A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India
| العنوان: | A Method for Amplicon Deep Sequencing of Drug Resistance Genes in Plasmodium falciparum Clinical Isolates from India |
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| المؤلفون: | Samuel C. Wassmer, Pavitra N. Rao, Swapna Uplekar, Sanjib Mohanty, Jane M. Carlton, Sriti Kayal, Sonal Kale, Om P. Singh, Akshaya K Mohanty, Prashant K. Mallick, Nabamita Bandyopadhyay |
| المصدر: | Journal of Clinical Microbiology |
| بيانات النشر: | American Society for Microbiology, 2016. |
| سنة النشر: | 2016 |
| مصطلحات موضوعية: | 0301 basic medicine, Microbiology (medical), Genotyping Techniques, 030231 tropical medicine, 030106 microbiology, Plasmodium falciparum, Drug Resistance, India, Drug resistance, Polymorphism, Single Nucleotide, Deep sequencing, 03 medical and health sciences, Antimalarials, 0302 clinical medicine, Genotype, medicine, Humans, Malaria, Falciparum, Alleles, Genetics, biology, Computational Biology, High-Throughput Nucleotide Sequencing, Ion semiconductor sequencing, Sequence Analysis, DNA, Amplicon, biology.organism_classification, medicine.disease, 3. Good health, Parasitology, Malaria |
| الوصف: | A major challenge to global malaria control and elimination is early detection and containment of emerging drug resistance. Next-generation sequencing (NGS) methods provide the resolution, scalability, and sensitivity required for high-throughput surveillance of molecular markers of drug resistance. We have developed an amplicon sequencing method on the Ion Torrent PGM platform for targeted resequencing of a panel of six Plasmodium falciparum genes implicated in resistance to first-line antimalarial therapy, including artemisinin combination therapy, chloroquine, and sulfadoxine-pyrimethamine. The protocol was optimized using 12 geographically diverse P. falciparum reference strains and successfully applied to multiplexed sequencing of 16 clinical isolates from India. The sequencing results from the reference strains showed 100% concordance with previously reported drug resistance-associated mutations. Single-nucleotide polymorphisms (SNPs) in clinical isolates revealed a number of known resistance-associated mutations and other nonsynonymous mutations that have not been implicated in drug resistance. SNP positions containing multiple allelic variants were used to identify three clinical samples containing mixed genotypes indicative of multiclonal infections. The amplicon sequencing protocol has been designed for the benchtop Ion Torrent PGM platform and can be operated with minimal bioinformatics infrastructure, making it ideal for use in countries that are endemic for the disease to facilitate routine large-scale surveillance of the emergence of drug resistance and to ensure continued success of the malaria treatment policy. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1098-660X 0095-1137 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bbe433af1f7d2d33f3b99f51f6a2bfb3Test http://europepmc.org/articles/PMC4879288Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....bbe433af1f7d2d33f3b99f51f6a2bfb3 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 1098660X 00951137 |
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