Development of a novel polymerase spiral reaction (PSR) assay for rapid and visual detection of Clostridium perfringens in meat

Establishment and application of a rapid visual detection method for Clostridium perfringens in chicken products based on helical loop-mediated isothermal amplification (HAMP)

Clostridium perfringens is a significant foodborne pathogen in chicken products. Rapid on-site detection of C. perfringens is crucial for mitigating the incidence of foodborne illnesses by enabling the prompt identification and recall of contaminated food products. A rapid and visual detection method for C. perfringens in chicken products was developed using helical loop-mediated isothermal amplification (HAMP) technology combined with SYBR Green I fluorescent staining. The reaction temperature, time, and reagent concentrations of HAMP technique were optimized firstly. HAMP displayed high specificity, effectively distinguishing C. perfringens from 18 other common pathogens in chicken products. HAMP also exhibited higher sensitivity (78 fg/µL) compared to endpoint PCR and real-time quantitative PCR (qPCR). The detection limit of HAMP for non-enriched samples was 6.8 × 102 CFU/g, which improved to 68 and 6.8 CFU/g after 5 and 10 h of enrichment, respectively. The detection limit of HAMP was lower by 2 and 1 orders of magnitude compared to endpoint PCR and qPCR under the same conditions. On-site testing of commercially available ready-to-eat chicken products showed that HAMP had the same results as traditional culture methods, indicating the significant potential of HAMP for on-site detection of C. perfringens. This method offered a rapid, accurate, and visual means of detecting C. perfringens in chicken products, making it well-suited for on-site testing. This research represented the first use of the HAMP method for detecting C. perfringens.

Polymerase Spiral Reaction (PSR) as a point-of-care diagnostic assay: A systematic review

INTRODUCTION

The current systematic review aimed to collect and analyze the comprehensive evidence regarding Polymerase Spiral Reaction (PSR) and to estimate its diagnostic performance and usefulness as a point-of-care (PoC) assay.

METHODS

Literature was retrieved systematically from 2015 to 2023 from PubMed and Scopus. Studies were screened and selected against pre-determined inclusion and exclusion criteria. Quality assessment and risk of bias were critiqued using QUADAS-2. A systematic, qualitative narrative synthesis was employed to synthesize the data.

RESULTS

11 studies were selected for the systematic review, testing diseases in humans utilizing PSR. Only 2 studies clinically validated the test with a sample size > 150. 5 studies were of poor quality; 3 studies were of moderate quality and 3 studies were deemed to be of high quality. 3 studies quantified the diagnostic throughput and reported clinical sensitivity and specificity of PSR approaching to be > 92% and ~ 100%, respectively.

CONCLUSION

Polymerase spiral reaction promises to be an optimistic isothermal assay; however, a huge research gap can be attributed to the lack of statistical and clinical evidence to validate the assay. Adequate research, focused on optimization, coupled with statistical and clinical validation, can help in estimating its true diagnostic potential and applicability.

REGISTRATION AND PROTOCOL

A detailed protocol of this review is registered and available in Prospero (registration number CRD42023406265).

Evaluation of reverse transcriptase-polymerase spiral reaction assay for rapid and sensitive detection of severe acute respiratory syndrome coronavirus 2

BACKGROUND AND AIM

Existing real-time reverse transcriptase PCR (RT-qPCR) has certain limitations for the point-of-care detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since it requires sophisticated instruments, reagents and skilled laboratory personnel. In this study, we evaluated an assay termed the reverse transcriptase-polymerase spiral reaction (RT-PSR) for rapid and visual detection of SARS-CoV-2.

METHODS

The RT-PSR assay was optimized using RdRp gene and evaluated for the detection of SARS-CoV-2. The time of 60min and a temperature of 63°C was optimized for targeting the RNA-dependent RNA polymerase gene of SARS-CoV-2. The sensitivity of the assay was evaluated by diluting the in-vitro transcribed RNA, which amplifies as low as ten copies.

RESULTS

The specific primers designed for this assay showed 100% specificity and did not react when tested with other lung infection-causing viruses and bacteria. The optimized assay was validated with 190 clinical samples in two phases, using automated RTPCR based TrueNat test, and the results were comparable.

CONCLUSIONS

The RT-PSR assay can be considered for rapid and sensitive detection of SARS-CoV-2, particularly in resource-limited settings. To our knowledge, there is as yet no RT-PSR-based kit developed for SARS-CoV-2.

Rapid detection of Actinobacillus pleuropneumoniae targeting the apxIVA gene for diagnosis of contagious porcine pleuropneumonia in pigs by Polymerase Spiral Reaction

Actinobacillus pleuropneumoniae is the primary etiological agent of contagious porcine pleuropneumonia associated with serious economic impact on pig husbandry worldwide. Diagnosis of the disease by existing techniques including isolation and identification bacteria followed by serotyping, serological techniques, conventional PCR, real-time PCR and LAMP assays are cumbersome, time consuming, costly and not suitable for rapid field application. A novel isothermal polymerase chain reaction (PSR) technique is standardized for all the reagents, incubation time and incubation temperature against A. pleuropneumoniae. Sensitivity of the assay was determined against various dilutions of purified DNA and total bacterial count. Specificity of the assay was determined against 11 closely related bacterial isolates. The relative sensitivity and specificity was compared with bacterial isolation, conventional PCR and real-time PCR assays. The PSR assay for specific detection was standardized at 64^o C for 30 minutes incubation in a water bath. The result was visible by the naked eye after centrifugation of the reaction mixture or after incorporation of SYBR Green dye as yellow-green fluorescence. The technique was found to be 100% specific and equally sensitive with real-time PCR and 10 times more sensitive than conventional PCR. The PSR assay could be applicable in detection of the organisms in porcine nasal swabs spiked with A. pleuropneumoniae. This is the first ever report on development of PSR for specific detection of A. pleuropneumoniae and can be applied for early diagnosis at field level.

Development of a Polymerase Spiral Reaction-Based Isothermal Assay for Rapid Identification of Thrips palmi

Thrips cause considerable economic losses to a wide range of food, feed, and forest crops. They also transmit several plant viruses. Being cryptic, it is often difficult to distinguish thrips species in crops and large consignments by conventional methods. Melon thrips (Thrips palmi Karny, Thysanoptera: Thripidae) is an invasive insect pest of vegetables, legumes, and ornamentals besides being vector to several viruses. It poses a threat to domestic and international plant biosecurity and can invade and establish in new areas. Here, we report a polymerase spiral reaction (PSR)-based isothermal assay for rapid, sensitive, specific, low-cost, and on-site detection of T. palmi. To the best of our knowledge, this is the first application of PSR in the identification of any insect species. A primer pair designed based on 3′-polymorphism of mtCOIII region can specifically identify T. palmi without any cross-reactivity with predominant thrips species. The assay uses crude lysate of a single thrips saving time and reagents involved in nucleic acid extraction. The presence of T. palmi is visualized by the appearance of bright fluorescence under ultraviolet light or a change in reaction color thus avoiding gel electrophoresis steps. The entire process can be completed in 70 min on-site using only an ordinary water bath. The assay is sensitive to detecting as little as 50 attograms of T. palmi template. The assay was validated with known thrips specimens and found to be efficient in diagnosing T. palmi under natural conditions. The described method will be useful for non-expert personnel to detect an early infestation, accidental introduction to a new area, restrict the spread of diseases and formulate appropriate management strategies.