Multiplex PCR and Oligonucleotide Microarray for Detection of Single-Nucleotide Polymorphisms Associated with
            <i>Plasmodium falciparum</i>
            Drug Resistance

Zhang, Guo Qing; Guan, Ya Yi; Sheng, Hai; Zheng, Bin; Wu, Song; Xiao, Hua; Tang, Lin

doi:10.1128/jcm.00081-08

Cited by 19 publications

(9 citation statements)

References 36 publications

(35 reference statements)

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“…If possible, primers were selected that contained more than one specific 3′-base, but five primers of the final set that were targeted to nuclear sequences matched this one base difference. Because genotyping based on single nucleotide polymorphisms (snips) is error-prone due to mutations [48], [49], we chose two genotype/strain-specific probes for all E. granulosus complex members. The exception was E. canadensis (G8/G10), where only one probe was selected due to its rare occurrence and close relationship to E. canadensis (G6/G7).…”

Section: Methodsmentioning

confidence: 99%

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

et al. 2013

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Echinococcus granulosus is characterized by high intra-specific variability (genotypes G1–G10) and according to the new molecular phylogeny of the genus Echinococcus, the E. granulosus complex has been divided into E. granulosus sensu stricto (G1–G3), E. equinus (G4), E. ortleppi (G5), and E. canadensis (G6–G10). The molecular characterization of E. granulosus isolates is fundamental to understand the spatio-temporal epidemiology of this complex in many endemic areas with the simultaneous occurrence of different Echinococcus species and genotypes. To simplify the genotyping of the E. granulosus complex we developed a single-tube multiplex PCR (mPCR) allowing three levels of discrimination: (i) Echinococcus genus, (ii) E. granulosus complex in common, and (iii) the specific genotype within the E. granulosus complex. The methodology was established with known DNA samples of the different strains/genotypes, confirmed on 42 already genotyped samples (Spain: 22 and Bulgaria: 20) and then successfully applied on 153 unknown samples (Tunisia: 114, Algeria: 26 and Argentina: 13). The sensitivity threshold of the mPCR was found to be 5 ng Echinoccoccus DNA in a mixture of up to 1 µg of foreign DNA and the specificity was 100% when template DNA from closely related members of the genus Taenia was used. Additionally to DNA samples, the mPCR can be carried out directly on boiled hydatid fluid or on alkaline-lysed frozen or fixed protoscoleces, thus avoiding classical DNA extractions. However, when using Echinococcus eggs obtained from fecal samples of infected dogs, the sensitivity of the mPCR was low (<40%). Thus, except for copro analysis, the mPCR described here has a high potential for a worldwide application in large-scale molecular epidemiological studies on the Echinococcus genus.

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Section: Methodsmentioning

confidence: 99%

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

et al. 2013

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“…The primers used in this study were designed by Zhang et al [28] to amplify regions containing single nucleotide polymorphisms (SNPs) covering genetic markers reported to be associated with the resistance of Plasmodium falciparum to some of the most commonly used antimalarial drugs such as chloroquine, me oquine, amodiaquine, sulfadoxinepyrimetamine and artemether. Pfcrt, pfmdr1, pfdhfr, pfdhps genes were detected at expected amplicon sizes from the malaria positive samples in this study.…”

Section: Discussionmentioning

confidence: 99%

Genetic markers associated with antimalarial drug resistance and haemoglobin genotypes among malaria patients in Kaduna State, Nigeria

Benjamin

Inabo

Muhammad

et al. 2020

Preprint

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Background Malaria is a disease of public health concern in Nigeria and sub-Saharan Africa. The emergence of drug resistance, particularly among P. falciparum strains, has been a major contributor to the global burden of malaria. This research was aimed at detecting genetic markers (pfcrt, pfmdr1, pfdhfr, pfdhps, pfatpase6) associated with antimalarial drug resistance and assessing the distribution of haemoglobin genotypes among malaria patients in of Kaduna State, Nigeria. Methods Three hundred (300) blood samples were collected from consenting individuals attending selected hospitals, in the three senatorial districts of Kaduna State, Nigeria. A structured questionnaire was used to obtain relevant data from the study participants. The samples were screened for malaria parasites by microscopy and malaria rapid diagnostic test kit. Deoxyribonucleic acid was extracted from one third of the malaria positive samples, and Polymerase Chain Reaction (PCR) was used for detection of the drug resistance genes. Pfcrt, pfmdr1, pfdhfr, pfdhps and pfatpase6 genes were detected at expected amplicon sizes from the malaria positive samples. The pfatpase6 PCR amplicons were sequenced and a phylogenetic tree was created using MEGA X to determine their relatedness to published sequences. Results Pfcrt (80%) had the highest prevalence, followed by pfdhfr (60%), pfmdr1 (36%) and pfdhps (8%). Pfatpase6 was also detected in 73.3% of the samples. The phylogenetic tree showed that all the pfatpase6 gene sequences (both the ones from this study and those published in NCBI Genbank) had the same origin and were closely related. However, the sequences from NCBI Genbank were from one clade; arising from a common ancestor (monophyletic) thus they were more closely related to themselves, than to the pfatpase6 sequences obtained in this study. Of all the malaria positive participants, those with HbAA (73%) haemoglobin genotype had the highest percentage followed by HbAS (23%), HbAC (3%) and HbSS (1). Conclusion We detected Plasmodium falciparum genes associated with drug resistance to commonly used antimalarials in the study area. Expression of these genes could have serious consequences in the treatment of malaria. The percentage of Plasmodium falciparum malaria was higher among persons with HbAA than those with HbAS, HbAC and HbS.

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“…Genotyping tests for the detection of drug resistance have been developed and applied in research as drug and pesticide resistance is of crucial importance in malaria control, both in Plasmodium and in the Anopheles mosquito vector, and also in the control of gastro-intestinal nematodes in livestock. Examples are: Plasmodium (Eldin de Pecoulas et al, 1995;Zindrou et al, 1996;Ranford-Cartwright et al, 2002;Djimde et al, 2004;Ferreira et al, 2006;Zhang et al, 2008;Wong et al, 2011) Trypanosoma (Delespaux et al, 2008) Haemonchus Humbert, 2000, 2002;Bo and Li, 2005;Tiwari et al, 2006;Walsh et al, 2007;Tiwari et al, 2007a,b;von Samson-Himmelstjerna et al, 2009;Rajat and Yadav, 2009), Teladorsagia (Elard et al, 1999;Humbert, 2000, 2002;Shayan et al, 2007), Trichostrongylus (Grant and Mascord, 1996;Humbert, 2000, 2002;Alvarez-Sanchez et al, 2005), Cyathostomum (Lake et al, 2009), and Wuchereria , Anopheles (Baek et al, 2006;Hoti et al, 2006;Tripet et al, 2006;Kim et al, 2007a,b;Djadid et al, 2009;Singh et al, 2009), Culex (de Chalegre et al, 2009Sarkar et al, 2011), Rhipicephalus (Guerrero et al, 2002) and Pediculus (Durand et al, 2007). These tests have the same technological advantages and disadvantages as DIQ tests.…”

Section: Assessment Of Intra-genomic Variation Determining Organism Cmentioning

confidence: 98%

Molecular diagnosis of infections and resistance in veterinary and human parasites

Hunt

2011

Veterinary Parasitology

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Multiplex PCR and Oligonucleotide Microarray for Detection of Single-Nucleotide Polymorphisms Associated with Plasmodium falciparum Drug Resistance

Cited by 19 publications

References 36 publications

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

A Multiplex PCR for the Simultaneous Detection and Genotyping of the Echinococcus granulosus Complex

Genetic markers associated with antimalarial drug resistance and haemoglobin genotypes among malaria patients in Kaduna State, Nigeria

Molecular diagnosis of infections and resistance in veterinary and human parasites

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