Rapid detection of Mycobacterium tuberculosis in sputum using CRISPR-Cas12b combined with cross-priming amplification in a single reaction

IMPORTANCE

In this study, we successfully established a new One-Pot method, named TB One-Pot, for detecting Mtb in sputum by combining CRISPR-cas12b-mediated trans-cleavage with cross-priming amplification (CPA). Our study evaluated the diagnostic performance of TB One-Pot in clinical sputum samples for tuberculosis. The findings provide evidence for the potential of TB One-Pot as a diagnostic tool for tuberculosis.

Development of cross-priming amplification (CPA) combined with colorimetric and lateral flow dipstick visualization for scale drop disease virus (SDDV) detection

Scale drop disease virus (SDDV) is one of the most important pathogens that causes scale drop disease (SDD) in Asian sea bass (Lates calcarifer). The outbreaks of this disease are one of the factors causing substantial losses in Asian sea bass aquaculture. In this study, the uracil-DNA glycosylase (UDG)-supplemented cross-priming amplification (UCPA) combined with a colorimetric detection method using the hydroxynaphthol blue (HNB) and lateral flow dipstick (LFD) for detection of SDDV was developed. The UDG was utilized to prevent carryover contamination, and the CPA reactions can be readily observed by HNB and LFD. The CPA primers and probe were designed to target the major capsid protein (MCP) gene of the SDDV. The optimized UCPA conditions were performed at the temperature of 61°C for 60 min. The UCPA assays demonstrated specificity to SDDV without cross-reaction to other tested viruses including red-spotted grouper nervous necrosis virus (RGNNV), infectious spleen and kidney necrosis virus (ISKNV) and Lates calcarifer herpes virus (LCHV), and other bacterial species commonly found in aquatic animals. The sensitivity of the UCPA-HNB and UCPA-LFD was 100 viral copies/µl and 10 pg of extracted total DNA, which was 10-fold more sensitive than that of conventional PCR. The UCPA-HNB and UCPA-LFD assays could be used to detect the SDDV infection in all 25 confirmed SDDV-infected fish samples. Therefore, the UCPA coupled with HNB and LFD was rapid, simple and effective and might be applied for diagnosis of SDDV infection.

Pathogenic and Virulence Factor Detection on Viable but Non-culturable Methicillin-Resistant Staphylococcus aureus

Food safety and foodborne infections and diseases have been a leading hotspot in public health, and methicillin-resistant Staphylococcus aureus (MRSA) has been recently documented to be an important foodborne pathogen, in addition to its recognition to be a leading clinical pathogen for some decades. Standard identification for MRSA has been commonly performed in both clinical settings and food routine detection; however, most of such so-called "standards," "guidelines," or "gold standards" are incapable of detecting viable but non-culturable (VBNC) cells. In this study, two major types of staphylococcal food poisoning (SFP), staphylococcal enterotoxins A (sea) and staphylococcal enterotoxins B (seb), as well as the panton-valentine leucocidin (pvl) genes, were selected to develop a cross-priming amplification (CPA) method. Limit of detection (LOD) of CPA for sea, seb, and pvl was 75, 107.5, and 85 ng/μl, indicating that the analytical sensitivity of CPA is significantly higher than that of conventional PCR. In addition, a rapid VBNC cells detection method, designated as PMA-CPA, was developed and further applied. PMA-CPA showed significant advantages when compared with PCR assays, in terms of rapidity, sensitivity, specificity, and accuracy. Compared with conventional VBNC confirmation methods, the PMA-CPA showed 100% accordance, which had demonstrated that the PMA-CPA assays were capable of detecting different toxins in MRSA in VBNC state. In conclusion, three CPA assays were developed on three important toxins for MRSA, and in combination with PMA, the PMA-CPA assay was capable of detecting virulent gene expression in MRSA in the VBNC state. Also, the above assays were further applied to real samples. As concluded, the PMA-CPA assay developed in this study was capable of detecting MRSA toxins in the VBNC state, representing first time the detection of toxins in the VBNC state.

Comparison of loop-mediated isothermal amplification (LAMP) and cross-priming amplification (CPA) for detection of African swine fever virus

The reliable and rapid diagnosis of infectious animal diseases presents an exceptionally im- portant aspect when considering their control and prevention. The paper describes the compara- tive evaluation of two rapid isothermal amplification methods for diagnosis of African swine fever (ASF). The robustness of loop-mediated isothermal amplification (LAMP) and the cross-priming amplification (CPA) were compared using samples obtained from ASF confirmed animals. Both assays were evaluated in order to define their diagnostic capabilities in terms of ASF diagnosis and reproducibility of the results. Investigations showed no cross-reactivity for other pig patho- gens and no significant differences in the specificity of both assays. The sensitivity of LAMP reached 90%, while that of CPA was 70%. In conclusion, both methods are suitable for imple- mentation in preliminary ASF diagnosis but further improvements are required to enhance their diagnostic sensitivity.

Label-Free Cross-Priming Amplification Coupled With Endonuclease Restriction and Nanoparticles-Based Biosensor for Simultaneous Detection of Nucleic Acids and Prevention of Carryover Contamination

Here, we reported on a label-free cross-priming amplification (CPA) scheme that utilized endonuclease restriction for simultaneous detection of nucleic acids and elimination of carryover contamination. Reaction mixtures were detected in a nanoparticle-based lateral flow biosensor (LFB). The assay exhibited attractive traits in that it did not require the use of labeled primers or labeled probes, and thus, the technique could prevent undesired results arising from unwanted hybridization between labeled primers or between a probe and labeled primer. Isothermal amplification and endonuclease restriction digestion were conducted in a single pot, and the use of a closed-tube amplification removed false-positive results due to contaminants. To validate the assay's applicability, we employed the novel technique to detect the pathogen Staphylococcus aureus in pure cultures and artificial blood samples. The assay could detect target bacterium in pure culture with a 100 fg.μL^-1 detection limit, and in spiked blood samples with a 700 cfu.mL^-1 detection limit. The whole process, including sample procedure (20-min), isothermal amplification (60-min), endonuclease digestion (10-min) and result reporting (within 2-min), could be finished within 95-min. As a poof-of-concept assay, the technique devised in the current report could be employed for detecting various other sequences if the specific CPA primers were available.

Development and evaluation of LAMP, CPA and IMSA methods for rapid detection of the AML1/ETO fusion gene in acute myeloid leukemia

The objective of the present study was to determine whether the loop-mediated isothermal amplification (LAMP), cross-priming amplification (CPA), and/or isothermal multiple-self-matching-initiated amplification (IMSA) methods can provide rapid detection of the runt related transcription factor 1/runt related transcription factor 1 translocation partner 1 (AML1/ETO) fusion gene in acute myeloid leukemia (AML). According to the sequence of the AML1/ETO fusion gene available in GenBank and the principles of the LAMP, CPA and IMSA methods, specific primers were designed to bind a conserved region of the AML1/ETO gene in each assay. Following optimization of the conditions for the LAMP, CPA and IMSA assays, the specificity and sensitivity of the assays were examined and compared. In addition, 41 clinical samples were assayed using the three methods. It was observed that a ladder-like pattern of DNA products was produced in AML1/ETO-positive samples in all three assays, whereas no DNA product was generated with the controls. The detection limit of the LAMP and CPA assays was 50 copies/tube, and for the IMSA assay was 10 copies/tube. This sensitivity was consistent, and improved in the latter case, compared with that of the reverse transcription-polymerase chain reaction (RT-PCR) assay. Furthermore, the detection rate for bone marrow or peripheral blood samples was 9.76%, and the agreement among the LAMP, CPA, IMSA and RT-PCR methods was 100%. Therefore, the LAMP, CPA and IMSA methods optimized in the present study provided rapid detection of the AML1/ETO fusion gene for an initial clinical diagnosis of AML. In addition, the LAMP, CPA and IMSA assays are straightforward to perform and do not require specialized instruments. Therefore, these three isothermal methods may be used to perform field tests or assays at resource-limited hospitals.

Detection of Chlamydia trachomatis and Neisseria gonorrhoeae based on cross-priming amplification

Rapid, sensitive and specific isothermal nucleic acid amplification methods of Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae (N. gonorrhoeae) have been developed based on cross-priming amplification (CPA). The amplicon of CPA can be detected by a disposable amplicon cross-contamination proof device. The whole assay takes 1-1·5 h from amplification to read out. Ten fold serial dilutions of quantified plasmids were used to test the CPA assay sensitivities, with the detection limits of 45 copies per reaction and 65 copies per reaction for C. trachomatis and N. gonorrhoeae respectively. The specificities of CPA assays for C. trachomatis and N. gonorrhoeae were tested by using total DNA extracted from nine other bacterial strains, and no cross-reactivity was detected. Eighty clinical cervical or vaginal swab specimens were tested by both CPA and real-time polymerase chain reaction (PCR) with the consistencies of 98·75% (79/80) and 97·5% (78/80) for C. trachomatis and N. gonorrhoeae respectively. Using real-time PCR as a reference standard, the clinical sensitivity (positive) and specificity (negative) of CPA was found to be 98·15% (53/54) and 100% (26/26) for C. trachomatis, and 93·75% (30/32) and 100% (48/48) for N. gonorrhoeae. Eight swab specimens tested positive for both C. trachomatis and N. gonorrhoeae simultaneously by real-time PCR and CPA assay. This study demonstrated that CPA is an affordable and accessible assay for C. trachomatis and N. gonorrhoeae detection, with high sensitivity and specificity.

SIGNIFICANCE AND IMPACT OF THE STUDY

Rapid and specific detection of the sexually transmitted pathogens Chlamydia trachomatis (C. trachomatis) and Neisseria gonorrhoeae (N. gonorrhoeae) would enable early treatment and management of their spread. Here, for the first time, a user friendly DNA isothermal amplification method named cross-priming amplification (CPA), was used to test C. trachomatis and N. gonorrhoeae with high sensitivity and specificity. The results indicate that CPA has great potential for improving C. trachomatis and N. gonorrhoeae diagnostics which could be particularly advantageous in resource-limited areas.

Development of cross-priming amplification for direct detection of the African Swine Fever Virus, in pig and wild boar blood and sera samples

African swine fever (ASF) is considered a major threat to the production of pigs worldwide. The ASF aetiological agent, ASFV, is the sole member of the Asfivirus genus, belonging to the Asfarviridae family. An effective ASF vaccine is not currently available, thus the only measures of ASF spread control include, reliable and fast diagnosis. Officially approved, diagnostic methods include, virus isolation, serological assays, including enzyme-linked immunosorbent assay and immunoperoxidase assay (IPT) and different modifications of the polymerase chain reaction (PCR). This paper describes the first development and application of a cross-priming amplification method (CPA) for the direct detection of genetic ASFV material, in blood and sera from pigs and wild boars. This method is specific only to ASFV DNA. The study showed that CPA had equal sensitivity, in comparison to the official, universal probe library (UPL) real-time PCR and reached 7·2 copies of standard plasmid DNA, containing a p72 gene fragment. This method was capable of detecting ASFV DNA in all examined blood samples, originating from pigs; n = 10 and wild boars; n = 76. The obtained results were also confirmed by the officially approved, real-time PCR. The developed CPA might be further used by local and county veterinary officers, hunters or pig farmers, for preliminary ASF diagnosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The spread of the African swine fever virus (ASFV) among infected pigs and wild boars, is currently one of the most important facets of virus transmission in eastern Europe. Cross-priming amplification (CPA) has been developed, for fast and direct development of genetic ASFV material in the blood and sera of infected pigs and wild boars. It has been shown that CPA is a rapid, sensitive and specific isothermal method for the detection of ASFV DNA, in directly collected blood or sera from pigs and wild boars.

Development of cross-priming amplification assays for rapid and sensitive detection of Aeromonas hydrophila

Aeromonas hydrophila has been increasingly implicated as the aetiologic agent of various human diseases. Therefore, reliable laboratory detection and identification of this bacterium has become clinically and epidemiologically desirable. We developed a nearly instrument-free, simple molecular method for rapid detection of Aer. hydrophila using a cross-priming amplification (CPA) assay with the desA gene as the target. The desA gene is crucial for the survival and growth of Aer. hydrophila under iron starvation. The results can be visualized as colour changes without opening the reaction tubes. No false-positive results were observed for the 33 non-Aer. hydrophila strains tested to evaluate assay specificity. The limit of detection for Aer. hydrophila was approximately 200 copies of desA per reaction (on reference plasmids) and 5 × 10(3)  CFU g(-1) Aer. hydrophila in simulated human stool, which is the same sensitivity as a qPCR assay. The performance of the CPA assay was also evaluated with 100 stool specimens from diarrhoea patients and 40 environmental water samples. In conclusion, the simplicity, cost-effectiveness and nearly instrument-free platform of the CPA assay make it practical for use in primary care facilities and smaller clinical laboratories.

SIGNIFICANCE AND IMPACT OF THE STUDY

Aeromonas hydrophila is a human pathogen that infects via exposed wounds or ingestion of contaminated water and food. In this study, a CPA-based PCR method was developed for specific, rapid, cost-effective detection of Aer. hydrophila, and the test results could be visualized without opening the reaction tubes. This is the first report on the application of the CPA method for the detection of Aer. hydrophila. This novel method could be practical for use in primary care facilities and smaller clinical laboratories.

Cross-priming amplification targeting the coagulase gene for rapid detection of coagulase-positive Staphylococci

AIMS

To develop and evaluate cross-priming amplification (CPA) combined with immuno-blotting for the detection of coagulase-positive Staphylococci including Staphylococcus aureus.

METHODS AND RESULTS

Twenty-four sets of cross and detection primers were designed according to four sequences of coagulase gene in Staph. aureus. The most specific primer pair was screened out for the next amplification and interaction. The specificity was evaluated in a total of 53 species of Staph. aureus and non-Staph. aureus. Two red lines indicating positive were always observed on the BioHelix Express strip for 12 subspecies of Staph. aureus. In contrast, only one signal line showing negative results was detected in all of non-Staph. aureus samples. The limit of detection (LOD) of CPA was 3·6 ± 2·7 fg for the genomic DNA, which is about 100 and 10 times sensitive than those of PCR and loop-mediated isothermal amplification respectively. For the pure culture of Staph. aureus and milk powders, the LODs of CPA were about 1·34 CFU per reaction and 5·2 ± 3·7 CFU per 100 g of milk powder respectively. The CPA method was also successfully applied to evaluate the contamination of Staph. aureus in 318 samples of daily food.

CONCLUSIONS

CPA is a very sensitive and rapid method to detect Staph. aureus by simple laboratory instrument.

SIGNIFICANCE AND IMPACT OF THE STUDY

It is the first report on the application of the CPA with immuno-blotting for detection of coagulase-positive Staphylococci including Staph. aureus.

The development and evaluation of cross-priming amplification for the detection of avian reovirus

AIMS

The aim of this study was to develop and evaluate cross-priming amplification (CPA) for the detection of avian reovirus (ARV).

METHODS AND RESULTS

Five specific primers were designed, on the basis of the σNS sequence of the S1133 ARV strain. Incubation temperature and primer concentrations were determined. The optimal incubation conditions in a water bath were 61.3°C for 45 min. No reverse transcription stage was required. The results were recorded under UV light illumination as a bright, greenish fluorescence in positive samples, and through the lack of this in negative controls and samples. Additionally, the gel electrophoresis performed during analysis showed the presence of ladder-like patterns, formed by hairpin-like CPA products. The developed CPA method was compared to reverse-transcription polymerase chain reaction (RT-PCR) and real-time RT-PCR. Sensitivity of CPA was estimated using seven dilutions of standard S1133 strain and reached 0.05 log10 TCID50 ml(-1). RT-PCR sensitivity reached 2.5 log10 TCID50 ml(-1) and was 1000 times lower than for CPA, whereas real-time RT-PCR sensitivity reached 1.5 log10 TCID50 ml(-1). Analysis of 32 RNAs extracted from field specimens showed the presence of an ARVσNS fragment in 4 (12.5%) samples. Interestingly, the positive samples originated from flocks affected by Marek's disease (MD) or fowl adenovirus (FadV). RT-PCR was unable to detect ARV, due to its lower sensitivity. However, the real-time RT-PCR that was conducted confirmed the CPA study.

CONCLUSIONS

CPA is a very sensitive and rapid method, which allows ARV detection using simple laboratory equipment.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report on the application of the CPA method for detection of ARV, using simple laboratory equipment.