Reliability of transport medium in the laboratory evaluation of corneal ulcers

In the eye of the ophthalmologist: the corneal microbiome in microbial keratitis

PURPOSE

To describe the bacterial findings by a targeted sequencing approach from corneal samples of patients with microbial keratitis and factors influencing culture outcome of indirectly inoculated corneal specimen.

METHODS

Prospective inclusion of patients fulfilling predefined criteria of microbial keratitis. Samples from the corneal lesion were collected and dispensed in liquid transport medium, from which both culture and targeted amplification and sequencing of the V3-V4 region of the 16S rRNA gene were carried out. Additional standard corneal culture from the corneal lesions was also performed. Factors influencing culture outcome of indirectly inoculated corneal samples were identified by a multivariate regression model incorporating quantitative data from sequencing.

RESULTS

Among the 94 included patients with microbial keratitis, contact lens wear (n = 69; 73%) was the most common risk factor. Contact lens wearers displayed significant differences in the bacterial community composition of the corneal lesion compared to no lens wearers, with higher abundance of Staphylococcus spp., Corynebacterium spp., and Stenotrophomonas maltophilia. Targeted sequencing detected a potential corneal pathogen in the highest proportional abundance among 9 of the 24 (38%) culture-negative patients with microbial keratitis. Age, bacterial density in the sample, and prior antibiotic treatment significantly influenced culture outcome of indirectly inoculated corneal samples.

CONCLUSION

Targeted sequencing may provide insights on pathogens in both culture negative episodes of microbial keratitis and among subgroups of patients with microbial keratitis as well as factors influencing culture outcome of indirectly inoculated corneal samples.

Urgent unmet needs in the care of bacterial keratitis: An evidence-based synthesis

Bacterial corneal infections, or bacterial keratitis (BK), are ophthalmic emergencies that frequently lead to irreversible visual impairment. Though increasingly recognized as a major cause of global blindness, modern paradigms of evidence-based care in BK have remained at a diagnostic and therapeutic impasse for over half a century. Current standards of management - based on the collection of corneal cultures and the application of broad-spectrum topical antibiotics - are beset by important yet widely underrecognized limitations, including approximately 30% of all patients who will develop moderate to severe vision loss in the affected eye. Though recent advances have involved a more clearly defined role for adjunctive topical corticosteroids, and novel therapies such as corneal crosslinking, overall progress to improve patient and population-based outcomes remains incommensurate to the chronic morbidity caused by this disease. Recognizing that the care of BK is guided by the clinical axiom, "time equals vision", this chapter offers an evidence-based synthesis for the clinical management of these infections, underscoring critical unmet needs in disease prevention, diagnosis, and treatment.

Impact of Sample Collection Order on the Diagnostic Performance of Metagenomic Deep Sequencing for Infectious Keratitis

PURPOSE

The purpose of this article was to evaluate the impact of sample collection order on the diagnostic yield of metagenomic deep sequencing (MDS) for determining the causative pathogen in infectious keratitis.

METHODS

We performed a cross-sectional diagnostic test evaluation among subjects with infectious keratitis at Aravind Eye Hospital in Madurai, India. All subjects underwent corneal scrapings of the affected eye to obtain potassium hydroxide smear, Gram stain, bacterial culture, and fungal culture, in this order. The order of MDS specimen collection relative to smear and culture samples was randomized and served as the primary predictor. Outcomes included the normalized copy number of pathogenic RNA detected by MDS, the proportion of MDS samples that were diagnostic, and the agreement of MDS results with cultures.

RESULTS

MDS samples from 46 subjects with corneal ulcers were evaluated. MDS was positive in 33 subjects (76%) and had 74% overall agreement with culture results. There was no association between order of MDS sample collection and normalized copy number of genetic material detected (P = 0.62) or the likelihood of MDS positivity (P = 0.46). However, the likelihood of agreement between MDS and cultures decreased when MDS corneal swabs were collected after other diagnostic corneal scrapings (P = 0.05).

CONCLUSIONS

The overall yield of MDS for detecting the cause of infectious keratitis was not affected by sample collection order. However, diagnostic agreement between MDS and cultures decreased when MDS samples were collected after other specimens. Additional investigation is warranted to determine whether this represents increased sensitivity of MDS compared with cultures or higher susceptibility to contaminants.

Bacterial keratitis: identifying the areas of clinical uncertainty

Bacterial keratitis is a common corneal infection that is treated with topical antimicrobials. By the time of presentation there may already be severe visual loss from corneal ulceration and opacity, which may persist despite treatment. There are significant differences in the associated risk factors and the bacterial isolates between high income and low- or middle-income countries, so that general management guidelines may not be appropriate. Although the diagnosis of bacterial keratitis may seem intuitive there are multiple uncertainties about the criteria that are used, which impacts the interpretation of investigations and recruitment to clinical studies. Importantly, the concept that bacterial keratitis can only be confirmed by culture ignores the approximately 50% of cases clinically consistent with bacterial keratitis in which investigations are negative. The aetiology of these culture-negative cases is unknown. Currently, the estimation of bacterial susceptibility to antimicrobials is based on data from systemic administration and achievable serum or tissue concentrations, rather than relevant corneal concentrations and biological activity in the cornea. The provision to the clinician of minimum inhibitory concentrations of the antimicrobials for the isolated bacteria would be an important step forward. An increase in the prevalence of antimicrobial resistance is a concern, but the effect this has on disease outcomes is yet unclear. Virulence factors are not routinely assessed although they may affect the pathogenicity of bacteria within species and affect outcomes. New technologies have been developed to detect and kill bacteria, and their application to bacterial keratitis is discussed. In this review we present the multiple areas of clinical uncertainty that hamper research and the clinical management of bacterial keratitis, and we address some of the assumptions and dogma that have become established in the literature.

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.

Paradox of complex diversity: Challenges in the diagnosis and management of bacterial keratitis

Bacterial keratitis continues to be one of the leading causes of corneal blindness in the developed as well as the developing world, despite swift progress since the dawn of the "anti-biotic era". Although, we are expeditiously developing our understanding about the different causative organisms and associated pathology leading to keratitis, extensive gaps in knowledge continue to dampen the efforts for early and accurate diagnosis, and management in these patients, resulting in poor clinical outcomes. The ability of the causative bacteria to subdue the therapeutic challenge stems from their large genome encoding complex regulatory networks, variety of unique virulence factors, and rapid secretion of tissue damaging proteases and toxins. In this review article, we have provided an overview of the established classical diagnostic techniques and therapeutics for keratitis caused by various bacteria. We have extensively reported our recent in-roads through novel tools for accurate diagnosis of mono- and poly-bacterial corneal infections. Furthermore, we outlined the recent progress by our group and others in understanding the sub-cellular genomic changes that lead to antibiotic resistance in these organisms. Finally, we discussed in detail, the novel therapies and drug delivery systems in development for the efficacious management of bacterial keratitis.

Diagnostic armamentarium of infectious keratitis: A comprehensive review

Infectious keratitis (IK) represents the leading cause of corneal blindness worldwide, particularly in developing countries. A good outcome of IK is contingent upon timely and accurate diagnosis followed by appropriate interventions. Currently, IK is primarily diagnosed on clinical grounds supplemented by microbiological investigations such as microscopic examination with stains, and culture and sensitivity testing. Although this is the most widely accepted practice adopted in most regions, such an approach is challenged by several factors, including indistinguishable clinical features shared among different causative organisms, polymicrobial infection, long diagnostic turnaround time, and variably low culture positivity rate. In this review, we aim to provide a comprehensive overview of the current diagnostic armamentarium of IK, encompassing conventional microbiological investigations, molecular diagnostics (including polymerase chain reaction and mass spectrometry), and imaging modalities (including anterior segment optical coherence tomography and in vivo confocal microscopy). We also highlight the potential roles of emerging technologies such as next-generation sequencing, artificial intelligence-assisted platforms. and tele-medicine in shaping the future diagnostic landscape of IK.

Corneal Culture in Infectious Keratitis: Effect of the Inoculation Method and Media on the Corneal Culture Outcome

Background: To compare two different methods of corneal culture in infectious keratitis: multiple sampling for direct inoculation and enrichment (standard method) and a single sample via transport medium for indirect inoculation (indirect inoculation method). Methods: Prospective inclusion of patients fulfilling predefined criteria of infectious keratitis undergoing corneal culture according to both studied methods in a randomized order. Results: The standard method resulted in a significantly higher proportion of positive culture outcomes among the 94 included episodes of infectious keratitis (61%; 57/94) than the indirect inoculation method (44%; 41/94) (p = 0.002) and a significantly higher proportion of microorganisms than the indirect inoculation method, with a Cohen’s kappa of 0.38 (95% CI: 0.28–0.49) for agreement between the methods. Subanalysis of culture results showed that direct inoculation on gonococcal agar only combined with the indirect inoculation method resulted in a similar rate of culture positive patients and proportion of detected microorganisms to the standard method. Conclusion: Indirect inoculation of one corneal sample cannot replace direct inoculation of multiple corneal samples without loss of information. A combination of directly and indirectly inoculated samples can reduce the number of corneal samples by four without statistically significant differences in culture outcome or in the proportion of detected microorganisms.

Does the sampling instrument influence corneal culture outcome in patients with infectious keratitis? A retrospective study comparing cotton tipped applicator with knife blade

Objective

This study aimed to compare the efficacy of a cotton tipped applicator and a knife blade in obtaining corneal samples in patients with infectious keratitis.

Methods and analysis

This is a retrospective cohort study of patients with suspected infectious keratitis during 2004–2014. Samples for corneal culture were obtained by a cotton tipped applicator and a knife blade, and directly inoculated on GC agar, blood agar and Sabouraud agar.

Results

In all, 355 patients were included. Corneal sampling by cotton tipped applicator yielded a significantly higher rate of patients with positive corneal culture, 156/355 (43.9%), compared with knife blade, 111/355 (31.3%) (p<0.001). On a patient level, the culture results obtained by the cotton tipped applicator and the knife blade were identical in 269/355 (76%) of the patients. The overall agreement between the two instruments on microbial level was 0.66 (Cohen’s kappa 95% CI 0.60 to 0.72).

Conclusion

Corneal sampling by cotton tipped applicator generated a higher rate of positive corneal cultures and a higher proportion of isolated microbes than by knife blade. Future studies with randomised sampling order are needed to establish which instrument, cotton tipped applicator or knife blade, is the most effective in sampling microbes for direct inoculation in patients with infectious 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.

A dot hybridization assay for the diagnosis of bacterial keratitis

Purpose

To evaluate a bacterial dot hybridization (BDH) assay for the diagnosis of bacterial keratitis (BK).

Methods

Sixty-one qualified corneal scrapings from 61 patients with suspected microbial keratitis were collected consecutively and prospectively. Among the 61 patients, 16 cases were BK and 45 cases were non-BK, including fungal keratitis, viral keratitis, parasitic keratitis, and non-microbial keratitis. Molecular diagnosis of BK in these corneal scrapes was performed using the BDH assay with three universal bacterial probes (PB1, PB2, and PB3) and three genus-specific probes (Aci, Klb, and Psu) to detect Acinetobacter, Klebsiella, and Pseudomonas, respectively. Signals were standardized after grayscale image transformation for objective validation using receiver operating characteristic (ROC) curves.

Results

The standardized intensities for the three universal probes differed statistically significantly between the BK group and the non-BK group. Based on the ROC curves, the sensitivities of PB1, PB2, and PB3 were 81.3%, 81.3%, and 93.8%, and the specificities were 71.1%, 88.9%, and 91.1%, respectively. The sensitivity and specificity of the Psu probe were 92% and 100%, respectively, while those of the Aci and Klb probes could not be estimated because there were no BK cases caused by Acinetobacter spp. or Klebsiella spp.

Conclusions

The BDH assay is an effective molecular approach to improve the diagnosis of BK. Because the bias from bacterial contamination on the ocular surface can be minimized with signal standardization, the assay has the potential to be adopted for routine clinical practice.

Impression membrane for the diagnosis of microbial keratitis

PURPOSE

To evaluate a corneal impression membrane (CIM) for isolation of bacteria, fungi and acanthamoeba in suspected microbial keratitis.

METHODS

Consecutive patients presenting with suspected microbial keratitis were included. For each patient, samples were collected in a random order using a surgical blade and a 4-mm-diameter polytetrafluoroethylene CIM disc, and transported in brain heart infusion broth. Risk factors, best corrected visual acuity (BCVA), size, location, depth and healing time of the ulcer were recorded. The microbial isolation rate was used to compare sampling methods.

RESULTS

130 patients were included (mean age 62.6 years, SD 19.0). An antimicrobial had been used prior to presentation in 36 (27.7%) patients. Mean major and minor ulcer diameters were 2.1 mm (SD 2.0) and 1.6 mm (SD 1.7). Mean healing time was 12.4 days (SD 13.6). BCVA at presentation and following healing was 0.7 (SD 0.7) and 0.62 (SD 0.7) (p=0.34). There were 66 isolates (50.8%); 53 (40.8%) using a CIM and 35 (26.9%) using a blade (p=0.02). ITALIC! Staphylococcus aureus and coagulase-negative staphylococci were the commonest isolates. Isolation rate was not influenced by organism type, although in four cases ITALIC! Acanthamoeba spp. were isolated; three using CIM and one a blade.

CONCLUSIONS

In this study, the isolation of microorganisms from cases of suspected microbial keratitis was significantly higher using a CIM than a surgical blade. A CIM may be a useful alternative or addition for sample collection in microbial keratitis.

The corneal ulcer one-touch study: a simplified microbiological specimen collection method

PURPOSE

To determine if a new, single-sample device (ESwab; Copan Diagnostics, Inc) can simplify the traditional multi-sample approach to specimen collection in infectious keratitis.

DESIGN

Prospective, diagnostic test evaluation.

METHODS

In this institutional study, patients with suspected infectious keratitis meeting traditional criteria for diagnostic corneal specimen collection and culture were randomized to the order of first specimen collection method: ESwab or a sample directly plated for growth on chocolate agar. This was followed by standard samples for blood agar, Gram stain, Sabouraud agar, thioglycolate broth, and brain heart infusion broth in all cases. The specimens collected using the 2 approaches were analyzed separately by the laboratory in a masked fashion. The main outcome measure was positive growth on cultured media.

RESULTS

Eighty-one eyes from 80 consecutive patients were sampled. Culture positivity rate for the multi-sample method and ESwab was 70% and 69%, respectively, with a 75% agreement rate. ESwab sensitivity was 84% (95% confidence interval [CI]: 72%-93%), with a specificity of 67% (95% CI: 45%-84%). Positive and negative predictive values of the ESwab were 86% (95% CI: 74%-94%) and 64% (95% CI: 43%-82%), respectively. There was no difference in positive culture reports with respect to the order of specimen collection technique used.

CONCLUSIONS

The single-sample ESwab method is a more accessible and less cumbersome approach to corneal culturing for ophthalmologists, particularly those in the community setting who do not have access to the full set of traditional culture materials. Culture results using this single-sample approach were comparable to the multi-sample method.

Corneal epithelial debridement for diagnosis and therapy of ocular surface disease

BACKGROUND

There is a wide range of ocular surface conditions that can be diagnosed or treated with epithelial debridement. The purpose of this study is to analyse the indications, instrumentation and outcomes of corneal epithelial debridement for anterior segment pathology.

METHODS

One hundred and thirty-three eyes of 129 patients with ocular surface disease were treated with epithelial debridement. Different methods were used, appropriate to the specific disease, aetiology and outcome measure.

RESULTS

The mean patient age was 56 years and 81 (60.9 per cent) were male. Sixty-two eyes (46.6 per cent) were undertaken for diagnosis and 71 (53.4 per cent) for therapy. Common indications for diagnostic corneal debridement included infective keratitis 48 (36.1 per cent), neoplasia 14 (10.5 per cent), while those for therapeutic corneal debridement included recurrent erosion 30 (22.5 per cent) and band keratopathy 16 (12.0 per cent). The most common post-operative complication was pain, occurring in all patients to some extent. Band keratopathy was seen to recur in two (12.5 per cent) of the treated eyes and there was a single relapse of recurrent erosion during the follow-up period.

CONCLUSION

The techniques presented can be undertaken in the office rather than a day procedural unit, improving time and cost-effectiveness for the ophthalmologist and patient.

Techniques, indications and complications of corneal debridement

The cornea is the most exposed surface of the eye and, as such, is vulnerable to external trauma and the risk of infection. Many corneal diseases alter shape, surface, and transparency and thus result in reduced vision. The external position of the cornea, however, lends itself to diagnostic and therapeutic maneuvers that are commonly performed and readily done in the clinic. More sophisticated techniques require the use of complex equipment such as excimer and femtosecond laser. Complications that develop from poor healing and/or secondary infection are best avoided with appropriate technique, antisepsis, and modification of wound healing. We review corneal debridement in the management of corneal disease.

Role of liquid culture media in the laboratory diagnosis of microbial keratitis

PURPOSE

To determine whether liquid culture media are helpful in the diagnosis of infectious keratitis.

DESIGN

Retrospective noncomparative case series.

SUBJECTS AND METHODS

This is a retrospective review of microbiology records of 114 corneal scraping samples from infectious keratitis patients. Samples were processed by corneal smear microscopy (potassium hydroxide with calcofluor white and Gram stains) and culture examination (5% sheep blood agar, sheep blood chocolate agar, Sabouraud dextrose agar, brain heart infusion, thioglycolate broth, and Robertson's cooked meat broth. Cases where at least 1 liquid medium was taken were included in the study and all cases were required to have significant growth in culture as per the institutional criteria. Results of smear examination and culture growth were analyzed.

RESULTS

Out of 114 cases, 44 (38.59%) were bacterial, 62 (54.38%) fungal, and 8 (7.01%) were mixed (bacteria + fungus) infection. Thirty-eight out of 44 cases of bacterial keratitis (86.36%) were diagnosed by solid media alone (criterion 1) and 6 of 44 (13.63%) required liquid media for diagnosis (P < .001). In fungal keratitis, 61 of 62 cases (98.38%) were diagnosed using solid media alone (criterion 1) while 1 case required liquid media for diagnosis. In mixed infection, none of the cases required liquid media for diagnosis of fungal component; however, all 8 cases required liquid media for establishing bacterial component.

CONCLUSIONS

Liquid culture media increase the chance of isolation of bacteria in pure bacterial and/or mixed infection; however, their role in isolating fungus is limited. Owing to overlap in clinical diagnosis of bacterial and fungal keratitis, we recommend inclusion of both solid and liquid culture media in the laboratory diagnosis of nonviral keratitis.

Fungal polymerase chain reaction testing in equine ulcerative keratitis

OBJECTIVE

To assess the diagnostic utility of fungal polymerase chain reaction (PCR) in forty-three horses with naturally acquired corneal ulcers presenting to a private practice.

METHODS

Routine evaluation of cytologic, histologic, and microbiologic samples was performed. Two PCR approaches were compared - generic and specific fungal nested PCR followed by sequencing and quantitative PCR (qPCR). PCRs were applied to pure control fungal cultures, corneal tissue from ulcerated eyes and in a subset of 9 horses, to swabs from contralateral normal eyes.

RESULTS

The expected fungus was identified by nested PCR and qPCR in all control fungal cultures. In all fungal culture-positive affected eyes (10/43), one or more fungi were identified by nested PCR and 4/10 were positive by qPCR. In 6/10 animals, the same fungus was identified by nested PCR and culture. Of these 6, only three were positive by qPCR. Fungal agents were identified by morphology in 8/10 horses. Diagnosis of fungal keratitis was reserved for only those cases in which the same fungus could be identified by PCR, culture, and morphology (5 horses). In 33/43 culture-negative affected eyes and in 6/9 unaffected eyes, one or more fungi were identified by nested PCR in 26 samples and by qPCR in 2 samples. Apart from Aspergillus spp, similar fungi were identified in affected and control eyes. Most eyes harbored mixed bacterial and fungal agents.

CONCLUSIONS

Nested PCR results confirmed all cytologically positive cases of fungal keratitis. Nested PCR identified a greater spectrum of agents than either culture or qPCR.

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.