Polymerase chain reaction identification in aqueous humor of patients with postoperative endophthalmitis

The diagnostic utility of nanopore targeted sequencing in suspected endophthalmitis

PURPOSE

This paper aimed to assess the diagnostic utility of a newly developed gene-based technology-nanopore targeted sequencing (NTS) in suspected endophthalmitis patients.

METHODS

This retrospective study included 43 patients (44 eyes) with suspected endophthalmitis. NTS was applied along with microbiological culture to detect unknown pathogens in intraocular fluid samples. The diagnostic utility of NTS was mainly evaluated from three aspects, including the positivity rate of bacterial/fungal presence, diagnostic turnaround time and the frequency of change in treatment based on etiology test results. Non-parametric, two-sided Wilcoxon rank sum test, the McNemar's test and the kappa statistic were used for statistical comparisons.

RESULTS

NTS showed significant advantages over traditional culture in positivity rates and diagnostic time (P < 0.001, kappa = 0.082; Z = -5.805, P < 0. 001). As regards antibiotic strategy, 17 patients (39.53%) and 5 patients (11.63%) underwent medication change following NTS and culture results respectively (P < 0.001, kappa = 0.335). With reasonable use of antibiotic and surgical intervention, most patients responded favorably, judged by significantly improved visual acuity (Z = -4.249, P < 0.001). The mean duration of hospitalization was 8.49 ± 2.45 days (range, 1-16 days).

CONCLUSION

The high efficiency feature of NTS in pathogen detection renders it a valuable supplementary to traditional culture. Additionally, it has facilitated patients' management for the early and precise diagnosis of endophthalmitis.

Endophthalmitis: Microbiology and Organism Identification Using Current and Emerging Techniques

Endophthalmitis is an ophthalmological emergency requiring timely and appropriate diagnosis and treatment. Microbiological methods of microscopy (Gram's staining) and culture are the current gold standard for organism identification. However, a significant proportion of endophthalmitis remains culture-negative-perhaps the inflammation is non-infectious in origin, results from a novel organism are unidentifiable or because the causative organism is non-culturable often due to pre-treatment with antibiotics. This review outlines the microbiological profile of endophthalmitis, current clinically used methods for organism identification, and the newer molecular techniques of polymerase chain reaction (PCR) and next-generation sequencing (NGS) technology as diagnostic tools for endophthalmitis. They offer the potential to improve organism identification rates and clinical outcomes in infectious diseases, representing an exciting future direction for organism identification in endophthalmitis. Based on the largest ophthalmic hospital in Australia, we highlight the key practical challenges faced by Australian diagnostic laboratories for their use in a clinical setting.

Application of High-Throughput Sequencing Technology in Identifying the Pathogens in Endophthalmitis

Infectious endophthalmitis is an important cause of vision loss worldwide. It is an inflammatory reaction caused by bacteria, fungi, and other micro-organisms and often occurs as a complication of intraocular surgery, especially following cataract surgery or intravitreal injection. The focus of the prevention and treatment of infectious endophthalmitis is the early detection of microbial flora, such as fungi or bacteria. Current identification methods for bacteria include Gram staining-based, culture-based, and polymerase chain reaction (PCR)-based methods. The matrix-assisted laser desorption/ionization time-of-flight mass spectrometry technology is now the standard identification method of bacteria and fungi after their isolation in culture. The remarkable sensitivity of PCR technology for the direct detection of micro-organisms in clinical samples makes it particularly useful in culture-positive and culture-negative endophthalmitis. Furthermore, PCR increases the rate of microorganism detection in intraocular samples by 20% and can provide a microbiology diagnosis in approximately 44.7–100% of the culture-negative cases. This review aims to introduce the development of different methods for the detection and identification of micro-organisms causing endophthalmitis through a literature review; introduce the research status of the first, second, and third-generation sequencing technologies in infectious endophthalmitis; and understand the research status of endophthalmitis microbial flora. For slow-growing and rare micro-organisms, high-throughput sequencing (HTS) offers advantages over conventional methods and provides a basis for the identification of pathogens in endophthalmitis cases with negative culture. It is a reliable platform for the identification of pathogenic bacteria of infectious endophthalmitis in the future and provides a reference for the clinical diagnosis and treatment of infectious endophthalmitis. The application of HTS technology may also be transformative for clinical microbiology and represents an exciting future direction for the epidemiology of ocular infections.

Acute postoperative endophthalmitis: Microbiology from the laboratory to the bedside

Postoperative endophthalmitis is a dreaded complication of intraocular surgery. Acute presentations need prompt management and good knowledge of differential diagnoses. In the last 10 years, progress in direct microbial detection and identification from intraocular samples included the use of blood culture systems and, more recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry, improving the rate of bacterial identification. Whatever the method used, diagnostic sensitivity is better for vitreous samples than for aqueous humor samples. Besides, molecular biology techniques have further improved the identification rate of infectious agents in intraocular samples. They also provide faster results compared to culture-based techniques. Quantitative real-time PCR (qPCR) can also determine the bacterial load in intraocular samples. Several studies have shown that intraocular bacterial loads in endophthalmitis patients are usually high, which helps differentiating infection from contamination. The prognostic value of qPCR remains to be validated. Whole genome DNA sequencing technologies facilitate direct and sequencing of single DNA molecules. They have the potential to increase the rate of microbiological identification. Some antibiotic resistance markers (e.g., methicillin resistance in staphylococci and vancomycin resistance in enterococci) may be detected earlier using molecular techniques (usually real-time PCR tests). Early determination of the involved microorganism and their antibiotic resistances can help establishing an earlier therapeutic strategy.

Microbiological diagnosis of endophthalmitis using nanopore targeted sequencing

BACKGROUND

Microorganism identification is critical for the early diagnosis and management of infectious endophthalmitis, but traditional culture can yield false-negative results. Nanopore targeted sequencing (NTS) is a third-generation sequencing technique with multiple advantages. This study aimed to test aqueous humour or vitreous fluid samples from presumed cases of infectious endophthalmitis using NTS to evaluate the feasibility of NTS in diagnosing endophthalmitis, especially for culture-negative cases.

METHODS

This prospective study enrolled patients who presented to the Department of Ophthalmology of Union Hospital (Wuhan, China) between June 2018 and December 2020. The samples were sent immediately for routine microbiology culture processing and NTS assay.

RESULTS

NTS identified microorganisms in 17 of 18 cases (94.4%) (eight culture-positive cases, nine culture-negative cases, and one case unavailable for culture). There was a high-quality match between culture and NTS for culture-positive cases. In the eight culture-negative cases and the case unavailable for culture, NTS detected either bacteria, fungi, or a mixture of bacteria and fungi in the intraocular fluids. The average waiting times for the results of bacterial and fungal cultures were 48 and 72 h, respectively. The average time for the NTS results was 12 h.

CONCLUSIONS

NTS appears to be a promising diagnostic platform for diagnosing infectious endophthalmitis, even for culture-negative cases.

Microbial diagnosis of endophthalmitis using nanopore amplicon sequencing

OBJECTIVES

We investigated whether nanopore amplicon sequencing of aqueous humor was capable of rapid pathogen identification in infectious endophthalmitis.

METHODS

5 cases of culture-positive bacterial endophthalmitis and 3 cases of fungal endophthalmitis (1 culture-positive and 2 presumed) were included. DNA was extracted from the aqueous humor and vitreous specimen, and PCR of bacterial rDNA (16S) and fungal rDNA (ITS1 and D1/2/3) was performed. Then, nanopore amplicon sequencing was performed for 2 h. The results of amplicon sequencing were compared to those of conventional culture studies.

RESULTS

In all cases, pathogens were identified by amplicon sequencing of aqueous humor specimens. In 3 cases of bacterial endophthalmitis, the identified microbes were confirmed by culture studies of both aqueous humor and vitreous specimens. In 2 cases of bacterial and 1 case of fungal endophthalmitis, the identified pathogens were confirmed only by culture studies of vitreous specimens. In all cases, amplicon sequencing identified pathogen in a shorter turnaround time than culture studies. In 2 cases with negative culture results, amplicon sequencing of aqueous humor identified fungal pathogens.

CONCLUSIONS

Our data demonstrates the potential of amplicon nanopore sequencing using aqueous humor to enable rapid, sensitive and less invasive microbial diagnosis of endophthalmitis.

Rational laboratory testing in uveitis: A Bayesian analysis

Uveitis encompasses a heterogeneous group of clinical entities with the common feature of intraocular inflammation. In addition to patient history and examination, a focused set of laboratory investigations is frequently necessary to establish a specific diagnosis. There is limited consensus among uveitis specialists regarding appropriate laboratory evaluation for many distinct patient presentations. The appropriateness of a laboratory test for a given case of uveitis will depend on patient-specific as well as epidemiologic factors. Bayesian analysis is a widely used framework for the interpretation of laboratory testing, but is seldom adhered to in clinical practice. Bayes theorem states that the predictive value of a particular laboratory test depends on the sensitivity and specificity of that test, as well as the prevalence of disease in the population being tested. In this review we will summarize the performance of commonly-utilized laboratory tests for uveitis, as well as the prevalence of uveitic diagnoses in different geographic practice settings. We will propose a logical framework for effective laboratory testing in uveitic disease through rigorous application of Bayesian analysis. Finally, we will demonstrate that while many highly sensitive laboratory tests offer an effective means to rule out associated systemic disease, limited test specificity and low pretest probability often preclude the diagnosis of systemic disease association with any high degree of certainty, even in the face of positive testing.

Using the West Midlands CONCERT to characterise regional incidence of acute-onset post cataract surgery endophthalmitis

BACKGROUND

Whilst research and innovation is embedded within the UK's National Health Service (NHS) constitution, Doctors-in-training have little opportunity to contribute to designing, leading and recruiting into clinical trials or cohort studies. We formed the West Midlands Collaborative Ophthalmology Network for Clinical Effectiveness & Research by Trainees (The West Midlands CONCERT) and undertook a characterisation of post cataract surgery endophthalmitis as a proof-of-concept study to test the feasibility of the CONCERT model.

METHODS

Doctors-in-training formed a collaborative working group to test the concept of delivering a pan-regional clinical effectiveness study across multiple hospital sites by performing retrospective analyses of post cataract endophthalmitis over a 6-year period.

RESULTS

Overall, 157,653 cataract surgeries were performed by participating centres accredited to deliver the Royal College of Ophthalmologists training curriculum. Thirty-eight cases of post cataract endophthalmitis were identified, giving an incidence of 2.41 per 10,000 cases (0.0241%). A further 15 endophthalmitis cases presented who had surgery in non-training centres, giving a total of 53 cases. The most common organisms were S. epidermidis (14 (51.9%)) and P. aeruginosa (5 (18.5%)). Anterior-chamber and vitreous sampling yielded positive culture in 33.3% (6/18) and 50.9% (27/53), respectively. At 6 months follow-up, 19 (51.4%) patients achieved visual acuities of ≤0.5 LogMAR. Repeat intravitreal injections (11 (20.8%)) and vitrectomy (n = 22 (41.5%)) were not associated with better outcomes.

CONCLUSIONS

Using post cataract endophthalmitis as a pilot cohort, this study highlights the feasibility of using the CONCERT model for studies across multiple sites. A UK-CONCERT could provide a powerful infrastructure enabling characterisation of patient cohorts and a platform for high-quality interventional studies, improving patient care.

Ocular bacterial infections: Pathogenesis and diagnosis

The human eye is a rigid asymmetric structure with unique defence system. Despite considerable resident microbiota, eye is exposed to external environment where a range of microorganisms also inhabits. Opportunistically, some of these microorganisms could associate with eye pathogen that could contact incidentally, leading to destructive visual consequences. Among such microbiota, bacteria form the major proportion concerning ocular complications worldwide. The succession of genome based approach through 16S rRNA gene based identification tremendously augmented the knowledge on diversity of ocular surface bacteria. Such evidence suggests that while few bacteria contribute towards normal ocular functions, considerable number of bacteria play active role in pathophysiology of ocular diseases. Thus, understanding the complexity of ocular microflora not only throw light on their critical role towards normal function of the eye, but also enlighten on certain visual exigencies. Under these circumstances, development of a rapid, reliable and cost effective method is essential that eventually evolve as a routine diagnostic protocol. Such precise prognostic modalities facilitate ophthalmologists to formulate pioneering therapeutics towards challenging ocular diseases.

Targeted High-Throughput Sequencing Identifies Predominantly Fungal Pathogens in Patients with Clinically Infectious, Culture-Negative Endophthalmitis in South India

To evaluate the clinical utility of high-throughput sequencing (HTS) approach-based analysis of the bacterial and fungal genome in vitreous fluids from patients clinically diagnosed as endophthalmitis, we subjected 75 vitreous fluids from clinically presumed infectious endophthalmitis patients to high-throughput sequencing (Illumina HiSeq 2500) after DNA extraction and amplification of the 16S rRNA for the detection of bacteria, and ITS 2 region for detection of fungal pathogens. As controls, we included vitreous biopsies from 70 patients diagnosed with other non-infectious retinal disorders. Following the construction of the curated microbial genome database and filtering steps to reduce ambiguousness/contaminants from the environment, the paired reads were analyzed. Our HTS reads revealed in almost all cases the same organism that was grown in culture (bacterial-14/15, fungal 3/3) by conventional microbiological workup. HTS additionally diagnosed the presence of microbes in 42/57 (73.7%) patients who were conventionally negative (fungal pathogens in 36/57, bacterial pathogens in 11/57, including five cases that showed the presence of both bacterial and fungal organisms). Aspergillus sp., Fusarium sp., Exserohilum sp., and Candida sp. were the most predominant genera in our cohort of culture-negative endophthalmitis cases. Heat map based microbial clustering analysis revealed that these organisms were taxonomically similar to the species identified by conventional culture methods. Interestingly, 4/70 control samples also showed the presence of bacterial reads, although their clinical significance is uncertain. HTS is useful in detecting pathogens in endophthalmitis cases that elude conventional attempts at diagnosis and can provide actionable information relevant to management, especially where there is a high index of suspicion of fungal endophthalmitis, particularly in tropical countries. Outcome analyses and clinical trials addressing the success and cost savings of HTS for the diagnosis of endophthalmitis are recommended.

New insights into culture negative endophthalmitis by unbiased next generation sequencing

The proof-of-concept, study to investigate the presence of microorganisms in presumed infectious endophthalmitis using Next generation sequencing (NGS) was carried out in vitreous biopsies from 34 patients with endophthalmitis, and thirty patients undergoing surgery for non-infectious retinal disorders as controls. Following DNA extraction using the Qiagen mini kit and PCR amplification of the V3–V4 regions of the bacterial 16S rRNA and ITS 2 region of fungus, they samples were sequenced on an Illumina HiSeq 2500 Machine. Paired reads were curated, taxonomically labeled, and filtered. Culture based diagnosis was achieved in 15/34 (44%) patients while NGS diagnosed the presence of microbes in 30/34 (88%) patients (bacteria in 26/30, fungi in 2/30, mixed infections in 2/30 cases). All 30 controls were negative for bacteria or fungus by NGS. There was good agreement between culture and NGS for culture-positive cases. Among culture negative cases, DNA of common culturable bacteria were identified like Streptococcus sp., Staphylococcus sp., Pseudomonas sp., Gemella sp., Haemophilus sp., Acinetobacter sp. The specificity of NGS with culture and clinical diagnosis was found to be 20% and 100% respectively and sensitivity of NGS with culture and clinical diagnosis was found to be 87.5% and 88% respectively. NGS appears to be promising diagnostic platform for the diagnosis of infectious culture negative endophthalmitis.

Utility of broad-range 16S rRNA PCR assay versus conventional methods for laboratory diagnosis of bacterial endophthalmitis in a tertiary care hospital

Background

Endophthalmitis, a sight-threatening intraocular infection, can be of postsurgical, post-traumatic or endogenous origin. Laboratory diagnosis-based appropriate therapy can be vision-saving. Conventional culture-based laboratory diagnosis takes time and lacks sensitivity. In this study a broad-range PCR assay was assessed against conventional and automated culture methods in vitreous specimens for accurate microbiological diagnosis.

Aims

To use broad-range PCR assay targeting 16S ribosomal RNA (rRNA) region of bacteria and to assess its performance vis-à-vis conventional and automated culture methods in the laboratory diagnosis of endophthalmitis.

Methods

Vitreous specimens from 195 patients with clinically diagnosed endophthalmitis were processed for classical and automated culture methods, antimicrobial sensitivity and broad-range PCR assay targeting 762 bp region of 16S rRNA followed by nucleotide sequencing by Sanger’s method. Causative agents were identified from the nucleotide sequences analysed against the GenBank database, and organisms were identified using the Clinical and Laboratory Standards Institute (CLSI) MM18A guidelines.

Results

Bacteria could be detected from 127 (65.13%) of the 195 vitreous specimens by broad-range PCR assay; bacterial isolation was possible from 17 (8.7%) and 60 (30.76%) of these specimens by conventional and automated culture methods, respectively (p<0.0001). PCR assay could detect two uncultured bacterium, and in five cases the bacterial identity could not be determined from NCBI database matching.

Conclusion

Broad-range PCR assay could provide definitive microbial diagnosis within 24 hours in significantly more patients (p<0.0001). Some rare organisms could be detected, useful in treatment modalities. Automated culture was significantly more sensitive than conventional culture.

Incidence, microbiology, and outcomes of endophthalmitis after 111,876 pars plana vitrectomies at a single, tertiary eye care hospital

Purpose

To describe the incidence, risk factors, clinical presentation, causative organisms, and outcomes in patients with endophthalmitis following pars plana vitrectomy (20G and minimally invasive vitrectomy surgery (MIVS).

Methods

Of 111,876 vitrectomies (70,585 20-G 41,291 MIVS) performed, 45 cases developed acute-onset, postoperative endophthalmitis.

Results

The rate of culture positive and culture negative endophthalmitis was 0.021% (2.1/10,000 surgeries) and 0.019% (1.9/10,000 surgeries) overall, 0.031% (3.1/10,000 surgeries) and 0.025% (2.5/10,000 surgeries) in 20G, and 0.005% (0.5/10,000 surgeries) and 0.007% (0.7/10,000 surgeries) in the MIVS group respectively. Potential predisposing factors were as follows: diabetes, 46.7%; vitrectomy for vascular retinopathies, 44.4%; and vitrectomy combined with anterior segment surgeries, 35.5%. The culture proven rates were 53.3% overall, 55.0% for 20G and 40.0% for MIVS. The most common organism was Pseudomonas aeruginosa for 20G. Klebsiella and Staphylococcus aureus were isolated in the two culture positive cases in MIVS group. The follow-up period for the patients with endophthalmitis was 586.14 ± 825.15 days. Seven were lost to follow up beyond one week. Of the remaining 38, 13 (34.2%) cases had a favorable visual outcome (i.e., best-corrected visual acuity [BCVA] > 5/200) and 24 (63.2%) had unfavorable visual outcome (BCVA < 5/200). Group with culture test results negative had significantly better outcomes (P < 0.05) as compared to those with positive.

Conclusions

MIVS does not increase the risk of endophthalmitis. Outcomes are poor despite appropriate treatment, particularly in cases with culture results positive.

Occurrence and risk factors for retinal detachment after pars plana vitrectomy in acute postcataract bacterial endophthalmitis

BACKGROUND/AIMS

To report the incidence, risk factors and prognosis of retinal detachment (RD) in patients who had vitrectomy for acute bacterial endophthalmitis after cataract surgery.

METHODS

123 patients with acute postcataract endophthalmitis, consecutively treated with pars plana vitrectomy (PPV) were included by the French Institutional Endophthalmitis Study group, in a prospective multicentre cohort study. Risk factors of RD were analysed using logistic regression.

RESULTS

At the 6-month follow-up, the rate of post-PPV RD was 13% (n=16). The risk factors of post-PPV RD were diabetes (OR=4.7 (1.4-15.4), p=0.01) and visualisation of retinal vasculitis on the posterior pole (OR=3.8 (1.1-13.9), p=0.03) at the time of PPV. Postoperative RD occurred in 56% (n=9) of cases in the first month, in 31% (n=5) in the second month and in 6% (n=1) in the third month, with a mean delay of 47±71 days after PPV. The macula was detached in 12 cases (75%) and proliferative vitreoretinopathy grade C was present in seven cases. Final successful reattachment of the retina was obtained in 60% (n=9/15) of cases, with one (7/9) or two surgeries (2/9). Final visual acuity after surgical repair was ≥20/40 in 19% of cases, compared with 43% in patients without RD (p=0.05).

CONCLUSIONS

RD is a major and severe complication of PPV performed in patients with acute postcataract endophthalmitis. Retinal vasculitis is a major risk factor of RD after PPV. Anatomical and functional outcome remain poor.

Identification of torque teno virus in culture-negative endophthalmitis by representational deep DNA sequencing

PURPOSE

To test the hypothesis that uncultured organisms may be present in cases of culture-negative endophthalmitis by use of deep DNA sequencing of vitreous biopsies.

DESIGN

Single-center, consecutive, prospective, observational study.

PARTICIPANTS

Aqueous or vitreous biopsies from 21 consecutive patients presenting with presumed infectious endophthalmitis and 7 vitreous samples from patients undergoing surgery for noninfectious retinal disorders.

METHODS

Traditional bacterial and fungal culture, 16S quantitative polymerase chain reaction (qPCR), and a representational deep-sequencing method (biome representational in silico karyotyping [BRiSK]) were applied in parallel to samples to identify DNA sequences corresponding to potential pathogens.

MAIN OUTCOME MEASURES

Presence of potential pathogen DNA in ocular samples.

RESULTS

Zero of 7 control eyes undergoing routine vitreous surgery yielded positive results for bacteria or virus by culture or 16S polymerase chain reaction (PCR). A total of 14 of the 21 samples (66.7%) from eyes harboring suspected infectious endophthalmitis were culture-positive, the most common being Staphylococcal and Streptococcal species. There was good agreement among culture, 16S bacterial PCR, and BRiSK methodologies for culture-positive cases (Fleiss' kappa of 0.621). 16S PCR did not yield a recognizable pathogen sequence in any culture-negative sample, whereas BRiSK suggested the presence of Streptococcus in 1 culture-negative sample. With the use of BRiSK, 57.1% of culture-positive and 100% of culture-negative samples demonstrated the presence of torque teno virus (TTV) sequences, compared with none in the controls (P=0.0005, Fisher exact test). The presence of TTV viral DNA was confirmed in 7 cases by qPCR. No other known viruses or potential pathogens were identified in these samples.

CONCLUSIONS

Culture, 16S qPCR, and BRiSK provide complementary information in presumed infectious endophthalmitis. The majority of culture-negative endophthalmitis samples did not contain significant levels of bacterial DNA. "Culture negativity" does not seem to be due to failure of growth of fastidious bacteria. The small DNA virus TTV was unexpectedly found in all culture-negative samples and some culture-positive samples. This study cannot distinguish whether TTV is a direct intraocular pathogen, an adjuvant for inflammation, a general marker of inflammation, or a commensal virus but provides a testable hypothesis for a pathogenic mechanism in culture-negative endophthalmitis.

Identification of causative pathogens in mouse eyes with bacterial keratitis by sequence analysis of 16S rDNA libraries

The clone library method using PCR amplification of the 16S ribosomal RNA (rRNA) gene was used to identify pathogens from corneal scrapings of C57BL/6-corneal opacity (B6-Co) mice with bacterial keratitis. All 10 samples from the eyes with bacterial keratitis showed positive PCR results. All 10 samples from the normal cornea showed negative PCR results. In all 10 PCR-positive samples, the predominant and second most predominant species accounted for 20.9 to 40.6% and 14.7 to 26.1%, respectively, of each clone library. The predominant species were Staphylococcus lentus, Pseudomonas aeruginosa, and Staphylococcus epidermidis. The microbiota analysis detected a diverse group of microbiota in the eyes of B6-Co mice with bacterial keratitis and showed that the causative pathogens could be determined based on percentages of bacterial species in the clone libraries. The bacterial species detected in this study were mostly in accordance with results of studies on clinical bacterial keratitis in human eyes. Based on the results of our previous studies and this study, the B6-Co mouse should be considered a favorable model for studying bacterial keratitis.

DNA extraction methods for panbacterial and panfungal PCR detection in intraocular fluids

PURPOSE

Three different methods of DNA extraction from intraocular fluids were compared with subsequent detection for bacterial and fungal DNA by universal PCR amplification.

MATERIAL AND METHODS

Three DNA extraction methods, from aqueous and vitreous humors, were evaluated to compare their relative efficiency. Bacterial (Gram positive and negative) and fungal strains were used in this study: Escherichia coli, Staphylococcus epidermidis and Candida albicans. The quality, quantification, and detection limit for DNA extraction and PCR amplification were analyzed. Validation procedures for 13 aqueous humor and 14 vitreous samples, from 20 patients with clinically suspected endophthalmitis were carried out.

RESULTS

The column-based extraction method was the most time-effective, achieving DNA detection limits ≥10(2) and 10(3 )CFU/100 µL for bacteria and fungi, respectively. PCR amplification detected 100 fg, 1 pg and 10 pg of genomic DNA of E. coli, S. epidermidis and C. albicans respectively. PCR detected 90.0% of the causative agents from 27 intraocular samples collected from 20 patients with clinically suspected endophthalmitis, while standard microbiological techniques could detect only 60.0%. The most frequently found organisms were Streptococcus spp. in 38.9% (n = 7) of patients and Staphylococcus spp. found in 22.2% (n = 4).

CONCLUSIONS

The column-based extraction method for very small inocula in small volume samples (50-100 µL) of aqueous and/or vitreous humors allowed PCR amplification in all samples with sufficient quality for subsequent sequencing and identification of the microorganism in the majority of them.

Detection of Escherichia fergusonii by PCR-based DNA sequencing in a case of delayed-onset chronic endophthalmitis after cataract surgery

We report a case of chronic low-grade endophthalmitis after cataract surgery presenting with recurrent episodes of severe anterior chamber reactions and hypopyon uveitis caused by Escherichia fergusonii, which was isolated from vitreous aspirate by polymerase chain reaction-based DNA sequencing. Polymerase chain reaction has emerged as an essential, powerful, and rapid laboratory diagnostic technique and a useful adjunct to the conventional gold standard.

FINANCIAL DISCLOSURE

No author has a financial or proprietary interest in any material or method mentioned.

Laboratory support in the diagnosis of uveitis

Intraocular inflammations are still a diagnostic challenge for ophthalmologists. It is often difficult to make a precise etiological diagnosis in certain situations. Recently, there have been several advances in the investigations of uveitis, which has helped the ophthalmologists a lot in the management of such clinical conditions. A tailored approach to laboratory diagnosis of uveitic cases should be directed by the history, patient's symptoms and signs, and clinical examination. This review summarizes various modalities of laboratory investigations and their role in the diagnosis of uveitis.

Principles and applications of molecular biology techniques for the microbiological diagnosis of acute post-operative endophthalmitis

The systematic microbiological evaluation of endophthalmitis allows the confirmation of the infectious nature of the disease and the possible adaptation of treatment at the individual level and, at the collective level, the epidemiological characterization of the bacterial spectrum of endophthalmitis. Long reserved for research, the use of molecular biology techniques to complement conventional culture techniques has become important for the diagnosis of endophthalmitis in recent years. These new diagnostic techniques are particularly useful for the microbiological study of bacteria that are difficult or impossible to grow because of their intrinsic properties, their presence in only a small inoculum, their sequestration on prosthetic materials, or their inactivation by prior antibiotic treatment. These techniques are based on the polymerase chain reaction (PCR), which allows the amplification and detection of extracted bacterial deoxyribonucleic acid (DNA) that is initially present in minute quantities in an ocular sample. In practice, these conventional or real-time PCRs allow either the a priori detection of bacterial DNA (universal PCR) or the identification of a specific DNA fragment of a bacterial genus or species (specific PCR). New techniques of PCR will allow more rapid bacterial identification and also characterization of genotypic properties, such as genes of virulence or antibiotic resistance.

A multicentre prospective study of post-traumatic endophthalmitis

PURPOSE

Study the clinical and microbiological characteristics and the prognostic factors of post-traumatic endophthalmitis.

METHODS

Seventeen eyes were included between 2004 and 2010, with clinical and microbiological data collected prospectively. Conventional cultures and panbacterial PCR were performed on aqueous and vitreous samples.

RESULTS

Clinical signs of endophthalmitis were observed soon after trauma (1.5 ± 2.5 days). Laceration with an intraocular foreign body (IOFB) was noted in 53% of the patients. At admission, all patients had aqueous humour (71%) and/or vitreous (53%) samples. Fifteen patients (88%) underwent a pars plana vitrectomy. Bacteria were identified in 77% of the cases: Staphylococcus epidermidis (n = 5), Streptococcus (n = 4), Bacillus (n = 2), Pseudomonas stuzeri (n = 1), and Streptococcus salivarius and Gemella haemolysans (multibacterial infection, n = 1). Progression toward phthisis was observed in 35% of the cases; 41% of the patients recuperated visual acuity (VA) ≥20/40. A good final visual prognosis (≥20/40) was significantly associated with initial VA better than light perception (0% versus 70%, p = 0.01) and absence of pupillary fibrin membrane (80% versus 20%, p = 0.05). There was no correlation between visual prognosis and age, the type of laceration (corneal or scleral) or presence of an IOFB. We found a statistical trend toward an association between bacterial virulence and poor final VA.

CONCLUSION

This series showed that better final VA outcomes were associated with initial VA better than light perception, S. epidermidis or culture-negative cases and absence of retinal detachment during the clinical course.

Real-time polymerase chain reaction in the diagnosis of acute postoperative endophthalmitis

PURPOSE

To evaluate the efficacy of quantitative real-time polymerase chain reaction (qPCR) in the diagnosis of postoperative bacterial endophthalmitis among patients who underwent cataract surgery at a tertiary care center.

DESIGN

Prospective experimental study.

METHODS

This was a single-center study of 64 eyes of 64 patients presenting with clinical signs and symptoms of endophthalmitis within 1 year of cataract surgery. Patients with glaucoma filtering or cornea surgery in the past year, postoperative trauma, fungal endophthalmitis, or preoperative inflammatory conditions were excluded. Vitreous samples were obtained during vitreous tap or vitrectomy and sent for both culture and qPCR with sequencing. Vitreous samples obtained from 50 patients undergoing vitrectomy for noninflammatory indications served as controls. The main outcome measures were the sensitivity of qPCR compared to culture and concordance of results of pathogen identification with sequencing vs phenotypic speciation.

RESULTS

qPCR detected 16s bacterial DNA in 37 patients (66%), compared to 19 (34%) with traditional culture. Only 1 patient had a positive result by culture (Nocardia species) but negative result by qPCR. For the 18 samples positive by both qPCR and culture, there was a 100% concordance in pathogen identification between sequencing and phenotypic speciation.

CONCLUSION

In cases of suspected bacterial endophthalmitis, qPCR offers an improved diagnostic yield and may be a useful adjunct to traditional culture. Further large-scale clinical studies are needed to elucidate the full clinical utility of qPCR.

Bilateral same-day intravitreal injections using a single vial and molecular bacterial screening for safety surveillance

PURPOSE

To evaluate the safety of bilateral same-day intravitreal injections using a single vial and to introduce a molecular surveillance system to screen bacterial drug contamination using eubacterial polymerase chain reaction (PCR).

METHODS

Retrospective review of the medical records of 135 patients who received 574 bilateral same-day intravitreal injections for various retinal diseases in 2 tertiary referral hospitals between January 2008 and March 2010 was performed. Data were obtained regarding the diagnosis, kinds of drugs injected, postinjection complications, and the result of molecular bacterial screening of the injected drugs. Drugs for bilateral intravitreal injections were drawn from a single vial and injected using separate syringes or needles. Molecular bacterial screening was performed using the remaining drug in the syringe by 16S ribosomal DNA real-time PCR.

RESULTS

A total of 574 injections (384 bevacizumab, 154 ranibizumab, and 36 triamcinolone) were administered on bilateral eyes of 135 patients. There were no complications, including endophthalmitis, uveitis, retinal tear, or retinal detachment. Of the 278 injections screened for bacterial contamination using eubacterial PCR, no cases (0%) showed drug contamination by bacteria. The sensitivity of eubacterial PCR for molecular bacterial screening was 10 colony-forming units (CFUs)/mL or lower.

CONCLUSION

Bilateral same-day intravitreal injections drawn from a single vial using separate syringes or needles are well tolerated by patients, and its safety profile may be equivalent to unilateral injections. The bacterial molecular surveillance system using eubacterial PCR demonstrated the safety of bilateral same-day intravitreal injections and may be used for safety surveillance and for timely intervention of possible drug-related endophthalmitis.

Real-time polymerase chain reaction test to discriminate between contamination and intraocular infection after cataract surgery

PURPOSE

To determine the usefulness of real-time polymerase chain reaction (PCR) assays in the diagnosis of postoperative bacterial endophthalmitis in clinically diagnosed infectious cases and to test for bacterial DNA in control samples collected from noninfected eyes.

SETTING

Federal University of São Paulo, Brazil.

DESIGN

Evaluation of diagnostic test or technology.

METHODS

This study comprised patients with clinically diagnosed infectious endophthalmitis after cataract surgery and vitreous samples (from noninflamed eyes obtained through vitrectomy) and aqueous samples (at end of phacoemulsification) from control patients at a single university setting. Universal and gram-specific real-time PCR, Gram staining, and culture were performed. Sensitivity and cycle thresholds were determined. Clinical and microbiologic data were also assessed.

RESULTS

The study evaluated 11 patients with infectious endophthalmitis (9 vitreous and 7 aqueous samples), 12 control vitreous samples, and 50 control aqueous samples. Gram and culture identified 80% and 75%, respectively, of patients with infectious endophthalmitis. Real-time PCR assays were positive in 91% of patients with a clinical diagnosis of endophthalmitis using aqueous samples, vitreous samples, or both. None of the 12 vitreous controls were positive by PCR. Two aqueous control samples were positive by real-time PCR. The cycle threshold cutoff value was 36 for universal PCR (sensitivity 93.8%; specificity 100%) and 38 for gram-specific PCR (sensitivity 93.8%; specificity 100%). Gram-positive microorganisms prevailed, and visual acuity varied according to the causative bacteria.

CONCLUSIONS

Real-time PCR provided fast and accurate diagnosis of bacterial endophthalmitis. As a quantitative technique, it may be useful in distinguishing between contamination and infection based on the cycle thresholds value.

Detection of bacterial DNA in acute and chronic cholecystitis

BACKGROUND

The incidence of bacterbilia in cholelithiasis remains controversial. The positivity of cultures ranges from 0 to 73 per cent. The aim of this study was to employ the polymerase chain reaction (PCR) to detect bacterial DNA in gallbladder bile extracted during elective laparoscopic cholecystectomy, and to compare PCR findings with those of bile culture.

METHODS

Bile samples from 84 laparoscopic cholecystectomies were collected for culture and PCR analysis.

RESULTS

Positive results for bacterbilia were found in 42 (50 per cent) of 84 patients by PCR but in only 16 patients (19 per cent) by culture (P < 0.001). Agreement between the two methods was seen in 44 samples (52 per cent), which were negative in 35 cases. Pathological examination showed chronic cholecystitis in 69 cases (82 per cent) and acute cholecystitis in 15 (18 per cent). Thirty-three (48 per cent) of the patients with chronic cholecystitis were PCR positive but only ten (14 per cent) were culture positive (P < 0.001). Only culture results correlated with findings on pathological examination (P = 0.033).

CONCLUSION

PCR is more sensitive in detecting bacterial contamination of gallbladder bile in cholecystitis than conventional culture. The clinical relevance of this high sensitivity remains unclear.

Applications of the polymerase chain reaction in clinical ophthalmology

Molecular biology has become a valuable component in many areas of medicine, including ophthalmology. Polymerase chain reaction (PCR) is the most widely used tool. It has proven to be a powerful technique in diagnosis and quantification of microorganisms and antibiotic resistance screening. For a growing number of ophthalmic conditions PCR testing can be conducted. It is therefore important that clinicians be knowledgeable about the indications, strengths, and limitations of the technique. The purpose of this review is to explore the current role of PCR in the diagnosis and management of eye disease.

Polymerase chain reaction in intraocular inflammation

Polymerase chain reaction (PCR) is a technique involving enzymatic amplification of nucleic acid sequences in repeated cycles of denaturation, oligonucleotide annealing and DNA polymerase extension. It is a powerful molecular biologic tool that allows the rapid production of analytic quantities of DNA from small amounts of starting material. PCR can be performed on nearly any ocular specimen or biopsy. For diagnosis of uveitis, the obtained sample is usually an anterior chamber paracentesis or vitreous tap. PCR potentially is more sensitive than culture for detection of many organisms. By utilizing a secondary detection system in concert with the initial PCR reaction, perfect specificity can be assured. The initial application of PCR diagnostics to ophthalmic disease was in the detection of viral uveitis. PCR has also been implicated in studies of noninfectious uveitis. The most common application is HLA typing. A universal bacterial PCR can be very helpful for the diagnosis of bacterial endophthalmitis at an early stage of the disease.

High prevalence of fastidious bacteria in 1520 cases of uveitis of unknown etiology

The etiologic evaluation of uveitis is frequently unsuccessful when noninvasive methods are used. We conducted a prospective study to evaluate systematic screening for pathogens of uveitis. All patients with uveitis referred to the participating tertiary ophthalmology departments from January 2001 to September 2007 underwent intraocular and serum specimen collection. The standardized protocol for laboratory investigations included universal polymerase chain reaction (PCR)-based detection of any bacteria and mycoses, specific PCR-based detection of fastidious (difficult-to-grow) bacteria and herpes viruses, and culture of vitreous fluid. Sera were tested for fastidious bacteria. Among the 1321 included patients (1520 specimens), infection was diagnosed in 147 (11.1%) patients: 78 (53%) were caused by fastidious bacteria that included spirochetes, Bartonella species, intracellular bacteria (Chlamydia species, Rickettsia species, Coxiella burnetii), and Tropheryma whipplei; 18 by herpes viruses; and 9 by fungi. Bartonella quintana, Coxiella burnetii, Paracoccus yeei, Aspergillus oryzae, and Cryptococcus albidus were found to be associated with uveitis for the first time, to our knowledge. We recommend applying a 1-step diagnostic procedure that incorporates intraocular, specific microbial PCR with serum analyses in tertiary centers to determine the etiology of uveitis.