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Cao X, Chang Y, Tao C, Chen S, Lin Q, Ling C, Huang S, Zhang H. Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus. Microbiol Spectr 2023; 11:e0487022. [PMID: 36943040 PMCID: PMC10100783 DOI: 10.1128/spectrum.04870-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
In order to ensure the prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infection, rapid and accurate detection of pathogens and their resistance phenotypes is a must. Therefore, this study aimed to develop a fast and precise nucleic acid detection platform for identifying S. aureus and MRSA. We initially constructed a CRISPR-Cas12a detection system by designing single guide RNAs (sgRNAs) specifically targeting the thermonuclease (nuc) and mecA genes. To increase the sensitivity of the CRISPR-Cas12a system, we incorporated PCR, loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA). Subsequently, we compared the sensitivity and specificity of the three amplification methods paired with the CRISPR-Cas12a system. Finally, the clinical performance of the methods was tested by analyzing the fluorescence readout of 111 clinical isolates. In order to visualize the results, lateral-flow test strip technology, which enables point-of-care testing, was also utilized. After comparing the sensitivity and specificity of three different methods, we determined that the nuc-LAMP-Cas12a and mecA-LAMP-Cas12a methods were the optimal detection methods. The nuc-LAMP-Cas12a platform showed a limit of detection (LOD) of 10 aM (~6 copies μL-1), while the mecA-LAMP-Cas12a platform demonstrated a LOD of 1 aM (~1 copy μL-1). The LOD of both platforms reached 4 × 103 fg/μL of genomic DNA. Critical evaluation of their efficiencies on 111 clinical bacterial isolates showed that they were 100% specific and 100% sensitive with both the fluorescence readout and the lateral-flow readout. Total detection time for the present assay was approximately 80 min (based on fluorescence readout) or 85 min (based on strip readout). These results indicated that the nuc-LAMP-Cas12a and mecA-LAMP-Cas12a platforms are promising tools for the rapid and accurate identification of S. aureus and MRSA. IMPORTANCE The spread of methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to global health. Isothermal amplification combined with the trans-cleavage activity of Cas12a has been exploited to generate diagnostic platforms for pathogen detection. Here, we describe the design and clinical evaluation of two highly sensitive and specific platforms, nuc-LAMP-Cas12a and mecA-LAMP-Cas12a, for the detection of S. aureus and MRSA in 111 clinical bacterial isolates. With a limit of detection (LOD) of 4 × 103 fg/μL of genomic DNA and a turnaround time of 80 to 85 min, the present assay was 100% specific and 100% sensitive using either fluorescence or the lateral-flow readout. The present assay promises clinical application for rapid and accurate identification of S. aureus and MRSA in limited-resource settings or at the point of care. Beyond S. aureus and MRSA, similar CRISPR diagnostic platforms will find widespread use in the detection of various infectious diseases, malignancies, pharmacogenetics, food contamination, and gene mutations.
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Affiliation(s)
- Xiaoying Cao
- Department of Plastic and Burn Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Yanbin Chang
- Department of Clinical Laboratory, Gansu Provincial Hospital, Lanzhou, People’s Republic of China
| | - Chunqing Tao
- Department of Plastic and Burn Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Sen Chen
- Department of Plastic and Burn Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Qiuxia Lin
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Chao Ling
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Shifeng Huang
- Department of Clinical Laboratory, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Hengshu Zhang
- Department of Plastic and Burn Surgery, the First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
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Xiao G, He X, Zhang S, Liu Y, Liang Z, Liu H, Zhang J, Ou M, Cai S, Lai W, Zhang T, Ren L, Zhang G. Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major Mycobacterium Species. J Clin Microbiol 2020; 58:e01368-19. [PMID: 31723010 PMCID: PMC6989083 DOI: 10.1128/jcm.01368-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis infection and nontuberculous mycobacteria (NTM) infections exhibit similar clinical symptoms; however, the therapies for these two types of infections are different. Therefore, the rapid and accurate identification of M. tuberculosis and NTM species is very important for the control of tuberculosis and NTM infections. In the present study, a Cas12a/guide RNA (gRNA)-based platform was developed to identify M. tuberculosis and most NTM species. By designing species-specific gRNA probes targeting the rpoB sequence, a Cas12a/gRNA-based platform successfully identified M. tuberculosis and six major NTM species (Mycobacterium abscessus, Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium fortuitum) without cross-reactivity. In a blind assessment, a total of 72 out of 73 clinical Mycobacterium isolates were correctly identified, which is consistent with previous rpoB sequencing results. These results suggest that the Cas12a/gRNA-based platform is a promising tool for the rapid, accurate, and cost-effective identification of both M. tuberculosis and NTM species.
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Affiliation(s)
- Guohui Xiao
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xing He
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Su Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yaya Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhihang Liang
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
| | - Houming Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Juanjuan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Shuhao Cai
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Wenjie Lai
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Lili Ren
- Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
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O'Donnell N, Corcoran D, Lucey B, Barrett A. Molecular-based mycobacterial identification in a clinical laboratory setting: a comparison of two methods. Br J Biomed Sci 2019. [DOI: 10.1080/09674845.2012.12069146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- N. O'Donnell
- Department of Medical Microbiology, Cork University Hospital
| | - D. Corcoran
- Department of Medical Microbiology, Cork University Hospital
| | - B. Lucey
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - A. Barrett
- Department of Medical Microbiology, Cork University Hospital
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Yang J, Qi XM, Wu YG. The Application Analysis of Multiplex Real-Time Polymerase Chain Reaction Assays for Detection of Pathogenic Bacterium in Peritoneal Dialysis-Associated Peritonitis. Blood Purif 2019; 47:337-345. [PMID: 30602148 DOI: 10.1159/000495780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/26/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND/AIMS To estimate the clinical value of bacterial detection in peritoneal dialysis-associated peritonitis (PDAP) by multiplex real-time polymerase chain reaction (RT-PCR). This study was undertaken to evaluate multiplex RT-PCR for identifying clinically significant bacteria in PDAP. METHODS Seventy peritoneal dialysate specimens were collected and traditional bacterial culture and universal primer RT-PCR detection of the bacterial were used. RESULTS The positive rate of traditional culture method was 65.71% (46/70) and that of universal primer RT-PCR was 81.42% (57/70). For 6 clinical commonly pathogenic bacteria, multiplex, and monoplex RT-PCR all detected 38 positive ones within the 57 specimens that were detected positive by universal primer RT-PCR. The results of the 2 methods were completely identical. Detecting bacteria by universal primer PCR and Monoplex RT-PCR needs 4-5 and 6-9 h, respectively, while multiplex RT-PCR needs less than 3 h. CONCLUSION Our results demonstrated that the multiplex RT-PCR can detect several kinds of bacteria simultaneously and it is also more practical and convenient than monoplex RT-PCR.
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Affiliation(s)
- Jing Yang
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiang-Ming Qi
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yong-Gui Wu
- Department of Nephropathy, The First Affiliated Hospital of Anhui Medical University, Hefei, China,
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Paine SK, Basu A, Choudhury RG, Bhattacharya B, Chatterjee S, Bhattacharya C. Multiplex PCR from Menstrual Blood: A Non-Invasive Cost-Effective Approach to Reduce Diagnostic Dilemma for Genital Tuberculosis. Mol Diagn Ther 2018; 22:391-396. [PMID: 29549658 DOI: 10.1007/s40291-018-0322-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AIM Genital tuberculosis (GTB) is a potent contributor to irreversible damage to the reproductive system and infertility in females. As no gold standard diagnostic tool is yet available, clinical suspicion and relatively insensitive approaches such as histopathology, laparoscopy and hysterosalpingogram are currently critical determinants in the diagnosis of GTB. Although a polymerase chain reaction (PCR)-based assay using endometrial tissue seems promising, sampling does require an invasive procedure. OBJECTIVE We hypothesized that menstrual blood may provide an alternate non-invasive source of samples for PCR-based GTB diagnosis. METHODS We enrolled 195 women with primary infertility in whom GTB was suspected. We obtained ethics committee approval from our institution and written informed consent from subjects. Endometrial tissue and menstrual blood was collected from the subjects and culture, histopathology, and multiplex PCR with both sample type was performed for each subject. RESULTS The sensitivity and specificity of multiplex PCR was, respectively, 90.2 and 86.1% for menstrual blood, 95.8 and 84.3% for endometrial tissue, and 64.8 and 93.2% for histopathology staining. CONCLUSIONS A strong clinical suspicion aided with multiplex PCR using menstrual blood may significantly reduce the diagnostic dilemma for GTB diagnosis in a non-invasive, sensitive, rapid, and cost-effective manner.
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Affiliation(s)
- Suman K Paine
- ICMR-Regional Medical Research Centre, NE Region, Assam, 786001, India.
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, India
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Keerthirathne TP, Magana-Arachchi DN, Madegedara D, Sooriyapathirana SS. Real time PCR for the rapid identification and drug susceptibility of Mycobacteria present in Bronchial washings. BMC Infect Dis 2016; 16:607. [PMID: 27782812 PMCID: PMC5080729 DOI: 10.1186/s12879-016-1943-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 10/19/2016] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Mycobacteria have a spectrum of virulence and different susceptibilities to antibiotics. Distinguishing mycobacterial species is vital as patients with non-tuberculous mycobacterial (NTM) infections present clinical features that are similar to those of patients with tuberculosis. Thus, rapid differentiation of Mycobacterium tuberculosis complex from NTM is critical to administer appropriate treatment. Hence the aim of the study was to rapid identification of mycobacterial species present in bronchial washings using multiplex real time Polymerase Chain Reaction (PCR) and to determine the drug susceptibility in identified mycobacterial species. METHODS Sputum smear negative bronchoscopy specimens (n = 150) were collected for a period of one year, from patients attending the General Hospital Kandy, Sri Lanka. The specimens were processed with modified Petroff's method and were cultured on Löwenstein- Jensen medium. DNA, extracted from the mycobacterial isolates were subjected to a SYBR green mediated real time multiplex, PCR assay with primers specific for the M. tuberculosis complex, M. avium complex, M. chelonae-M.abscessus group and M. fortuitum group. DNA sequencing was performed for the species confirmation, by targeting the 16S rRNA gene and the drug susceptibility testing was performed for the molecularly identified isolates of M. tuberculosis and NTM. RESULTS The optimized SYBR Green mediated multiplex real-time PCR assay was able to identify the presence of genus Mycobacterium in 25 out of 26 AFB positive isolates, two M. tuberculosis complex, three M. avium complex and two isolates belonging to M. chelonae-M. abscessus group. DNA sequencing confirmed the presence of M. tuberculosis, M. chelonae-M. abscessus, M. intracellulare, M. avium, Rhodococcus sp. and M. celatum. Remaining isolates were identified as Mycobacterium sp. All the NTM isolates were sensitive to amikacin and seven were resistant to ciproflaxacin. Twenty two of the NTM isolates and the isolate Rhodococcus was resistant to clarithromycin. The two isolates of M. tuberculosis were sensitive to all first line anti tuberculosis drugs. CONCLUSION The optimized SYBR Green mediated multiplex real time PCR assay could be an effective tool for the rapid differentiation of pathogenic M. tuberculosis complex from the opportunistic nontuberculous mycobacteria and also it confirmed the presence of NTM in 15.3 % of the study population.
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Shen J, Guan Y, Zhang J, Tang J, Lu X, Zhang C. Application of microarray technology for the detection of intracranial bacterial infection. Exp Ther Med 2013; 7:496-500. [PMID: 24396433 PMCID: PMC3881033 DOI: 10.3892/etm.2013.1443] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/20/2013] [Indexed: 01/03/2023] Open
Abstract
The aim of this study was to assess the value of microarray technology for the detection of intracranial bacterial infection. A small gene chip was prepared based on the four pathogens commonly known to cause intracranial infection and the corresponding six types of common resistance genes in The Affiliated Hospital of Nantong University and The Affiliated Haian People’s Hospital of Nantong University. Cerebrospinal fluid samples were then collected from 30 patients with clinically diagnosed intracranial infection for the detection of the bacteria and resistance genes. The results were compared with the bacterial culture and sensitivity test results from the Department of Clinical Laboratories. The laboratory bacterial culture took 4–5 days, and revealed that 12 cases were positive and 18 cases were negative for bacteria. The microarray analysis took 1 day, and bacteria and resistance genes were detected in 15 cases. The 16S gene and drug resistance genes were detected in 8 cases; however, the bacterial strain was not identified. Seven cases appeared negative for bacteria and resistance genes. Microarray technology is rapid, sensitive and suitable for use in the detection of intracranial infections and other diseases for which conventional bacterial culture has a low positive rate.
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Affiliation(s)
- Jianhong Shen
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Yixiang Guan
- Department of Surgery, Affiliated Haian People's Hospital of Nantong University, Haian, Jiangsu 226600, P.R. China
| | - Jianping Zhang
- Department of Surgery, Affiliated Haian People's Hospital of Nantong University, Haian, Jiangsu 226600, P.R. China
| | - Jianwu Tang
- Department of Infectious Disease, Affiliated Haian People's Hospital of Nantong University, Haian, Jiangsu 226600, P.R. China
| | - Xiaojian Lu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, P.R. China
| | - Chunxiu Zhang
- Shanghai Biochip National Engineering Research Center, Shanghai 201203, P.R. China
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Rapid detection of Mycobacterium tuberculosis in clinical samples by multiplex polymerase chain reaction (mPCR). World J Microbiol Biotechnol 2013; 29:2389-95. [PMID: 23807412 DOI: 10.1007/s11274-013-1407-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 06/17/2013] [Indexed: 10/26/2022]
Abstract
Although the multi-copy and specific element IS6110 provides a good target for the detection of Mycobacterium tuberculosis complex by PCR techniques, the emergence of IS6110-negative strains suggested that false negative may occur if IS6110 alone is used as the target for detection. In this report, a multiplex polymerase chain reaction (mPCR) system was developed using primers derived from the insertion sequence IS6110 and an IS-like elements designated as B9 (GenBank accession no. U78639.1) to overcome the problem of detecting negative or low copy IS6110 containing strains of M. tuberculosis. The mPCR was evaluated using 346 clinical samples which included 283 sputum, 19 bronchial wash, 18 pleural fluid, 9 urine, 7 CSF, 6 pus, and 4 gastric lavage samples. Our results showed that the sensitivity (93.1 %) and specificity (89.6 %) of the mPCR system exceeds that of the conventional method of microscopy and culture. The mPCR assay provides an efficient strategy to detect and identify M. tuberculosis from clinical samples and enables prompt diagnosis when rapid identification of infecting mycobacteria is necessary.
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Rogers JT, Procop GW, Steelman CK, Abramowsky CR, Tuohy MT, Shehata BM. Clinical utility of DNA amplification and sequencing to identify a strain of Mycobacterium avium in paraffin-embedded, formalin-fixed biopsies from an immunosuppressed child. Pediatr Dev Pathol 2012; 15:315-7. [PMID: 22550970 DOI: 10.2350/11-07-1061-cr.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nontuberculous mycobacterial (NTM) infections are serious, though rare, in patients with severe combined immunodeficiency who have received bone marrow transplants. A 5-year-old female patient underwent stem cell/bone marrow transplant with disseminated NTM. Real-time polymerase chain reaction (PCR) using a fluorescence resonance energy transfer (FRET) probe for detection and identification of NTM was performed. The FRET-based real-time PCR assay amplified mycobacterial DNA, and the postamplification melt curve analysis classified the organism as a NTM. The pyrosequence of the hypervariable region A definitively identified the infecting organism as Mycobacterium avium. Real-time PCR along with melt curve analysis and pyrosequencing provides faster, definitive identification of mycobacteria, as compared to bacterial culture. In this case report, we emphasize the importance of utilizing molecular means for fast and accurate diagnosis.
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Affiliation(s)
- John T Rogers
- Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA
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