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Participants were finger pricked, blood drops were collected for rapid diagnosis with <jats:italic>P. falciparum<\/jats:italic> histidine-rich protein 11 rapid diagnostic test kit and the ultra-sensitive Alere <jats:italic>Pf<\/jats:italic> malaria RDT, Blood smears for microscopy and dried blood spots on Whatman filter paper for molecular analysis were made. Real time PCR targeting the var acidic terminal sequence (varATS) gene of <jats:italic>P. falciparum<\/jats:italic> was carried out on a CFX 96 real time system thermocycler (BioRad) in discriminating malaria infections. For each run, laboratory strain of <jats:italic>P. falciparum<\/jats:italic> 3D7 and nuclease free water were used as positive and negative controls respectively. Additionally, High resolution melt analyses was employed for genotyping of the different drug resistance markers.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Out of one hundred and twenty-one pregnant women sampled, the SD Bioline\u2122 Malaria Ag <jats:italic>P.f<\/jats:italic> HRP2-based malaria rapid diagnostic test (mRDT) detected eight (0.06%) cases, the ultra-sensitive Alere\u2122 malaria Ag <jats:italic>P.f<\/jats:italic> rapid diagnostic test mRDT had similar outcome in the same samples as detected by the HRP2-based mRDT. Microscopy and RT-PCR confirmed four out of the eight infections detected by both rapid diagnostic tests as true positive and RT-PCR further detected three false negative samples by the two mRDTs providing a sub-microscopic malaria prevalence of 3.3%. Single nucleotide polymorphism in <jats:italic>Pf<\/jats:italic>dhps gene associated with sulphadoxine resistance revealed the presence of S613 mutant genotypes in three of the seven positive isolates and isolates with mixed wild\/mutant genotype at codon A613S. Furthermore, four mixed genotypes at the A581G codon were also recorded while the other <jats:italic>Pf<\/jats:italic>dhps codons (A436G, A437G and K540E) showed the presence of wild type alleles. In the <jats:italic>Pf<\/jats:italic>dhfr gene, there were mutations in 28.6%, 28.6%, and 85.7% at the I51, R59 and N108 codons respectively. Mixed wild and mutant type genotypes were also observed in 28.6% each of the N51I, and C59R codons. For the <jats:italic>Pf<\/jats:italic>crt, two haplotypes CVMNK and CVIET were observed. The SVMNT was altogether absent. Triple mutant CVIET 1(14.3%) and triple mutant\u2009+\u2009wild genotype CVIET\u2009+\u2009CVMNK 1(14.3%) were observed. The <jats:italic>Pf<\/jats:italic>mdr1 haplotypes were single mutants <jats:bold>Y<\/jats:bold>YND 1(14.3%); N<jats:bold>F<\/jats:bold>ND 1(14.3%) and double mutants <jats:bold>YF<\/jats:bold>ND 4(57.1%); <jats:bold>Y<\/jats:bold>Y<jats:bold>D<\/jats:bold>D 1(14.3%).<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13104-024-06763-2","type":"journal-article","created":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T15:02:19Z","timestamp":1715266939000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Sub-microscopic Plasmodium falciparum infections and multiple drug resistant single nucleotide polymorphic alleles in pregnant women from southwestern Nigeria"],"prefix":"10.1186","volume":"17","author":[{"given":"Agatha N.","family":"Ibekpobaoku","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mary A.","family":"Oboh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatou","family":"Faal","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth","family":"Adeniji","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olusola","family":"Ajibaye","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel T.","family":"Idowu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred","family":"Amambua-Ngwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,9]]},"reference":[{"key":"6763_CR1","unstructured":"WHO. 2020. 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Verbal and written informed consent was obtained from all pregnant women included in this study after detailed explanation of the study objectives to each of them. 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