Functional metagenomic profile of the lacrimal sac microbial communities in primary acquired nasolacrimal duct obstruction: The Lacriome paper 2

PCR-based characterization of nasal and ocular surface flora and functional analysis of bacterial metabolic pathways in congenital nasolacrimal duct obstruction

PURPOSE

To evaluate the role of Streptococcus pneumoniae, Staphylococcus aureus, Haemophilus influenzae, Serratia marcescens, and Moraxella catarrhalis in the nasal and ocular surface flora, along with their metabolic activities in children with unilateral congenital nasolacrimal duct obstruction (CNLDO).

METHODS

Swabs were taken from the bilateral inferior meatus and ocular surface of 26 children with unilateral CNLDO before probing. Nasal and ocular surface swabs from non-operated eyes of children who underwent unilateral blepharoptosis or strabismus surgery formed the control group. The quantitative polymerase chain reaction (qPCR) method was used to analyze the samples.

RESULTS

The detection of Streptococcus pneumoniae in the nasal flora, Staphylococcus aureus in the ocular surface flora, and Haemophilus influenzae and Serratia marcescens in both the nasal and ocular surface flora was higher on the obstructed sides of children with CNLDO compared to the controls (p < 0.05). Obstructed sides in children with CNLDO showed a significant difference for Moraxella catarrhalis in the ocular surface and Streptococcus pneumoniae, Staphylococcus aureus, Serratia marcescens, and Moraxella catarrhalis in the nasal flora compared to the patent sides (p < 0.05). Metabolite analysis revealed that betaine, L-carnitine, L-leucine, and L-alanine were negatively regulated in the presence of these bacteria.

CONCLUSIONS

Significant changes in bacterial composition in the nasal and ocular surface flora may be a cause or a result of CNLDO. More comprehensive microbiological studies that evaluate the entire microbiome would be helpful in understanding CNLDO.

The microbiome and the eye: a new era in ophthalmology

The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.

Alterations of Lacrimal Sac Microbiota in Failed Dacryocystorhinostomy: The Lacriome Paper 6

PURPOSE

To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR).

METHODS

A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the IlluminaTM platform following DNA extraction and library preparation. The downstream analysis of the samples was performed using various software packaged in the Squeeze Metapipeline v1.3.0 and marker gene-based metagenomic phylogenetic analysis using MetaPhlAn4.

RESULTS

The five major phyla identified across the samples of failed DCR include Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria (Figure 1). The prevalent species include Stenotrophomonas maltophilia, Pseudomonas juntendi, Streptococcus pneumoniae, Acinetobacter ursingii, Citrobacter koseri, and Cutibacterium acnes (Figure 2). Among the other organisms identified, few were from genera candida and mezorhizobium. Among the viruses, the most abundant was the BeAn 58058 virus. It was interesting to note the occasional presence of plasmodium and toxoplasma species. The functional category distribution of KEGG (Kyoto encyclopedia of genes and genomes) data showed microbial metabolism to be the most involved function, followed by cellular processes.

CONCLUSION

This is the first whole metagenome sequencing of the lacrimal sac contents from failed DCR patients. The organisms identified varied significantly from those isolated from patients with primary acquired nasolacrimal duct obstruction (PANDO) using similar techniques and reflect altered lacrimal microbiota in surgically unsuccessful DCRs.

Clinical characteristics and cytological changes in mucinous obstruction diagnosed by dacryoendoscopy

To analyze the clinical characteristics of mucinous obstruction diagnosed by dacryoendoscopy and compared the cytological changes with membranous obstruction using a modified liquid-based thin prep cytology method. A retrospective chart review was conducted on 53 eyes of 51 patients with mucus obstruction based on dacryoendoscopic findings from January 2022 to October 2022. Liquid-based thin-prep cytology was performed by irrigating the inside of the nasolacrimal drainage system with saline during dacryoendoscopy-guided silicone tube intubation. Pathological findings were analyzed through a comparison of mucinous obstruction with membranous obstruction as determined by dacryoendoscopic findings. The modified liquid-based thin prep cytology technique had a higher cytology detection rate across all cases. Mucinous obstruction exhibited a significantly higher number of successful canalicular irrigation test cases compared to membranous obstruction. In mucinous obstruction, epithelial squamous cells were more frequently detected in pre-sac obstruction, whereas columnar epithelial cells were predominant in post-sac obstruction. Inflammatory cells showed a stronger correlation with primary change and post-sac obstruction. Bacterial colonies were observed exclusively in cases of mucinous obstruction. The use of a modified liquid-based thin prep cytology method enables the examination of histopathological changes in the lacrimal passage in primary acquired nasolacrimal duct obstruction (PANDO), particularly in cases of mucinous obstruction, without the need for invasive biopsies. These findings enhance the understanding of the etiopathogenesis of mucinous obstruction, complementing knowledge of membranous obstruction in PANDO.

Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5

PURPOSE

To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO).

METHODS

A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database.

RESULTS

The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples.

CONCLUSION

The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.

Etiopathogenesis of primary acquired nasolacrimal duct obstruction (PANDO)

Primary acquired nasolacrimal duct obstruction, or PANDO, is a common adult lacrimal drainage disorder. The current treatment modality of dacryocystorhinostomy to bypass the obstructed nasolacrimal duct has excellent outcomes. However, the understanding of the disease etiopathogenesis needs to be revisited. There are not many studies that specifically assessed any hypothesis or ones that convincingly put forth the presumed or confirmed interpretations regarding the PANDO pathogenesis or the mechanisms or pathways involved therein. Histopathological evidence points to recurrent inflammation of the nasolacrimal duct, subsequent fibrosis, and the resultant obstruction. The disease etiopathogenesis is considered multifactorial. Several implicated suspects include anatomical narrowing of the bony nasolacrimal duct, vascular factors, local hormonal imbalance, microbial influence, nasal abnormalities, autonomic dysregulation, surfactants, lysosomal dysfunction, gastroesophageal reflux, tear proteins, and deranged local host defenses. The present work reviewed the literature on the etiopathogenesis of primary acquired nasolacrimal duct obstruction (PANDO) to gain insights into the present state of the understanding and the high-value translational implications of precisely decoding the disease etiology.

Microbial Metagenomics of the Extubated Lacrimal Stents Following Dacryocystorhinostomy: The Lacriome Paper 4

PURPOSE

To study the metagenome of the microbes present on the extubated lacrimal stents following a dacryocystorhinostomy.

METHODS

A prospective study was performed on 10 consecutive extubated lacrimal stents obtained for the metagenomic analysis from the patients following an endoscopic dacryocystorhinostomy. The stents were extubated at 4 weeks postoperatively under endoscopic guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta pipeline or MG-RAST pipeline.

RESULTS

The taxonomic hit distribution across the stent samples showed that bacteria were the most common isolates (mean, 69.70%), followed by viruses (mean, 0.02%) and archaea (0.003%). The 3 major phyla identified were Firmicutes, Actinobacteria, and Proteobacteria. The prevalent organisms include Pseudomonas aeruginosa, Staphylococcus aureus, Corynebacterium accolens, Dolosigranulum pigrum, Citrobacter koserii, Staphylococcus epidermidis, E. coli, and Hemophilus influenza . The functional subsystem profiling demonstrated microbial genes associated with metabolism, cellular, and information processing. The functional subsystem categories were metabolism involving carbohydrates, amino acids, DNA and RNA, cell wall or cell capsule biogenesis, membrane transport, virulence, and defense mechanisms.

CONCLUSIONS

The present study is the first whole metagenome sequencing of the microbes isolated from the extubated lacrimal stents. The stents harbor diverse microbial communities with distinct ecosystem dynamics. Further studies on microbes-host interactions in the early postoperative period would provide valuable insights.

Metagenomics of infective canaliculitis: The Lacriome paper 3

PURPOSE

To study the metagenomics of the microbes isolated from the canaliculus of patients with infective canaliculitis.

METHODS

A prospective study was performed on five consecutive canalicular samples obtained for the metagenomic analysis from the patients with infective canaliculitis who underwent non-incisional canalicular curettage at a tertiary care Dacryology service. The canalicular concretions were collected intraoperatively soon after a canalicular curettage and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina™ platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta™ pipeline or MG-RAST™ pipeline.

RESULTS

The taxonomic hit distribution across the samples showed that bacteria were the most common isolates (mean-80.5%), followed by viruses (mean-0.74%), and archaea (0.01%). The five major phyla identified across the samples of infective canaliculitis were, Fusobacteria, Bacteroidetes, Proteobacteria, Actinobacteria, and Firmicutes. The prevalent organisms include Fusobacterium nucelatum, Fusobacterium periodonticum, Parvimonas micra, Prevotella oris, Selonomonas noxia, Pseudopropionobacterium propoinicum, Campylobacter showae, and Streptococcus anginosus, amongst few others. Actinomycetes israelii was noted in all the samples, though it was not the most abundant. The microbial gene mapping and protein prediction demonstrated proteins with known functions to range from 69.91% to 87.09% across the samples. The functional subsystem profiling demonstrated genes associated with carbohydrate, amino acid, and co-enzyme transport and metabolism, cell wall or cell membrane biogenesis, energy production and conversion, transcription, translation, and cellular communications.

CONCLUSION

This is the first whole metagenome sequencing of infective canaliculitis. Infected canaliculi harbor diverse microbial communities, including bacteria, viruses, and archaea. Functional analysis has provided newer insights into the ecosystem dynamics and strategies of microbial communities.