CRISPR-Based Diagnostics for Detection of Microorganisms and Beyond

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Microbial Biotechnology".

Deadline for manuscript submissions: 30 June 2024 | Viewed by 1452

Special Issue Editor

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Guest Editor
1. College of Life Sciences, Shanghai Normal University, Shanghai, China
2. Shanghai Tolo Biotechnology Co., Ltd., Shanghai, China
Interests: CRISPR; CRISPR diagnostics; cas engineering; nucleic acid detection; non-nucleic acid detection

Special Issue Information

Dear Colleagues,

Unlike CRISPR Cas9, Cas12 and Cas13 possess trans-cleavage activities against single-stranded nucleic acids, the activities of which have been employed to develop the next-generation CRISPR diagnostic (CRISPR-Dx) systems. So far, dozens of CRISPR-Dx systems have been successfully created, most of which are used in the detection of infectious diseases, non-infectious diseases, SNPs and non-nucleic acid targets. Although CRISPR-Dx technologies have shown merits in accuracy, sensitivity, rapidness and portability, there is still a lot of room for improvement in the detection of microorganisms.

Knowledge in this field will aid in understanding how CRISPR technologies facilitate the development of convenient methods for the sensitive and specific detection of microorganisms, which may include both target nucleic acids and target non-nucleic acids. As the Guest Editor of this Special Issue, I invite you to submit research articles, review articles, and short communications related to CRISPR-based technologies for the detection of microorganisms and beyond.

Prof. Dr. Jin Wang
Guest Editor

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  • CRISPR Diagnostics
  • Cas
  • microorganisms
  • next-generation diagnostics
  • molecular diagnostics
  • pathogen detection
  • DNA detection
  • RNA detection
  • amplification-free diagnostics
  • non-nucleic acid detection

Published Papers (1 paper)

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14 pages, 3326 KiB  
A One-Pot Convenient RPA-CRISPR-Based Assay for Salmonella enterica Serovar Indiana Detection
by Jiansen Gong, Di Zhang, Lixia Fu, Yongyi Dong, Kun Wu, Xinhong Dou and Chengming Wang
Microorganisms 2024, 12(3), 519; - 5 Mar 2024
Viewed by 844
Salmonella enterica serovar Indiana (S. Indiana) is among the most prevalent serovars of Salmonella and is closely associated with foodborne diseases worldwide. In this study, we combined a recombinase polymerase amplification (RPA) technique with clustered regularly interspaced short palindromic repeat (CRISPR) and [...] Read more.
Salmonella enterica serovar Indiana (S. Indiana) is among the most prevalent serovars of Salmonella and is closely associated with foodborne diseases worldwide. In this study, we combined a recombinase polymerase amplification (RPA) technique with clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated (Cas) protein Cas12b (CRISPR/Cas12b)-based biosensing in a one-pot platform to develop a novel one-step identification method for S. Indiana infection diagnosis. The entire RPA-CRISPR/Cas12b reaction can be completed at 41 °C within 1 h without the need for specific instruments. The optimal concentrations of Cas12b and single-guide RNA (sgRNA) for the reaction were the same at 250 nM. The single-stranded DNA (ssDNA) reporter 8C-FQ (5′-/6-FAM/CCCCCCCC/BHQ1/-3′) presented the best performance in the reaction compared with the other reporters. The limit of detection (LoD) of the RPA-CRISPR/Cas12b assay was 14.4 copies per reaction. As for specificity, we successfully identified four S. Indiana strains among twenty-two Salmonella strains without any false-positive results, presenting 100% accuracy for S. Indiana, and no cross-reactions were observed in eight other pathogens. Moreover, a total of 109 chicken carcasses were classified by the S. Indiana RPA-CRISPR assay and PCR methods from three processing points, including 43 post-shedding, 35 post-evisceration, and 31 post-chilling. There were 17 S. Indiana-positive samples identified during the whole processing step, consisting of nine post-shedding, five post-evisceration, and three post-chilling. The corresponding S. Indiana-positive rates of post-shedding, post-evisceration, and post-chilling were 20.93% (9/43), 14.29% (5/35), and 9.68% (3/31), respectively. Results from the S. Indiana one-step RPA-CRISPR/Cas12b assay were totally in agreement with those obtained using a traditional culture method, demonstrating 100% agreement with no false-positive or false-negative results observed. Altogether, the RPA-CRISPR/Cas12b assay developed in this study represents a promising, accurate, and simple diagnostic tool for S. Indiana detection. Full article
(This article belongs to the Special Issue CRISPR-Based Diagnostics for Detection of Microorganisms and Beyond)
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