Specific detection of fungal pathogens by 18S rRNA gene PCR in microbial keratitis

Clinical Evaluation of a Novel CRISPR-Cas12a-Based RID-MyC Assay for the Diagnosis of Fungal Endophthalmitis

OBJECTIVE

This study evaluated the RID-MyC (Rapid Identification of Mycoses using clustered regularly interspaced short palindromic repeats [CRISPR]) assay, a CRISPR/Cas12a-based diagnostic tool, for its efficacy in diagnosing fungal endophthalmitis (FE) compared with panfungal polymerase chain reaction (PCR) and culture methods.

DESIGN

A comparative cross-sectional study assessing the performance of the RID-MyC assay against established diagnostic modalities for FE.

SUBJECTS

The study included 133 intraocular samples from 117 patients with suspected microbial endophthalmitis.

METHODS

The study compared the sensitivity, specificity, positive predictive value, and negative predictive value of the RID-MyC assay against panfungal PCR and culture. The limit of detection for Aspergillus flavus and Candida albicans was determined for both RID-MyC and panfungal PCR across 3 different media: nuclease-free water, aqueous humor, and vitreous humor. Discrepancy analysis was conducted for discordant results, incorporating clinical outcomes and responses to antifungal treatment.

MAIN OUTCOME MEASURES

The study primarily assessed the sensitivity, specificity, positive predictive value, and negative predictive value for clinical samples. Time to diagnosis was also evaluated.

RESULTS

The RID-MyC assay demonstrated a sensitivity of 88.24% (95% confidence interval [CI], 63.56%-98.54%) and specificity of 93.1% (95% CI, 86.86%-96.98%), with positive predictive value and negative predictive value of 65.22% (95% CI, 48.45%-78.91%) and 98.18% (95% CI, 93.62%-99.50%), respectively. Discrepancy analysis enhanced sensitivity to 90.48% (95% CI, 69.62%-98.83%) and specificity to 96.43% (95% CI, 91.11%-99.02%). The RID-MyC assay was 10- to 1000-fold more sensitive than panfungal PCR in detecting A. flavus and C. albicans in intraocular specimens. The time to diagnosis with the RID-MyC assay was consistently <2 hours.

CONCLUSIONS

The RID-MyC assay may advance the rapid and precise diagnosis of FE, with possible relevance to other invasive fungal conditions.

FINANCIAL DISCLOSURE(S)

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Causative Agents of Fungal Keratitis in Northeastern Iran: A 3-Year Tertiary Care Hospital Study

Infectious keratitis is a significant ocular disease that, if left untreated, can lead to blindness. Fungi are among the causative agents that can result in severe symptoms. Keratitis infections are prevalent globally, with a higher incidence reported in tropical and subtropical regions. The current research focused on the molecular diagnosis of fungal keratitis and its prevalence over a 3-year period in northeastern Iran. The study involved the collection of 38 corneal scraping specimens from the Eye Specialized Hospital of Khatam in Mashhad, northeastern Iran. These specimens were cultured on Sabouraud dextrose agar, and the isolates were identified using DNA-based techniques. Among the patients studied (n = 38), 22 (58%) cases were caused by Aspergillus species (A. flavus, n = 17, A. fumigatus, n = 3; A. terreus, n = 1; A. tubingensis, n = 1), seven (18%) by Neocosmospora species (N. falciformis, n = 4; N. solani, n = 3), three (7%) by Candida albicans, two (5%) by Fusarium annulatum, and one case each (2%) by Penicillium chrysogenum, Cladosporium cladosporioides, and Cytospora sp. In addition, one case had a combined infection of A. flavus and P. glabrum. The results indicate a higher incidence of fungal keratitis in males, particularly in the age range of 40-60 years. Aspergillus sp., and specifically A. flavus, had the highest prevalence. Cladosporium cladosporioides is reported for the first time in this area as causal agent of keratitis. Additionally, this is the first report of keratitis likely caused by Cytospora species.

[Microbiological diagnosis of ocular surface infections aside from virology]

The ocular surface is a structure exposed to multiple stresses that can directly or indirectly lead to infectious contamination and compromise visual function. This significant risk justifies multidisciplinary care, often in an emergency context, bringing together ophthalmologists and microbiologists to optimize and guide microbiological testing on small volume samples and ensure the most appropriate treatment. Herein, we present the various steps leading to microbiological diagnosis, from pre-analytical requirements, sampling methods, transport conditions, and then to the analytical steps of pathogen identification. These are based on microscopic examination associated with culture techniques, pathogen identification using mass spectrometry and molecular biology approaches and finally, antimicrobial susceptibility testing. Molecular biology methods have become important for the diagnosis and detection of antibiotic resistance genes, improving the identification rate of microorganisms, reducing the time needed to obtain results, and thus improving therapeutic management. Nevertheless, direct microbiological examination and culture remain the gold standards in the diagnosis of many ocular infections.

Development and Clinical Evaluation of a CRISPR/Cas12a-Based Nucleic Acid Detection Platform for the Diagnosis of Keratomycoses

Objective

The objective of this study was to develop a rapid and accurate clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a-based molecular diagnostic assay (Rapid Identification of Mycoses using CRISPR, RID-MyC assay) to detect fungal nucleic acids and to compare it with existing conventional mycologic methods for the diagnosis of fungal keratitis (FK).

Design

This study was structured as a development and validation study focusing on the creation and assessment of the RID-MyC assay as a novel diagnostic modality for FK.

Subjects

Participants comprised 142 individuals presenting with suspected microbial keratitis at 3 tertiary care institutions in South India.

Methods

The RID-MyC assay utilized recombinase polymerase amplification targeting the 18S ribosomal RNA gene for isothermal amplification, followed by a CRISPR/Cas12a reaction. This was benchmarked against microscopy, culture, and polymerase chain reaction for the diagnosis of FK.

Main Outcome Measures

The primary outcome measures focused on the analytical sensitivity and specificity of the RID-MyC assay in detecting fungal nucleic acids. Secondary outcomes measured the assay's diagnostic sensitivity and specificity for FK, including its concordance with conventional diagnostic methods.

Results

The RID-MyC assay exhibited a detection limit ranging from 13.3 to 16.6 genomic copies across 4 common fungal species. In patients with microbial keratitis, the RID-MyC assay showed substantial agreement with microscopy (kappa = 0.714) and fair agreement with culture (kappa = 0.399). The assay demonstrated a sensitivity of 93.27% (95% confidence interval [CI], 86.62%-97.25%) and a specificity of 89.47% (95% CI, 66.86%-98.70%) for FK diagnosis, with a median diagnostic time of 50 minutes (range, 35-124 minutes).

Conclusions

The RID-MyC assay, utilizing CRISPR-Cas12a technology, offers high diagnostic accuracy for FK. Its potential for point-of-care use could expedite and enhance the precision of fungal diagnostics, presenting a promising solution to current diagnostic challenges.

Financial Disclosures

Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

Microbiological culture versus 16S/18S rRNA gene PCR-sanger sequencing for infectious keratitis: a three-arm, diagnostic cross-sectional study

Background

To compare the diagnostic performance of microbiological culture and 16S/18S rRNA gene polymerase chain reaction (PCR)-Sanger sequencing for infectious keratitis (IK) and to analyse the effect of clinical disease severity on test performance and inter-test concordance.

Methods

This was a three-arm, diagnostic cross-sectional study. We included all eligible patients who presented with presumed bacterial/fungal keratitis to the Queen's Medical Centre, Nottingham, UK, between June 2021 and September 2022. All patients underwent simultaneous culture (either direct or indirect culture, or both) and 16S (pan-bacterial)/18S (pan-fungal) ribosomal RNA (rRNA) PCR-Sanger sequencing. The bacterial/fungal genus and species identified on culture were confirmed using matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry. Relevant clinical data were also collected to analyze for any potential clinico-microbiological correlation. Main outcome measures included the diagnostic yield, test accuracy (including sensitivity and specificity), and inter-test agreement [including percent agreement and Cohen's kappa (k)].

Results

A total of 81 patients (86 episodes of IK) were included in this study. All organisms identified were of bacterial origin. Diagnostic yields were similar among direct culture (52.3%), indirect culture (50.8%), and PCR (43.1%; p = 0.13). The addition of PCR enabled a positive diagnostic yield in 3 (9.7%) direct culture-negative cases. Based on composite reference standard, direct culture had the highest sensitivity (87.5%; 95% CI, 72.4-95.3%), followed by indirect culture (85.4%; 95% CI, 71.6-93.5%) and PCR (73.5%; 95% CI, 59.0-84.6%), with 100% specificity noted in all tests. Pairwise comparisons showed substantial agreement among the three tests (percent agreement = 81.8-86.2%, Cohen's k = 0.67-0.72). Clinico-microbiological correlation demonstrated higher culture-PCR concordance in cases with greater infection severity.

Conclusions

This study highlights a similar diagnostic performance of direct culture, indirect culture and 16S rRNA PCR for bacterial keratitis, with substantial inter-test concordance. PCR serves as a useful diagnostic adjuvant to culture, particularly in culture-negative cases or those with lesser disease severity (where culture-PCR concordance is lower).

Diagnostic Performance of a Molecular Assay in Synovial Fluid Targeting Dominant Prosthetic Joint Infection Pathogens

Prosthetic joint infection (PJI) is one of the most serious complications of joint replacement surgery among orthopedic surgeries and occurs in 1 to 2% of primary surgeries. Additionally, the cause of PJIs is mostly bacteria from the Staphylococcus species, accounting for more than 98%, while fungi cause PJIs in only 1 to 2% of cases and can be difficult to manage. The current gold-standard microbiological method of culturing synovial fluid is time-consuming and produces false-negative and -positive results. This study aimed to identify a novel, accurate, and convenient molecular diagnostic method. The DreamDX primer-hydrolysis probe set was designed for the pan-bacterial and pan-fungal detection of DNA from pathogens that cause PJIs. The sensitivity and specificity of DreamDX primer-hydrolysis probes were 88.89% (95% CI, 56.50-99.43%) and 97.62% (95% CI, 87.68-99.88%), respectively, compared with the microbiological method of culturing synovial fluid, and receiver operating characteristic (ROC) area under the curve (AUC) was 0.9974 (*** p < 0.0001). It could be concluded that the DreamDX primer-hydrolysis probes have outstanding potential as a molecular diagnostic method for identifying the causative agents of PJIs, and that host inflammatory markers are useful as adjuvants in the diagnosis of PJIs.

Rapid, Ultrasensitive, and Visual Detection of Pathogens Based on Cation Dye-Triggered Gold Nanoparticle Electrokinetic Agglutination Analysis

Rapid prescribing of the right antibiotic is the key to treat infectious diseases and decelerate the challenge of bacterial antibiotic resistance. Herein, by targeting the 16S rRNA of bacteria, we developed a cation dye-triggered electrokinetic gold nanoparticle (AuNP) agglutination (CD-TEAA) method, which is rapid, visual, ultrasensitive, culture-independent, and low in cost. The limit of detection (LOD) is as low as 1 CFU mL-1 Escherichia coli. The infection identifications of aseptic fluid samples (n = 11) and urine samples with a clinically suspected urinary tract infection (UTI, n = 78) were accomplished within 50 and 30 min for each sample, respectively. The antimicrobial susceptibility testing (AST) of UTI urine samples was achieved within 2.5 h. In ROC analysis of urine, the sensitivity and specificity were 100 and 96% for infection identification, and 100 and 98% for AST, respectively. Moreover, the overall cost of materials for each test is about US$0.69. Therefore, the CD-TEAA method is a superior approach to existing, time-consuming, and expensive methods, especially in less developed areas.

Recent Advances in Diagnosis and Treatment Approaches in Fungal Keratitis: A Narrative Review

Fungal keratitis represents a potentially sight-threatening infection associated with poor prognosis, as well as financial burden. Novel diagnostic methods include polymerase-chain-reaction (PCR)-based approaches, metagenomic deep sequences, in vivo confocal microscopy, and antifungal susceptibility testing. The ideal therapeutic approaches and outcomes have been widely discussed in recent times, with early therapy being of the utmost importance for the preservation of visual acuity, minimizing corneal damage and reducing the scar size. However, combination therapy can be more efficacious compared to monotherapy. Understanding the pathogenesis, early diagnosis, and prevention strategies can be of great importance. In this narrative, we discuss the recent progress that may aid our understanding of the diagnosis, treatment, and prevention of mycotic keratitis.

Utility of investigation for suspected microbial keratitis: a diagnostic accuracy study

PURPOSE

The true disease status of a population with suspected microbial keratitis (MK) cannot be verified. There is not an accurate (gold) reference standard to confirm infection and inter-test comparisons of sensitivity and specificity therefore lead to bias with questionable estimates of test utility. We present an alternative method to report results.

METHODS

We used a decision to treat as the definition for MK. We retrospectively compared the results of corneal culture and polymerase chain reaction (PCR) as these are objective tests available for the three principal groups of pathogens. We then estimated the potential contribution of positive results, either alone or in combination, to support the working diagnosis.

RESULTS

We included 2021 (77.4%) eyes with suspected bacterial keratitis, 365 (14.0%) with suspected acanthamoeba keratitis, and 226 (8.6%) with suspected fungal keratitis, all treated between July 2013 and December 2019. In these groups, there were 51.6% positive culture and 6.5% positive PCR results for bacteria, 19.0% and 40.5% for acanthamoeba, and 28.3% and 15.0% for fungi. Between groups the differences in the proportions of positive results from culture and PCR was statistically significant (P < 0.001). The added benefit of PCR to the result of culture in identifying a potential pathogen was 1.4% for bacteria (P = 0.6292), 24.4% for acanthamoeba (P = 0.0001), and 5.8% for fungi (P = 0.3853).

CONCLUSIONS

For suspected MK a comparison of the test positivity rate is an easily comprehensible outcome measure of test utility.

Radiometal chelators for infection diagnostics

Infection of native tissues or implanted devices is common, but clinical diagnosis is frequently difficult and currently available noninvasive tests perform poorly. Immunocompromised individuals (for example transplant recipients, or those with cancer) are at increased risk. No imaging test in clinical use can specifically identify infection, or accurately differentiate bacterial from fungal infections. Commonly used [18F]fluorodeoxyglucose (18FDG) positron emission computed tomography (PET/CT) is sensitive for infection, but limited by poor specificity because increased glucose uptake may also indicate inflammation or malignancy. Furthermore, this tracer provides no indication of the type of infective agent (bacterial, fungal, or parasitic). Imaging tools that directly and specifically target microbial pathogens are highly desirable to improve noninvasive infection diagnosis and localization. A growing field of research is exploring the utility of radiometals and their chelators (siderophores), which are small molecules that bind radiometals and form a stable complex allowing sequestration by microbes. This radiometal-chelator complex can be directed to a specific microbial target in vivo, facilitating anatomical localization by PET or single photon emission computed tomography. Additionally, bifunctional chelators can further conjugate therapeutic molecules (e.g., peptides, antibiotics, antibodies) while still bound to desired radiometals, combining specific imaging with highly targeted antimicrobial therapy. These novel therapeutics may prove a useful complement to the armamentarium in the global fight against antimicrobial resistance. This review will highlight current state of infection imaging diagnostics and their limitations, strategies to develop infection-specific diagnostics, recent advances in radiometal-based chelators for microbial infection imaging, challenges, and future directions to improve targeted diagnostics and/or therapeutics.

Implementation of Genetic Engineering and Novel Omics Approaches to Enhance Bioremediation: A Focused Review

Bioremediation itself is considered to be a cost effective soil clean-up technique and preferred over invasive physical and chemical treatments. Besides increasing efficiency, application of genetic engineering has led to reduction in the time duration required to achieve remediation, overcoming the so called 'Achilles heel' of Bioremediation. Omics technologies, namely genomics, transcriptomics, proteomics, and metabolomics, are being employed extensively to gain insights at genetic level. A wise synchronised application of these approaches can help scrutinize complex metabolic pathways, and molecular changes in response to heavy metal stress, and also its fate i.e., uptake, transport, sequestration and detoxification. In the present review, an account of some latest achievements made in the field is presented.

Diagnostic methods for the etiological assessment of infectious corneal pathology (Review)

Infectious keratitis is a leading cause of visual morbidity, including blindness, all across the globe, especially in developing countries. Prompt and adequate treatment is mandatory to maintain corneal integrity and to recover the best possible final visual acuity. Although in most of the cases practitioners chose to employ empirical broad-spectrum antimicrobial medication that is usually effective, in some instances, they face the need to identify the causative agent to establish the appropriate therapy. An extensive search was conducted on published literature before December 2020 concerning the main laboratory investigations used to identify the microbial agents found in infectious keratitis, their indications, advantages, and disadvantages, as well as the results reported by other studies concerning different diagnostic tools. At present, the gold standard for diagnosis is still considered to be the isolation of microorganisms in cultures, along with the examination of smears, but other newer techniques, such as polymerase chain reaction (PCR), next-generation sequencing (NGS), and in vivo confocal microscopy (IVCM) have gained popularity in the last decades. Currently, these newer methods have proved to be valuable adjuvants in making the diagnosis, but technological advances hold promise that, in the future, these methods will have increased performance and availability, and may become the new gold standard, replacing the classic cultures and smears.

Fungal Keratitis: Diagnostic Characteristics of the Potassium Hydroxide Preparation With Calcofluor White in Northern California

PURPOSE

The incidence of fungal keratitis demonstrates significant geographic and climatic variation. We report on the characteristics of the potassium hydroxide/calcofluor white (KOH-CFW) preparation observed at a tertiary center in Northern California, a region with a low incidence of fungal keratitis.

METHODS

Culture-proven cases of microbial keratitis during a 5-year period were retrospectively reviewed. The sensitivity, specificity, and posttest probabilities were determined for the KOH-CFW assay. These results were compared with documented clinical impression and values reported in the literature.

RESULTS

Three hundred three of 368 episodes of microbial keratitis during the study period documented the results of a fungal culture, KOH-CFW assay, and a clinical impression. Twenty-one (6.9%) of these cultures were positive for fungal organisms. The sensitivity and specificity of the KOH-CFW test were 29% and 93%, respectively. Clinicians' initial clinical impression based solely on patients' history and examination, without the aid of any histopathologic or biochemical test results, demonstrated a sensitivity and specificity of 33% and 89%, respectively.

CONCLUSIONS

The observed sensitivity and specificity of the KOH-CFW preparation are significantly lower than many previously reported values. In regions with low incidence of fungal keratitis, the KOH-CFW preparation may have diagnostic performance similar to that of the clinical impression formed only on the basis of history and physical examination.

Recent Perspectives in the Management of Fungal Keratitis

Mycotic keratitis is common in warm, humid regions with a varying profile of pathogenic fungi according to geographical origin, socioeconomic status, and climatic condition. Clinical diagnosis can be challenging in difficult cases and those refractory to treatment. Fungal hyphae on microscopic examination and culture isolation have been the gold standard in the laboratory diagnosis of fungal keratitis. A culture isolate of the aetiological fungus is essential to perform antifungal susceptibility testing. As the culture isolation of fungi is time-consuming, causing delays in the initiation of treatment, newer investigative modalities such as in vivo confocal microscopy and molecular diagnostic methods have recently gained popularity. Molecular diagnostic techniques now help to obtain a rapid diagnosis of fungal keratitis. Genomic approaches are based on detecting amplicons of ribosomal RNA genes, with internal transcribed spacers being increasingly adopted. Metagenomic deep sequencing allows for rapid and accurate diagnosis without the need to wait for the fungus to grow. This is also helpful in identifying new emerging strains of fungi causing mycotic keratitis. A custom-tear proteomic approach will probably play an important diagnostic role in future in the management of mycotic keratitis. Positive repeat cultures are being suggested as an important gauge indicative of a poor prognosis. Positive repeat fungal cultures help to modify a treatment regimen by increasing its frequency, providing the addition of another topical and oral antifungal agent along with close follow-up for perforation and identifying need for early therapeutic keratoplasty. The role of collagen crosslinking in the treatment of fungal keratitis is not convincingly established. Rapid detection by multiplex PCR and antifungal susceptibility testing of the pathogenic fungi, adopted into a routine management protocol of fungal keratitis, will help to improve treatment outcome. Early therapy is essential in minimizing damage to the corneal tissue, thereby providing a better outcome. The role of conventional therapy with polyenes, systemic and targeted therapy of antifungal agents, newer azoles and echinocandins in fungal keratitis has been widely studied in recent times. Combination therapy can be more efficacious in comparison to monotherapy. Given the diversity of fungal aetiology, the emergence of new corneal pathogenic fungi with varying drug susceptibilities, increasing the drug resistance to antifungal agents in some genera and species, it is perhaps time to adopt recent molecular methods for precise identification and incorporate antifungal susceptibility testing as a routine.

Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Ocular Infections

The variety and complexity of ocular infections have increased significantly in the last decade since the publication of Cumitech 13B, Laboratory Diagnosis of Ocular Infections (L. D. Gray, P. H. Gilligan, and W. C. Fowler, Cumitech 13B, Laboratory Diagnosis of Ocular Infections, 2010). The purpose of this practical guidance document is to review, for individuals working in clinical microbiology laboratories, current tools used in the laboratory diagnosis of ocular infections. This document begins by describing the complex, delicate anatomy of the eye, which often leads to limitations in specimen quantity, requiring a close working bond between laboratorians and ophthalmologists to ensure high-quality diagnostic care. Descriptions are provided of common ocular infections in developed nations and neglected ocular infections seen in developing nations. Subsequently, preanalytic, analytic, and postanalytic aspects of laboratory diagnosis and antimicrobial susceptibility testing are explored in depth.

Identification and molecular characterization of Subramaniula asteroides causing human fungal keratitis: a case report

Background

Keratitis due to by filamentous fungi are not easy to diagnose thus causing a delay in correct therapy. There are many descriptions of keratitis due to Candida, Fusarium and Aspergillus genera. Subramaniula genus has only recently been reported to cause human infections and there are few descriptions of eye infections due to this filamentous fungus. Diagnosis of fungal keratitis is usually based on microscopic and cultural techniques of samples obtained by corneal swabbing or scraping. Considering the amount of time required to obtain culture results it is wise to use other diagnostic methods, such as molecular analyses. Therapeutic options against these fungi are limited by low tissue penetration in the eye due to ocular barriers. We describe the first case of S. asteroides human keratitis treated with isavuconazole.

Case presentation

We describe a rare case of fungal keratitis unresponsive to antimicrobial treatment in a 65-year-old male patient without a history of diabetes or immunological diseases. He reported that the onset of symptoms occurred during a long holiday in Cape Verde Island. Initial treatment with topical antibiotics associated to steroids were ineffective, allowing a slow clinical progression of disease to corneal perforation. On admission in our Hospital, slit-lamp examination of the left eye showed conjunctival congestion and hyperemia, a large inferior corneal ulceration with brown pigment, corneal edema, about 3 mm of hypopyon and irido-lenticular synechiae. The slow clinical progression of the disease to corneal perforation and the aspect of the ulcer were consistent with a mycotic etiology. Molecular methods used on fungal colonies isolated by Sabouraud’s dextrose agar cultures allowed the identification of Subramaniula asteroids from corneal scraping. Antimicrobial test showed a good susceptibility of this filamentous fungus to voriconazole and isavuconazole. Moreover, this fungal keratitis was successfully treated with isavuconazole, without side effects, observing a progressive clinical improvement.

Conclusions

Molecular methods may be useful for the identification of filamentous fungal keratitis on scraping samples thus shortening the time of diagnosis. Systemic therapy by isavuconazole could be useful to treat the filamentous fungal keratitis, reducing the possible adverse effects due to the use of voriconazole by systemic administration.

Survey and Evaluation of Spacecraft-Associated Aluminum-Degrading Microbes and Their Rapid Identification Methods

Aluminum corrosion has become a major obstacle in spacecraft construction given that aluminum is used extensively throughout the construction process. Despite its many attributes in strength and durability, aluminum is susceptible to corrosion, in particular, corrosion due to microbial contamination. Scientists have encountered a number of problems with microbial aluminum corrosion within spacecraft components. Here, we summarize recent findings with regard to the phenomenon of microbiologically influenced corrosion (MIC) on space stations in the context of microbial strains isolated from the Mir space station (Mir) and the International Space Station (ISS). Given that strains found on spacecraft are of terrestrial origin, an understanding of the contribution of Al-corrosive microbes to corrosion and related risks to space travel and astronaut health is essential for implementation of prevention strategies. Accordingly, an efficient rapid identification method of microbes with the capability to degrade aluminum is proposed. In particular, onboard implementation of a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is addressed. The use of a MALDI-TOF MS on board spacecraft will be crucial to future successes in space travel given that traditional methods of identifying corrosive species are far more time-consuming. Identification of microbes by way of a MALDI-TOF MS may also aid in the study of microbial corrosion and be a valuable asset for MIC prevention.

Filamentous Fungal Keratitis in Taiwan: Based on Molecular Diagnosis

Purpose

To analyze the epidemiological pattern, demographics, risk factors, and treatment outcomes of filamentous fungal keratitis at a tertiary hospital in Taiwan.

Methods

We recruited 65 patients (65 eyes) with culture-proven filamentous fungal keratitis who received diagnosis and treatment at Chang Gung Memorial Hospital between 2015 and 2018. All isolates were examined through conventional morphological identification and subjected to molecular identification with internal transcribed spacer sequencing. Data on patient demographics, predisposing factors, and treatment outcomes were collected.

Results

In total, filamentous fungi belonged to 16 genera were identified. Fusarium spp. (29 cases [44.6%]) was the most commonly isolated organism overall, followed by Colletotrichum spp. and Purpureocillium linacinum (seven cases [10.8% for each]), and Aspergillus spp. (six cases [9.2%]). Some fungi that have not been regarded as human pathogens were also identified, such as Paracremonium and Phellinum. Among 52 (80%) patients with predisposing factors, 30 (46.2%) had trauma. The ulcers of 33 (50.8%) patients resolved with medical treatment only. Additionally, six patients (9.2%) had corneal perforation, and nine patients (13.9%) required therapeutic/destructive surgical interventions including therapeutic penetrating keratoplasty (seven patients) or evisceration (two patients). Only 16 patients (24.6%) had final visual acuity of 20/40 or better.

Conclusions

Through molecular diagnosis, a high diversity of fungal pathogens was revealed along with an increasing incidence of Colletotrichumspp. and Purpureocilliumspp. in Taiwan. The most common risk factor for filamentous fungal keratitis was trauma. The visual outcomes were guarded.

Translational Relevance

The molecular diagnosis provides insight into accurate identification, which affects the epidemiology and diversity of pathogens of filamentous fungal keratitis.

The Spectrum of Microbial Keratitis: An Updated Review

Background:

In microbial keratitis, infection of the cornea can threaten vision through permanent corneal scarring and even perforation resulting in the loss of the eye. A literature review was conducted by Karsten, Watson and Foster (2012) to determine the spectrum of microbial keratitis. Since this publication, there have been over 2600 articles published investigating the causative pathogens of microbial keratitis.

Objective:

To determine the current spectrum of possible pathogens implicated in microbial keratitis relative to the 2012 study.

Methods:

An exhaustive literature review was conducted of all the peer-reviewed articles reporting on microbial pathogens implicated in keratitis. Databases including MEDLINE, EMBASE, Scopus and Web of Science were searched utilising their entire year limits (1950-2019).

Results:

Six-hundred and eighty-eight species representing 271 genera from 145 families were implicated in microbial keratitis. Fungal pathogens, though less frequent than bacteria, demonstrated the greatest diversity with 393 species from 169 genera that were found to cause microbial keratitis. There were 254 species of bacteria from 82 genera, 27 species of amoeba from 11 genera, and 14 species of virus from 9 genera, which were also identified as pathogens of microbial keratitis.

Conclusion:

The spectrum of pathogens implicated in microbial keratitis is extremely diverse. Bacteria were most commonly encountered and in comparison, to the review published in 2012, further 456 pathogens have been identified as causative pathogens of microbial keratitis. Therefore, the current review provides an important update on the potential spectrum of microbes, to assist clinicians in the diagnosis and treatment of microbial keratitis.

An Omics Approach to Diagnosing or Investigating Fungal Keratitis

Fungal keratitis (FK) is one of the most severe corneal infectious diseases. FK often leads to poor visual prognosis and thus requires accurate diagnosis. Conventional approaches, including clinical diagnoses, smears, and cultures, often fail to provide reliable diagnostic value. Omics approaches, such as those using genomic, metagenomic, and tear proteomic data sources, provide promising features for improving the diagnosis and monitoring the progression of FK. Genomic approaches are based mainly on detecting amplicons of ribosomal RNA genes, and internal transcribed spacers are gradually gaining popularity in clinical practices. A metagenomic approach based on 16S rRNA genes may help monitor the dynamic change of conjunctival microbiota associated with an FK event, whereas that based on shot-gun and 18S rRNA target enrichment sequencing could have the potential to diagnose FK using clinical samples. A tear proteomic approach may provide comprehensive information about ocular surface defense and injury during FK. Representative up- and down-regulated proteins during FK could also be used as biomarkers to determine the clinical course and develop a treatment strategy in different stages of FK. Consequently, a personalized tear proteomic approach will soon play a key role in FK management.

The persistent dilemma of microbial keratitis: Global burden, diagnosis, and antimicrobial resistance

Microbial keratitis is a potentially blinding condition that must be treated emergently to preserve vision. Although long recognized as a significant cause of corneal blindness, our understanding of its true global scale, associated burden of disease, and etiological patterns remains somewhat limited. Current epidemiological data suggest that microbial keratitis may be epidemic in parts of the world-particularly within South, South-East, and East Asia-and may exceed 2 million cases per year worldwide. Etiological patterns vary between economically developed and developing countries, with bacterial predominance in the former and fungal predominance in the latter. The key to effective management lies in timely diagnosis; however, the current gold standard of stain and culture remains time consuming and often yields no clinically useful results. For this reason, there are attempts to develop highly sensitive and accurate molecular diagnostic tools to provide rapid diagnosis, inform treatment decision making, and minimize the threat of antimicrobial resistance. We provide an overview of these key areas and of avenues for further research toward the goal of more effectively addressing the problem of microbial keratitis on both an individual and public health level.

Fungal Keratitis: Epidemiology, Rapid Detection, and Antifungal Susceptibilities of Fusarium and Aspergillus Isolates from Corneal Scrapings

Fungal aetiology of keratitis/corneal ulcer is considered to be one of the leading causes of ocular morbidity, particularly in developing countries including India. More importantly, Fusarium and Aspergillus are reported commonly implicating corneal ulcer and against this background the present work was undertaken so as to understand the current epidemiological trend of the two fungal keratitis. During the project period, a total of 500 corneal scrapings were collected from suspected mycotic keratitis patients, of which 411 (82.2%) were culture positive for bacteria, fungi, and parasites. Among fungal aetiologies, Fusarium (216, 52.5% of 411) and Aspergillus (68, 16.5% of 411) were predominantly determined. While the study revealed a male preponderance with both the fungal keratitis , it further brought out that polyene compounds (natamycin and amphotericin B) and azoles were active, respectively, against Fusarium spp. and Aspergillus spp. Additionally, 94.1% of culture proven Fusarium keratitis and, respectively, 100% and 63.6% of A. flavus and A. fumigatus were confirmed by multiplex PCR. The sensitivity of the PCR employed in the present study was noted to be 10 fg/μl, 1 pg/μl, and 300 pg/μl of DNA, respectively, for Fusarium, A. flavus, and A. fumigatus. Alarming fact was that Fusarium and Aspergillus regionally remained to be the common cause of mycotic keratitis and the Fusarium isolates had a higher antifungal resistance than Aspergillus strains against most of the test drugs.

Diagnosis of Superficial Mycoses by a Rapid and Effective PCR Method from Samples of Scales, Nails and Hair

Superficial mycoses are the most frequently diagnosed affections of the stratum corneum of the skin, nails and hair. It is generally caused by the presence of yeasts and dermatophytes. Onychomycosis is the most common infection with an incidence of 80-90% in Europe generally produced by Trichophyton rubrum. The aim of this study is to compare the traditional diagnostic techniques of superficial mycoses with a homemade and wide-spectrum fungal polymerase chain reaction (PCR) technique that amplifies a specific region of the 18S ribosomal RNA (rRNA) directly from samples of scales, nails and hair. A total of 626 clinical samples (obtained in the Basurto University Hospital, Bilbao, Spain) were analysed by traditional culture, microscopy and PCR. DNA extraction was carried out by using an extraction buffer and bovine serum, and amplification of samples and performance of the PCR were checked by conventional agarose gel electrophoresis with subsequent sequencing of amplified samples. A total of 211 samples (34%) resulted in positive diagnosis with at least one of the two applied methods: culture (21%) and PCR (22%). Despite the low percentage of identification achieved by the sequencing technique (40%), the value contributed by the amplification of the 18S region of the rRNA was considered important in the identification as it showed a high predictive values for both positive and negative diagnoses (90.9% and 94.6%, respectively). The proposed PCR method has been confirmed as a complementary, rapid, and effective method in the diagnosis of superficial mycoses. Additionally, it reduces the time to obtain satisfactory results from 4 weeks to 7 h.

[Diagnostic and therapeutic contribution of microbiological analysis in severe microbial keratitis at Reims University Hospital between 2012 and 2014]

PURPOSE

To investigate the contribution of microbial analysis in the diagnosis and management of severe microbial keratitis.

MATERIAL AND METHOD

This is a monocentric retrospective study at the University Hospital of Reims from January 2012 to December 2014. Corneal scrapings with infectious keratitis were subjected to routine bacterial and fungal culture. PCR was also performed to detect various viral DNA (VZV, CMV, EBV, HSV 1 & 2, adenovirus) and Acanthamoeba sp. DNA. All contact lens cases were analyzed if available.

RESULTS

One hundred and six patients were hospitalized, including 30 contact lens wearers (28.3%). Sixty-four bacterial cultures were positive (68%). Twenty-five different bacterial species were identified with a majority of gram-positive bacteria (67.92%). Among contact lens wearers, the initial VA was better than non-wearers (P=0.0004) and 37% of bacteria identified (a plurality) were gram positive. Of 11 contact lens case analyzed, in only one case (3.3%) did the result correlate with the corneal culture. Only 9 samples from the 323 viral DNA extractions and real time PCR were positive (2.8%); 7 were HSV1. No prior antiviral therapy had been started. Fungal culture was positive in 2 of the 97 corneal samples taken and 63.6% of the contact lens cases (7/11 cases). Only one of the 40 Acanthamoeba sp. PCR's was positive.

CONCLUSION

The systematic performance of microbiological investigations is a good diagnostic approach given the polymorphism of clinical presentations of corneal ulcers, which can sometimes be extremely misleading. Culture of contact lens cases appears ineffective for the detection and determination of the causative microorganism. The high incidence of Staphylococcus in bacterial keratitis and the prevalence of infections with gram-positive bacteria in contact lens wearers were noted.

Filamentous fungal infections of the cornea: a global overview of epidemiology and drug sensitivity

Fungal keratitis is a serious suppurative, usually ulcerative corneal infection which may result in blindness or reduced vision. Epidemiological studies indicate that the occurrence of fungal keratitis is higher in warm, humid regions with agricultural economy. The most frequent filamentous fungal genera among the causal agents are Fusarium, Aspergillus and Curvularia. A more successful therapy of fungal keratitis relies on precise identification of the pathogen to the species level using molecular tools. As the sequence analysis of the internal transcribed spacer (ITS) region of the ribosomal RNA gene cluster (rDNA) is not discriminative enough to reveal a species-level diagnosis for several filamentous fungal species highly relevant in keratitis infections, analysis of other loci is also required for an exact diagnosis. Molecular identifications may also reveal the involvement of fungal species which were not previously reported from corneal infections. The routinely applied chemotherapy of fungal keratitis is based on the topical and systemic administration of polyenes and azole compounds. Antifungal susceptibility testing of the causal agents is of special importance due to the emergence and spread of resistance. Testing the applicability of further available antifungals and screening for new, potential compounds for the therapy of fungal keratitis are of highlighted interest.

Detection of fungi by conventional methods and semi-nested PCR in patients with presumed fungal keratitis

Background and Purpose:

Fungal keratitis is a suppurative, ulcerative, and sight-threatening infection of the cornea that sometimes leads to blindness. The aims of this study were: recuperating facilities for laboratory diagnosis, determining the causative microorganisms, and comparing conventional laboratory diagnostic tools and semi-nested PCR.

Materials and Methods:

Sampling was conducted in patients with suspected fungal keratitis. Two corneal scrapings specimens, one for direct smear and culture and the other for semi- nested PCR were obtained.

Results:

Of the 40 expected cases of mycotic keratitis, calcofluor white staining showed positivity in 25%, culture in 17.5%, KOH in 10%, and semi-nested PCR in 27.5%. The sensitivities of semi-nested PCR, KOH, and CFW were 57.1%, 28.5%, and 42% while the specificities were 78.7%, 94%, and 78.7%, respectively. The time taken for PCR assay was 4 to 8 hours, whereas positive fungal cultures took at least 5 to 7 days.

Conclusion:

Due to the increasing incidence of fungal infections in people with weakened immune systems, uninformed using of topical corticosteroids and improper use of contact lens, fast diagnosis and accurate treatment of keratomycosis seems to be essential. Therefore, according to the current study, molecular methods can detect mycotic keratitis early and correctly leading to appropriate treatment.

Novel intein-containing DNA specific primers for rapid identification of Candida glabrata using Real-Time PCR assays

Candida glabrata is an opportunistic human pathogen known to cause systemic and vaginal candidiasis. Rapid detection of Candida glabrata is indispensable for appropriate selection of antifungal drugs for chemotherapy. The study describes a unique intein-containing DNA fragment for specific detection of C. glabrata. The designed oligonucleotides detected C. glabrata (Ct mean: 24.75 ± 1.1 and Tm: 70.08 ± 0.23°C) in Real-Time PCR assays. The fluorescent signals were negative when the primers were tested for cross-species and cross-genera amplifications. In conclusion, our study recommends a novel primer set for developing a quick identification system which does not require laborious and time-consuming experimentations.

Autochthonous blastomycosis of the adrenal: first case report from Asia

Systemic endemic mycoses, such as blastomycosis, are rare in Asia and have been reported as health risks among travelers who visit or reside in an endemic area. Adrenal involvement is rarely seen in blastomycosis and has never been reported from Asia. We report the first case of blastomycosis with bilateral involvement of the adrenals in a diabetic patient residing in the state of Arunachal Pradesh, India.

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.

Biochemical and biophysical response to calcium chloride stress in Aspergillus niger and its role in malachite green degradation

Filamentous fungi show great promise in remediation of environmental contaminants such as industrial dyes. In the current study, Aspergillus niger (Genbank ID: JF437542) decolorized 82 % of the test dye malachite green (MG; 50 mg/l) during cultivation for 24 h. The organism decolorized only 6 % of the MG at higher concentration (250 mg MG/l) during the same time period and growth was inhibited at this higher MG concentration. Exposing A. niger to different types of stress resulted in variable impacts on ability to decolorize MG. CaCl2 had the largest positive impact on decolorization. A. niger cultures treated with CaCl2 (1 M) decolorized 46 % of the MG (250 mg/l) in 1 h compared to 6 % in untreated control cultures. CaCl2 also increased catalase production in A. niger which strongly supported a direct relationship between stress response and decolorizing ability. Spectrophotometric measurement confirmed MG decolorization while Fourier transform infrared spectroscopy suggested that biodegradation of MG occurred. Cultures treated with CaCl2 accumulated fewer toxic MG by-products than untreated cultures. CaCl2-induced stress increased the permeability and conductivity of the fungal cell membrane. An observed increase in medium [H(+)] also suggested a change in Ca(2+)/H(+) exchange capacity in the fungal cell. Calcium ions had a pronounced effect on membrane properties and this may have had an important impact on signal transduction. We conclude that A. niger decolorizes MG and that CaCl2 enhances this process; the CaCl2 effect appears to be associated with stress response.

PCR for the molecular diagnosis of mycotic keratitis

Mycotic keratitis, an infection of the cornea caused by fungi, is a medical emergency, with patients presenting with considerable pain and distress. For effective management of the condition, a specific diagnosis must be made rapidly to permit early initiation of antifungal therapy. Currently, direct microscopic examination and culture of corneal material constitute the 'gold standard' for diagnosis. However, rapid, sensitive yet specific tests are needed to detect a small number of, or nonviable, fungi. PCR has many potential advantages when used as a diagnostic aid for mycotic keratitis; the present review covers these advantages, and possible limitations. An expert assessment is also made of studies that have used PCR for the diagnosis of mycotic keratitis. The review concludes with a Five-year view of the potential impact of PCR in management of mycotic keratitis.

A highly sensitive method for molecular diagnosis of fungal keratitis: a dot hybridization assay

PURPOSE

Fungal keratitis (FK) is an important cause of ocular morbidity, especially for people living in the agricultural communities of the developing world. Current diagnostic methods may lack sensitivity (direct microscopy) or are time consuming (culture). The aim of this study was to develop a dot hybridization assay for sensitive and rapid diagnosis of FK.

DESIGN

Evaluation of diagnostic test or technology.

PARTICIPANTS AND CONTROLS

Fifty corneal scrapes (49 patients) from consecutive cases of clinically suspected microbial keratitis were analyzed prospectively.

METHODS

Molecular detection of fungi in the scrapes was performed by amplification of the internal transcribed spacer region (ITS) that contained the target gene (5.8S rRNA gene) by polymerase chain reaction (PCR), followed by hybridization of the PCR product to a fungus-specific oligonucleotide probe immobilized on a nylon membrane. The results were compared with those obtained by gram-stain microscopy, culture, and gel electrophoresis of the PCR products. Discrepant results were resolved by cloning and resequencing of the amplified ITS fragments.

MAIN OUTCOME MEASURES

Performance of the dot hybridization assay, including sensitivity, specificity, and positive and negative predictive values, was evaluated.

RESULTS

Ten scrapes demonstrated positive results by both the dot hybridization assay and culture. However, 11 scrapes demonstrated positive results by the dot hybridization assay, but demonstrated negative results by culture, and 10 of the 11 samples were considered to be positive for FK by cloning and resequencing of the amplified ITS fragment and by a pathologic examination or clinical course review. The sensitivities for diagnosis of FK by the dot hybridization assay and culture were 100% and 50%, respectively, whereas the specificities were 96.7% and 100%, respectively.

CONCLUSIONS

The dot hybridization assay is a highly sensitive and specific diagnostic tool for FK. The method provides a much higher sensitivity than that of culture (100% vs. 50%; P<0.001). The hybridization procedure can be finished within a working day. It is expected that the method can have an impact on the diagnosis and treatment of FK in the future.

FINANCIAL DISCLOSURE(S)

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Diagnosis of fungal keratitis: current options

INTRODUCTION

Fungal keratitis is prevalent in tropical regions of the world and is being increasingly recognized as an important cause of ocular morbidity. Early diagnosis and appropriate treatment are essential to avoid blindness. Clinical impression is often suggestive but clinical features may vary considerably and no one clinical feature may be pathognomonic of fungal infection.

AREAS COVERED

This review describes a combination of methods for the diagnosis of fungal keratitis. Both in vivo and in vitro techniques are described along with their advantages and limitations. In vivo confocal microscopy has made it easier for ophthalmologists to back up their clinical suspicion. In vitro methods include microscopy and culture for fungi. A wide range of conventional and molecular techniques are currently available that provide rapid diagnosis of fungal keratitis.

EXPERT OPINION

Owing to the sensitivity and specificity of over 80%, when available, confocal microscopy could be useful for the diagnosis of fungal keratitis in the clinic. Among the laboratory techniques, a 10% potassium hydroxide wet mount or Gram stain are simple and sensitive enough to be adopted as office methods by ophthalmologists to rule out fungal etiology in patients with microbial keratitis. Empiric antifungal therapy is discouraged and confirmation of the diagnosis prior to institution of treatment is recommended.

Diagnosis of infectious diseases of the eye

Specific therapy of ocular infections often requires etiological diagnosis that is a combined effect of observation of characteristic clinical features and microbiological investigations. Clinical impression is central to guiding the laboratory investigation, and the aim of laboratory investigation is to confirm or rule out the clinical diagnosis. However, clinical features may vary considerably, and no one clinical feature may be pathognomonic of a particular pathogen. In addition, there may be a racial, geographical, and climatic difference in the distribution and type of causative agents associated with infections. Ophthalmologists have at their disposal in vivo and in vitro methods of diagnosis of ocular infections. The expertise of the clinician and the microbiologist along with the facilities available, determine the success with accurate diagnosis. A wide range of conventional and molecular techniques are available that not only provide rapid diagnosis for known common infections but have the potential to bring to the fore unknown organisms that may be associated with ocular infections.

Evaluation of molecular diagnosis in fungal keratitis. Ten years of experience

Purpose

The aims of this study were to assess the utility of polymerase chain reaction (PCR) in diagnosing fungal keratitis in the last decade in our center and to review the molecular diagnosis of mycotic keratitis.

Methods

A retrospective nonrandomized investigation was undertaken at Vissum Corporación Instituto Oftalmologico de Alicante to evaluate 27 corneal samples of 20 patients with proven fungal keratitis from January 2000 to December 2009. Corneal samples (21 corneal scrapings, 5 biopsies, and 1 cornea) were evaluated by Gram stain or calcofluor stain, culture, and PCR. The detection and molecular identification were carried out by DNA amplification and sequencing of the internal transcribed spacer and 5.8S rRNA region from the corneal samples.

Results

PCR detected all the samples that were positive by conventional methods. Four samples were positive by PCR and showed negative results by culture and stain. Combination of microscopy and culture gave positive results in 21 of the 27 samples of patients with mycotic keratitis. Stains showed a 66.7% of positive results, culture showed 59.3%, and PCR showed 92.6%. The time taken for PCR assay was 4 to 8 h whereas positive fungal cultures took 1 to 35 days. Identification at species level by molecular methods was possible in all cases except one. Identification at species level by conventional methods only was possible in eight cases.

Conclusions

PCR not only proved to be an effective rapid method for the diagnosis of fungal keratitis but was also more sensitive than stain and culture methods. Fungal PCR must be added as the screening diagnosis test when an early mycotic keratitis is suspected. Molecular identification is the gold standard technique for the identification of corneal fungal pathogens.

Pythium insidiosum keratitis in contact lens wear: a case report

PURPOSE

The purpose of this study was to report a case of contact lens-related Pythium insidiosum corneal ulcer.

METHODS

The authors conducted an interventional case report. We report the clinical presentations, histopathologic findings, and treatments of a patient with P. insidiosum keratitis associated with contact lens wear.

RESULTS

A 22-year-old Thai woman presented to our clinic with a nonresponsive, progressive corneal ulcer of the left eye. Slit lamp examination showed a large central ulcer measuring 5.4 x 5.2 mm with underlying dense stromal infiltrates surrounded by subepithelial and superficial stromal opacity in a reticular pattern along with radial perineural-like infiltrates. Histopathologic examination revealed broad, branched, thin-walled nonparallel hyaline hyphae with rare septates consistent with P. insidiosum. The corneal culture confirmed the diagnosis. The infection recurred after multiple therapeutic penetrating keratoplasties. Enucleation was eventually performed to eradicate the infection. No definite report of contact lens-related P. insidiosum keratitis existed in the literature.

CONCLUSION

Pythium keratitis may present with central ulcer and radial keratoneuritis similar to acanthamoeba keratitis. Contact lens wear can be a risk factor for this infection. Increasing awareness, early diagnosis, and intervention may improve the prognosis.