{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T22:02:26Z","timestamp":1793397746657,"version":"4.5.0"},"reference-count":99,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T00:00:00Z","timestamp":1687910400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.<\/jats:p>","DOI":"10.3389\/fmicb.2023.1186424","type":"journal-article","created":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T10:02:22Z","timestamp":1687946542000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":92,"title":["Clinical metagenomics\u2014challenges and future prospects"],"prefix":"10.3389","volume":"14","author":[{"given":"Maliha","family":"Batool","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Galloway-Pe\u00f1a","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,6,28]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"7965","DOI":"10.1038\/s41598-020-64739-1","article-title":"Clinical utility and cost-effectiveness of bacterial 16S rRNA and targeted PCR based diagnostic testing in a UK microbiology laboratory network","volume":"10","author":"Aggarwal","year":"2020","journal-title":"Sci. Rep."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"18852","DOI":"10.1038\/s41598-021-98452-4","article-title":"Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics","volume":"11","author":"Arroyo M\u00fchr","year":"2021","journal-title":"Sci. Rep."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1356","DOI":"10.1016\/j.chest.2020.11.008","article-title":"Added diagnostic utility of clinical metagenomics for the diagnosis of pneumonia in immunocompromised adults","volume":"159","author":"Azar","year":"2021","journal-title":"Chest"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-020-63970-0","article-title":"Cell free DNA from respiratory pathogens is detectable in the blood plasma of cystic fibrosis patients","volume":"10","author":"Barrett","year":"2020","journal-title":"Sci. Rep."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1038\/s41564-018-0349-6","article-title":"Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease","volume":"4","author":"Blauwkamp","year":"2019","journal-title":"Nat. Microbiol."},{"key":"ref6","doi-asserted-by":"publisher","first-page":"e2115285119","DOI":"10.1073\/pnas.2115285119","article-title":"Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system","volume":"119","author":"Bohl","year":"2022","journal-title":"Proc. Natl. Acad. Sci."},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e01491","DOI":"10.1128\/mBio.01491-15","article-title":"Virome capture sequencing enables sensitive viral diagnosis and comprehensive virome analysis","volume":"6","author":"Briese","year":"2015","journal-title":"MBio"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1093\/clinchem\/hvab143","article-title":"Molecular diagnosis of pneumonia (including multiplex panels)","volume":"68","author":"Buchan","year":"2022","journal-title":"Clin. Chem."},{"key":"ref9","doi-asserted-by":"publisher","first-page":"O468","DOI":"10.1111\/1469-0691.12490","article-title":"Comparison of peptide nucleic acid fluorescence in situ hybridization assays with culture-based matrix-assisted laser desorption\/ionization-time of flight mass spectrometry for the identification of bacteria and yeasts from blood cultures and cerebrospinal fluid cultures","volume":"20","author":"Calderaro","year":"2014","journal-title":"Clin. Microbiol. Infect."},{"key":"ref10","article-title":"Principles of diagnostic medical microbiology","volume-title":"Jawetz, Melnick, & Adelberg\u2019s medical microbiology, 27e","author":"Carroll","year":"2019"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"105025","DOI":"10.1016\/j.jcv.2021.105025","article-title":"A metagenomics workflow for SARS-CoV-2 identification, co-pathogen detection, and overall diversity","volume":"145","author":"Casta\u00f1eda-Mogoll\u00f3n","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref12","doi-asserted-by":"publisher","first-page":"646","DOI":"10.1111\/crj.13538","article-title":"Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases","volume":"16","author":"Chen","year":"2022","journal-title":"Clin. Respir. J."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"4014","DOI":"10.21037\/jtd-20-1232","article-title":"Comparison of metagenomic next-generation sequencing technology, culture and GeneXpert MTB\/RIF assay in the diagnosis of tuberculosis","volume":"12","author":"Chen","year":"2020","journal-title":"J. Thorac. Dis."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"2080","DOI":"10.21037\/apm-20-2578","article-title":"Metagenomic next-generation sequencing of radial ultrasound bronchoscopy-guided\" cocktail\" specimens as an efficient method for the diagnosis of focal pulmonary infections: a randomised study","volume":"10","author":"Chen","year":"2021","journal-title":"Annals Palliat Med"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"S416","DOI":"10.1093\/cid\/ciaa1516","article-title":"Clinical utility of in-house metagenomic next-generation sequencing for the diagnosis of lower respiratory tract infections and analysis of the host immune response","volume":"71","author":"Chen","year":"2020","journal-title":"Clin. Infect. Dis."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1016\/j.ijid.2021.04.057","article-title":"Clinical usefulness of metagenomic next-generation sequencing for the diagnosis of central nervous system infection in people living with HIV","volume":"107","author":"Chen","year":"","journal-title":"Int. J. Infect. Dis."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"001259","DOI":"10.1099\/jmm.0.001259","article-title":"The clinical significance of simultaneous detection of pathogens from bronchoalveolar lavage fluid and blood samples by metagenomic next-generation sequencing in patients with severe pneumonia","volume":"70","author":"Chen","year":"","journal-title":"J. Med. Microbiol."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1111\/crj.13369","article-title":"Clinical and etiological analysis of co-infections and secondary infections in COVID-19 patients: an observational study","volume":"15","author":"Chen","year":"2021","journal-title":"Clin. Respir. J."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"Chiu","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref20","author":"Chiu","year":""},{"key":"ref21","doi-asserted-by":"publisher","first-page":"1453","DOI":"10.1007\/s40265-021-01572-4","article-title":"The potential role of clinical metagenomics in infectious diseases: therapeutic perspectives","volume":"81","author":"d\u2019Humi\u00e8res","year":"2021","journal-title":"Drugs"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"1536","DOI":"10.3389\/fcimb.2022.950531","article-title":"Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia","volume":"12","author":"Deng","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref23","doi-asserted-by":"publisher","first-page":"201","DOI":"10.1016\/j.jare.2021.09.012","article-title":"Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections","volume":"38","author":"Diao","year":"2022","journal-title":"J. Adv. Res."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.cll.2013.03.001","article-title":"MALDI-TOF mass spectrometry for microorganism identification","volume":"33","author":"Dingle","year":"2013","journal-title":"Clin. Lab. Med."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-020-05746-5","article-title":"The diagnostic value of metagenomic next\u2043 generation sequencing in infectious diseases","volume":"21","author":"Duan","year":"2021","journal-title":"BMC Infect. Dis."},{"key":"ref26","doi-asserted-by":"publisher","first-page":"2020","DOI":"10.1093\/cid\/ciab742","article-title":"Microbial cell-free DNA identifies etiology of bloodstream infections, persists longer than conventional blood cultures, and its duration of detection is associated with metastatic infection in patients with staphylococcus aureus and gram-negative bacteremia","volume":"74","author":"Eichenberger","year":"2022","journal-title":"Clin. Infect. Dis."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13073-014-0114-2","article-title":"Clinical detection and characterization of bacterial pathogens in the genomics era","volume":"6","author":"Fournier","year":"2014","journal-title":"Genome Med."},{"key":"ref28","author":"Fry","year":""},{"key":"ref29","doi-asserted-by":"publisher","first-page":"1250","DOI":"10.3389\/fcimb.2021.745156","article-title":"Evaluations of clinical utilization of metagenomic next-generation sequencing in adults with fever of unknown origin","volume":"11","author":"Fu","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref30","doi-asserted-by":"publisher","first-page":"942","DOI":"10.1038\/nbt.3601","article-title":"Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies","volume":"34","author":"Gohl","year":"2016","journal-title":"Nat. Biotechnol."},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e02916","DOI":"10.1128\/JCM.02916-20","article-title":"Metagenomic sequencing as a pathogen-agnostic clinical diagnostic tool for infectious diseases: a systematic review and meta-analysis of diagnostic test accuracy studies","volume":"59","author":"Govender","year":"2021","journal-title":"J. Clin. Microbiol."},{"key":"ref32","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1016\/B978-0-323-54391-0.00008-4","article-title":"Chapter 8\u2014when to perform lumbar puncture in infants at risk for meningitis in the neonatal intensive care unit","volume-title":"Infectious disease and pharmacology","author":"Greenberg","year":"2019"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"605","DOI":"10.1080\/14737159.2018.1487292","article-title":"The challenge of diagnostic metagenomics","volume":"18","author":"Greninger","year":"2018","journal-title":"Expert Rev. Mol. Diagn."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13059-016-0904-5","article-title":"Depletion of abundant sequences by hybridization (DASH): using Cas9 to remove unwanted high-abundance species in sequencing libraries and molecular counting applications","volume":"17","author":"Gu","year":"2016","journal-title":"Genome Biol."},{"key":"ref35","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/s41591-020-1105-z","article-title":"Rapid pathogen detection by metagenomic next-generation sequencing of infected body fluids","volume":"27","author":"Gu","year":"2021","journal-title":"Nat. Med."},{"key":"ref36","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1146\/annurev-pathmechdis-012418-012751","article-title":"Clinical metagenomic next-generation sequencing for pathogen detection","volume":"14","author":"Gu","year":"2019","journal-title":"Annu. Rev. Pathol."},{"key":"ref37","doi-asserted-by":"publisher","first-page":"9","DOI":"10.3389\/fmed.2022.952636","article-title":"Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia","volume":"9","author":"Guo","year":"2022","journal-title":"Front. Med."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"919","DOI":"10.1128\/JCM.03050-15","article-title":"Depletion of human DNA in spiked clinical specimens for improvement of sensitivity of pathogen detection by next-generation sequencing","volume":"54","author":"Hasan","year":"2016","journal-title":"J. Clin. Microbiol."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"11194","DOI":"10.1038\/s41598-020-68159-z","article-title":"A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting","volume":"10","author":"Hasan","year":"2020","journal-title":"Sci. Rep."},{"key":"ref40","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1093\/jpids\/piz032","article-title":"Prospective cohort study of next-generation sequencing as a diagnostic modality for unexplained encephalitis in children","volume":"9","author":"Haston","year":"2020","journal-title":"J Pediatr Infect Diseases Soc"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13073-022-01097-9","article-title":"High-dimensional investigation of the cerebrospinal fluid to explore and monitor CNS immune responses","volume":"14","author":"Heming","year":"2022","journal-title":"Genome Med."},{"key":"ref42","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1093\/ilar\/ilv017","article-title":"Analyses of intestinal microbiota: culture versus sequencing","volume":"56","author":"Hiergeist","year":"2015","journal-title":"ILAR J."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1093\/cid\/ciaa035","article-title":"Clinical impact of metagenomic next-generation sequencing of plasma cell-free DNA for the diagnosis of infectious diseases: a multicenter retrospective cohort study","volume":"72","author":"Hogan","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref44","volume-title":"Next-generation sequencing for infectious diseases diagnostics\u2014Is it worth the hype?","author":"Huanyu Wang","year":"2021"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-021-83812-x","article-title":"A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification","volume":"11","author":"Jia","year":"2021","journal-title":"Sci. Rep."},{"key":"ref46","author":"Jiang","year":""},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e02473","DOI":"10.1128\/spectrum.02473-21","article-title":"Improving suspected pulmonary infection diagnosis by Bronchoalveolar lavage fluid metagenomic next-generation sequencing: a multicenter retrospective study","volume":"10","author":"Jin","year":"2022","journal-title":"Microbiol Spectr"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"1133","DOI":"10.1093\/clinchem\/hvab061","article-title":"Clinical evaluation of an improved metagenomic next-generation sequencing test for the diagnosis of bloodstream infections","volume":"67","author":"Jing","year":"2021","journal-title":"Clin. Chem."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1093\/clinchem\/hvac097","article-title":"Cell-free DNA as biomarker for sepsis by integration of microbial and host information","volume":"68","author":"Jing","year":"2022","journal-title":"Clin. Chem."},{"key":"ref50","doi-asserted-by":"publisher","first-page":"845","DOI":"10.3390\/cimb43020061","article-title":"Next-generation sequencing (NGS) in COVID-19: a tool for SARS-CoV-2 diagnosis, monitoring new strains and phylodynamic modeling in molecular epidemiology","volume":"43","author":"John","year":"2021","journal-title":"Curr. Issues Mol. Biol."},{"key":"ref51","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41564-022-01237-2","article-title":"Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults","volume":"7","author":"Kalantar","year":"2022","journal-title":"Nat. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2020\/2367505","article-title":"The value of combined radial endobronchial ultrasound-guided transbronchial lung biopsy and metagenomic next-generation sequencing for peripheral pulmonary infectious lesions","volume":"2020","author":"Li","year":"2020","journal-title":"Can. Respir. J."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"e24498","DOI":"10.1002\/jcla.24498","article-title":"Clinical application of metagenomic next-generation sequencing technology in the diagnosis and treatment of pulmonary infection pathogens: a prospective single-center study of 138 patients","volume":"36","author":"Li","year":"2022","journal-title":"J. Clin. Lab. Anal."},{"key":"ref54","doi-asserted-by":"publisher","first-page":"1152","DOI":"10.1007\/s40615-021-01056-x","article-title":"Influenza and pneumonia mortality across the 30 biggest US cities: assessment of overall trends and racial inequities","volume":"9","author":"Lippert","year":"2022","journal-title":"J. Racial Ethn. Health Disparities"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"2309","DOI":"10.3390\/microorganisms9112309","article-title":"Clinical application of metagenomic next-generation sequencing in patients with hematologic malignancies suffering from sepsis","volume":"9","author":"Liu","year":"2021","journal-title":"Microorganisms"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"104691","DOI":"10.1016\/j.jcv.2020.104691","article-title":"Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: wet lab procedure","volume":"134","author":"L\u00f3pez-Labrador","year":"2021","journal-title":"J. Clin. Virol."},{"key":"ref58","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1093\/clinchem\/hvab173","article-title":"The role of metagenomics and next-generation sequencing in infectious disease diagnosis","volume":"68","author":"Miller","year":"2022","journal-title":"Clin. Chem."},{"key":"ref59","doi-asserted-by":"publisher","first-page":"e01739","DOI":"10.1128\/JCM.01739-19","article-title":"Point-counterpoint: should we be performing metagenomic next-generation sequencing for infectious disease diagnosis in the clinical laboratory?","volume":"58","author":"Miller","year":"2020","journal-title":"J. Clin. Microbiol."},{"key":"ref60","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1101\/gr.238170.118","article-title":"Laboratory validation of a clinical metagenomic sequencing assay for pathogen detection in cerebrospinal fluid","volume":"29","author":"Miller","year":"2019","journal-title":"Genome Res."},{"key":"ref61","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1016\/j.phoj.2022.08.005","article-title":"Comparison of flowcytometry and conventional cytology for diagnosis of CNS involvement in hematologic malignancies","volume":"7","author":"Mokhtari","year":"2022","journal-title":"Pediatr Hematol Oncol J"},{"key":"ref62","doi-asserted-by":"publisher","first-page":"104247","DOI":"10.1016\/j.ebiom.2022.104247","article-title":"Real-time metagenomics-based diagnosis of community-acquired meningitis: a prospective series, southern France","volume":"84","author":"Morsli","year":"","journal-title":"EBioMedicine"},{"key":"ref63","doi-asserted-by":"publisher","first-page":"461","DOI":"10.3390\/pathogens10040461","article-title":"Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: a case report","volume":"10","author":"Morsli","year":"","journal-title":"Pathogens"},{"key":"ref64","doi-asserted-by":"publisher","first-page":"13","DOI":"10.3389\/fmicb.2022.926240","article-title":"Direct metagenomic diagnosis of community-acquired meningitis: state of the art","volume":"13","author":"Morsli","year":"","journal-title":"Front. Microbiol."},{"key":"ref65","doi-asserted-by":"publisher","first-page":"2037","DOI":"10.1007\/s10096-021-04205-6","article-title":"Direct next-generation sequencing diagnosis of echovirus 9 meningitis, France","volume":"40","author":"Morsli","year":"","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref66","doi-asserted-by":"publisher","first-page":"953","DOI":"10.3389\/fcimb.2021.684965","article-title":"Prospective evaluation of a rapid clinical metagenomics test for bacterial pneumonia","volume":"11","author":"Mu","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref67","doi-asserted-by":"publisher","first-page":"3378","DOI":"10.1038\/s41598-022-07260-x","article-title":"Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics","volume":"12","author":"Olausson","year":"2022","journal-title":"Sci. Rep."},{"key":"ref68","doi-asserted-by":"publisher","first-page":"403","DOI":"10.5588\/ijtld.21.0055","article-title":"Detection of Mycobacterium tuberculosis cell-free DNA to diagnose TB in pediatric and adult patients","volume":"25","author":"Pollock","year":"2021","journal-title":"Int. J. Tuberc. Lung Dis."},{"key":"ref69","doi-asserted-by":"publisher","first-page":"3722","DOI":"10.1128\/JCM.01641-14","article-title":"Exploring the potential of next-generation sequencing in detection of respiratory viruses","volume":"52","author":"Prachayangprecha","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"ref71","doi-asserted-by":"publisher","first-page":"e83","DOI":"10.1093\/nar\/gkz418","article-title":"FLASH: a next-generation CRISPR diagnostic for multiplexed detection of antimicrobial resistance sequences","volume":"47","author":"Quan","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref72","doi-asserted-by":"publisher","first-page":"600","DOI":"10.3390\/v14030600","article-title":"Next-generation sequencing for confronting virus pandemics","volume":"14","author":"Quer","year":"2022","journal-title":"Viruses"},{"key":"ref73","doi-asserted-by":"publisher","first-page":"547","DOI":"10.1038\/s41582-020-0374-y","article-title":"Metagenomics for neurological infections\u2014expanding our imagination","volume":"16","author":"Ramachandran","year":"2020","journal-title":"Nat. Rev. Neurol."},{"key":"ref74","doi-asserted-by":"publisher","first-page":"e0218318","DOI":"10.1371\/journal.pone.0218318","article-title":"Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda","volume":"14","author":"Ramesh","year":"2019","journal-title":"PLoS One"},{"key":"ref75","doi-asserted-by":"publisher","first-page":"1245","DOI":"10.1093\/cid\/cir692","article-title":"Broad-range 16S rRNA gene polymerase chain reaction for diagnosis of culture-negative bacterial infections","volume":"53","author":"Rampini","year":"2011","journal-title":"Clin. Infect. Dis."},{"key":"ref76","doi-asserted-by":"publisher","first-page":"2492","DOI":"10.1074\/mcp.TIR119.001559","article-title":"Fast and accurate bacterial species identification in urine specimens using LC-MS\/MS mass spectrometry and machine learning*[S]","volume":"18","author":"Roux-Dalvai","year":"2019","journal-title":"Mol. Cell. Proteomics"},{"key":"ref77","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1016\/S0140-6736(19)32989-7","article-title":"Global, regional, and national sepsis incidence and mortality, 1990\u20132017: analysis for the global burden of disease study","volume":"395","author":"Rudd","year":"2020","journal-title":"Lancet"},{"key":"ref78","doi-asserted-by":"publisher","first-page":"e65226","DOI":"10.1371\/journal.pone.0065226","article-title":"Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections","volume":"8","author":"Salipante","year":"2013","journal-title":"PLoS One"},{"key":"ref79","doi-asserted-by":"publisher","first-page":"778","DOI":"10.1093\/cid\/cix881","article-title":"Understanding the promises and hurdles of metagenomic next-generation sequencing as a diagnostic tool for infectious diseases","volume":"66","author":"Simner","year":"2018","journal-title":"Clin. Infect. Dis."},{"key":"ref80","first-page":"4","article-title":"The SEP-SEQ trial: clinical validation of the Karius plasma next-generation sequencing test for pathogen detection in sepsis","volume-title":"Open forum infectious diseases","author":"Thair","year":"2017"},{"key":"ref81","doi-asserted-by":"publisher","first-page":"747","DOI":"10.1016\/j.cmi.2018.10.001","article-title":"The use of broad-range bacterial PCR in the diagnosis of infectious diseases: a prospective cohort study","volume":"25","author":"Tkadlec","year":"2019","journal-title":"Clin. Microbiol. Infect."},{"key":"ref82","doi-asserted-by":"publisher","first-page":"771","DOI":"10.3389\/fmicb.2015.00771","article-title":"Primer and platform effects on 16S rRNA tag sequencing","volume":"6","author":"Tremblay","year":"2015","journal-title":"Front. Microbiol."},{"key":"ref84","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/s12879-018-3629-0","article-title":"Comparison of an in-house real-time duplex PCR assay with commercial HOLOGIC\u00ae APTIMA assays for the detection of Neisseria gonorrhoeae and Chlamydia trachomatis in urine and extra-genital specimens","volume":"19","author":"Venter","year":"2019","journal-title":"BMC Infect. Dis."},{"key":"ref85","doi-asserted-by":"publisher","first-page":"706","DOI":"10.1016\/j.cmi.2019.12.013","article-title":"Diagnostic challenges of central nervous system infection: extensive multiplex panels versus stepwise guided approach","volume":"26","author":"Vetter","year":"2020","journal-title":"Clin. Microbiol. Infect."},{"key":"ref86","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1038\/s41587-018-0006-x","article-title":"Capturing sequence diversity in metagenomes with comprehensive and scalable probe design","volume":"37","author":"Metsky","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"ref87","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-25129-w","article-title":"Molecular detection of fungal pathogens in clinical specimens by 18S rDNA high-throughput screening in comparison to ITS PCR and culture","volume":"8","author":"Wagner","year":"2018","journal-title":"Sci. Rep."},{"key":"ref88","doi-asserted-by":"publisher","first-page":"891","DOI":"10.2147\/IDR.S395700","article-title":"Clinical diagnosis application of metagenomic next-generation sequencing of plasma in suspected Sepsis","volume":"16","author":"Wang","year":"2023","journal-title":"Infect Drug Resist"},{"key":"ref89","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.ijid.2019.01.032","article-title":"Community acquired Stenotrophomonas maltophilia discitis: diagnosis aided by shotgun metagenomic sequencing","volume":"81","author":"Wang","year":"2019","journal-title":"Int. J. Infect. Dis."},{"key":"ref90","doi-asserted-by":"publisher","first-page":"1853","DOI":"10.3389\/fcimb.2022.957073","article-title":"The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China","volume":"12","author":"Wang","year":"2022","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref91","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1093\/jbcr\/irz047","article-title":"Clinical utility of PNA-FISH for burn wound diagnostics: a noninvasive, culture-independent technique for rapid identification of pathogenic organisms in burn wounds","volume":"40","author":"Weaver","year":"2019","journal-title":"J. Burn Care Res."},{"key":"ref92","doi-asserted-by":"publisher","first-page":"2408","DOI":"10.1056\/NEJMoa1401268","article-title":"Actionable diagnosis of neuroleptospirosis by next-generation sequencing","volume":"370","author":"Wilson","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref93","doi-asserted-by":"publisher","first-page":"2327","DOI":"10.1056\/NEJMoa1803396","article-title":"Clinical metagenomic sequencing for diagnosis of meningitis and encephalitis","volume":"380","author":"Wilson","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"ref95","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"ref96","doi-asserted-by":"publisher","first-page":"e32117","DOI":"10.1097\/MD.0000000000032117","article-title":"Clinical and chest computed tomography features associated with severe Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing: a multicenter, retrospective, observational study","volume":"101","author":"Xu","year":"2022","journal-title":"Medicine"},{"key":"ref97","doi-asserted-by":"publisher","first-page":"2","DOI":"10.3389\/fepid.2022.926695","article-title":"Metagenomic pathogen sequencing in resource-scarce settings: lessons learned and the road ahead","volume":"2","author":"Yek","year":"2022","journal-title":"Front Epidemiol"},{"key":"ref98","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s10096-023-04586-w","article-title":"Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis","volume":"42","author":"Zhang","year":"2023","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"ref99","doi-asserted-by":"publisher","first-page":"e9623","DOI":"10.7717\/peerj.9623","article-title":"Metagenomic next-generation sequencing for the clinical diagnosis and prognosis of acute respiratory distress syndrome caused by severe pneumonia: a retrospective study","volume":"8","author":"Zhang","year":"2020","journal-title":"PeerJ"},{"key":"ref100","doi-asserted-by":"publisher","first-page":"030006052210897","DOI":"10.1177\/03000605221089795","article-title":"Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections","volume":"50","author":"Zhang","year":"2022","journal-title":"J. Int. Med. Res."},{"key":"ref101","doi-asserted-by":"publisher","first-page":"694756","DOI":"10.3389\/fcimb.2021.694756","article-title":"The diagnostic value of metagenomic next\u2013generation sequencing in lower respiratory tract infection","volume":"11","author":"Zheng","year":"2021","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"ref102","doi-asserted-by":"publisher","first-page":"1259","DOI":"10.1016\/j.jmoldx.2021.06.007","article-title":"Clinical impact of metagenomic next-generation sequencing of bronchoalveolar lavage in the diagnosis and management of pneumonia: a multicenter prospective observational study","volume":"23","author":"Zhou","year":"2021","journal-title":"J. Mol. Diagn."},{"key":"ref103","doi-asserted-by":"publisher","first-page":"2165","DOI":"10.3389\/fpubh.2021.738412","article-title":"Metagenomic next-generation sequencing vs. traditional microbiological tests for diagnosing varicella-zoster virus central nervous system infection. Frontiers","volume":"9","author":"Zhu","year":"2022","journal-title":"Front. Public Health"}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1186424\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,28]],"date-time":"2023-06-28T10:02:28Z","timestamp":1687946548000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2023.1186424\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,6,28]]},"references-count":99,"alternative-id":["10.3389\/fmicb.2023.1186424"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2023.1186424","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,28]]},"article-number":"1186424"}}