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(CRISPR diagnosis) - Coggle Diagram

- - - - FLASH
        
        multiplexed detection of AMR sequences
        
        test the resistance of S. aureus strains
        
        important in the detection of MRSA infection vancomycin-resistant E. faecalis
        
        detected, in respiratory fluids and dried blood spots, subattomolar levels of drug-resistant Gram-positive bacteria and the malaria parasite Plasmodium falciparum.
      - Muller et al.
        
        directly identify specific resistance genes (blaCTX-M, blaNDM, and blaKPC) on plasmid molecules
        
        test yields sequence information within hours, making it ideal for rapidly tracking infections
        
        novel DNA labelling technique
        
        target any 20 bp sequence dramatically improves the detection of markers with specific characteristics
      - CAS-EXPAR
        
        based on the isothermal exponential nucleic acid amplification
        
        has the advantages of rapid and site-specific nucleic acid detection
        
        does not require exogenous priming
        
        also detect DNA methylation and L. monocytogenes total RNA
      - targeting the quinolone drug resistance gene gyrA mutation
      - Sun et al
        
        a fluorescence-sensing method based on CRISPR-Cas9 for bacterial detection
      - NASBA
        
        Zika virus (ZIKV) in infected monkey
      - LEOPARD
        
        enables the multiplexed detection
        of different RNA sequences with single-nucleotide specificity2
    - - DetectR
        
        quickly detects individual DNA or RNA, and allows the identification of individual base mismatches
        
        Cas12a from Lachnospiraceae bacterium (LbCas12a) or other organisms is guided to dsDNA targets by a complementary crRNA, triggering collateral cleavage of short ssDNA reporters carrying a fluorophore and a quencher.
        
        was optimized to detect the N (nucleoprotein) and E (envelope small membrane protein) genes of the SARS-CoV-2 genome
      - diagnose M. tuberculosis in clinical samples and identify strains and subspecies of the bacterium
        
        CRISPR-MTB
      - diagnostic value of CRISPR-Cas12 in paediatric tuberculosis
      - quick detection of E. coli and S. aureus with high sensitivity and specificity.
      - identify target sequences corresponding to carbapenem resistance genes, such as blaKPC, blaNDM, and blaOXA
      - label-free impedance assay
        
        less than an hour
        
        comparable to those of qPCR
      - HOLMES
      - E-CRISPR
        
        human papillomavirus and parvovirus B19 DNA with a LOD of ~50 pM
      - COVID
      - STOPCovid (for SHERLOCK testing in one pot)
        
        Cas12-based one-pot assay, integrated RT-LAMP-based preamplification with CRISPR-mediated detection in a one-step workflow
        
        STOPCovid has a sensitivity comparable to that of RT–qPCR, with a LOD of 100 copies of viral genome per reaction.
    - - Cas-TSPE system
        
        detect various pathogens, including E. coli, S. Typhi, P. aeruginosa, S. aureus, S. pyogenes, and E. faecalis.
      - CMP
        
        rapid detection of pathogens in milk samples
        
        S. pyogenes and S. Typhi in samples
        
        higher sensitivity than PCR
  - - - SHERLOCK
        
        viral particles
        
        The SHERLOCK-based detection of SARS-CoV-2 initially consisted of a two-step assay comprising RPA-based preamplification, followed by T7 transcription and Cas13a-mediated target recognition86
        
        In May 2020, a modified SHERLOCK-based two-step assay using RT-LAMP instead of RT-RPA received emergency use authorization from the United States Food and Drug Administration for the CRISPR-based detection of SARS-CoV-2
      - SHERLOCKv2 [
        
        simultaneously detects multiple viral nucleic acids in 90 min
        
        enabled the quantitative multiplexed sensing of nucleic acids and the target detection at zeptomolar (10–21 M) concentrations, and introduced a lateral-flow readout based on an immunochromatographic assay, where cleaved reporter molecules are detected through antibody-conjugated gold nanoparticles on a paper strip22,34.
      - HUDSON + SHERLOCK (SHINE )
        
        detect pathogens in patient samples at concentrations as low as 1 copy/μL
        
        combined the preamplification reaction and CRISPR-based detection into a single-step reaction that uses HUDSON to accelerate SARS-CoV-2 viral extraction in nasal swabs and saliva samples
      - APC-Cas
        
        Salmonella in milk samples
      - Schultzhaus
        
        the detection of the lcrV virulence gene
        
        lcrV gene exists in a plasmid with a corresponding low copy number and cannot be recognized by qPCR
      - detects BK polyomavirus DNA and cytomegalovirus DNA from patient-derived blood and urine samples 32284553
      - In a panel of five possible targeting crRNAs for different pathogenic strains and gDNA isolated from E. coli and Pseudomonas aeruginosa (Fig. 2G), SHERLOCK correctly genotyped strains and showed low cross-reactivity (Fig. 2H). Additionally, we were able to use SHERLOCK to distinguish between clinical isolates of Klebsiella pneu-moniae with two different resistance genes: Klebsiella pneumoniae carbapenemase (KPC) and New Delhi metallo-beta-lactamase 1 (NDM-1)
        
        Nucleic acid detection with CRISPR-Cas13a/C2c2
        
        Staphylococcus aureus
        
        When combined with RPA, we detected two DNA targets (the P. aeruginosa acyltransferase gene and the S. aureus thermonuclease gene) (Fig. 1G) down to the attomo-lar range
        
        Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6
      - Salmonella enteritidis92
      - n a different Cas13-based approach, the integration of multiple crRNAs, the usage of a Cas13a homologue from Leptotrichia buccalis (Lbu) and the measurement of fluorescence over time enabled the detection of SARS-Cov-2 RNA extracted from nasal swabs down to 1.27 × 108 copies per ml (1.65 × 103 copies per μl in the Cas13 reaction). Importantly, this was achieved without the need for preamplification, and the assay was compatible with readout using a portable fluorescence-detection device44
      - CARMEN