References:

<HIDE>

[1]AzoulayE,RussellL,van de LouwA,et al.,2020.Diagnosis of severe respiratory infections in immunocompromised patients.Intensive Care Med,46(2):298-314.

[2]BajajJS,AcharyaC,SikaroodiM,et al.,2020.Cost-effectiveness of integrating gut microbiota analysis into hospitalisation prediction in cirrhosis.GastroHep,2(2):79-86.

[3]BlauwkampTA,ThairS,RosenMJ,et al.,2019.Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.Nat Microbiol,4(4):663-674.

[4]ChenHB,YinYY,GaoH,et al.,2020.Clinical utility of in-house metagenomic next-generation sequencing for the diagnosis of lower respiratory tract infections and analysis of the host immune response.Clin Infect Dis,71(Suppl 4):S416-S426.

[5]ChiangAD,DekkerJP,2020.From the pipeline to the bedside: advances and challenges in clinical metagenomics.J Infect Dis,221(Suppl 3):S331-S340.

[6]ChiuCY,MillerSA,2019.Clinical metagenomics.Nat Rev Genet,20(6):341-355.

[7]del FabbroC,ScalabrinS,MorganteM,et al.,2013.An extensive evaluation of read trimming effects on Illumina NGS data analysis.PLoS ONE,8(12):e85024.

[8]DuanHX,LiX,MeiAH,et al.,2021.The diagnostic value of metagenomic next-generation sequencing in infectious diseases.BMC Infect Dis,21:62.

[9]DyeC,2014.After 2015: infectious diseases in a new era of health and development.Philos Trans R Soc B Biol Sci,369(1645):20130426.

[10]FangXW,MeiQ,FanXQ,et al.,2020.Diagnostic value of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in ventilator-associated pneumonia patients.Front Microbiol,11:599756.

[11]FariaNR,QuickJ,ClaroIM,et al.,2017.Establishment and cryptic transmission of Zika virus in Brazil and the Americas.Nature,546(7658):406-410.

[12]FlurinL,WolfMJ,MutchlerMM,et al.,2022.Targeted metagenomic sequencing-based approach applied to 2146 tissue and body fluid samples in routine clinical practice.Clin Infect Dis,75(10):1800-1808.

[13]FlygareS,SimmonK,MillerC,et al.,2016.Taxonomer: an interactive metagenomics analysis portal for universal pathogen detection and host mRNA expression profiling.Genome Biol,17:111.

[14]FooxJ,TigheSW,NicoletCM,et al.,2021.Performance assessment of DNA sequencing platforms in the ABRF next-generation sequencing study.Nat Biotechnol,39(9):1129-1140.

[15]GallonP,ParekhM,FerrariS,et al.,2019.Metagenomics in ophthalmology: hypothesis or real prospective?Biotechnol Rep (Amst),23:e00355.

[16]GaoD,YuQF,WangGQ,et al.,2016.Diagnosis of a malayan filariasis case using a shotgun diagnostic metagenomics assay.Parasit Vectors,9:86.

[17]GengSK,MeiQ,ZhuCY,et al.,2021.Metagenomic next-generation sequencing technology for detection of pathogens in blood of critically ill patients.Int J Infect Dis,103:81-87.

[18]GosiewskiT,Ludwig-GalezowskaAH,HuminskaK,et al.,2017.Comprehensive detection and identification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method—the observation of DNAemia.Eur J Clin Microbiol Infect Dis,36(2):329-336.

[19]GranerodJ,AmbroseHE,DaviesNWS,et al.,2010.Causes of encephalitis and differences in their clinical presentations in England: a multicentre, population-based prospective study.Lancet Infect Dis,10(12):835-844.

[20]GuW,MillerS,ChiuCY,2019.Clinical metagenomic next-generation sequencing for pathogen detection.Annu Rev Pathol,14:319-338.

[21]GuW,DengXD,LeeM,et al.,2021.Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids.Nat Med,27:115-124.

[22]GuoYF,LiHN,ChenHB,et al.,2021.Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue.eBioMedicine,73:103639.

[23]HasanMR,RawatA,TangP,et al.,2016.Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing.J Clin Microbiol,54(4):919-927.

[24]HanDS,LiZY,LiR,et al.,2019.mNGS in clinical microbiology laboratories: on the road to maturity.Crit Rev Microbiol,45(5-6):668-685.

[25]HeatherJM,ChainB,2016.The sequence of sequencers: the history of sequencing DNA.Genomics,107(1):1-8.

[26]HongDK,BlauwkampTA,KerteszM,et al.,2018.Liquid biopsy for infectious diseases: sequencing of cell-free plasma to detect pathogen DNA in patients with invasive fungal disease.Diagn Microbiol Infect Dis,92(3):210-213.

[27]HuangJ,LiangXM,XuanYK,et al.,2017.A reference human genome dataset of the BGISEQ-500 sequencer.Gigascience,6(5):gix024.

[28]HuangJ,JiangEL,YangDL,et al.,2020.Metagenomic next-generation sequencing versus traditional pathogen detection in the diagnosis of peripheral pulmonary infectious lesions.Infect Drug Resist,13:567-576.

[29]JingCD,ChenHB,LiangY,et al.,2021.Clinical evaluation of an improved metagenomic next-generation sequencing test for the diagnosis of bloodstream infections.Clin Chem,67(8):1133-1143.

[30]KorostinD,KuleminN,NaumovV,et al.,2020.Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing.PLoS ONE,15(3):e0230301.

[31]LalithaP,PrajnaNV,SikhaM,et al.,2021.Evaluation of metagenomic deep sequencing as a diagnostic test for infectious keratitis.Ophthalmology,128(3):473-475.

[32]LamyB,DargèreS,ArendrupMC,et al.,2016.How to optimize the use of blood cultures for the diagnosis of bloodstream infections?A state-of-the art. Front Microbiol,7:697.

[33]LiN,CaiQQ,MiaoQ,et al.,2021.High-throughput metagenomics for identification of pathogens in the clinical settings.Small Methods,5(1):2000792.

[34]LiuDL,ZhouHW,XuT,et al.,2021.Multicenter assessment of shotgun metagenomics for pathogen detection.eBioMedicine,74:103649.

[35]LiuX,ChenYL,OuyangH,et al.,2021.Tuberculosis diagnosis by metagenomic next-generation sequencing on bronchoalveolar lavage fluid: a cross-sectional analysis.Int J Infect Dis,104:50-57.

[36]LiuYX,QinY,ChenT,et al.,2021.A practical guide to amplicon and metagenomic analysis of microbiome data.Protein Cell,12(5):315-330.

[37]LowL,NakamichiK,AkileswaranL,et al.,2022.Deep metagenomic sequencing for endophthalmitis pathogen detection using a Nanopore platform.Am J Ophthalmol,242:243-251.

[38]MarotzCA,SandersJG,ZunigaC,et al.,2018.Improving saliva shotgun metagenomics by chemical host DNA depletion.Microbiome,6:42.

[39]MaxamAM,GilbertW,1977.A new method for sequencing DNA.Proc Natl Acad Sci USA,74(2):560-564.

[40]MiaoQ,MaYY,WangQQ,et al.,2018.Microbiological diagnostic performance of metagenomic next-generation sequencing when applied to clinical practice.Clin Infect Dis,67(suppl_2):S231-S240.

[41]MillerS,NaccacheSN,SamayoaE,et al.,2019.Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid.Genome Res,29(5):831-842.

[42]MuSR,HuL,ZhangY,et al.,2021.Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia.Front Cell Infect Microbiol,11:684965.

[43]NaccacheSN,FedermanS,VeeraraghavanN,et al.,2014.A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples.Genome Res,24(7):1180-1192.

[44]National Medical Products Administration,2024.Citing Electronic Sources of Information.No.20183220257.https://www.nmpa.gov.cn/datasearch/search-info.html?nmpa=aWQ9YmIwNjM4Zjk5NzBiM2ZjYWUxMmU4NjE1NGE4NjBiZDYmaXRlbUlkPWZmODA4MDgxODNjYWQ3NTAwMTgzY2I2NmZlNjkwMjg1

[45]National Medical Products Administration,2024.Citing Electronic Sources of Information.No.20183220258.https://www.nmpa.gov.cn/datasearch/search-info.html?nmpa=aWQ9ZGZjNWJjYWJhMzI4YTY3MDdmOWM0MWUzODFmY2Q4NTkmaXRlbUlkPWZmODA4MDgxODNjYWQ3NTAwMTgzY2I2NmZlNjkwMjg1

[46]NelsonMT,PopeCE,MarshRL,et al.,2019.Human and extracellular DNA depletion for metagenomic analysis of complex clinical infection samples yields optimized viable microbiome profiles.Cell Rep,26(8):2227-2240.e5.

[47]ParekhM,RomanoV,FranchA,et al.,2020.Shotgun sequencing to determine corneal infection.Am J Ophthalmol Case Rep,19:100737.

[48]PengJM,DuB,QinHY,et al.,2021.Metagenomic next-generation sequencing for the diagnosis of suspected pneumonia in immunocompromised patients.J Infect,82(4):22-27.

[49]PiantadosiA,MukerjiSS,YeS,et al.,2021.Enhanced virus detection and metagenomic sequencing in patients with meningitis and encephalitis.mBio,12(4):e0114321.

[50]PrachayangprechaS,SchapendonkCME,KoopmansMP,et al.,2014.Exploring the potential of next-generation sequencing in detection of respiratory viruses.J Clin Microbiol,52(10):3722-3730.

[51]QianYY,WangHY,ZhouY,et al.,2020.Improving pulmon

[52]ary infection diagnosis with metagenomic next generation sequencing.Front Cell Infect Microbiol,10:567615.

[53]QuickJ,LomanNJ,DuraffourS,et al.,2016.Real-time, portable genome sequencing for Ebola surveillance.Nature,530(7589):228-232.

[54]QuinceC,WalkerAW,SimpsonJT,et al.,2017.Shotgun metagenomics, from sampling to analysis.Nat Biotechnol,35(9):833-844.

[55]RamachandranPS,WilsonMR,2020.Metagenomics for neuro‑logical infections ‒ expanding our imagination. Nat Rev Neurol,16(10):547-556.

[56]RhodesA,EvansLE,AlhazzaniW,et al.,2017.Surviving sepsis campaign: international guidelines for management of sepsis and septic shock: 2016.Intensive Care Med,43(3):304-377.

[57]SalipanteSJ,SenguptaDJ,RosenthalC,et al.,2013.Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.PLoS ONE,8(5):e65226.

[58]SalterSJ,CoxMJ,TurekEM,et al.,2014.Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.BMC Biol,12:87.

[59]SangerF,CoulsonAR,1975.A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase.J Mol Biol,94(3):441-448.

[60]SchatzMC,DelcherAL,SalzbergSL,2010.Assembly of large genomes using second-generation sequencing.Genome Res,20(9):1165-1173.

[61]StrongMJ,XuGR,MoriciL,et al.,2014.Microbial contamin

[62]ation in next generation sequencing: implications for sequence-based analysis of clinical samples.PLoS Pathog,10(11):e1004437.

[63]SunX,SongL,YangWJ,et al.,2020.Nanopore sequencing and its clinical applications.Methods Mol Biol,2204:13-32.

[64]ThomasT,GilbertJ,MeyerF,2012.Metagenomics—a guide from sampling to data analysis.Microb Inform Exp,2:3.

[65]ThorburnF,BennettS,ModhaS,et al.,2015.The use of next generation sequencing in the diagnosis and typing of respiratory infections.J Clin Virol,69:96-100.

[66]van DijkEL,JaszczyszynY,NaquinD,et al.,2018.The third revolution in sequencing technology.Trends Genet,34(9):666-681.

[67]WagnerK,SpringerB,PiresVP,et al.,2018.Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture.Sci Rep,8:6964.

[68]WangYH,ZhaoY,BollasA,et al.,2021.Nanopore sequencing technology, bioinformatics and applications.Nat Biotechnol,39(11):1348-1365.

[69]WilsonMR,NaccacheSN,SamayoaE,et al.,2014.Actionable diagnosis of neuroleptospirosis by next-generation sequencing.N Engl J Med,370(25):2408-2417.

[70]WilsonMR,O'DonovanBD,GelfandJM,et al.,2018.Chronic meningitis investigated via metagenomic next-generation sequencing.JAMA Neurol,75(8):947-955.

[71]WilsonMR,SampleHA,ZornKC,et al.,2019.Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis.N Engl J Med,380(24):2327-2340.

[72]XiaoTT,ZhouWH,2020.The third generation sequencing: the advanced approach to genetic diseases.Transl Pediatr,9(2):163-173.

[73]XingXW,ZhangJT,MaYB,et al.,2020.Metagenomic next-generation sequencing for diagnosis of infectious encephalitis and meningitis: a large, prospective case series of 213 patients.Front Cell Infect Microbiol,10:88.

[74]YangL,SongJX,WangYB,et al.,2021.Metagenomic next-generation sequencing for pulmonary fungal infection diag

[75]nosis: lung biopsy versus bronchoalveolar lavage fluid.Infect Drug Resist,14:4333-4359.

[76]ZhangW,WuTF,GuoMM,et al.,2019.Characterization of a new bunyavirus and its derived small RNAs in the brown citrus aphid,Aphiscitricidus.Virus Genes,55(4):557-561.

[77]ZhangXX,GuoLY,LiuLL,et al.,2019.The diagnostic value of metagenomic next-generation sequencing for identifyingStreptococcuspneumoniae in paediatric bacterial meningitis.BMC Infect Dis,19:495.

[78]ZhangY,CuiP,ZhangHC,et al.,2020.Clinical application and evaluation of metagenomic next-generation sequencing in suspected adult central nervous system infection.J Transl Med,18:199.

[79]ZhengY,QiuXJ,WangT,et al.,2021.The diagnostic value of metagenomic next-generation sequencing in lower respiratory tract infection.Front Cell Infect Microbiol,11:694756.

[80]ZhouX,WuHL,RuanQL,et al.,2019.Clinical evaluation of diagnosis efficacy of activeMycobacteriumtuberculosis complex infection via metagenomic next-generation sequencing of direct clinical samples.Front Cell Infect Microbiol,9:351.

[81]ZhuN,ZhouDB,LiSQ,2021.Diagnostic accuracy of metagenomic next-generation sequencing in sputum-scarce or smear-negative cases with suspected pulmonary tuberculosis.BioMed Res Int,2021:9970817.

[82]ZhuYG,TangXD,LuYT,et al.,2018.Contemporary situation of community-acquired pneumonia in China: a systematic review.J Transl Int Med,6(1):26-31.