55102_CR30","doi-asserted-by":"publisher","first-page":"440","DOI":"10.1016\/j.pt.2010.05.002","volume":"26","author":"JB Koenderink","year":"2010","unstructured":"Koenderink, J. B., Kavishe, R. A., Rijpma, S. R. & Russel, F. G. M. The ABCs of multidrug resistance in malaria. Trends Parasitol. 26, 440\u2013446 (2010).","journal-title":"Trends Parasitol."},{"key":"55102_CR31","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1111\/1755-0998.12634","volume":"17","author":"M Gautier","year":"2017","unstructured":"Gautier, M., Klassmann, A. & Vitalis, R. rehh 2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure. Mol. Ecol. Resour. 17, 78\u201390 (2017).","journal-title":"Mol. Ecol. Resour."},{"key":"55102_CR32","doi-asserted-by":"publisher","first-page":"645","DOI":"10.1016\/j.ijpara.2008.11.015","volume":"39","author":"W Leber","year":"2009","unstructured":"Leber, W. et al. A unique phosphatidylinositol 4-phosphate 5-kinase is activated by ADP-ribosylation factor in Plasmodium falciparum. Int. J. Parasitol. 39, 645\u2013653 (2009).","journal-title":"Int. J. Parasitol."},{"key":"55102_CR33","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1007031","volume":"14","author":"C Lehmann","year":"2018","unstructured":"Lehmann, C. et al. Plasmodium falciparum dipeptidyl aminopeptidase 3 activity is important for efficient erythrocyte invasion by the malaria parasite. PLoS Pathog. 14, e1007031 (2018).","journal-title":"PLoS Pathog."},{"key":"55102_CR34","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01897-22","volume":"13","author":"X Zhu","year":"2022","unstructured":"Zhu, X. et al. The Plasmodium falciparum nuclear protein phosphatase NIF4 is required for efficient merozoite invasion and regulates artemisinin sensitivity. mBio 13, e0189722 (2022).","journal-title":"mBio"},{"key":"55102_CR35","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.43362","volume":"8","author":"DK Gupta","year":"2019","unstructured":"Gupta, D. K. et al. The Plasmodium liver-specific protein 2 (LISP2) is an early marker of liver stage development. eLife 8, e43362 (2019).","journal-title":"eLife"},{"key":"55102_CR36","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1111\/mmi.12083","volume":"87","author":"Y Orito","year":"2013","unstructured":"Orito, Y. et al. Liver-specific protein 2: a Plasmodium protein exported to the hepatocyte cytoplasm and required for merozoite formation. Mol. Microbiol. 87, 66\u201379 (2013).","journal-title":"Mol. Microbiol."},{"key":"55102_CR37","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1038\/ng.3189","volume":"47","author":"O Miotto","year":"2015","unstructured":"Miotto, O. et al. Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nat. Genet. 47, 226\u2013234 (2015).","journal-title":"Nat. Genet."},{"key":"55102_CR38","doi-asserted-by":"publisher","first-page":"e01542","DOI":"10.1128\/AAC.01542-19","volume":"64","author":"RC Henrici","year":"2019","unstructured":"Henrici, R. C., van Schalkwyk, D. A. & Sutherland, C. J. Modification of pfap2\u03bc and pfubp1 markedly reduces ring-stage susceptibility of plasmodium falciparum to artemisinin in vitro. Antimicrob. Agents Chemother. 64, e01542\u201319 (2019).","journal-title":"Antimicrob. Agents Chemother."},{"key":"55102_CR39","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1111\/j.1365-2958.2007.05753.x","volume":"65","author":"P Hunt","year":"2007","unstructured":"Hunt, P. et al. Gene encoding a deubiquitinating enzyme is mutated in artesunate- and chloroquine-resistant rodent malaria parasites. Mol. Microbiol. 65, 27\u201340 (2007).","journal-title":"Mol. Microbiol."},{"key":"55102_CR40","doi-asserted-by":"publisher","DOI":"10.1038\/srep03318","volume":"3","author":"S Borrmann","year":"2013","unstructured":"Borrmann, S. et al. Genome-wide screen identifies new candidate genes associated with artemisinin susceptibility in Plasmodium falciparum in Kenya. Sci. Rep. 3, 3318 (2013).","journal-title":"Sci. Rep."},{"key":"55102_CR41","doi-asserted-by":"publisher","first-page":"9109","DOI":"10.1073\/pnas.85.23.9109","volume":"85","author":"AF Cowman","year":"1988","unstructured":"Cowman, A. F., Morry, M. J., Biggs, B. A., Cross, G. A. & Foote, S. J. Amino acid changes linked to pyrimethamine resistance in the dihydrofolate reductase-thymidylate synthase gene of Plasmodium falciparum. Proc. Natl Acad. Sci. Usa. 85, 9109\u20139113 (1988).","journal-title":"Proc. Natl Acad. Sci. Usa."},{"key":"55102_CR42","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1126\/science.1074045","volume":"298","author":"ABS Sidhu","year":"2002","unstructured":"Sidhu, A. B. S., Verdier-Pinard, D. & Fidock, D. A. Chloroquine resistance in plasmodium falciparum malaria parasites conferred by pfcrt mutations. Science 298, 210\u2013213 (2002).","journal-title":"Science"},{"key":"55102_CR43","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/s41564-023-01377-z","volume":"8","author":"A Amambua-Ngwa","year":"2023","unstructured":"Amambua-Ngwa, A. et al. Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nat. Microbiol. 8, 1213\u20131226 (2023).","journal-title":"Nat. Microbiol."},{"key":"55102_CR44","doi-asserted-by":"publisher","unstructured":"Mok, S. et al. Mapping the genomic landscape of multidrug resistance in Plasmodium falciparum and its impact on parasite fitness. Preprint at BioRxiv https:\/\/doi.org\/10.1101\/2023.06.02.543338 (2023).","DOI":"10.1101\/2023.06.02.543338"},{"key":"55102_CR45","doi-asserted-by":"publisher","first-page":"1124","DOI":"10.1073\/pnas.94.4.1124","volume":"94","author":"W Sirawaraporn","year":"1997","unstructured":"Sirawaraporn, W., Sathitkul, T., Sirawaraporn, R., Yuthavong, Y. & Santi, D. V. Antifolate-resistant mutants of Plasmodium falciparum dihydrofolate\u2009reductase. Proc. Natl Acad. Sci. 94, 1124\u20131129 (1997).","journal-title":"Proc. Natl Acad. Sci."},{"key":"55102_CR46","doi-asserted-by":"publisher","first-page":"13944","DOI":"10.1073\/pnas.94.25.13944","volume":"94","author":"T Triglia","year":"1997","unstructured":"Triglia, T., Menting, J. G. T., Wilson, C. & Cowman, A. F. Mutations in dihydropteroate synthase are responsible for sulfone and sulfonamide resistance in Plasmodium\u2009falciparum. Proc. Natl Acad. Sci. Usa. 94, 13944\u201313949 (1997).","journal-title":"Proc. Natl Acad. Sci. Usa."},{"key":"55102_CR47","doi-asserted-by":"publisher","first-page":"759422","DOI":"10.3389\/fphar.2021.759422","volume":"12","author":"JP Gil","year":"2021","unstructured":"Gil, J. P. & Fan\u00e7ony, C. Plasmodium falciparum Multidrug Resistance Proteins (pfMRPs). Front. Pharmacol. 12, 759422 (2021).","journal-title":"Front. Pharmacol."},{"key":"55102_CR48","first-page":"66","volume":"4","author":"SA Peel","year":"2001","unstructured":"Peel, S. A. The ABC transporter genes of Plasmodium falciparum and drug resistance. Drug Resist. Updat. Rev. Comment. Antimicrob. Anticancer Chemother. 4, 66\u201374 (2001).","journal-title":"Drug Resist. Updat. Rev. Comment. Antimicrob. Anticancer Chemother."},{"key":"55102_CR49","doi-asserted-by":"publisher","first-page":"E5455","DOI":"10.1073\/pnas.1414221111","volume":"111","author":"MB Jim\u00e9nez-D\u00edaz","year":"2014","unstructured":"Jim\u00e9nez-D\u00edaz, M. B. et al. (+)-SJ733, a clinical candidate for malaria that acts through ATP4 to induce rapid host-mediated clearance of Plasmodium. Proc. Natl Acad. Sci. Usa. 111, E5455\u2013E5462 (2014).","journal-title":"Proc. Natl Acad. Sci. Usa."},{"key":"55102_CR50","doi-asserted-by":"publisher","first-page":"1060202","DOI":"10.3389\/fcimb.2022.1060202","volume":"12","author":"CBG Barnes","year":"2022","unstructured":"Barnes, C. B. G., Dans, M. G., Jonsdottir, T. K., Crabb, B. S. & Gilson, P. R. PfATP4 inhibitors in the medicines for malaria venture malaria box and pathogen box block the schizont-to-ring transition by inhibiting egress rather than invasion. Front. Cell. Infect. Microbiol. 12, 1060202 (2022).","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"55102_CR51","doi-asserted-by":"publisher","DOI":"10.1128\/mbio.01178-22","volume":"13","author":"F Mohring","year":"2022","unstructured":"Mohring, F. et al. Cation ATPase (ATP4) orthologue replacement in the malaria parasite plasmodium knowlesi reveals species-specific responses to ATP4-targeting drugs. mBio 13, e0117822 (2022).","journal-title":"mBio"},{"key":"55102_CR52","doi-asserted-by":"publisher","first-page":"50","DOI":"10.1038\/nature12876","volume":"505","author":"F Ariey","year":"2014","unstructured":"Ariey, F. et al. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 505, 50\u201355 (2014).","journal-title":"Nature"},{"key":"55102_CR53","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1128\/AAC.42.7.1811","volume":"42","author":"LK Basco","year":"1998","unstructured":"Basco, L. K., Tahar, R. & Ringwald, P. Molecular basis of in vivo resistance to sulfadoxine-pyrimethamine in african adult patients infected with plasmodium falciparum malaria parasites. Antimicrob. Agents Chemother. 42, 1811\u20131814 (1998).","journal-title":"Antimicrob. Agents Chemother."},{"key":"55102_CR54","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1128\/AAC.49.2.733-740.2005","volume":"49","author":"MD Hastings","year":"2005","unstructured":"Hastings, M. D. et al. Novel Plasmodium vivax dhfr alleles from the indonesian archipelago and papua new guinea: association with pyrimethamine resistance determined by a saccharomyces cerevisiae expression system. Antimicrob. Agents Chemother. 49, 733\u2013740 (2005).","journal-title":"Antimicrob. Agents Chemother."},{"key":"55102_CR55","doi-asserted-by":"publisher","first-page":"3018","DOI":"10.1073\/pnas.87.8.3018","volume":"87","author":"DS Peterson","year":"1990","unstructured":"Peterson, D. S., Milhous, W. K. & Wellems, T. E. Molecular basis of differential resistance to cycloguanil and pyrimethamine in Plasmodium falciparum malaria. Proc. Natl Acad. Sci. Usa. 87, 3018\u20133022 (1990).","journal-title":"Proc. Natl Acad. Sci. Usa."},{"key":"55102_CR56","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1073\/pnas.1216457110","volume":"110","author":"RW Moon","year":"2013","unstructured":"Moon, R. W. et al. Adaptation of the genetically tractable malaria pathogen Plasmodium knowlesi to continuous culture in human erythrocytes. Proc. Natl Acad. Sci. 110, 531\u2013536 (2013).","journal-title":"Proc. Natl Acad. Sci."},{"key":"55102_CR57","doi-asserted-by":"publisher","DOI":"10.21769\/BioProtoc.3522","volume":"10","author":"F Mohring","year":"2020","unstructured":"Mohring, F., Hart, M. N., Patel, A., Baker, D. A. & Moon, R. W. CRISPR-Cas9 genome editing of plasmodium knowlesi. Bio-Protoc. 10, e3522 (2020).","journal-title":"Bio-Protoc."},{"key":"55102_CR58","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1016\/j.molbiopara.2003.10.019","volume":"134","author":"AVD Wel","year":"2004","unstructured":"Wel, A. V. D., Kocken, C. H. M., Pronk, T. C., Franke-Fayard, B. & Thomas, A. W. New selectable markers and single crossover integration for the highly versatile Plasmodium knowlesi transfection system. Mol. Biochem. Parasitol. 134, 97\u2013104 (2004).","journal-title":"Mol. Biochem. Parasitol."},{"key":"55102_CR59","doi-asserted-by":"publisher","first-page":"3051","DOI":"10.1093\/jac\/dkx279","volume":"72","author":"DA van Schalkwyk","year":"2017","unstructured":"van Schalkwyk, D. A., Moon, R. W., Blasco, B. & Sutherland, C. J. Comparison of the susceptibility of Plasmodium knowlesi and Plasmodium falciparum to antimalarial agents. J. Antimicrob. Chemother. 72, 3051\u20133058 (2017).","journal-title":"J. Antimicrob. Chemother."},{"key":"55102_CR60","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1016\/j.jinf.2023.06.013","volume":"87","author":"DA Prah","year":"2023","unstructured":"Prah, D. A. et al. Asymptomatic Plasmodium falciparum infection evades triggering a host transcriptomic response. J. Infect. 87, 259\u2013262 (2023).","journal-title":"J. Infect."},{"key":"55102_CR61","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29306-4","volume":"13","author":"LJ Plenderleith","year":"2022","unstructured":"Plenderleith, L. J. et al. Zoonotic origin of the human malaria parasite Plasmodium malariae from African apes. Nat. Commun. 13, 1868 (2022).","journal-title":"Nat. Commun."},{"key":"55102_CR62","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1086\/338566","volume":"185","author":"JG Kublin","year":"2002","unstructured":"Kublin, J. G. et al. Molecular markers for failure of sulfadoxine-pyrimethamine and chlorproguanil-dapsone treatment of Plasmodium falciparum malaria. J. Infect. Dis. 185, 380\u2013388 (2002).","journal-title":"J. Infect. Dis."},{"key":"55102_CR63","doi-asserted-by":"publisher","first-page":"857","DOI":"10.4269\/ajtmh.13-0129","volume":"89","author":"JA Flegg","year":"2013","unstructured":"Flegg, J. A. et al. Trends in antimalarial drug use in Africa. Am. J. Trop. Med. Hyg. 89, 857\u2013865 (2013).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"55102_CR64","doi-asserted-by":"publisher","first-page":"687","DOI":"10.4269\/ajtmh.1999.60.687","volume":"60","author":"B Singh","year":"1999","unstructured":"Singh, B. et al. A genus- and species-specific nested polymerase chain reaction malaria detection assay for epidemiologic studies. Am. J. Trop. Med. Hyg. 60, 687\u2013692 (1999).","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"55102_CR65","doi-asserted-by":"publisher","first-page":"975","DOI":"10.1128\/JCM.01858-08","volume":"47","author":"SE Shokoples","year":"2009","unstructured":"Shokoples, S. E., Ndao, M., Kowalewska-Grochowska, K. & Yanow, S. K. Multiplexed real-time PCR assay for discrimination of Plasmodium species with improved sensitivity for mixed infections. J. Clin. Microbiol. 47, 975\u2013980 (2009).","journal-title":"J. Clin. Microbiol."},{"key":"55102_CR66","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giab008","volume":"10","author":"P Danecek","year":"2021","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. GigaScience 10, giab008 (2021).","journal-title":"GigaScience"},{"key":"55102_CR67","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1038\/ng.806","volume":"43","author":"MA DePristo","year":"2011","unstructured":"DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491\u2013498 (2011).","journal-title":"Nat. Genet."},{"key":"55102_CR68","doi-asserted-by":"publisher","first-page":"1292","DOI":"10.1093\/bioinformatics\/btu005","volume":"30","author":"SA Assefa","year":"2014","unstructured":"Assefa, S. A. et al. estMOI: estimating multiplicity of infection using parasite deep sequencing data. Bioinformatics 30, 1292\u20131294 (2014).","journal-title":"Bioinformatics"},{"key":"55102_CR69","doi-asserted-by":"publisher","first-page":"731","DOI":"10.21105\/joss.00731","volume":"3","author":"SD Turner","year":"2018","unstructured":"Turner, S. D. qqman: an R package for visualizing GWAS results using Q-Q and Manhattan plots. J. Open Source Softw. 3, 731 (2018).","journal-title":"J. Open Source Softw."},{"key":"55102_CR70","doi-asserted-by":"publisher","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","volume":"37","author":"BQ Minh","year":"2020","unstructured":"Minh, B. Q. et al. IQ-TREE 2: New models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530\u20131534 (2020).","journal-title":"Mol. Biol. Evol."},{"key":"55102_CR71","doi-asserted-by":"publisher","first-page":"1655","DOI":"10.1101\/gr.094052.109","volume":"19","author":"DH Alexander","year":"2009","unstructured":"Alexander, D. H., Novembre, J. & Lange, K. Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19, 1655\u20131664 (2009).","journal-title":"Genome Res."},{"key":"55102_CR72","doi-asserted-by":"publisher","DOI":"10.1186\/s12936-018-2349-7","volume":"17","author":"SF Schaffner","year":"2018","unstructured":"Schaffner, S. F., Taylor, A. R., Wong, W., Wirth, D. F. & Neafsey, D. E. hmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar. J. 17, 196 (2018).","journal-title":"Malar. J."},{"key":"55102_CR73","doi-asserted-by":"publisher","first-page":"D808","DOI":"10.1093\/nar\/gkad1003","volume":"52","author":"J Alvarez-Jarreta","year":"2024","unstructured":"Alvarez-Jarreta, J. et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Res. 52, D808\u2013D816 (2024).","journal-title":"Nucleic Acids Res."},{"key":"55102_CR74","doi-asserted-by":"publisher","first-page":"W276","DOI":"10.1093\/nar\/gkac240","volume":"50","author":"F Madeira","year":"2022","unstructured":"Madeira, F. et al. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 50, W276\u2013W279 (2022).","journal-title":"Nucleic Acids Res."},{"key":"55102_CR75","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","volume":"25","author":"AM Waterhouse","year":"2009","unstructured":"Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189\u20131191 (2009).","journal-title":"Bioinformatics"},{"key":"55102_CR76","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1038\/nmeth.3213","volume":"12","author":"J Yang","year":"2015","unstructured":"Yang, J. et al. The I-TASSER Suite: protein structure and function prediction. Nat. Methods 12, 7\u20138 (2015).","journal-title":"Nat. Methods"},{"key":"55102_CR77","doi-asserted-by":"publisher","first-page":"1605","DOI":"10.1002\/jcc.20084","volume":"25","author":"EF Pettersen","year":"2004","unstructured":"Pettersen, E. F. et al. UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605\u20131612 (2004).","journal-title":"J. Comput. Chem."},{"key":"55102_CR78","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.45829","volume":"8","author":"F Mohring","year":"2019","unstructured":"Mohring, F. et al. Rapid and iterative genome editing in the malaria parasite Plasmodium knowlesi provides new tools for P. vivax research. eLife 8, e45829 (2019).","journal-title":"eLife"},{"key":"55102_CR79","doi-asserted-by":"publisher","first-page":"e01635","DOI":"10.1128\/mbio.01635-22","volume":"13","author":"A Patel","year":"2022","unstructured":"Patel, A., Nofal, S. D., Blackman, M. J. & Baker, D. A. CDC50 orthologues in plasmodium falciparum have distinct roles in merozoite egress and trophozoite maturation. mBio 13, e01635\u201322 (2022).","journal-title":"mBio"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-55102-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-55102-3","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-55102-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,30]],"date-time":"2024-12-30T13:02:44Z","timestamp":1735563764000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-55102-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,30]]},"references-count":79,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["55102"],"URL":"https:\/\/doi.org\/10.1038\/s41467-024-55102-3","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-4396572\/v1","asserted-by":"object"}]},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,30]]},"assertion":[{"value":"27 May 2024","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"27 November 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"30 December 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"10779"}}