{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,19]],"date-time":"2026-03-19T12:22:31Z","timestamp":1773922951072,"version":"3.50.1"},"reference-count":53,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T00:00:00Z","timestamp":1606348800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI104423"],"award-info":[{"award-number":["AI104423"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["P20 GM104420, P30 GM103324"],"award-info":[{"award-number":["P20 GM104420, P30 GM103324"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>Antifolate resistance is significant in Kenya and presumed to result from extensive use and cross-resistance between antifolate antimalarials and antibiotics, including cotrimoxazole\/Bactrim used for HIV-1 chemotherapy. However, little is known about antifolate-resistant malaria in the context of newly diagnosed HIV-1 co-infection prior to administration of HIV-1 chemotherapy. Blood samples from a cross-sectional study of asymptomatic adult Kenyans enrolled during voluntary HIV testing were analyzed by PCR for<jats:italic>Plasmodium<\/jats:italic>spp. More than 95% of volunteers with identifiable parasite species (132 HIV-1 co-infected) were infected with<jats:italic>Plasmodium falciparum<\/jats:italic>alone or<jats:italic>P. falciparum<\/jats:italic>with<jats:italic>Plasmodium ovale<\/jats:italic>and\/or<jats:italic>Plasmodium malariae<\/jats:italic>. Deep sequencing was used to screen for mutations in<jats:italic>P. falciparum dihydrofolate reductase (dhfr)<\/jats:italic>(N51I, C59R, S108N, I164L) and<jats:italic>dihydropteroate synthase (dhps)<\/jats:italic>(S436H, A437G, K540E, A581G) from 1133 volunteers. Individual mutations in DHPS but not DHFR correlated with HIV-1 status. DHFR haplotype diversity was significantly different among volunteers by gender and HIV-1 status. DHPS haplotype diversity by HIV-1 status was significantly different between volunteers paired by age and gender, indicating that patterns of resistance were independent of these variables. Molecular simulations for a novel DHPS mutation (I504T) suggested that the mutated protein has increased affinity for the endogenous ligand DHPPP and decreased affinity for drug binding. A sub-group of monoclonal infections revealed that age and parasitemia were not correlated and enabled identification of a rare septuple-mutant haplotype (IRNL-HGEA). In our study, adult Kenyans newly diagnosed with HIV-1 infection were predominantly infected with moderately resistant<jats:italic>P. falciparum<\/jats:italic>, with patterns of infecting parasite genotypes significantly associated with HIV-1 status. Together with the discovery of DHPS I504T, these data indicate that antifolate resistance continues to evolve in Kenya. Further, they highlight the need to understand the effects of associated mutations on both fitness and resistance of<jats:italic>P. falciparum<\/jats:italic>in the context of HIV-1 co-infection to better inform treatment for asymptomatic malaria.<\/jats:p>","DOI":"10.3389\/fcimb.2020.600112","type":"journal-article","created":{"date-parts":[[2020,11,26]],"date-time":"2020-11-26T04:24:37Z","timestamp":1606364677000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":7,"title":["Plasmodium falciparum DHFR and DHPS Mutations Are Associated With HIV-1 Co-Infection and a Novel DHPS Mutation I504T Is Identified in Western Kenya"],"prefix":"10.3389","volume":"10","author":[{"given":"Brandi K.","family":"Torrevillas","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sarah M.","family":"Garrison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexander J.","family":"McKeeken","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dharmeshkumar","family":"Patel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James T.","family":"Van Leuven","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nathaniel I.","family":"Dizon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karina I.","family":"Rivas","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicholas J.","family":"Hathaway","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeffrey A.","family":"Bailey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John N.","family":"Waitumbi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carolyne M.","family":"Kifude","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janet","family":"Oyieko","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"V. Ann","family":"Stewart","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shirley","family":"Luckhart","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2020,11,26]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.softx.2015.06.001","article-title":"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers","author":"Abraham","year":"2015","journal-title":"SoftwareX"},{"key":"B2","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1186\/1475-2875-13-233","article-title":"Distinct patterns of diversity, population structure and evolution in the AMA1 genes of sympatric Plasmodium falciparum and Plasmodium vivax populations of Papua New Guinea from an area of similarly high transmission","volume":"13","author":"Arnott","year":"2014","journal-title":"Malaria J."},{"key":"B3","doi-asserted-by":"publisher","first-page":"e8497 (1:11)","DOI":"10.1371\/journal.pone.0008497","article-title":"Contrasting population structures of the genes encoding ten leading vaccine-candidate antigens of the human malaria parasite, Plasmodium falciparum","volume":"4","author":"Barry","year":"2009","journal-title":"PLoS One"},{"key":"B4","doi-asserted-by":"publisher","first-page":"S107","DOI":"10.1093\/infdis\/jit610","article-title":"Sex bias in the outcome of human tropical infectious diseases: influence of steroid hormones","volume":"209","author":"Bernin","year":"2014","journal-title":"J. Infect. Dis."},{"key":"B5","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"B6","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: an ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"B7","doi-asserted-by":"publisher","first-page":"3273","DOI":"10.1111\/febs.15196","article-title":"The structure of Plasmodium falciparum hydroxymethyldihydropterin pyrophosphokinase-dihydropteroate synthase reveals the basis of sulfa resistance","volume":"287","author":"Chitnumsub","year":"","journal-title":"FEBS J."},{"key":"B8","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1093\/bfgp\/elz008","article-title":"The genomic architecture of antimalarial drug resistance","volume":"18","author":"Cowell","year":"2019","journal-title":"Brief Funct. Genomics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"2156","DOI":"10.1093\/bioinformatics\/btr330","article-title":"The variant call format and VCFtools","volume":"27","author":"Danecek","year":"2011","journal-title":"Bioinformatics"},{"key":"B10","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1475-2875-3-33","article-title":"Competitive release of drug resistance following drug treatment of mixed Plasmodium chabaudi infections","volume":"3","author":"de Roode","year":"2004","journal-title":"Malaria J."},{"key":"B11","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/s12936-015-1039-y","article-title":"The role of gender on malaria preventive behaviour among rural households in Kenya","volume":"15","author":"Diiro","year":"2016","journal-title":"Malaria J."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1","DOI":"10.18637\/jss.v022.i04","article-title":"The ade4 Package: Implementing the Duality Diagram for Ecologists","volume":"22","author":"Dray","year":"2007","journal-title":"J. Stat. Soft."},{"key":"B13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1006\/expr.1998.4274","article-title":"Plasmodium falciparum: Detection of polymorphisms in the dihydrofolate reductase and dihydropteroate synthetase genes by PCR and restriction digestion","volume":"89","author":"Duraisingh","year":"1998","journal-title":"Exp. Parasitol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1016\/S1473-3099(11)70031-7","article-title":"Consequences of HIV infection on malaria and therapeutic implications: a systematic review","volume":"11","author":"Flateau","year":"2011","journal-title":"Lancet Infect. Dis."},{"key":"B15","doi-asserted-by":"publisher","first-page":"331","DOI":"10.1093\/infdis\/jiu448","article-title":"Demographic evidence of sex differences in vulnerability to infectious diseases: Table 1","volume":"211","author":"Garenne","year":"2015","journal-title":"J. Infect. Dis."},{"key":"B16","doi-asserted-by":"publisher","first-page":"e21 (1:13)","DOI":"10.1093\/nar\/gkx1201","article-title":"SeekDeep: single-base resolution de novo clustering for amplicon deep sequencing","volume":"46","author":"Hathaway","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B17","doi-asserted-by":"publisher","first-page":"2135","DOI":"10.1002\/jcc.23354","article-title":"CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data","volume":"34","author":"Huang","year":"2013","journal-title":"J. Comput. Chem."},{"key":"B18","doi-asserted-by":"publisher","first-page":"680","DOI":"10.1093\/bioinformatics\/btq003","article-title":"CD-HIT Suite: a web server for clustering and comparing biological sequences","volume":"26","author":"Huang","year":"2010","journal-title":"Bioinformatics"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1066","DOI":"10.1016\/S0140-6736(01)06201-8","article-title":"Plasmodium falciparum cross-resistance between trimethoprim and pyrimethamine","volume":"358","author":"Iyer","year":"2001","journal-title":"Lancet"},{"key":"B20","doi-asserted-by":"publisher","first-page":"1367","DOI":"10.1016\/S0006-3495(99)77298-X","article-title":"The role of proline and glycine in determining the backbone flexibility of a channel-forming peptide","volume":"76","author":"Jacob","year":"1999","journal-title":"Biophys. J."},{"key":"B21","doi-asserted-by":"publisher","first-page":"597","DOI":"10.1016\/S0022-2836(02)00470-9","article-title":"On the role of the crystal environment in determining protein side-chain conformations","volume":"320","author":"Jacobson","year":"2002","journal-title":"J. Mol. Biol."},{"key":"B22","doi-asserted-by":"publisher","first-page":"351","DOI":"10.1002\/prot.10613","article-title":"A hierarchical approach to all-atom protein loop prediction","volume":"55","author":"Jacobson","year":"2004","journal-title":"Proteins: Struc. Funct. Bioinf."},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pntd.0007223","article-title":"The prevalence and antifolate drug resistance profiles of Plasmodium falciparum in study participants randomized to discontinue or continue cotrimoxazole prophylaxis","volume":"13","author":"Juma","year":"2019","journal-title":"PLoS Negl Trop. Dis."},{"key":"B24","doi-asserted-by":"publisher","first-page":"876","DOI":"10.1097\/00006454-199709000-00011","article-title":"Effects of malaria infection in human immunodeficiency virus type 1-infected Ugandan children","volume":"16","author":"Kalyesubula","year":"1997","journal-title":"Pediatr. Infect. Dis. J."},{"key":"B25","doi-asserted-by":"publisher","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B26","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"B27","unstructured":"Data available from NCBI GenBank (https:\/\/www.ncbi.nlm.nih.gov\/) LuckhartS. TorrevillasB. K. GarrisonS. M. McKeekenA. J. PatelD. Van LeuvenJ. T. Assembled population-level haplotypes of P. falciparum dhfr (PopSet: 1927947099: MT886986 - MT886999), dhps (PopSet: 1927947063: MT886968 - MT886985), csp (PopSet: 1927946859: MT886866 - MT886967) and ama1 domain 1 (PopSet: 1927947308: MT887090 - MT887221) and domain 2 (PopSet: 1927947128: MT887000 - MT887089).2020"},{"key":"B28","unstructured":"RCSB PDB homepage, released 08-28-2018 ManickamY. KarlH. SharmaA. 2018"},{"key":"B29","doi-asserted-by":"publisher","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a map-reduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"B30","doi-asserted-by":"publisher","first-page":"1198","DOI":"10.1086\/374555","article-title":"Uncommon asymptomatic Plasmodium falciparum infections in Gabonese children","volume":"36","author":"Missinou","year":"2003","journal-title":"Clin. Infect. Dis."},{"key":"B31","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1093\/infdis\/jit415","article-title":"Ordered accumulation of mutations conferring resistance to sulfadoxine-pyrimethamine in the Plasmodium falciparum parasite","volume":"209","author":"Mita","year":"2014","journal-title":"J. Infect. Dis."},{"key":"B32","doi-asserted-by":"crossref","first-page":"141","DOI":"10.38150\/sajeb.1(3).p141-146","article-title":"Human host preference of Anopheles mosquitoes collected from students hostels in a Nigerian university","volume":"1","author":"Okwa","year":"2011","journal-title":"South Asian J. Exp. Biol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1590","DOI":"10.1086\/514159","article-title":"Mutations in Plasmodium falciparum dihydrofolate reductase and dihydropteroate synthase and epidemiologic patterns of pyrimethamine-sulfadoxine use and resistance","volume":"176","author":"Plowe","year":"1997","journal-title":"J. Infect. Dis."},{"key":"B35","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1186\/s13104-015-1270-1","article-title":"Effects of HIV-1 infection on malaria parasitemia in milo sub-location, western Kenya","volume":"8","author":"Rutto","year":"2015","journal-title":"BMC Res. Notes"},{"key":"B36","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1093\/bioinformatics\/btq706","article-title":"phangorn: phylogenetic analysis in R","volume":"27","author":"Schliep","year":"2011","journal-title":"Bioinformatics"},{"key":"B37","article-title":"Maestro","volume-title":"Schr\u00f6dinger Release 2020-2: Maestro.","year":"2020"},{"key":"B38","doi-asserted-by":"publisher","first-page":"2661","DOI":"10.1073\/pnas.0611182104","article-title":"Conformational entropy of alanine versus glycine in protein denatured states","volume":"104","author":"Scott","year":"2007","journal-title":"PNAS"},{"key":"B39","unstructured":"SettlesM. msettles\/dbcAmplicons.2019"},{"key":"B40","doi-asserted-by":"publisher","first-page":"608","DOI":"10.1093\/infdis\/jiv088","article-title":"Asymptomatic multiclonal Plasmodium falciparum infections carried through the dry season predict protection against subsequent clinical malaria","volume":"212","author":"Sond\u00e9n","year":"2015","journal-title":"J. Infect. Dis."},{"key":"B41","doi-asserted-by":"publisher","first-page":"42","DOI":"10.4269\/ajtmh.1996.55.42","article-title":"Impairment of a pregnant woman\u2019s acquired ability to limit Plasmodium falciparum by infection with human immunodeficiency virus type-1","volume":"55","author":"Steketee","year":"1996","journal-title":"Am. J. Trop. Med. Hyg"},{"key":"B42","doi-asserted-by":"publisher","first-page":"1883","DOI":"10.1093\/cid\/cix1123","article-title":"The relative contribution of symptomatic and asymptomatic Plasmodium vivax and Plasmodium falciparum infections to the infectious reservoir in a low-endemic setting in Ethiopia","volume":"66","author":"Tadesse","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"B43","doi-asserted-by":"publisher","first-page":"1998","DOI":"10.1093\/infdis\/jit392","article-title":"Pooled deep sequencing of Plasmodium falciparum isolates: an efficient and scalable tool to quantify prevailing malaria drug-resistance genotypes","volume":"208","author":"Taylor","year":"2013","journal-title":"J. Infect. Dis."},{"key":"B44","doi-asserted-by":"publisher","first-page":"3807","DOI":"10.1093\/emboj\/17.14.3807","article-title":"Allelic exchange at the endogenous genomic locus in Plasmodium falciparum proves the role of dihydropteroate synthase in sulfadoxine-resistant malaria","volume":"17","author":"Triglia","year":"1998","journal-title":"EMBO J."},{"key":"B45","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1093\/infdis\/jiu044","article-title":"Differential prevalence of transporter polymorphisms in symptomatic and asymptomatic falciparum malaria infections in Uganda","volume":"210","author":"Tukwasibwe","year":"2014","journal-title":"J. Infect. Dis."},{"key":"B46","doi-asserted-by":"publisher","first-page":"2629","DOI":"10.1098\/rspb.2007.0873","article-title":"Transmission stage investment of malaria parasites in response to in-host competition","volume":"274","author":"Wargo","year":"2007","journal-title":"Proc. R. Soc. B"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1051","DOI":"10.1016\/S0140-6736(00)02727-6","article-title":"Effect of HIV-1 and increasing immunosuppression on malaria parasitaemia and clinical episodes in adults in rural Uganda: a cohort study","volume":"356","author":"Whitworth","year":"2000","journal-title":"Lancet"},{"key":"B48","doi-asserted-by":"publisher","first-page":"3190","DOI":"10.1074\/jbc.272.6.3190","article-title":"Glycine residues provide flexibility for enzyme active sites","volume":"272","author":"Yan","year":"1997","journal-title":"J. Biol. Chem."},{"key":"B49","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/1471-2105-13-134","article-title":"Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction","volume":"13","author":"Ye","year":"2012","journal-title":"BMC Bioinf."},{"key":"B50","doi-asserted-by":"publisher","first-page":"14962","DOI":"10.1074\/jbc.RA118.004558","article-title":"Structure of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase\u2013dihydropteroate synthase from Plasmodium vivax sheds light on drug resistance","volume":"293","author":"Yogavel","year":"2018","journal-title":"J. Biol. Chem."},{"key":"B51","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/2041-210X.12628","article-title":"ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data","volume":"8","author":"Yu","year":"2017","journal-title":"Methods Ecol. Evol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1016\/j.meegid.2016.01.021","article-title":"Genetic diversity of the Plasmodium falciparum apical membrane antigen I gene in parasite population from the China\u2013Myanmar border area","volume":"39","author":"Zhu","year":"2016","journal-title":"Infect Genet. Evol."},{"key":"B53","doi-asserted-by":"publisher","first-page":"2359","DOI":"10.1002\/jcc.21816","article-title":"SwissParam: A fast force field generation tool for small organic molecules","volume":"32","author":"Zoete","year":"2011","journal-title":"J. Comput. Chem."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2020.600112\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,29]],"date-time":"2022-11-29T22:30:47Z","timestamp":1669761047000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fcimb.2020.600112\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,26]]},"references-count":53,"alternative-id":["10.3389\/fcimb.2020.600112"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2020.600112","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,26]]},"article-number":"600112"}}