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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article  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.

CAS  Article