Rudd KE, Johnson SC, Agesa KM, Shackelford KA, Tsoi D, Kievlan DR, Colombara DV, Ikuta KS, Kissoon N, Finfer S, et al. Global, regional, and national sepsis incidence and mortality, 1990–2017: analysis for the Global Burden of Disease Study. Lancet. 2020;395(10219):200–11.
Article
PubMed
Google Scholar
Defeating meningitis by 2030: baseline situation analysis. https://www.who.int/initiatives/defeating-meningitis-by-2030. Accessed 27 June 2022.
McGloughlin S, Richards GA, Nor MBM, Prayag S, Baker T, Amin P. Sepsis in tropical regions: report from the task force on tropical diseases by the World Federation of Societies of Intensive and Critical Care Medicine. J Crit Care. 2018;46:115–8.
Article
PubMed
Google Scholar
Kumalo A, Kassa T, Mariam ZS, Daka D, Tadesse AH. Bacterial profile of adult sepsis and their antimicrobial susceptibility pattern at Jimma University specialized hospital, south West Ethiopia. Health Sci J. 2016;10(2):1.
Google Scholar
Grumaz S, Grumaz C, Vainshtein Y, Stevens P, Glanz K, Decker SO, Hofer S, Weigand MA, Brenner T, Sohn K. Enhanced performance of next-generation sequencing diagnostics compared with standard of care microbiological diagnostics in patients suffering from septic shock. Crit Care Med. 2019;47(5):e394–402.
Article
PubMed
Google Scholar
Jordana-Lluch E, Gimenez M, Quesada MD, Ausina V, Martro E. Improving the diagnosis of bloodstream infections: PCR coupled with mass spectrometry. Biomed Res Int. 2014;2014: 501214.
Article
PubMed
Google Scholar
Weiss SL, Fitzgerald JC, Balamuth F, Alpern ER, Lavelle J, Chilutti M, Grundmeier R, Nadkarni VM, Thomas NJ. Delayed antimicrobial therapy increases mortality and organ dysfunction duration in pediatric sepsis. Crit Care Med. 2014;42(11):2409–17.
Article
CAS
PubMed
Google Scholar
Obaro S. Updating the diagnosis of bacterial meningitis. Lancet Infect Dis. 2019;19(11):1160–1.
Article
PubMed
Google Scholar
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. 2019;380(24):2327–40.
Article
CAS
PubMed
Google Scholar
Mishra D, Satpathy G, Wig N, Fazal F, Ahmed NH, Panda SK. Evaluation of 16S rRNA broad range PCR assay for microbial detection in serum specimens in sepsis patients. J Infect Public Health. 2020;13(7):998–1002.
Article
PubMed
Google Scholar
Sinha M, Jupe J, Mack H, Coleman TP, Lawrence SM, Fraley SI. Emerging technologies for molecular diagnosis of sepsis. Clin Microbiol Rev. 2018. https://doi.org/10.1128/CMR.00089-17.
Article
PubMed Central
PubMed
Google Scholar
Petersen LM, Martin IW, Moschetti WE, Kershaw CM, Tsongalis GJ. Third-generation sequencing in the clinical laboratory: exploring the advantages and challenges of Nanopore sequencing. J Clin Microbiol. 2019. https://doi.org/10.1128/JCM.01315-19.
Article
PubMed Central
PubMed
Google Scholar
Goldberg B, Sichtig H, Geyer C, Ledeboer N, Weinstock GM. Making the leap from research laboratory to clinic: challenges and opportunities for next-generation sequencing in infectious disease diagnostics. mBio. 2015;6(6):e01888-01815.
Article
CAS
PubMed
Google Scholar
Forbes JD, Knox NC, Ronholm J, Pagotto F, Reimer A. Metagenomics: the next culture-independent game changer. Front Microbiol. 2017;8:1069.
Article
PubMed
Google Scholar
Rang FJ, Kloosterman WP, de Ridder J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 2018;19(1):90.
Article
PubMed
Google Scholar
Gonzalez-Recio O, Gutierrez-Rivas M, Peiro-Pastor R, Aguilera-Sepulveda P, Cano-Gomez C, Jimenez-Clavero MA, Fernandez-Pinero J. Sequencing of SARS-CoV-2 genome using different nanopore chemistries. Appl Microbiol Biotechnol. 2021;105(8):3225–34.
Article
CAS
PubMed
Google Scholar
Cao Y, Li J, Chu X, Liu H, Liu W, Liu D. Nanopore sequencing: a rapid solution for infectious disease epidemics. Sci China Life Sci. 2019;62(8):1101–3.
Article
PubMed
Google Scholar
Nakagawa S, Inoue S, Kryukov K, Yamagishi J, Ohno A, Hayashida K, Nakazwe R, Kalumbi M, Mwenya D, Asami N, et al. Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia. Clin Transl Immunol. 2019;8(11): e01087.
Article
Google Scholar
Hong NTT, Nghia HDT, Thanh TT, Lan NPH, Ny NTH, Ngoc NM, Hang VTT, Chau LTM, Quynh VX, Diem LT, et al. Cerebrospinal fluid MinION sequencing of 16S rRNA gene for rapid and accurate diagnosis of bacterial meningitis. J Infect. 2020;80(4):469–96.
Article
CAS
PubMed
Google Scholar
Ashikawa S, Tarumoto N, Imai K, Sakai J, Kodana M, Kawamura T, Ikebuchi K, Murakami T, Mitsutake K, Maesaki S, et al. Rapid identification of pathogens from positive blood culture bottles with the MinION nanopore sequencer. J Med Microbiol. 2018;67(11):1589–95.
Article
CAS
PubMed
Google Scholar
Anson LW, Chau K, Sanderson N, Hoosdally S, Bradley P, Iqbal Z, Phan H, Foster D, Oakley S, Morgan M, et al. DNA extraction from primary liquid blood cultures for bloodstream infection diagnosis using whole genome sequencing. J Med Microbiol. 2018;67(3):347–57.
Article
CAS
PubMed
Google Scholar
Udaondo Z, Jenjaroenpun P, Wongsurawat T, Meyers E, Anderson C, Lopez J, Mohan M, Tytarenko R, Walker B, Ussery D, et al. Two cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin-resistant phenotype and its detection using oxford nanopore sequencing. Open Forum Infect Dis. 2020;7(6):180.
Article
Google Scholar
Grumaz C, Hoffmann A, Vainshtein Y, Kopp M, Grumaz S, Stevens P, Decker SO, Weigand MA, Hofer S, Brenner T, et al. Rapid next-generation sequencing-based diagnostics of bacteremia in septic patients. J Mol Diagn. 2020;22(3):405–18.
Article
CAS
PubMed
Google Scholar
Moon J, Kim N, Kim TJ, Jun JS, Lee HS, Shin HR, Lee ST, Jung KH, Park KI, Jung KY, et al. Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: a pilot study. Int J Med Microbiol. 2019;309(6): 151338.
Article
CAS
PubMed
Google Scholar
Faria NR, Sabino EC, Nunes MR, Alcantara LC, Loman NJ, Pybus OG. Mobile real-time surveillance of Zika virus in Brazil. Genome Med. 2016;8(1):97.
Article
PubMed
Google Scholar
Quick J, Loman NJ, Duraffour S, Simpson JT, Severi E, Cowley L, Bore JA, Koundouno R, Dudas G, Mikhail A, et al. Real-time, portable genome sequencing for Ebola surveillance. Nature. 2016;530(7589):228–32.
Article
CAS
PubMed
Google Scholar
Bull RA, Adikari TN, Ferguson JM, Hammond JM, Stevanovski I, Beukers AG, Naing Z, Yeang M, Verich A, Gamaarachchi H, et al. Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nat Commun. 2020;11(1):6272.
Article
CAS
PubMed
Google Scholar
Freed NE, Vlkova M, Faisal MB, Silander OK. Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and Oxford Nanopore Rapid Barcoding. Biol Methods Protoc. 2020;5(1):bpaa014.
Article
PubMed
Google Scholar
Mount HR, Boyle SD. Aseptic and bacterial meningitis: evaluation, treatment, and prevention. Am Fam Physician. 2017;96(5):314–22.
PubMed
Google Scholar
Trung NT, Hien TT, Huyen TT, Quyen DT, Van Son T, Hoan PQ, Phuong NT, Lien TT, Binh MT, Van Tong H, et al. Enrichment of bacterial DNA for the diagnosis of blood stream infections. BMC Infect Dis. 2016;16:235.
Article
PubMed
Google Scholar
Trung NT, Thau NS, Bang MH, Song LH. PCR-based Sepsis@Quick test is superior in comparison with blood culture for identification of sepsis-causative pathogens. Sci Rep. 2019;9(1):13663.
Article
PubMed
Google Scholar
Zeng YH, Koblizek M, Li YX, Liu YP, Feng FY, Ji JD, Jian JC, Wu ZH. Long PCR-RFLP of 16S-ITS-23S rRNA genes: a high-resolution molecular tool for bacterial genotyping. J Appl Microbiol. 2013;114(2):433–47.
Article
CAS
PubMed
Google Scholar
Klindworth A, Pruesse E, Schweer T, Peplies J, Quast C, Horn M, Glockner FO. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41(1): e1.
Article
CAS
PubMed
Google Scholar
Wertheim HF, Nguyen HN, Taylor W, Lien TT, Ngo HT, Nguyen TQ, Nguyen BN, Nguyen HH, Nguyen HM, Nguyen CT, et al. Streptococcus suis, an important cause of adult bacterial meningitis in northern Vietnam. PLoS ONE. 2009;4(6): e5973.
Article
PubMed
Google Scholar
Huong VT, Thanh LV, Phu VD, Trinh DT, Inui K, Tung N, Oanh NT, Trung NV, Hoa NT, Bryant JE, et al. Temporal and spatial association of Streptococcus suis infection in humans and porcine reproductive and respiratory syndrome outbreaks in pigs in northern Vietnam. Epidemiol Infect. 2016;144(1):35–44.
Article
CAS
PubMed
Google Scholar
Wertheim HF, Nghia HD, Taylor W, Schultsz C. Streptococcus suis: an emerging human pathogen. Clin Infect Dis. 2009;48(5):617–25.
Article
PubMed
Google Scholar
Goyette-Desjardins G, Auger JP, Xu J, Segura M, Gottschalk M. Streptococcus suis, an important pig pathogen and emerging zoonotic agent-an update on the worldwide distribution based on serotyping and sequence typing. Emerg Microbes Infect. 2014;3(6): e45.
PubMed Central
PubMed
Google Scholar
Hasan MR, Sundararaju S, Tang P, Tsui KM, Lopez AP, Janahi M, Tan R, Tilley P. A metagenomics-based diagnostic approach for central nervous system infections in hospital acute care setting. Sci Rep. 2020;10(1):11194.
Article
PubMed
Google Scholar
Stebner A, Ensser A, Geissdorfer W, Bozhkov Y, Lang R. Molecular diagnosis of polymicrobial brain abscesses with 16S-rDNA-based next-generation sequencing. Clin Microbiol Infect. 2021;27(1):76–82.
Article
CAS
PubMed
Google Scholar
Morrell M, Fraser VJ, Kollef MH. Delaying the empiric treatment of candida bloodstream infection until positive blood culture results are obtained: a potential risk factor for hospital mortality. Antimicrob Agents Chemother. 2005;49(9):3640–5.
Article
CAS
PubMed
Google Scholar
Ibrahim EH, Sherman G, Ward S, Fraser VJ, Kollef MH. The influence of inadequate antimicrobial treatment of bloodstream infections on patient outcomes in the ICU setting. Chest. 2000;118(1):146–55.
Article
CAS
PubMed
Google Scholar
Seymour CW, Gesten F, Prescott HC, Friedrich ME, Iwashyna TJ, Phillips GS, Lemeshow S, Osborn T, Terry KM, Levy MM. Time to treatment and mortality during mandated emergency care for sepsis. N Engl J Med. 2017;376(23):2235–44.
Article
PubMed
Google Scholar
Desnos-Ollivier M, Patel S, Spaulding AR, Charlier C, Garcia-Hermoso D, Nielsen K, Dromer F. Mixed infections and In Vivo evolution in the human fungal pathogen Cryptococcus neoformans. mBio. 2010. https://doi.org/10.1128/mBio.00091-10.
Article
PubMed Central
PubMed
Google Scholar
Zhu X, Yan S, Yuan F, Wan S. The applications of Nanopore sequencing technology in pathogenic microorganism detection. Can J Infect Dis Med Microbiol. 2020;2020:6675206.
Article
PubMed
Google Scholar
Santibanez P, Garcia-Garcia C, Portillo A, Santibanez S, Garcia-Alvarez L, de Toro M, Oteo JA. What does 16S rRNA gene-targeted next generation sequencing contribute to the study of infective endocarditis in heart-valve tissue? Pathogens. 2021. https://doi.org/10.3390/pathogens11010034.
Article
PubMed Central
PubMed
Google Scholar
Morsli M, Kerharo Q, Delerce J, Roche PH, Troude L, Drancourt M. Haemophilus influenzae meningitis direct diagnosis by metagenomic next-generation sequencing: a case report. Pathogens. 2021. https://doi.org/10.3390/pathogens10040461.
Article
PubMed Central
PubMed
Google Scholar