Clinical diagnostic value of targeted next‑generation sequencing for infectious diseases (Review)

Chen,Qiuyue; Yi,Jie; Liu,Yiwei; Yang,Chenglin; Sun,Yujie; Du,Juan; Liu,Yi; Gu,Dejian; Liu,Hao; Xu,Yingchun; Chen,Yu

doi:10.3892/mmr.2024.13277

Clinical diagnostic value of targeted next‑generation sequencing for infectious diseases (Review)

Authors:
- Qiuyue Chen
- Jie Yi
- Yiwei Liu
- Chenglin Yang
- Yujie Sun
- Juan Du
- Yi Liu
- Dejian Gu
- Hao Liu
- Yingchun Xu
- Yu Chen
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Affiliations: Department of Laboratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing 100000, P.R. China, Emergency Department, The 305th Hospital of the People's Liberation Army of China, Beijing 100000, P.R. China, Department of Medicine, GenePlus‑Beijing, Beijing 100000, P.R. China
Published online on: July 2, 2024 https://doi.org/10.3892/mmr.2024.13277
Article Number: 153

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Abstract

As sequencing technology transitions from research to clinical settings, due to technological maturity and cost reductions, metagenomic next‑generation sequencing (mNGS) is increasingly used. This shift underscores the growing need for more cost‑effective and universally accessible sequencing assays to improve patient care and public health. Therefore, targeted NGS (tNGS) is gaining prominence. tNGS involves enrichment of target pathogens in patient samples based on multiplex PCR amplification or probe capture with excellent sensitivity. It is increasingly used in clinical diagnostics due to its practicality and efficiency. The present review compares the principles of different enrichment methods. The high positivity rate of tNGS in the detection of pathogens was found in respiratory samples with specific instances. tNGS maintains high sensitivity (70.8‑95.0%) in samples with low pathogen loads, including blood and cerebrospinal fluid. Furthermore, tNGS is effective in detecting drug‑resistant strains of Mycobacterium tuberculosis, allowing identification of resistance genes and guiding clinical treatment decisions, which is difficult to achieve with mNGS. In the present review, the application of tNGS in clinical settings and its current limitations are assessed. The continued development of tNGS has the potential to refine diagnostic accuracy and treatment efficacy and improving infectious disease management. However, further research to overcome technical challenges such as workflow time and cost is required.

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1	Lozano R, Naghavi M, Foreman K, Lim S, Shibuya K, Aboyans V, Abraham J, Adair T, Aggarwal R, Ahn SY, et al: Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: A systematic analysis for the global burden of disease study 2010. Lancet. 380:2095–2128. 2012. View Article : Google Scholar : PubMed/NCBI
2	Chiu CY and Miller SA: Clinical metagenomics. Nat Rev Genet. 20:341–355. 2019. View Article : Google Scholar : PubMed/NCBI
3	Li N, Cai Q, Miao Q, Song Z, Fang Y and Hu B: High-throughput metagenomics for identification of pathogens in the clinical settings. Small Methods. 5:20007922021. View Article : Google Scholar : PubMed/NCBI
4	Wilson MR, Naccache SN, Samayoa E, Biagtan M, Bashir H, Yu G, Salamat SM, Somasekar S, Federman S, Miller S, et al: Actionable diagnosis of neuroleptospirosis by next-generation sequencing. N Engl J Med. 370:2408–2417. 2014. View Article : Google Scholar : PubMed/NCBI
5	Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, Wall GD, et al: Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 4:663–674. 2019. View Article : Google Scholar : PubMed/NCBI
6	Wilson MR, Sample HA, Zorn KC, Arevalo S, Yu G, Neuhaus J, Federman S, Stryke D, Briggs B, Langelier C, et al: Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis. N Engl J Med. 380:2327–2340. 2019. View Article : Google Scholar : PubMed/NCBI
7	Ramachandran PS and Wilson MR: Metagenomics for neurological infections-expanding our imagination. Nat Rev Neurol. 16:547–556. 2020. View Article : Google Scholar : PubMed/NCBI
8	Han D, Li R, Shi J, Tan P, Zhang R and Li J: Liquid biopsy for infectious diseases: A focus on microbial cell-free DNA sequencing. Theranostics. 10:5501–5513. 2020. View Article : Google Scholar : PubMed/NCBI
9	Zheng Y, Qiu X, Wang T and Zhang J: The Diagnostic value of metagenomic next-generation sequencing in lower respiratory tract infection. Front Cell Infect Microbiol. 11:6947562021. View Article : Google Scholar : PubMed/NCBI
10	Zhu N, Zhang D, Wang W, Li X, Yang B, Song J, Zhao X, Huang B, Shi W, Lu R, et al: A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med. 382:727–733. 2020. View Article : Google Scholar : PubMed/NCBI
11	Gu L, Liu W, Ru M, Lin J, Yu G, Ye J, Zhu ZA, Liu Y, Chen J, Lai G and Wen W: The application of metagenomic next-generation sequencing in diagnosing Chlamydia psittaci pneumonia: A report of five cases. BMC Pulm Med. 20:652020. View Article : Google Scholar : PubMed/NCBI
12	Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, et al: Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice. Clin Infect Dis. 67 (Suppl 2):S231–S240. 2018. View Article : Google Scholar : PubMed/NCBI
13	Shi CL, Han P, Tang PJ, Chen MM, Ye ZJ, Wu MY, Shen J, Wu HY, Tan ZQ, Yu X, et al: Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect. 81:567–574. 2020. View Article : Google Scholar : PubMed/NCBI
14	Zhang Y, Cui P, Zhang HC, Wu HL, Ye MZ, Zhu YM, Ai JW and Zhang WH: Clinical application and evaluation of metagenomic next-generation sequencing in suspected adult central nervous system infection. J Transl Med. 18:1992020. View Article : Google Scholar : PubMed/NCBI
15	Zhou Y, Xu Y, Gong Y, Zhang Y, Lu Y, Wang C, Yao R, Li P, Guan Y, Wang J, et al: Clinical factors associated with circulating tumor DNA (ctDNA) in primary breast cancer. Mol Oncol. 13:1033–1046. 2019. View Article : Google Scholar : PubMed/NCBI
16	Ji XC, Zhou LF, Li CY, Shi YJ, Wu ML, Zhang Y, Fei XF and Zhao G: Reduction of human DNA contamination in clinical cerebrospinal fluid specimens improves the sensitivity of metagenomic next-generation sequencing. J Mol Neurosci. 70:659–666. 2020. View Article : Google Scholar : PubMed/NCBI
17	Bal A, Pichon M, Picard C, Casalegno JS, Valette M, Schuffenecker I, Billard L, Vallet S, Vilchez G, Cheynet V, et al: Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow. BMC Infect Dis. 18:5372018. View Article : Google Scholar : PubMed/NCBI
18	Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, Parkes D, Freeman C, Dhalla F, Patel SY, et al: Sequencing of human genomes with nanopore technology. Nat Commun. 10:18692019. View Article : Google Scholar : PubMed/NCBI
19	Gu W, Crawford ED, O'Donovan BD, Wilson MR, Chow ED, Retallack H and DeRisi JL: Depletion of abundant sequences by hybridization (DASH): Using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications. Genome Biol. 17:412016. View Article : Google Scholar : PubMed/NCBI
20	Gu W, Miller S and Chiu CY: clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol. 14:319–338. 2019. View Article : Google Scholar : PubMed/NCBI
21	Wylie TN, Wylie KM, Herter BN and Storch GA: Enhanced virome sequencing using targeted sequence capture. Genome Res. 25:1910–1920. 2015. View Article : Google Scholar : PubMed/NCBI
22	Zhao N, Cao J, Xu J, Liu B, Liu B, Chen D, Xia B, Chen L, Zhang W, Zhang Y, et al: Targeting RNA with next- and third-generation sequencing improves pathogen identification in clinical samples. Adv Sci (Weinh). 8:e21025932021. View Article : Google Scholar : PubMed/NCBI
23	Medicine CSoL: Expert consensus on the standardized management of bioinformatics analysis for the detection of pathogenic microorganisms in mNGS. Chin J Lab Med. 44:799–807. 2021.
24	Wang Q, Wu B, Yang D, Yang C, Jin Z, Cao J and Feng J: Optimal specimen type for accurate diagnosis of infectious peripheral pulmonary lesions by mNGS. BMC Pulm Med. 20:2682020. View Article : Google Scholar : PubMed/NCBI
25	Fang X, Mei Q, Fan X, Zhu C, Yang T, Zhang L, Geng S and Pan A: Diagnostic value of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in ventilator-associated pneumonia patients. Front Microbiol. 11:5997562020. View Article : Google Scholar : PubMed/NCBI
26	Mongkolrattanothai K, Naccache SN, Bender JM, Samayoa E, Pham E, Yu G, Dien Bard J, Miller S, Aldrovandi G and Chiu CY: Neurobrucellosis: Unexpected answer from metagenomic next-generation sequencing. J Pediatric Infect Dis Soc. 6:393–398. 2017.PubMed/NCBI
27	Mason A, Foster D, Bradley P, Golubchik T, Doumith M, Gordon NC, Pichon B, Iqbal Z, Staves P, Crook D, et al: Accuracy of different bioinformatics methods in detecting antibiotic resistance and virulence factors from staphylococcus aureus whole-genome sequences. J Clin Microbiol. 56:e01815–17. 2018. View Article : Google Scholar : PubMed/NCBI
28	Singh RR: Target enrichment approaches for next-generation sequencing applications in oncology. Diagnostics (Basel). 12:15392022. View Article : Google Scholar : PubMed/NCBI
29	Xiao M, Liu X, Ji J, Li M, Li J, Yang L, Sun W, Ren P, Yang G, Zhao J, et al: Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples. Genome Med. 12:572020. View Article : Google Scholar : PubMed/NCBI
30	Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ and Lipkin WI: Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis. mBio. 6:e01491–15. 2015. View Article : Google Scholar : PubMed/NCBI
31	Bonsall D, Ansari MA, Ip C, Trebes A, Brown A, Klenerman P, Buck D; STOP-HCV Consortium, ; Piazza P, Barnes E and Bowden R: ve-SEQ: Robust, unbiased enrichment for streamlined detection and whole-genome sequencing of HCV and other highly diverse pathogens. F1000Res. 4:10622015. View Article : Google Scholar : PubMed/NCBI
32	Piantadosi A, Mukerji SS, Ye S, Leone MJ, Freimark LM, Park D, Adams G, Lemieux J, Kanjilal S, Solomon IH, et al: Enhanced virus detection and metagenomic sequencing in patients with meningitis and encephalitis. mBio. 12:e01143212021. View Article : Google Scholar : PubMed/NCBI
33	Wang ZY, Li LL, Cao XL, Li P, Du J, Zou MJ and Wang LL: Clinical application of amplification-based versus amplification-free metagenomic next-generation sequencing test in infectious diseases. Front Cell Infect Microbiol. 13:11381742023. View Article : Google Scholar : PubMed/NCBI
34	Zhang D, Zhang J, Du J, Zhou Y, Wu P, Liu Z, Sun Z, Wang J, Ding W, Chen J, et al: Optimized sequencing adaptors enable rapid and real-time metagenomic identification of pathogens during runtime of sequencing. Clin Chem. 68:826–836. 2022. View Article : Google Scholar : PubMed/NCBI
35	Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, et al: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol. 5:443–454. 2020. View Article : Google Scholar : PubMed/NCBI
36	Miller S, Naccache SN, Samayoa E, Messacar K, Arevalo S, Federman S, Stryke D, Pham E, Fung B, Bolosky WJ, et al: Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid. Genome Res. 29:831–842. 2019. View Article : Google Scholar : PubMed/NCBI
37	Kalantar KL, Carvalho T, de Bourcy CFA, Dimitrov B, Dingle G, Egger R, Han J, Holmes OB, Juan YF, King R, et al: IDseq-An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience. 9:giaa1112020. View Article : Google Scholar : PubMed/NCBI
38	Nugen SR, Leonard B and Baeumner AJ: Application of a unique server-based oligonucleotide probe selection tool toward a novel biosensor for the detection of Streptococcus pyogenes. Biosens Bioelectron. 22:2442–2448. 2007. View Article : Google Scholar : PubMed/NCBI
39	Siegwald L, Touzet H, Lemoine Y, Hot D, Audebert C and Caboche S: Assessment of common and emerging bioinformatics pipelines for targeted metagenomics. PLoS One. 12:e01695632017. View Article : Google Scholar : PubMed/NCBI
40	Simner PJ, Miller HB, Breitwieser FP, Pinilla Monsalve G, Pardo CA, Salzberg SL, Sears CL, Thomas DL, Eberhart CG and Carroll KC: Development and optimization of metagenomic next-generation sequencing methods for cerebrospinal fluid diagnostics. J Clin Microbiol. 56:e00472–18. 2018. View Article : Google Scholar : PubMed/NCBI
41	Gaston DC, Miller HB, Fissel JA, Jacobs E, Gough E, Wu J, Klein EY, Carroll KC and Simner PJ: Evaluation of metagenomic and targeted next-generation sequencing workflows for detection of respiratory pathogens from bronchoalveolar lavage fluid specimens. J Clin Microbiol. 60:e00526222022. View Article : Google Scholar : PubMed/NCBI
42	Gauduchon V, Chalabreysse L, Etienne J, Célard M, Benito Y, Lepidi H, Thivolet-Béjui F and Vandenesch F: Molecular diagnosis of infective endocarditis by PCR amplification and direct sequencing of DNA from valve tissue. J Clin Microbiol. 41:763–766. 2003. View Article : Google Scholar : PubMed/NCBI
43	Marín M, Muñoz P, Sánchez M, Del Rosal M, Alcalá L, Rodríguez-Créixems M and Bouza E; Group for the Management of Infective Endocarditis of the Gregorio Marañón Hospital (GAME), : Molecular diagnosis of infective endocarditis by real-time broad-range polymerase chain reaction (PCR) and sequencing directly from heart valve tissue. Medicine (Baltimore). 86:195–202. 2007. View Article : Google Scholar : PubMed/NCBI
44	Vondracek M, Sartipy U, Aufwerber E, Julander I, Lindblom D and Westling K: 16S rDNA sequencing of valve tissue improves microbiological diagnosis in surgically treated patients with infective endocarditis. J Infect. 62:472–478. 2011. View Article : Google Scholar : PubMed/NCBI
45	Maneg D, Sponsel J, Müller I, Lohr B, Penders J, Madlener K and Hunfeld KP: Advantages and limitations of direct PCR amplification of bacterial 16S-rDNA from resected heart tissue or swabs followed by direct sequencing for diagnosing infective endocarditis: A retrospective analysis in the routine clinical setting. Biomed Res Int. 2016:79238742016. View Article : Google Scholar : PubMed/NCBI
46	Peeters B, Herijgers P, Beuselinck K, Verhaegen J, Peetermans WE, Herregods MC, Desmet S and Lagrou K: Added diagnostic value and impact on antimicrobial therapy of 16S rRNA PCR and amplicon sequencing on resected heart valves in infective endocarditis: A prospective cohort study. Clin Microbiol Infect. 23:888.e1–888.e5. 2017. View Article : Google Scholar : PubMed/NCBI
47	Kim MS, Chang J, Kim MN, Choi SH, Jung SH, Lee JW and Sung H: Utility of a direct 16S rDNA PCR and sequencing for etiological diagnosis of infective endocarditis. Ann Lab Med. 37:505–510. 2017. View Article : Google Scholar : PubMed/NCBI
48	Santibáñez P, García-García C, Portillo A, Santibáñez S, García-Álvarez L, de Toro M and Oteo JA: What does 16S rRNA gene-targeted next generation sequencing contribute to the study of infective endocarditis in heart-valve tissue? Pathogens. 11:342021. View Article : Google Scholar : PubMed/NCBI
49	Flurin L, Wolf MJ, Fisher CR, Cano Cevallos EJ, Vaillant JJ, Pritt BS, DeSimone DC and Patel R: Pathogen detection in infective endocarditis using targeted metagenomics on whole blood and plasma: A prospective pilot study. J Clin Microbiol. 60:e00621222022. View Article : Google Scholar : PubMed/NCBI
50	Hong HL, Flurin L, Greenwood-Quaintance KE, Wolf MJ, Pritt BS, Norgan AP and Patel R: 16S rRNA gene PCR/sequencing of heart valves for diagnosis of infective endocarditis in routine clinical practice. J Clin Microbiol. 61:e00341232023. View Article : Google Scholar : PubMed/NCBI
51	Poulsen SH, Søgaard KK, Fuursted K and Nielsen HL: Evaluating the diagnostic accuracy and clinical utility of 16S and 18S rRNA gene targeted next-generation sequencing based on five years of clinical experience. Infect Dis (Lond). 55:767–775. 2023. View Article : Google Scholar : PubMed/NCBI
52	Hong HL, Flurin L, Thoendel MJ, Wolf MJ, Abdel MP, Greenwood-Quaintance KE and Patel R: Targeted versus shotgun metagenomic sequencing-based detection of microorganisms in sonicate fluid for periprosthetic joint infection diagnosis. Clin Infect Dis. 76:e1456–e1462. 2023. View Article : Google Scholar : PubMed/NCBI
53	Fida M, Wolf MJ, Hamdi A, Vijayvargiya P, Esquer Garrigos Z, Khalil S, Greenwood-Quaintance KE, Thoendel MJ and Patel R: Detection of pathogenic bacteria from septic patients using 16s ribosomal RNA gene-targeted metagenomic sequencing. Clin Infect Dis. 73:1165–1172. 2021. View Article : Google Scholar : PubMed/NCBI
54	Okuda KI, Yoshii Y, Yamada S, Chiba A, Hironaka I, Hori S, Yanaga K and Mizunoe Y: Detection of bacterial DNA from central venous catheter removed from patients by next generation sequencing: A preliminary clinical study. Ann Clin Microbiol Antimicrob. 17:442018. View Article : Google Scholar : PubMed/NCBI
55	Flurin L, Wolf MJ, Greenwood-Quaintance KE, Sanchez-Sotelo J and Patel R: Targeted next generation sequencing for elbow periprosthetic joint infection diagnosis. Diagn Microbiol Infect Dis. 101:1154482021. View Article : Google Scholar : PubMed/NCBI
56	Miller RJ, Chow B, Pillai D and Church D: Development and evaluation of a novel fast broad-range 16S ribosomal DNA PCR and sequencing assay for diagnosis of bacterial infective endocarditis: Multi-year experience in a large Canadian healthcare zone and a literature review. BMC Infect Dis. 16:1462016. View Article : Google Scholar : PubMed/NCBI
57	Mularoni A, Mikulska M, Barbera F, Graziano E, Medaglia AA, Di Carlo D, Monaco F, Bellavia D, Cascio A, Raffa G, et al: Molecular analysis with 16S rRNA PCR/sanger sequencing and molecular antibiogram performed on DNA extracted from valve improve diagnosis and targeted therapy of infective endocarditis: A prospective study. Clin Infect Dis. 76:e1484–e1491. 2023. View Article : Google Scholar : PubMed/NCBI
58	Flurin L, Hemenway JJ, Fisher CR, Vaillant JJ, Azad M, Wolf MJ, Greenwood-Quaintance KE, Abdel MP and Patel R: Clinical use of a 16S ribosomal RNA gene-based sanger and/or next generation sequencing assay to test preoperative synovial fluid for periprosthetic joint infection diagnosis. mBio. 13:e01322222022. View Article : Google Scholar : PubMed/NCBI
59	Sabat AJ, van Zanten E, Akkerboom V, Wisselink G, van Slochteren K, de Boer RF, Hendrix R, Friedrich AW, Rossen JWA and Kooistra-Smid AMDM: Targeted next-generation sequencing of the 16S-23S rRNA region for culture-independent bacterial identification-increased discrimination of closely related species. Sci Rep. 7:34342017. View Article : Google Scholar : PubMed/NCBI
60	Flurin L, Wolf MJ, Mutchler MM, Daniels ML, Wengenack NL and Patel R: Targeted metagenomic sequencing-based approach applied to 2146 tissue and body fluid samples in routine clinical practice. Clin Infect Dis. 75:1800–1808. 2022. View Article : Google Scholar : PubMed/NCBI
61	Cheng LL, Li SY and Zhong NS: New characteristics of COVID-19 caused by the Omicron variant in Guangzhou. Zhonghua Jie He He Hu Xi Za Zhi. 46:441–443. 2023.(In Chinese). PubMed/NCBI
62	Ramos N, Panzera Y, Frabasile S, Tomás G, Calleros L, Marandino A, Goñi N, Techera C, Grecco S, Fuques E, et al: A multiplex-NGS approach to identifying respiratory RNA viruses during the COVID-19 pandemic. Arch Virol. 168:872023. View Article : Google Scholar : PubMed/NCBI
63	Danilenko AV, Kolosova NP, Shvalov AN, Ilyicheva TN, Svyatchenko SV, Durymanov AG, Bulanovich JA, Goncharova NI, Susloparov IM, Marchenko VY, et al: Evaluation of HA-D222G/N polymorphism using targeted NGS analysis in A(H1N1)pdm09 influenza virus in Russia in 2018–2019. PLoS One. 16:e02510192021. View Article : Google Scholar : PubMed/NCBI
64	Chao L, Li J, Zhang Y, Pu H and Yan X: Application of next generation sequencing-based rapid detection platform for microbiological diagnosis and drug resistance prediction in acute lower respiratory infection. Ann Transl Med. 8:16442020. View Article : Google Scholar : PubMed/NCBI
65	Lin R, Xing Z, Liu X, Chai Q, Xin Z, Huang M, Zhu C, Luan C, Gao H, Du Y, et al: Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children. J Med Microbiol. 72:2023. View Article : Google Scholar : PubMed/NCBI
66	Ip M, Liyanapathirana V, Ang I, Fung KS, Ng TK, Zhou H and Tsang DN: Direct detection and prediction of all pneumococcal serogroups by target enrichment-based next-generation sequencing. J Clin Microbiol. 52:4244–4252. 2014. View Article : Google Scholar : PubMed/NCBI
67	Li F, Wang Y, Zhang Y, Shi P, Cao L, Su L, Zhu Q, Wang L, Lu R, Tan W and Shen J: Etiology of severe pneumonia in children in alveolar lavage fluid using a high-throughput gene targeted amplicon sequencing assay. Front Pediatr. 9:6591642021. View Article : Google Scholar : PubMed/NCBI
68	Dai Y, Sheng K and Hu L: Diagnostic efficacy of targeted high-throughput sequencing for lower respiratory infection in preterm infants. Am J Transl Res. 14:8204–8214. 2022.PubMed/NCBI
69	Li S, Tong J, Li H, Mao C, Shen W, Lei Y and Hu P: L. pneumophila infection diagnosed by tNGS in a lady with lymphadenopathy. Infect Drug Resist. 16:4435–4442. 2023. View Article : Google Scholar : PubMed/NCBI
70	Zhang Y, Jiang X, Ye W and Sun J: Clinical features and outcome of eight patients with Chlamydia psittaci pneumonia diagnosed by targeted next generation sequencing. Clin Respir J. 17:915–930. 2023. View Article : Google Scholar : PubMed/NCBI
71	Du ZM and Chen P: Co-infection of Chlamydia psittaci and Tropheryma whipplei: A case report. World J Clin Cases. 11:7144–7149. 2023. View Article : Google Scholar : PubMed/NCBI
72	Ren HQ, Zhao Q, Jiang J, Yang W, Fu AS and Ge YL: Acute heart failure due to pulmonary Aspergillus fumigatus and Cryptococcus neoformans infection associated with COVID-19. Clin Lab; 69. 2023
73	Li S, Tong J, Liu Y, Shen W and Hu P: Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection. J Infect. 85:e127–e129. 2022. View Article : Google Scholar : PubMed/NCBI
74	Kunasol C, Dondorp AM, Batty EM, Nakhonsri V, Sinjanakhom P, Day NPJ and Imwong M: Comparative analysis of targeted next-generation sequencing for Plasmodium falciparum drug resistance markers. Sci Rep. 12:55632022. View Article : Google Scholar : PubMed/NCBI
75	Mensah BA, Aydemir O, Myers-Hansen JL, Opoku M, Hathaway NJ, Marsh PW, Anto F, Bailey J, Abuaku B and Ghansah A: Antimalarial drug resistance profiling of plasmodium falciparum infections in ghana using molecular inversion probes and next-generation sequencing. Antimicrob Agents Chemother. 64:e01423–19. 2020. View Article : Google Scholar : PubMed/NCBI
76	Deng X, Achari A, Federman S, Yu G, Somasekar S, Bártolo I, Yagi S, Mbala-Kingebeni P, Kapetshi J, Ahuka-Mundeke S, et al: Author correction: Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance. Nat Microbiol. 5:5252020. View Article : Google Scholar : PubMed/NCBI
77	Boltz VF, Rausch J, Shao W, Hattori J, Luke B, Maldarelli F, Mellors JW, Kearney MF and Coffin JM: Ultrasensitive single-genome sequencing: accurate, targeted, next generation sequencing of HIV-1 RNA. Retrovirology. 13:872016. View Article : Google Scholar : PubMed/NCBI
78	Li Q, Huang W, Zhang S, Zheng Y, Lv Q, Kong D, Zhang L, Zhang Y, Zhao Z, Wang M, et al: Target-enriched sequencing enables accurate identification of bloodstream infections in whole blood. J Microbiol Methods. 192:1063912022. View Article : Google Scholar : PubMed/NCBI
79	Jiang J, Lv M, Yang K, Zhao G and Fu Y: A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS. Open Life Sci. 18:202207382023. View Article : Google Scholar : PubMed/NCBI
80	Chen W, Wu Y and Zhang Y: Next-generation sequencing technology combined with multiplex polymerase chain reaction as a powerful detection and semiquantitative method for herpes simplex virus type 1 in adult encephalitis: A case report. Front Med (Lausanne). 9:9053502022. View Article : Google Scholar : PubMed/NCBI
81	Yang HH, He XJ, Nie JM, Guan SS, Chen YK and Liu M: Central nervous system aspergillosis misdiagnosed as Toxoplasma gondii encephalitis in a patient with AIDS: A case report. AIDS Res Ther. 19:402022. View Article : Google Scholar : PubMed/NCBI
82	Gao D, Hu Y, Jiang X, Pu H, Guo Z and Zhang Y: Applying the pathogen-targeted next-generation sequencing method to pathogen identification in cerebrospinal fluid. Ann Transl Med. 9:16752021. View Article : Google Scholar : PubMed/NCBI
83	McGill F, Tokarz R, Thomson EC, Filipe A, Sameroff S, Jain K, Bhuva N, Ashraf S, Lipkin WI, Corless C, et al: Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis. J Infect. 84:499–510. 2022. View Article : Google Scholar : PubMed/NCBI
84	Li J, Zhang L, Yang X, Wang P, Feng L, Guo E and Chen Y: Diagnostic significance of targeted next-generation sequencing in central nervous system infections in neurosurgery of pediatrics. Infect Drug Resist. 16:2227–2236. 2023. View Article : Google Scholar : PubMed/NCBI
85	Huang C, Huang Y, Wang Z, Lin Y, Li Y, Chen Y, Chen X, Zhang C, Li W, Zhang W, et al: Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis. Front Microbiol. 14:11813482023. View Article : Google Scholar : PubMed/NCBI
86	Hulten KG, Genta RM, Kalfus IN, Zhou Y, Zhang H and Graham DY: Comparison of culture with antibiogram to next-generation sequencing using bacterial isolates and formalin-fixed, paraffin-embedded gastric biopsies. Gastroenterology. 161:1433–1442.e2. 2021. View Article : Google Scholar : PubMed/NCBI
87	Ferreira I, Lepuschitz S, Beisken S, Fiume G, Mrazek K, Frank BJH, Huber S, Knoll MA, von Haeseler A, Materna A, et al: Culture-free detection of antibiotic resistance markers from native patient samples by hybridization capture sequencing. Microorganisms. 9:16722021. View Article : Google Scholar : PubMed/NCBI
88	Jouet A, Braet SM, Gaudin C, Bisch G, Vasconcellos S, Epaminondas Nicacio de Oliveira do Livramento RE, Prado Palacios YY, Fontes AB, Lucena N, Rosa P, et al: Hi-plex deep amplicon sequencing for identification, high-resolution genotyping and multidrug resistance prediction of Mycobacterium leprae directly from patient biopsies by using deeplex Myc-Lep. EBioMedicine. 93:1046492023. View Article : Google Scholar : PubMed/NCBI
89	Jouet A, Gaudin C, Badalato N, Allix-Béguec C, Duthoy S, Ferré A, Diels M, Laurent Y, Contreras S, Feuerriegel S, et al: Deep amplicon sequencing for culture-free prediction of susceptibility or resistance to 13 anti-tuberculous drugs. Eur Respir J. 57:20023382021. View Article : Google Scholar : PubMed/NCBI
90	Cabibbe AM, Spitaleri A, Battaglia S, Colman RE, Suresh A, Uplekar S, Rodwell TC and Cirillo DM: Application of targeted next-generation sequencing assay on a portable sequencing platform for culture-free detection of drug-resistant tuberculosis from clinical samples. J Clin Microbiol. 58:e00632–20. 2020. View Article : Google Scholar : PubMed/NCBI
91	Mesfin AB, Araia ZZ, Beyene HN, Mebrahtu AH, Suud NN, Berhane YM, Hailu DT, Kassahun AZ, Auguet OT, Dean AS, et al: First molecular-based anti-TB drug resistance survey in Eritrea. Int J Tuberc Lung Dis. 25:43–51. 2021. View Article : Google Scholar : PubMed/NCBI
92	Mansoor H, Hirani N, Chavan V, Das M, Sharma J, Bharati M, Oswal V, Iyer A, Morales M, Joshi A, et al: Clinical utility of target-based next-generation sequencing for drug-resistant TB. Int J Tuberc Lung Dis. 27:41–48. 2023. View Article : Google Scholar : PubMed/NCBI
93	Sibandze DB, Kay A, Dreyer V, Sikhondze W, Dlamini Q, DiNardo A, Mtetwa G, Lukhele B, Vambe D, Lange C, et al: Rapid molecular diagnostics of tuberculosis resistance by targeted stool sequencing. Genome Med. 14:522022. View Article : Google Scholar : PubMed/NCBI
94	Kambli P, Ajbani K, Kazi M, Sadani M, Naik S, Shetty A, Tornheim JA, Singh H and Rodrigues C: Targeted next generation sequencing directly from sputum for comprehensive genetic information on drug resistant Mycobacterium tuberculosis. Tuberculosis (Edinb). 127:1020512021. View Article : Google Scholar : PubMed/NCBI
95	Wu X, Liang R, Xiao Y, Liu H, Zhang Y, Jiang Y, Liu M, Tang J, Wang W, Li W, et al: Application of targeted next generation sequencing technology in the diagnosis of Mycobacterium tuberculosis and first line drugs resistance directly from cell-free DNA of bronchoalveolar lavage fluid. J Infect. 86:399–401. 2023. View Article : Google Scholar : PubMed/NCBI
96	Colman RE, Anderson J, Lemmer D, Lehmkuhl E, Georghiou SB, Heaton H, Wiggins K, Gillece JD, Schupp JM, Catanzaro DG, et al: Rapid drug susceptibility testing of drug-resistant Mycobacterium tuberculosis isolates directly from clinical samples by use of amplicon sequencing: A proof-of-concept study. J Clin Microbiol. 54:2058–2067. 2016. View Article : Google Scholar : PubMed/NCBI
97	Iyer A, Ndlovu Z, Sharma J, Mansoor H, Bharati M, Kolan S, Morales M, Das M, Issakidis P, Ferlazzo G, et al: Operationa-lising targeted next-generation sequencing for routine diagnosis of drug-resistant TB. Public Health Action. 13:43–49. 2023. View Article : Google Scholar : PubMed/NCBI
98	Leung KS, Tam KK, Ng TT, Lao HY, Shek RC, Ma OCK, Yu SH, Chen JX, Han Q, Siu GK and Yam WC: Clinical utility of target amplicon sequencing test for rapid diagnosis of drug-resistant Mycobacterium tuberculosis from respiratory specimens. Front Microbiol. 13:9744282022. View Article : Google Scholar : PubMed/NCBI
99	Comín J, Viñuelas J, Lafoz C, Cebollada A, Ibarz D, Iglesias MJ and Samper S: Rapid identification of lineage and drug resistance in clinical samples of Mycobacterium tuberculosis. Microorganisms. 11:14672023. View Article : Google Scholar : PubMed/NCBI
100	Zhang G, Zhang H, Zhang Y, Hu X, Tang M and Gao Q: Targeted next-generation sequencing technology showed great potential in identifying spinal tuberculosis and predicting the drug resistance. J Infect. 87:e110–e112. 2023. View Article : Google Scholar : PubMed/NCBI
101	Murphy SG, Smith C, Lapierre P, Shea J, Patel K, Halse TA, Dickinson M, Escuyer V, Rowlinson MC and Musser KA: Direct detection of drug-resistant Mycobacterium tuberculosis using targeted next generation sequencing. Front Public Health. 11:12060562023. View Article : Google Scholar : PubMed/NCBI
102	Song J, Du W, Liu Z, Che J, Li K and Che N: Application of amplicon-based targeted NGS technology for diagnosis of drug-resistant tuberculosis using FFPE specimens. Microbiol Spectr. 10:e01358212022. View Article : Google Scholar : PubMed/NCBI
103	Wilson MR, O'Donovan BD, Gelfand JM, Sample HA, Chow FC, Betjemann JP, Shah MP, Richie MB, Gorman MP, Hajj-Ali RA, et al: Chronic meningitis investigated via metagenomic next-generation sequencing. JAMA Neurol. 75:947–955. 2018. View Article : Google Scholar : PubMed/NCBI