A 13-year retrospective review of polymerase chain reaction testing for infectious agents from ocular samples

Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study

PURPOSE

We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS).

METHODS

In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS.

RESULTS

All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal.

CONCLUSION

Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.

Apollo Rising: Acute Conjunctivitis Outbreak in India, 2022

Purpose

To identify pathogens associated with the 2022 conjunctivitis outbreak in Tamil Nadu, India.

Methods

This prospective study was conducted in November of 2022. Patients with presumed acute infectious conjunctivitis presenting to the Aravind Eye Clinic in Madurai, India were eligible. Anterior nares and conjunctival samples from participants were obtained and processed for metagenomic RNA deep sequencing (RNA-seq).

Results

Samples from 29 patients were sequenced. A pathogen was identified in 28/29 (97%) patients. Coxsackievirus A24v, a highly infectious RNA virus, was the predominant pathogen and detected in 23/29 patients. Human adenovirus D (HAdV-D), a DNA virus commonly associated with conjunctivitis outbreaks, was detected in the remaining patients (5/29). Hemorrhagic conjunctiva was documented in both HAdV-D and coxsackievirus A24v affected patients but was not the predominant clinical presentation. Phylogenetic analysis of coxsackievirus A24v revealed a recent divergence from the 2015 outbreak.

Conclusions

Coxsackievirus A24v and HAdV-D were co-circulating during the 2022 conjunctivitis outbreak in Tamil Nadu, India. Clinical findings were similar between patients with HAD-V and coxsackievirus A24v associated conjunctivitis. As high-throughput technologies become more readily accessible and cost-effective, unbiased pathogen surveillance may prove useful for outbreak surveillance and control.

Case Series: Unbiased Deep Sequencing Analysis of Acute Infectious Conjunctivitis in an Ambulatory Eye Center in Berkeley, California

SIGNIFICANCE

Acute infectious conjunctivitis poses significant challenges to eye care providers. It can be highly transmissible, and because etiology is often presumed, correct treatment and management can be difficult. This study uses unbiased deep sequencing to identify causative pathogens of infectious conjunctivitis, potentially allowing for improved approaches to diagnosis and management.

PURPOSES

This study aimed to identify associated pathogens of acute infectious conjunctivitis in a single ambulatory eye care center.

CASE REPORTS

This study included patients who presented to the University of California Berkeley eye center with signs and symptoms suggestive of infectious conjunctivitis. From December 2021 to July 2021, samples were collected from seven subjects (ages ranging from 18 to 38). Deep sequencing identified associated pathogens in five of seven samples, including human adenovirus D, Haemophilus influenzae , Chlamydia trachomatis , and human coronavirus 229E.

CONCLUSIONS

Unbiased deep sequencing identified some unexpected pathogens in subjects with acute infectious conjunctivitis. Human adenovirus D was recovered from only one patient in this series. Although all samples were obtained during the COVID-19 pandemic, only one case of human coronavirus 229E and no SARS-CoV-2 were identified.

Variability and cost implications of three generations of the Roche LightCycler® 480

Real time PCR has become a dominant method for the highly sensitive detection of pathogens in clinical material. Real time PCR can generate a fluorescence signal by using fluorescence labelled probes, allowing us to detect and semi quantify the amount of amplified DNA. Here we test the variability of the detection system and cost implications of three different versions of the LightCycler® 480 (LC480), focusing on the intensity of fluorescence and Cq in monoplex and multiplex rtPCRs.

For gastro-intestinal pathogens there was no correlation between the intensity of fluorescence and the Cq value in the different LC480 types. For probes with the dyes FAM^TM, HEX^TM, Cy5 and Red610 a higher fluorescence intensity was seen in LC480 type II and III compared to LC480 type I. After lowering the probe concentration for the Cy5 dye three-fold (from 0.3μM to 0.1μM) the Cq value remains the same and the intensity of fluorescence decreases. For the LC480 type II and III the difference in fluorescence intensity was much more extreme. The concentration of the different labelled probes can be lowered at least six-fold in LC480 type II and III cyclers while maintaining a fluorescence intensity as high as achieved in the LC480 type I with undiluted probe. In conclusion, the strength of the fluorescence signal of the LightCycler® 480 type III is superior to that of LightCycler® 480 types I and II, allowing the use of lower probe concentrations for all dyes, particularly for the dyes Red610 and Cy5. This results in a two thirds reduction in PCR probe costs. Switching to these newer machines for real-time PCR can reduce dye labelled probe consumption and thus reduce costs significantly.

Progressive outer retinal necrosis in an immunocompromised patient presenting with bilateral retrobulbar optic neuritis

Background: Progressive outer retinal necrosis (PORN) is a necrotizing chorioretinopathy caused by herpes simplex virus, varicella-zoster virus, or cytomegalovirus.

Objective: To describe the clinical morphology of PORN presenting with asymmetrical isolated bilateral retrobulbar optic neuropathy.

Method: The medical records of a 45-year-old human immunodeficiency virus infected patient presenting with bilateral visual loss at King Chulalongkorn Memorial Hospital were reviewed with respect for the privacy of patient.

Result: Gradual visual loss progressed to no light perception in the right eye and 20/200 in the left eye within 1 month. The patient was initially diagnosed with retrobulbar optic neuritis in both eyes. The investigations included MRI, vitreous tapping, lumbar puncture, and serological testing. MRI elicited enhancement around both optic nerves, which suggested optic neuritis. Thereafter, multifocal areas of retinal necrosis developed with rapid progression and additional cutaneous zoster lesions were established. These findings led to a diagnosis of PORN. The patient was promptly treated with intravenous ganciclovir, anti-retroviral therapy, and vitrectomy with endophotocoagulation and silicone injection. Unfortunately, his visual prognosis in the left eye was still poor

Conclusion: PORN was uncommonly present with bilateral isolated optic neuropathy before retinal lesions developed. Retrobulbar optic neuropathy from herpetic infection in immunocompromised patients should be considered despite a normal fundus at initial presentation. Early diagnosis and prompt intervention may preserve vision. This case demonstrates the importance of careful physical examination and follow up of retinal lesions.

Sensitivity of the Standard Chlamydia trachomatis Culture Method Is Improved After One Additional In Vitro Passage

BACKGROUND

Chlamydia trachomatis causes the most common bacterial sexually transmitted infection (STI) worldwide. Although highly sensitive nucleic acid amplification tests (NAATs) are used to routinely diagnose chlamydial infection, C. trachomatis isolation by cell culture is still preferred for legal cases and epidemiological studies because of its high specificity; however, the sensitivity of traditional two-passage diagnostic cultures is significantly lower than that of NAATs. Therefore, we sought to analyze if additional in vitro passaging of clinical samples would improve detection sensitivity of C. trachomatis.

METHODS

Clinical swabs (n = 428) were collected from Tianjin Medical University General Hospital, grown in McCoy cells for up to five passages, and analyzed for the presence of inclusions by iodine staining. Results were confirmed by routine PCR-based methods.

RESULTS

Viable C. trachomatis organisms were detected in 91 (21.26%) swabs with the traditional two-passage protocol, which increased to 145 (33.88%) and 149 (34.81%) following three and four passages, respectively. Thus, the standard protocol yielded a false-negative rate of nearly 39%. Subsequent PCR-based diagnostics revealed a concordance rate of 80.98% between these two methods without any false negatives.

CONCLUSION

The results of this study support the use of a three-passage Chlamydia culture procedure to increase the detection sensitivity of this method.

Designing novel and simple competitive internal amplification control for reliable PCR diagnosis of herpes simplex virus

Background:

PCR is a molecular technique for herpes simplex virus (HSV) detection that can cause life-threatening infections such as encephalitis and keratitis. However, the main issues, false-negative results causing by PCR inhibitors, of this technique that reduce PCR efficiency. To overcome this problem, a competitive internal amplification control (IAC) was constructed for conventional PCR using the PCR-cloning technique.

Objectives:

The purpose of this study is the design of competitive IAC for PCR diagnosis of HSV, which in fact is the main cause of keratitis and viral encephalitis in developed countries.

Materials and Methods:

Composite primers for PCR amplification of Leishmania major kDNA (kinetoplast DNA) were designed and optimized to use as IAC-HSV. IAC-HSV amplified in a non-stringent condition, ligated into pTZ57R plasmid vector, and transformed into Escherichia coli JM207 and then cloned. Resulting IAC was used for 105 CSF and 78 keratitis specimens.

Results:

PCR amplicons for HSV and IAC-HSV were 454-bp and 662-bp, respectively. Detection limit of IAC was determined as 1000 plasmids per PCR reaction. IAC sensitivity for HSV detection was determined as 1000 plasmids per PCR reaction. IAC sensitivity for HSV detection was 500 copies/mL of HSV DNA. Among all specimens, 7 inhibited specimens were detected.

Conclusions:

Indeed, using other DNA as an IAC is expected to detect false-negative results and amplification of the DNA is the key tool to examine the accuracy of amplification and detection steps. This internal amplification control is applicable for early reliable diagnosis of HSV in different loads of virus in different specimens.

Role of molecular diagnostics in ocular microbiology

Although microbial culture remains the gold standard for diagnosis of many ocular infections, the technique is limited by low yield, inability to detect certain organisms, and potentially long delays to results. DNA-based molecular diagnostic techniques use detection of specific nucleic acid sequences as evidence for presence of suspected pathogens. The polymerase chain reaction (PCR) is a powerful molecular biology technique that allows for detection of fewer than 10 copies of pathogen genome. Recent technical advances in PCR have permitted quantitation of pathogen load using quantitative PCR (qPCR), and have permitted multiplexing of primer sets. Use of pan-bacterial and pan-fungal primers for ribosomal DNA sequences has allowed diagnosis of bacterial and fungal infections using molecular techniques. In this review, we highlight recent advances in the application of PCR to the diagnosis of anterior segment and posterior segment ocular infectious diseases.

[Delayed course of Acanthamoeba keratitis]

A 35-year-old male presented with corneal ulceration on the left eye with a history of treatment over several months. At the first visit in our department we saw an elliptically shaped ulcerative stromal keratitis with circular peripheral neovascularization. There was organized hypopyon with hyphemia. The best corrected visual acuity (BCVA) was light perception. The patient had used contact lenses for many years. Under the suspicion of herpetic keratitis due to a positive "dendrite" the patient had undergone antiviral therapy for 6 months in a different department. Our diagnosis was Acanthamoeba keratitis. We performed penetrating excimer laser keratoplasty-à-chaud (8.0 × 7.0 mm/8.1 × 7.1 mm) with simultaneous cryotherapy of the mid-peripheral cornea. The topical therapy was polyhexamethylene biguanide, propamidine isoethionate, neomycin and steroids in intervals. A repeat penetrating excimer laser keratoplasty (8.5 × 7.5 mm/8.6 × 7.6 mm) with simultaneous amniotic membrane patch and lateral tarsorrhaphy was performed 2 months later due to melting of the graft with positive Seidel test. After successful surgery of the mature cataract the BCVA was 20/25. In a patient with a positive contact lens history acanthamoeba keratitis should always be considered as a differential diagnosis to herpes simplex keratitis in the early course of the disease.

What is causing the corneal ulcer? Management strategies for unresponsive corneal ulceration

Infectious keratitis represents a significant cause of ocular morbidity in the United States. The work-up and treatment of presumed infectious keratitis (PIK) has changed in the past two decades. The development of newer topical antibiotics has enabled broad-spectrum antibiotic coverage with good tissue penetration. The majority of PIK cases respond well to this strategy. The small numbers of cases that do not respond to the treatment are the cases that offer a diagnostic and therapeutic challenge. This review will describe different algorithms that can be followed for the successful management of patients with difficult or progressive PIK. These algorithms are based on scientific work and on our empirical clinical experience. The review will also present three different clinical cases of PIK that were managed according to the algorithms presented in this review.