Rapid specific detection of oral bacteria using Cas13-based SHERLOCK

References

• Griffen AL, Beall CJ, Campbell JH, et al. Distinct and complex bacterial profiles in human periodontitis and health revealed by 16S pyrosequencing. Isme J. 2012;6(6):1176–11. DOI:10.1038/ismej.2011.191
   PubMed Web of Science ®Google Scholar
• Kumar PS, Griffen AL, Barton JA, et al. New bacterial species associated with chronic periodontitis. J Dent Res. 2003;82(5):338–344. DOI:10.1177/154405910308200503
   PubMed Web of Science ®Google Scholar
• Li X, Kolltveit KM, Tronstad L, et al. Systemic diseases caused by oral infection. Clin Microbiol Rev. 2000;13:547–558.
   PubMed Web of Science ®Google Scholar
• Freire M, Nelson KE, Edlund A. The oral host–microbial interactome: an ecological chronometer of health? Trends Microbiol. 2021;29:551–561.
   PubMed Web of Science ®Google Scholar
• Wade WG. The oral microbiome in health and disease. Pharmacol Res. 2013;69:137–143.
   PubMed Web of Science ®Google Scholar
• Abusleme L, Dupuy AK, Dutzan N, et al. The subgingival microbiome in health and periodontitis and its relationship with community biomass and inflammation. Isme J. 2013;7(5):1016–1025. DOI:10.1038/ismej.2012.174
   PubMed Web of Science ®Google Scholar
• Tanner ACR, Kressirer CA, Rothmiller S, et al. The caries microbiome: implications for reversing dysbiosis. Adv Dent Res. 2018;29:78–85.
   PubMedGoogle Scholar
• Kressirer CA, Smith DJ, King WF, et al. Scardovia wiggsiae and its potential role as a caries pathogen. J Oral Biosci. 2017;59(3):135–141. DOI:10.1016/j.job.2017.05.002
   PubMed Web of Science ®Google Scholar
• Gross EL, Leys EJ, Gasparovich SR, et al. Bacterial 16S sequence analysis of severe caries in young permanent teeth. J Clin Microbiol. 2010;48(11):4121–4128. DOI:10.1128/JCM.01232-10
   PubMed Web of Science ®Google Scholar
• Hajishengallis G. Immunomicrobial pathogenesis of periodontitis: keystones, pathobionts, and host response. Trends Immunol. 2014;35:3–11.
   PubMed Web of Science ®Google Scholar
• Chen Y, Huang Z, Tang Z, et al. More than just a periodontal pathogen –the research progress on Fusobacterium nucleatum. Front Cell Infect Microbiol. 2022;12:815318.
   PubMed Web of Science ®Google Scholar
• Han YW. Fusobacterium nucleatum: a commensal-turned pathogen. Curr Opin Microbiol. 2015;23:141–147.
   PubMed Web of Science ®Google Scholar
• Dominy SS, Lynch C, Ermini F, et al. Porphyromonas gingivalis in Alzheimer’s disease brains: evidence for disease causation and treatment with small-molecule inhibitors. Sci Adv. 2019;5(1):eaau3333. DOI:10.1126/sciadv.aau3333
   PubMed Web of Science ®Google Scholar
• Wu H, Qiu W, Zhu X, et al. The periodontal pathogen Fusobacterium nucleatum exacerbates alzheimer’s pathogenesis via specific pathways. Front Aging Neurosci. 2022;14:912709.
   PubMed Web of Science ®Google Scholar
• Oravital home - Preventing oral systemic diseases. Available from: https://www.oravital.com/.
   Google Scholar
• Bristle: oral health test. Available from: https://www.bristlehealth.com/product-oral-health-test.
   Google Scholar
• Kellner MJ, Koob JG, Gootenberg JS, et al. SHERLOCK: nucleic acid detection with CRISPR nucleases. Nat Protoc. 2019;14(10):2986–3012.
   PubMed Web of Science ®Google Scholar
• Gootenberg JS, Abudayyeh OO, Lee JW, et al. Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438–442. DOI:10.1126/science.aam9321
   PubMed Web of Science ®Google Scholar
• de Puig H, Lee RA, Najjar D, et al. Minimally instrumented SHERLOCK (miSHERLOCK) for CRISPR-based point-of-care diagnosis of SARS-CoV-2 and emerging variants. Sci Adv. 2021;7(32):eabh2944. DOI:10.1126/sciadv.abh2944
   PubMed Web of Science ®Google Scholar
• Cunningham CH, Hennelly CM, Lin JT, et al. A novel CRISPR-based malaria diagnostic capable of Plasmodium detection, species differentiation, and drug-resistance genotyping. EBioMedicine. 2021;68:103415.
   PubMed Web of Science ®Google Scholar
• Piepenburg O, Williams CH, Stemple DL, et al. DNA detection using recombination proteins. PLoS Biol. 2006;4(7):e204.
   PubMed Web of Science ®Google Scholar
• Lobato IM, O’Sullivan CK. Recombinase polymerase amplification: basics, applications and recent advances. Trends Anal Chem. 2018;98:19–35.
   PubMed Web of Science ®Google Scholar
• Ghouneimy A, Mahas A, Marsic T, et al. CRISPR-Based diagnostics: challenges and potential solutions toward point-of-care applications. ACS Synth Biol. 2023;12:1–16.
   PubMed Web of Science ®Google Scholar
• Blanco-Miguez A, Beghini F, Cumbo F, et al. Extending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4. 2022; 2022.08.22.504593 Preprint at. DOI:10.1101/2022.08.22.504593
   Google Scholar
• Untergasser A, Cutcutache I, Koressaar T, et al. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115. DOI:10.1093/nar/gks596
   PubMed Web of Science ®Google Scholar
• Lorenz R, Bernhart SH, Höner Zu Siederdissen C, et al. ViennaRNA Package 2.0. Algorithms Mol Biol. 2011;6(1):26. DOI:10.1186/1748-7188-6-26
   PubMed Web of Science ®Google Scholar
• Lemos J, Palmer SR, Zeng L, et al. The biology of Streptococcus mutans. Microbiol Spectr. 2019;7(1):1–7. DOI:10.1128/microbiolspec.GPP3-0051-2018
   Web of Science ®Google Scholar
• Ajdić D, McShan WM, McLaughlin RE, et al. Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen. Proc Natl Acad Sci. 2002;99(22):14434–14439. DOI:10.1073/pnas.172501299
   PubMed Web of Science ®Google Scholar
• Downes J, Mantzourani M, Beighton D, et al. Scardovia wiggsiae sp. Nov., isolated from the human oral cavity and clinical material, and emended descriptions of the genus Scardovia and Scardovia inopinata. Int J Syst Evol Microbiol. 2011;61(1):25–29. DOI:10.1099/ijs.0.019752-0
   PubMedGoogle Scholar
• Oscarsson J, Claesson R, Lindholm M, et al. Tools of Aggregatibacter actinomycetemcomitans to evade the host response. J Clin Med. 2019;8:1079.
   PubMed Web of Science ®Google Scholar
• Nedergaard S, Kobel CM, Nielsen MB, et al. Whole genome sequencing of aggregatibacter actinomycetemcomitans cultured from blood stream infections reveals three major phylogenetic groups including a novel lineage expressing serotype a membrane O Polysaccharide. Pathogens. 2019;8(4):256. DOI:10.3390/pathogens8040256
   PubMed Web of Science ®Google Scholar
• How KY, Song KP, Chan KG. Porphyromonas gingivalis: an overview of periodontopathic pathogen below the gum line. Front Microbiol. 2016;7:53.
   PubMed Web of Science ®Google Scholar
• Chastain-Gross RP, Xie G, Bélanger M, et al. Genome sequence of porphyromonas gingivalis strain 381. Genome Announc. 2017;5(2): e01467-16. doi:10.1128/genomeA.01467-16.
   Google Scholar
• Zawadzki PJ, Perkowski K, Padzik M, et al. Examination of oral microbiota diversity in adults and older adults as an approach to prevent spread of risk factors for human infections. BioMed Res Int. 2017;2017:1–7.
   Web of Science ®Google Scholar
• Traglia GM, Chua K, Centrón D, et al. Whole-genome sequence analysis of the naturally competent Acinetobacter baumannii clinical isolate A118. Genome Biol Evol. 2014;6:2235–2239.
   PubMed Web of Science ®Google Scholar
• Botelho-Nevers E, Gouriet F, Lepidi H, et al. Chronic nasal infection caused by Klebsiella rhinoscleromatis or Klebsiella ozaenae: two forgotten infectious diseases. Int J Infect Dis. 2007;11(5):423–429. DOI:10.1016/j.ijid.2006.10.005
   PubMed Web of Science ®Google Scholar
• Conlan S, Kong HH, Segre JA. Species-level analysis of DNA sequence data from the NIH human microbiome project. PLoS ONE. 2012;7:e47075.
   PubMed Web of Science ®Google Scholar
• Rafiq Z, Sam N, Vaidyanathan R. Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India. Mem Inst Oswaldo Cruz. 2016;111:144–146.
   PubMed Web of Science ®Google Scholar
• McCormack M, Smith AJ, Akram AN, et al. Staphylococcus aureus and the oral cavity: an overlooked source of carriage and infection? Am J Infect Control. 2015;43(1):35–37. DOI:10.1016/j.ajic.2014.09.015
   PubMed Web of Science ®Google Scholar
• Zubair S, Fischer A, Liljander A, et al. Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel. Stand Genomic Sci. 2015;10(1):109. DOI:10.1186/s40793-015-0098-6
   PubMedGoogle Scholar
• Chipashvili O, Utter DR, Bedree JK, et al. Episymbiotic Saccharibacteria suppresses gingival inflammation and bone loss in mice through host bacterial modulation. Cell Host Microbe. 2021;29:1649–1662.e7.
   PubMed Web of Science ®Google Scholar
• Tavares LJ, Klein MI, Panariello BHD, et al. An in vitro model of Fusobacterium nucleatum and Porphyromonas gingivalis in single- and dual-species biofilms. J Periodontal Implant Sci. 2018;48:12.
   PubMed Web of Science ®Google Scholar
• Kim S, Song M, Roh B-D, et al. Inhibition of Streptococcus mutans biofilm formation on composite resins containing ursolic acid. Restor Dent Endod. 2013;38:65–72.
   PubMedGoogle Scholar
• Arvikar SL, Hasturk H, Strle K, et al. Periodontal inflammation and distinct inflammatory profiles in saliva and gingival crevicular fluid compared with serum and joints in rheumatoid arthritis patients. J Periodontol. 2021;92:1379–1391.
   PubMed Web of Science ®Google Scholar
• Escapa IF, Chen T, Huang Y, et al. New insights into human nostril microbiome from the Expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract. mSystems. 2018;3(6): e00187-18. DOI:10.1128/mSystems.00187-18.
   PubMed Web of Science ®Google Scholar
• Callahan BJ, McMurdie PJ, Rosen MJ, et al. DADA2: high-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581–583. DOI:10.1038/nmeth.3869
   PubMed Web of Science ®Google Scholar
• Katoh K, Misawa K, Kuma K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002;30:3059–3066.
   PubMed Web of Science ®Google Scholar
• Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–1973.
   PubMed Web of Science ®Google Scholar
• Nguyen L-T, Schmidt HA, von Haeseler A, et al. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–274.
   PubMed Web of Science ®Google Scholar
• Gut Microbiome Testing. Health supplements & probiotics. Viome.com. Available from: https://www.viome.com.
   Google Scholar
• Aas JA, Paster BJ, Stokes LN, et al. Defining the normal bacterial flora of the oral cavity. J Clin Microbiol. 2005;43:5721–5732.
   PubMed Web of Science ®Google Scholar
• Eren AM, Borisy GG, Huse SM, et al. Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci. 2014;111:E2875–2884.
   PubMed Web of Science ®Google Scholar
• Baumgartner D, Johannsen B, Specht M, et al. OralDisk: a chair-side compatible molecular platform using whole saliva for monitoring oral health at the dental practice. Biosensors (Basel). 2021;11(11):423. DOI:10.3390/bios11110423
   PubMedGoogle Scholar
• OralDNA Labs. Available from: https://www.oraldna.com/.
   Google Scholar
• Chandrasekaran SS, Agrawal S, Fanton A, et al. Rapid detection of SARS-CoV-2 RNA in saliva via Cas13. Nat Biomed Eng. 2022;6:944–956.
   PubMed Web of Science ®Google Scholar
• Lee RA, Puig HD, Nguyen PQ, et al. Ultrasensitive CRISPR-based diagnostic for field-applicable detection of Plasmodium species in symptomatic and asymptomatic malaria. Proc Natl Acad Sci. 2020;117(41):25722–25731. DOI:10.1073/pnas.2010196117
   PubMed Web of Science ®Google Scholar
• Notomi T, Okayama H, Masubuchi H, et al. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000;28:e63.
   PubMed Web of Science ®Google Scholar
• Maekawa T, Krauss J, Abe T, et al. Porphyromonas gingivalis manipulates complement and TLR signaling to uncouple bacterial clearance from inflammation and promote dysbiosis. Cell Host Microbe. 2014;15(6):768–778. DOI:10.1016/j.chom.2014.05.012
   PubMed Web of Science ®Google Scholar
• Ackerman CM, Myhrvold C, Thakku SG, et al. Massively multiplexed nucleic acid detection with Cas13. Nature. 2020;582(7811):277–282. DOI:10.1038/s41586-020-2279-8
   PubMed Web of Science ®Google Scholar