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Chen F, Liu B, Chen M, Jiang Z, Zhou Z, Wu P, Zhang M, Jin H, Li L, Lu L, Shang H, Liu L, Chen W, Xu J, Sun R, Wang G, Zheng J, Qi J, Yang B, Zeng L, Li Y, Lv H, Zhao N, Wang W, Cai J, Liu Y, Luo W, Zhang J, Zhang Y, Fan J, Dan H, He X, Huang W, Sun L, Yan Q. A Two-color Single-molecule Sequencing Platform and Its Clinical Applications. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae006. [PMID: 38862429 DOI: 10.1093/gpbjnl/qzae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 06/13/2024]
Abstract
DNA sequencers have become increasingly important research and diagnostic tools over the past 20 years. In this study, we developed a single-molecule desktop sequencer, GenoCare 1600 (GenoCare), which utilizes amplification-free library preparation and two-color sequencing-by-synthesis chemistry, making it more user-friendly compared with previous single-molecule sequencing platforms for clinical use. Using the GenoCare platform, we sequenced an Escherichia coli standard sample and achieved a consensus accuracy exceeding 99.99%. We also evaluated the sequencing performance of this platform in microbial mixtures and coronavirus disease 2019 (COVID-19) samples from throat swabs. Our findings indicate that the GenoCare platform allows for microbial quantitation, sensitive identification of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and accurate detection of virus mutations, as confirmed by Sanger sequencing, demonstrating its remarkable potential in clinical application.
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Affiliation(s)
- Fang Chen
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Bin Liu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Meirong Chen
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Zefei Jiang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Zhiliang Zhou
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Ping Wu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Meng Zhang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Huan Jin
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Linsen Li
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Liuyan Lu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Huan Shang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Lei Liu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Weiyue Chen
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Jianfeng Xu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Ruitao Sun
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | | | - Jiao Zheng
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Jifang Qi
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Bo Yang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Lidong Zeng
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Yan Li
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Hui Lv
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Nannan Zhao
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Wen Wang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Jinsen Cai
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Yongfeng Liu
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Weiwei Luo
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Juan Zhang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Yanhua Zhang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Jicai Fan
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Haitao Dan
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Xuesen He
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Wei Huang
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Lei Sun
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
| | - Qin Yan
- GeneMind Biosciences Co., Ltd., Shenzhen 518000, China
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Pinhata JMW, Brandao AP, Gallo JF, Oliveira RSD, Ferrazoli L. GenoType MTBDRsl for detection of second-line drugs and ethambutol resistance in multidrug-resistant Mycobacterium tuberculosis isolates at a high-throughput laboratory. Diagn Microbiol Infect Dis 2023; 105:115856. [PMID: 36446302 DOI: 10.1016/j.diagmicrobio.2022.115856] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/13/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022]
Abstract
We assessed the performance of MTBDRsl for detection of resistance to fluoroquinolones, aminoglycosides/cyclic peptides, and ethambutol compared to BACTEC MGIT 960 by subjecting simultaneously to both tests 385 phenotypically multidrug-resistant-Mycobacterium tuberculosis isolates from Sao Paulo, Brazil. Discordances were resolved by Sanger sequencing. MTBDRsl correctly detected 99.7% of the multidrug-resistant isolates, 87.8% of the pre-XDR, and 73.9% of the XDR. The assay showed sensitivity of 86.4%, 100%, 85.2% and 76.4% for fluoroquinolones, amikacin/kanamycin, capreomycin and ethambutol, respectively. Specificity was 100% for fluoroquinolones and aminoglycosides/cyclic peptides, and 93.6% for ethambutol. Most fluoroquinolone-discordances were due to mutations in genome regions not targeted by the MTBDRsl v. 1.0: gyrA_H70R and gyrB_R446C, D461N, D449V, and N488D. Capreomycin-resistant isolates with wild-type rrs results on MTBDRsl presented tlyA mutations. MTBDRsl presented good performance for detecting resistance to second-line drugs and ethambutol in clinical isolates. In our setting, multidrug-resistant. isolates presented mutations not targeted by the molecular assay.
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Affiliation(s)
- Juliana Maira Watanabe Pinhata
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, São Paulo, Brazil.
| | - Angela Pires Brandao
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, São Paulo, Brazil; Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana Failde Gallo
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, São Paulo, Brazil
| | - Rosângela Siqueira de Oliveira
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, São Paulo, Brazil
| | - Lucilaine Ferrazoli
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz (IAL), São Paulo, São Paulo, Brazil
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