Next-Generation Sequencing of Plasmodium vivax Patient Samples Shows Evidence of Direct Evolution in Drug-Resistance Genes

Patients with antiretroviral therapy interruption have a high risk of virological failure when re-initiating antiretroviral therapy (ART), especially those with HIV drug resistance. Next-generation sequencing may provide close scrutiny on their minority drug resistance variant. A cross-sectional study was conducted in patients with ART interruption in five regions in China in 2016. Through Sanger and next-generation sequencing in parallel, HIV drug resistance was genotyped on their plasma samples. Rates of HIV drug resistance were compared by the McNemar tests. In total, 174 patients were included in this study, with a median 12 (interquartile range (IQR), 6–24) months of ART interruption. Most (86.2%) of them had received efavirenz (EFV)/nevirapine (NVP)-based first-line therapy for a median 16 (IQR, 7–26) months before ART interruption. Sixty-one (35.1%) patients had CRF07_BC HIV-1 strains, 58 (33.3%) CRF08_BC and 35 (20.1%) CRF01_AE. Thirty-four (19.5%) of the 174 patients were detected to harbor HIV drug-resistant variants on Sanger sequencing. Thirty-six (20.7%), 37 (21.3%), 42 (24.1%), 79 (45.4%) and 139 (79.9) patients were identified to have HIV drug resistance by next-generation sequencing at 20% (v.s. Sanger, p = 0.317), 10% (v.s. Sanger, p = 0.180), 5% (v.s. Sanger, p = 0.011), 2% (v.s. Sanger, p < 0.001) and 1% (v.s. Sanger, p < 0.001) of detection thresholds, respectively. K65R was the most common minority mutation, of 95.1% (58/61) and 93.1% (54/58) in CRF07_BC and CRF08_BC, respectively, when compared with 5.7% (2/35) in CRF01_AE (p < 0.001). In 49 patients that followed-up a median 10 months later, HIV drug resistance mutations at >20% frequency such as K103N, M184VI and P225H still existed, but with decreased frequencies. The prevalence of HIV drug resistance in ART interruption was higher than 15% in the survey. Next-generation sequencing was able to detect more minority drug resistance variants than Sanger. There was a sharp increase in minority drug resistance variants when the detection threshold was below 5%.

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Next generation sequencing reveals limitation of qPCR methods in quantifying emerging antibiotic resistance genes (ARGs) in the environment

Applied Microbiology and Biotechnology ◽

10.1007/s00253-021-11202-4 ◽

2021 ◽

Author(s):

Bo Li ◽

Tao Yan

Keyword(s):

Antibiotic Resistance ◽

Next Generation Sequencing ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Next Generation ◽

Generation Sequencing

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Next-Generation Sequencing for Typing and Detection of Resistance Genes: Performance of a New Commercial Method during an Outbreak of Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli

Journal of Clinical Microbiology ◽

10.1128/jcm.00313-14 ◽

2014 ◽

Vol 52 (7) ◽

pp. 2454-2460 ◽

Cited By ~ 24

Author(s):

J. Veenemans ◽

I. T. Overdevest ◽

E. Snelders ◽

I. Willemsen ◽

Y. Hendriks ◽

...

Keyword(s):

Escherichia Coli ◽

Next Generation Sequencing ◽

Resistance Genes ◽

Beta Lactamase ◽

Next Generation ◽

Extended Spectrum Beta Lactamase ◽

Extended Spectrum ◽

Commercial Method ◽

Generation Sequencing

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Identification and characterization of candidateRlm4blackleg resistance genes inBrassica napususing next-generation sequencing

Plant Biotechnology Journal ◽

10.1111/j.1467-7652.2012.00716.x ◽

2012 ◽

Vol 10 (6) ◽

pp. 709-715 ◽

Cited By ~ 28

Author(s):

Reece Tollenaere ◽

Alice Hayward ◽

Jessica Dalton-Morgan ◽

Emma Campbell ◽

Joanne R.M. Lee ◽

...

Keyword(s):

Next Generation Sequencing ◽

Resistance Genes ◽

Next Generation ◽

Identification And Characterization ◽

Generation Sequencing

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geno2pheno[ngs-freq]: a genotypic interpretation system for identifying viral drug resistance using next-generation sequencing data

Nucleic Acids Research ◽

10.1093/nar/gky349 ◽

2018 ◽

Vol 46 (W1) ◽

pp. W271-W277 ◽

Cited By ~ 18

Author(s):

Matthias Döring ◽

Joachim Büch ◽

Georg Friedrich ◽

Alejandro Pironti ◽

Prabhav Kalaghatgi ◽

...

Keyword(s):

Drug Resistance ◽

Next Generation Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Interpretation System ◽

Generation Sequencing

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Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02474-17 ◽

2018 ◽

Vol 62 (4) ◽

pp. e02474-17 ◽

Cited By ~ 20

Author(s):

Eldin Talundzic ◽

Shashidhar Ravishankar ◽

Julia Kelley ◽

Dhruviben Patel ◽

Mateusz Plucinski ◽

...

Keyword(s):

Drug Resistance ◽

Next Generation Sequencing ◽

Deep Sequencing ◽

Artemisinin Resistance ◽

The United States ◽

Imported Malaria ◽

Chloroquine Resistance ◽

Next Generation ◽

Content Type ◽

Generation Sequencing

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.

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