Development and evaluation of multiplex real-time PCR for diagnosis of HSV-1, VZV, CMV, and Toxoplasma gondii in patients with infectious uveitis

A Chromatography Test Strip of Exonuclease III-Amplified Aptamer for Rapid Identification of Prorocentrum minimum

Recently, the scale and frequency of harmful algae blooms (HABs) have gradually increased, posing a serious threat to human health, marine ecosystems and economic development. For early warning, a method is required that can quickly detect and monitor microalgae. It is proposed to use aptamer targeted to Prorocentrum minimum, along with exonuclease III (Exo III), gold nanoparticles, target single-stranded DNA and hairpin structure probe to construct a new method, i.e. aptamer-lateral flow dipstick (LFD) based on Exo III-assisted signal amplification assay (ALBEA). The key conditions, including signal amplification and LFD detection, are optimized. Under the optimal conditions, the detection limit of ALBEA was 1.25 cells mL-1. The cross-reactivity test showed no positive result except for P. minimum, indicating that the method is highly specific. The anti-interference test confirmed that the technique was not affected by the presence of other microalgae. The tested results of P. minimum cultured under different nutrient conditions and different growth stages demonstrated that the method is not affected by the cell state. Furthermore, the test results of simulated natural water samples further validated the practicality of the ALBEA. In conclusion, the established ALBEA offers a sensitive, specific and user-friendly tool, which can be used for the rapid detection of P. minimum and also provides a reference for the detection of other microalgae.

Detection of Mycobacterium tuberculosis DNA in intraocular fluid of 11 suspected tuberculous uveitis patients by multiplex PCR

BACKGROUND

This study aims to detect Mycobacterium tuberculosis complex (MTBC) DNA in intraocular fluid from clinically suspected tuberculous uveitis patients using multiplex polymerase chain reaction (PCR) and investigate the diagnostic utility of multiplex PCR for tuberculous uveitis.

METHODS

Primers targeting three specific genes (MPB64, CYP141, and IS6110) within the MTBC genome were designed. Multiplex PCR was conducted using DNA from the H37Rv strain as well as DNA extracted from fluids of confirmed tuberculosis patients to assess primer specificity and method feasibility. Intraocular fluid samples were collected during the initial visit for multiplex PCR detection of MTBC DNA. The results of multiplex PCR tests were correlated with intraocular fluid findings and clinical profiles of patients clinically diagnosed with tuberculous uveitis who underwent standard antituberculosis therapy.

RESULTS

Multiplex PCR was employed to detect MTBC DNA in intraocular fluid samples from 15 patients clinically suspected of having tuberculous uveitis, with no amplification bands observed in the DNA lanes for the three target genes. T-cell spot test (T-SPOT) results were positive in 11 patients (100%), while purified protein derivative (PPD) tests were positive in 5 patients (45.5%). Abnormal chest CT findings were noted in 4 patients (36.4%), including one case of active pulmonary tuberculosis and three cases of inactive pulmonary tuberculosis. Retinal vasculitis was observed in 6 eyes (46.2%), panuveitis in 5 eyes (38.5%), and intermediate uveitis in 2 eyes (15.4%). The average duration of antituberculosis therapy administered to the 11 patients was 7.1 months (range: 6-10 months). The medium LogMAR Best Corrected Visual Acuity (BCVA) significantly improved at the last follow-up (Z=-2.371, P = 0.018).

CONCLUSIONS

Standard antituberculosis therapy demonstrated effectiveness in treating 11 patients clinically suspected of having tuberculous uveitis despite the absence of detectable MTBC DNA in intraocular fluid via multiplex PCR. Further investigation is warranted to elucidate the role of PCR in diagnosing ocular tuberculosis among Chinese individuals.

Diagnostic and therapeutic results of aqueous real-time polymerase chain reaction in infectious uveitis

OBJECTIVE

This study was aimed primarily at describing the results of aqueous real-time polymerase chain reaction (RT-PCR) and reporting the rate of therapeutic modifications directly attributable to this procedure (profitability). Our secondary outcome was to compare demographic and clinical characteristics between patients with RT-PCR positivity and those with RT-PCR negative results.

DESIGN

Retrospective observational study conducted at the Uveitis Service of San Raffaele Hospital (Milan, Italy) between November 2016 and July 2022.

PARTICIPANTS

Patients with infectious uveitis suspect (anterior, intermediate, posterior uveitis, or panuveitis).

METHODS

Patients with suspected infectious uveitis underwent aqueous RT-PCR for detection of herpes simplex 1 (HSV-1), herpes simplex 2 (HSV-2), varicella zoster virus (VZV), cytomegalovirus (CMV), and Toxoplasma gondii.

RESULTS

Sixty-five eyes of 61 patients (60 ±16 years of age; 54% males) were included. Aqueous RT-PCR tested positive in 58% and negative in 42% of patients. CMV and HSV-1 were the most frequently detected pathogens. RT-PCR confirmed clinical suspicion in 38% of patients and altered the presumed etiologic diagnosis and treatment in 20% of patients. Profitability was associated with CMV positivity. HSV-1 positivity was related to iris atrophy. CMV positivity was correlated with keratic precipitates. Vitritis and retinitis were related to VZV, CMV, and T. gondii detection. Synechiae, retinitis, and neuritis were related to positive tests regardless of the pathogen investigated. Early complications related to paracentesis were rarely reported.

CONCLUSION

Aqueous RT-PCR was a safe semi-invasive tool to confirm a presumptive diagnosis and to change initial suspicion in ambiguous cases of herpetic uveitis. Thus aqueous RT-PCR may alter therapeutic management.

Congenital Toxoplasmosis Diagnosis: Current Approaches and New Insights

PURPOSE

The aim of this study is to describe and discuss current disadvantages in congenital toxoplasmosis (CT) diagnosis, and what can be improved or changed through new perspectives and technological advances.

METHODS

We used Pubmed, Cochrane, and EBSCO databases to research publications from 10 years to date describing current diagnostic methods for CT. The keywords used for this Mini-Review were Toxoplasma gondii, congenital toxoplasmosis, diagnosis, and prospects using Boolean operators such as AND, OR, identifying scientific publications highlighting the importance of implementing new diagnostic methods.

RESULTS

Current diagnosis methods have several disadvantages, i.e., time-consuming, low sensitivity or specificity, and non-cost effective, that bring up the necessity of improving or developing new approaches. Recombinant proteins can help improve specificity by generating tests that use circulating strains in a specific geographical region, SAG1 and BAG1, as they are expressed during a particular stage of the disease (acute or chronic, respectively), for its use in serological diagnoses, such as capture ELISA and immunochromatography. Point of Care (POC) tests are methods performed at the patient care site, which leads to rapid patient treatment; despite the advantages, several improvements and perspectives are necessary to be implemented globally.

CONCLUSIONS

Although already established diagnosis methods for CT may be sufficient in some regions, there is still a persistent demand to develop tests with higher throughput, cost, and time reduction in developing countries, where prevalence is high. New approaches in CT diagnosis, such as recombinant proteins, capture ELISA, immunochromatography, and POC tests methods, can increase performance in terms of specificity and sensitivity simplifying diagnostic tests' requirements.

An All-in-One Highly Multiplexed Diagnostic Assay for Rapid, Sensitive, and Comprehensive Detection of Intraocular Pathogens

PURPOSE

Intraocular infections are sight-threatening conditions that can lead to vision loss. Rapid identification of the etiologies plays a key role in early initiation of effective therapy to save vision. However, current diagnostic modalities are time consuming and lack sensitivity and inclusiveness. We present here a newly developed comprehensive ocular panel designed to improve diagnostic yields and provide a tool for rapid and sensitive pathogen detection.

DESIGN

Experimental laboratory investigation.

METHODS

A panel containing 46 pathogens and 2 resistance/virulence markers that are commonly detected in intraocular infections was developed. Genomic targets were scrutinized for stretches predicted to be specific for a particular species while being conserved across different strains. A set of primers for sample enrichment, and two 50mer NanoString compatible probes were then designed for each target. Probe-target hybrids were detected and quantified using the NanoString nCounter SPRINT Profiler. Diagnostic feasibility was assessed in a pilot clinical study testing samples from infectious retinitis (n = 15) and endophthalmitis (n = 12) patients, for which the etiologies were confirmed by polymerase chain reaction (PCR) or culture.

RESULTS

Analytical studies demonstrated highly sensitive detection of a broad spectrum of pathogens, including bacteria, viruses, and parasites, with limits of detection being as low as 2.5 femtograms per reaction. We also found excellent target specificity, with minimal cross-reactivity detected. The custom-designed NanoString ocular panel correctly identified the causative agent from all clinical specimens positive for a variety of pathogens.

CONCLUSION

This highly multiplexed panel for pathogen detection offers a sensitive, comprehensive, and uniform assay run directly on ocular fluids that could significantly improve diagnostics of sight-threatening intraocular infections.

Polymerase chain reaction test for diagnosis of infectious uveitis

BACKGROUND

To study the clinical utility of broad-range real-time Polymerase Chain Reaction (PCR) assay in patients suspected for infectious uveitis and to analyze the clinical relevance.

METHODS

Medical records of patients with uveitis were assessed in whom PCR analysis of intraocular fluids was performed between January 2018 and February 2021. Intraocular samples were investigated for cytomegalovirus (CMV), Epstein-Barr virus (EBV), varicella zoster virus (VZV), herpes simplex viruses type 1 and 2 (HSV_1,2), human T-lymphotropic virus type 1 (HTLV-1), Toxoplasma gondii and also for bacterial 16 S and fungal 18 S/28S ribosomal DNA (rDNA).

RESULTS

Aqueous paracentesis and vitreous sampling was done for 151 (81.2%) and 35 (18.8%) patients, respectively. Most of the patients had panuveitis (61.3%). PCR results were positive in 69 out of 186 patients (37%) according to the following order: CMV (18 cases), VZV (18 cases), fungal 18s/28s rDNA (17 cases), HSV (9 cases), bacterial 16s rDNA (3 cases), HTLV-1 (2 cases), and Toxoplasma gondii (2 cases). PCR positivity rate was 5.8% in patients with undifferentiated panuveitis. EBV was not detected at all. Initial treatment was changed in 38 patients (20%) based on PCR results. The overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of PCR test for aqueous samples was 82%, 91%, 96%, and 87%, respectively. No significant adverse effect related to sampling was reported.

CONCLUSION

PCR analysis of intraocular fluids in patients with suspected infectious uveitis plays an important role in confirming diagnosis or changing treatment with good predictive value. However, routine PCR test in patients with undifferentiated panuveitis in order to rule out possible underlying infectious etiology had low benefit.

An update on immunological and molecular tests and their impact in infectious uveitis

Early diagnosis of infectious uveitis can lead to prompt initiation of treatment to minimize vision-threatening sequelae. As various infectious etiologies of uveitis share similar clinical features, advancements in polymerase chain reaction (PCR) and metagenomic next-generation sequencing (MDS) have shown significant promise in improving diagnostic capabilities. Various techniques of PCR, including real-time, multiplex, comprehensive, and broad-range, have increased the armamentarium for infectious uveitis diagnosis. Additionally, metagenomic deep sequencing technology has provided a methodology to identify causative pathogens as well as novel etiologies of uveitis. This review discusses the diagnostic tools available for infectious uveitis and highlights the advantages and disadvantages of the techniques.

Improved Detection of Herpesviruses from Diluted Vitreous Specimens Using Hydrogel Particles

Infectious uveitis is a sight-threatening infection commonly caused by herpesviruses. Vitreous humor is often collected for molecular confirmation of the causative agent during vitrectomy and mixed in large volumes of buffered saline, diluting the pathogen load. Here, we explore affinity-capture hydrogel particles (Nanotrap®) to concentrate low abundant herpesviruses from diluted vitreous. Simulated samples were prepared using porcine vitreous spiked with HSV-1, HSV-2, VZV and CMV at 105 copies/mL. Pure undiluted samples were used to test capturing capability of three custom Nanotrap particles (red, white and blue) in a vitreous matrix. We found that all particles demonstrated affinity to the herpesviruses, with the Red Particles having both good capture capability and ease of handling for all herpesviruses. To mimic diluted vitrectomy specimens, simulated-infected vitreous were then serially diluted in 7 mL TE buffer. Diluted samples were subjected to an enrichment protocol using the Nanotrap Red particles. Sensitivity of pathogen detection by qPCR in diluted vitreous increased anywhere between 2.3 to 26.5 times compared to non-enriched specimens. This resulted in a 10-fold increase in the limit of detection for HSV-1, HSV-2 and VZV. These data demonstrated that Nanotrap particles can capture and concentrate HSV-1, HSV-2, VZV and CMV in a vitreous matrix.

A review of the current and emerging detection methods of marine harmful microalgae

In recent years, the scale and frequency of outbreaks of harmful algal blooms (HABs) have increased year by year due to the intensification of seawater eutrophication and global climate change. HABs have become a global marine ecological and environmental problem, which poses a serious threat to human health, marine ecological security, and economic development. The establishment of detection technology for harmful microalgae is fundamental to the early warning and prevention of HABs. To date, several detection methods have been developed for harmful microalgae, they however lack a unified classification standard. It is difficult to use a reasonable mix of all the developed methods to improve the accuracy of detection results. Here, all of the established detection methods for harmful microalgae were reviewed, including morphological structure-based detection methods, cytochrome-based detection techniques, immunoassays, and nucleic acid-based detection methods. The principles, advantages, and weaknesses of these methods were highlighted. Their application in the detection of harmful microalgae was summarized. Overall, different detection methods are suitable for different purposes. Further development of more accurate, cost-effective, efficient, and rapid detection technology is required in the future. This review is expected to provide a reference for research related to the monitoring of marine environment, early warning of HABs, and the molecular identification of harmful microalgae.

Usefulness of aqueous and vitreous humor analysis in infectious uveitis

OBJECTIVE

To evaluate the role of intraocular fluid analysis as a diagnostic aid for uveitis.

METHODS

Twenty-eight samples (27 patients including 3 HIV-infected patients) with active (n=24) or non-active (n=4) uveitis were submitted to aqueous (AH; n=12) or vitreous humor (VH) analysis (n=16). All samples were analyzed by quantitative PCR for herpes simplex virus (HSV), varicella zoster virus (VZV), cytomegalovirus (CMV), Epstein-Barr virus (EBV) and Toxoplasma gondii.

RESULTS

The positivity of the PCR in AH was 41.7% (5/12), with 50% (2/4) in immunocompetent and 67% (2/3) in HIV+ patients. The positivity of the PCR in VH was 31.2% (5/16), with 13% (1/8) in immunocompetent and 50% (4/8) in immunosuppressed HIV negative patients. The analysis was a determinant in the diagnostic definition in 58% of HA and 50% of VH.

CONCLUSION

Even in posterior uveitis, initial AH analysis may be helpful. A careful formulation of possible clinical diagnosis seems to increase the chance of intraocular sample analysis being meaningful.

Newborn Glaucoma: Do not Forget Infections

Intrauterine infections can affect various structures of the developing fetal eye. Rubella infection results in congenital cataracts, keratopathy, retinopathy and less commonly, glaucoma. Ophthalmic manifestations of intrauterine cytomegalovirus (CMV) infection have been reported to be chorioretinitis, optic nerve colobomas, and corneal opacities, but have not been implicated in congenital cataract or congenital glaucoma. Concurrent infection with both rubella and CMV virus has not been reported. We report concurrent rubella and CMV infection in a baby born with corneal opacification, severe congenital glaucoma, and congenital cataract. It is important to recognize these babies early and investigate for intrauterine infections rather than assume they are all primary congenital glaucoma. Involvement of the cornea, glaucoma, and cataract make management of these babies a major challenge requiring a multidisciplinary team approach.

Diagnostic vitrectomy: a case series in a single referral center

OBJECTIVE

To study the results and safety of diagnostic vitrectomy in patients with unknown etiology panuveitis.

METHODS

A retrospective descriptive observational study was carried out in which a total of 29 patients (37 eyes) were included, who underwent a vitreous biopsy due to acute intraocular inflammatory processes. In all, demographic and clinical data were collected. We studied the specific samples extraction methods and their diagnosic processing.

RESULTS

Of the 29 patients analyzed, 18 were men. Mean of age was 63.11 years old (standard deviation: 14.55). The most frequent initial symptom was visual acuity decrease, with mean initial visual acuity being 20/40, excluding 8 eyes that had vision lower than 20/200. 21 presented unilateral ocular involvement. Vitrectomy was performed in all of them obtaining a dry sample. Vitrectomy was performed in all of the patients obtaining a dry sample. Moreover, the following techniques were done: 5 retinal biopsies, obtaining 5 muestras diluidas, 1 subretinal abscess aspirate and 1 aqueous humor aspirate. The most frequent processing technique that was used was cytology in 25 eyes, followed by PCR (polymerase chain reaction) in 11 eyes and culture in 10 eyes. Diagnosis was achieved in 94.5% of patients. Main diagnosis found was lymphoma, followed by toxoplasmosis.

CONCLUSIONS

Diagnostic vitrectomy is very important in ophthalmic inflammation identification. Different techniques for obtaining and processing can be used.

Novel 2019-coronavirus on new year's Eve

An ongoing apocalyptic outbreak of a new virus causing pneumonia-like clusters in Wuhan city, China, has gleamed the world. The outbreak, confirmed on the New Year's Eve 2020, has known no boundaries since then. The number has surpassed that of Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS), and is uninterruptedly escalating. Being an RNA virus, it has a propensity to mutate due to the low proofreading capacity of RNA-dependent RNA polymerase. Step-wise mutations have led to the gradual spillover of virus and after crossing the inter-species interface, the virus has adapted itself for a stable human-to-human transmission. The disease caused by severe acute respiratory syndrome coronavirus (CoV)-2 (SARS-CoV-2) can prove deadlier if the so-called 'super-spreading events' emerge with time. Recent research has shown the maximum homology of 99% of SARS-CoV-2 to pangolins associated coronavirus, owing to which these can serve as potential intermediate host. India is responding swiftly to the emergency situation, and the whole of the country is under lockdown since 25 March 2020, to ensure social distancing. All the international flights are padlocked and the travellers are being screened at airports and seaports via thermal sensors, and quarantine for a period of 14 days is recommended. Three hundred and forty-five patients across the country tested positive with six fatalities as of 22 March 2020. No specific anti-CoV drugs are currently available. Patients are being treated with protease drugs are inhibitors, remdesivir, chloroquine, angiotensin-converting enzyme 2 inhibitors, ivermectin, sarilumab and tocilizumab, though none of these is Food and Drug Administration approved and are undergoing trials. Preventive measures such as social distancing, quarantine, cough etiquettes, proper hand washing, cleaning and decontaminating the surfaces are the mainstay for curbing the transmission of this virus. The present review highlights the update of novel SARS-CoV-2 in context to the Indian scenario.

Institutional outbreak of varicella in a child welfare institute in Chandigarh, North India

Introduction

Varicella outbreaks are known to occur in developing nations as vaccine coverage is still low.

Material and Methods

In the present study, an institutional outbreak from Chandigarh, India, is reported wherein the utility of non-invasive samples such as saliva and urine was studied for the molecular diagnosis of varicella by conventional polymerase chain reaction (PCR), real-time PCR and real-time loop-mediated isothermal amplification (real-time LAMP).

Results

The results of the present study showed that saliva and urine samples can be used for outbreak investigation of varicella compared to varicella-zoster virus DNA in vesicular swab samples with reasonable sensitivity.

Conclusion

Thus, molecular techniques may be useful in the early identification of the outbreak and timely isolation, and the treatment of cases can further prevent its spread.

Real-Time Multiplex PCR Analysis in Infectious Uveitis

Introduction: Infectious uveitis is a serious inflammatory condition that often causes grave ocular morbidity including permanent vision loss and damage to the structures of the eye. The most common causes of infectious uveitis include herpesviruses and Toxoplasma gondii. Traditionally, these infections have been identified and differentiated based on characteristic clinical examination findings; however, there is often overlap between these presentations and the unique cause of a given patient's infection is not always clear. Therefore, a reliable and fast method for definitively diagnosing infectious uveitis would be helpful and potentially sight-saving. Several groups have recently found experimental success with real-time multiplex polymerase chain reaction (PCR) techniques. Methods: A comprehensive review of the literature was undertaken to further understand the current state of real-time multiplex PCR and its clinical use. Search terms including "real time multiplex PCR", "infectious uveitis", and "uveitis diagnosis" were used. Appropriate English-language articles were included in this review. Results: Publications from four main groups (two from the United States, one from Japan, and one from India) citing success with real-time multiplex PCR were compared and contrasted. All four groups used the same technique to develop a highly sensitive and specific multiplex PCR analysis and found that their tests maintained high sensitivity and specificity during validation testing. These tests confirmed clinical suspicions in the majority of cases of infectious uveitis, but there were also cases of clinical misdiagnosis that were corrected based on molecular pathogen detection. These patients were then initiated on appropriate antimicrobial therapy with subsequent clinical improvement. Discussion: Real-time multiplex PCR is a highly sensitive and specific laboratory assay that allows for rapid and reliable molecular diagnosis of causative agents in infectious uveitis. This in turn facilitates swift initiation of effective therapy and prevents long-term ocular damage and vision loss.

Digital droplet polymerase chain reaction analysis of common viruses in the aqueous humour of patients with Posner-Schlossman syndrome in Chinese population

BACKGROUND

To compare the detection results consistency of quantitative polymerase chain reaction (qPCR) and digital droplet polymerase chain reaction (ddPCR), and determine the value of ddPCR for viral detection in the aqueous humour.

METHODS

A total of 130 aqueous humour samples were collected, including 60 patients with Posner-Schlossman syndrome (PSS) in case group and 70 elderly patients with senile cataract in control group. The target nucleic acid fragments of human cytomegalovirus (HCMV), herpes simplex virus, Epstein-Barr virus and varicella zoster virus in aqueous humour were analysed by qPCR and ddPCR, respectively, for the diagnosis and curative effect monitoring of pathogen-induced PSS. Samples with inconsistent results were verified by next-generation sequencing.

RESULTS

There were 27 and 20 HCMV-positive cases detected in the case group by ddPCR and qPCR, respectively. ddPCR increased the sensitivity for the HCMV virus detection from 400 to 100 copies/mL. No other pathogens were found in this study. The results of ddPCR were consistent with that of next generation sequencing. The mean (SD) of Lg (HCMV copies/mL) detected by ddPCR and qPCR were 1.66 (1.92) and 1.10 (1.61), respectively (P < 0.001). Compared with qPCR, results of ddPCR showed better consistency with validity of clinical treatment. All patients with ddPCR-positive results had good validity on antiviral therapy, exhibiting anterior chamber inflammation remission, resolution of corneal oedema and good IOP control within 1 month.

CONCLUSIONS

HCMV was the leading cause of pathogen-induced PSS in the Chinese population. ddPCR was a promising tool for early detection, accurate diagnosis and therapeutic validity monitoring of pathogen-induced PSS. The high sensitivity of ddPCR could avoid repeated anterior chamber tap.

Rapid Detection and Identification of Uveitis Pathogens by Qualitative Multiplex Real-Time PCR

Purpose

Infectious uveitis is a serious sight-threatening infection commonly caused by herpesviruses and Toxoplasma gondii. Etiologic diagnosis based on the clinical evaluation is often challenging. We developed and validated a multiplex real-time PCR assay coupled with high-resolution melting (HRM) for rapid detection and identification of herpes simplex viruses 1 and 2 (HSV-1 and HSV-2), varicella-zoster virus (VZV), cytomegalovirus (CMV), and T. gondii.

Methods

The assay was designed to target pathogen genome regions that yield products with distinct melting temperatures. Analytical specificity, sensitivity, and precision of HRM identification were determined. Clinical validation was performed by testing 108 intraocular fluids collected from eyes suffering with infectious uveitis (n = 30) and controls (n = 78).

Results

A nonoverlapping high-precision profile for each pathogen was generated following HRM (coefficient of variation 0%). The assay was highly sensitive, with a limit of detection of 20 genome copies for herpesviruses and 200 genome copies for T. gondii. The intra- and interassay variability of cycle threshold (Ct) measurement was ≤4% and ≤6%, respectively. Thirteen intraocular specimens collected from suspected cases of infectious uveitis were positive (mean Ct values varied from 19.4 to 27.7). Melting profiles of positive cases were consistent with HSV-2 (n = 5), VZV (n = 5), CMV (n = 2), and T. gondii (n = 1). Amplicon identities were confirmed by sequencing. Control intraocular samples from patients without a clinical diagnosis of infectious uveitis were all negative.

Conclusions

This assay allows rapid, sensitive, and reliable detection and identification of the most common known causes of infectious uveitis, making early pathogen information-based intervention possible.