Rapid and economical drug resistance profiling with Nanopore MinION for clinical specimens with low bacillary burden of Mycobacterium tuberculosis

被引：21

作者：

Chan, Wai Sing ^{[1
]}

Au, Chun Hang ^{[1
]}

Chung, Yvonne ^{[1
]}

Leung, Henry Chi Ming ^{[2
,3
]}

Ho, Dona N. ^{[1
]}

Wong, Elaine Yue Ling ^{[1
]}

Lam, Tak Wah ^{[2
,3
]}

Chan, Tsun Leung ^{[1
]}

Ma, Edmond Shiu Kwan ^{[1
]}

Tang, Bone Siu Fai ^{[1
]}

机构：

[1] Hong Kong Sanat & Hosp, Dept Pathol, Hong Kong, Peoples R China

[2] Univ Hong Kong, Dept Comp Sci, Hong Kong, Peoples R China

[3] L3 Bioinformat Ltd, Hong Kong, Peoples R China

来源：

BMC RESEARCH NOTES | 2020年 / 13卷 / 01期

关键词：

Antibiotic resistance; Illumina MiSeq; MDR-TB; Nanopore MinION; NGS; Tuberculosis; XDR-TB; Xpert MTB; RIF;

D O I：

10.1186/s13104-020-05287-9

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

ObjectiveWe designed and tested a Nanopore sequencing panel for direct tuberculosis drug resistance profiling. The panel targeted 10 resistance-associated loci. We assessed the feasibility of amplifying and sequencing these loci from 23 clinical specimens with low bacillary burden.ResultsAt least 8 loci were successfully amplified from the majority for predicting first- and second-line drug resistance (14/23, 60.87%), and the 12 specimens yielding all 10 targets were sequenced with Nanopore MinION and Illumina MiSeq. MinION sequencing data was corrected by Nanopolish and recurrent variants were filtered. A total of 67,082 bases across all consensus sequences were analyzed, with 67,019 bases called by both MinION and MiSeq as wildtype. For the 41 single nucleotide variants (SNVs) called by MiSeq with 100% variant allelic frequency (VAF), 39 (95.1%) were called by MinION. For the 22 mixed bases called by MiSeq, a SNV with the highest VAF (70%) was called by MinION. With short assay time, reasonable reagent cost as well as continuously improving sequencing chemistry and signal correction pipelines, this Nanopore method can be a viable option for direct tuberculosis drug resistance profiling in the near future.

引用

页数：7

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