Conjunctival transcriptome profiling of Solomon Islanders with active trachoma in the absence of Chlamydia trachomatis infection

Vasileva, Hristina; Butcher, Robert; Pickering, Harry; Sokana, Oliver; Jack, Kelvin; Solomon, Anthony W.; Holland, Martin J.

doi:10.1186/s13071-018-2682-2

Cited by 5 publications

(2 citation statements)

References 36 publications

(49 reference statements)

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“…2a). This is in line with the hypothesis that active trachoma in the paci c islands has a distinct pathogenesis to that in Sub-Saharan Africa (9). The proportion of mast cells was only estimated by a small number of deconvolution methods, and did not reach statistical signi cance.…”

Section: Resultssupporting

confidence: 85%

Deconvolution of Bulk Transcriptomics Data Suggests Changes in Conjunctival Immune Cell Populations in Trachoma

Barton

Holland

2022

Preprint

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Objective: Trachoma, a neglected tropical disease caused by ocular infection with Chlamydia trachomatis, progresses from repeated infections and conjunctivitis to scarring, trichiasis and blindness. It is yet unknown which immune cells are responsible for mediating pathogenesis. Our objective was to deconvolute bulk transcriptomics data in order to estimate how conjunctival immune cell populations change in active and scarring trachoma. Results: Six deconvolution methods (quanTIseq, TIMER, MCP-counter, xCell, EPIC, and CIBERSORT) were used to estimate the relative abundance of cell populations in five bulk transcriptomic datasets. Cell types from each deconvolution method were mapped to one another using the Immunedeconv R package. In active disease, B cells, neutrophils, natural killer cells, CD4+ T cells and CD8+ T cells were raised (direction of change the same for at least 75% of methods, p<0.05 for at least two methods by logistic regression). B cells and neutrophils were raised in trachomatous scarring and inflammation, while the relative abundance of CD8+ T cells was decreased. In those with scarring and no inflammation, monocyte/macrophages, neutrophils and CD8+ T cells were decreased compared with controls.

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Section: Resultssupporting

confidence: 85%

Deconvolution of Bulk Transcriptomics Data Suggests Changes in Conjunctival Immune Cell Populations in Trachoma

Barton

Holland

2022

Preprint

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“…Second, individuals diagnosed as having TF might have conjunctivitis precipitated by a stimulus other than C. trachomatis infection. Scientific understanding of the diseases that cause a similar presentation to TF is currently incomplete [57][58][59], and disentangling them from trachoma requires further research. Finally, for the TT analysis in Brazil, we did not include gender effects.…”

Section: Plos Neglected Tropical Diseasesmentioning

confidence: 99%

Using model-based geostatistics for assessing the elimination of trachoma

Sasanami,

Amoah,

Diori

et al. 2023

PLoS Negl Trop Dis

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Background Trachoma is the commonest infectious cause of blindness worldwide. Efforts are being made to eliminate trachoma as a public health problem globally. However, as prevalence decreases, it becomes more challenging to precisely predict prevalence. We demonstrate how model-based geostatistics (MBG) can be used as a reliable, efficient, and widely applicable tool to assess the elimination status of trachoma. Methods We analysed trachoma surveillance data from Brazil, Malawi, and Niger. We developed geostatistical Binomial models to predict trachomatous inflammation—follicular (TF) and trachomatous trichiasis (TT) prevalence. We proposed a general framework to incorporate age and gender in the geostatistical models, whilst accounting for residual spatial and non-spatial variation in prevalence through the use of random effects. We also used predictive probabilities generated by the geostatistical models to quantify the likelihood of having achieved the elimination target in each evaluation unit (EU). Results TF and TT prevalence varied considerably by country, with Brazil showing the lowest prevalence and Niger the highest. Brazil and Malawi are highly likely to have met the elimination criteria for TF in each EU, but, for some EUs, there was high uncertainty in relation to the elimination of TT according to the model alone. In Niger, the predicted prevalence varied significantly across EUs, with the probability of having achieved the elimination target ranging from values close to 0% to 100%, for both TF and TT. Conclusions We demonstrated the wide applicability of MBG for trachoma programmes, using data from different epidemiological settings. Unlike the standard trachoma prevalence survey approach, MBG provides a more statistically rigorous way of quantifying uncertainty around the achievement of elimination prevalence targets, through the use of spatial correlation. In addition to the analysis of existing survey data, MBG also provides an approach to identify areas in which more sampling effort is needed to improve EU classification. We advocate MBG as the new standard method for analysing trachoma survey outputs.

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Prevalence of Trachoma after Implementation of Trachoma Elimination Interventions in Oromia Regional State, Ethiopia: Results of Impact Surveys in 131 Evaluation Units Covering 139 Districts

Miecha

Dejene²,

Adugna

et al. 2022

Ophthalmic Epidemiology

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Purpose To determine the prevalence of trachomatous inflammation—follicular (TF), trachomatous trichiasis (TT), water, sanitation, and hygiene (WASH) access in 131 evaluation units (EUs) after implementation of trachoma elimination interventions in Oromia Region, Ethiopia. Methodology A population-based cross-sectional survey was conducted in each EU using the World Health Organization-recommended two-stage cluster-sampling methodology. Twenty-six clusters, each with a mean of 30 households were enumerated in each EU. All residents aged ≥1 year in selected households were examined for TF and TT. Information on WASH access in surveyed households was also collected through questioning the household head and direct observation. Results A total of 419,858 individuals were enumerated in 131 EUs, of whom 396,134 (94%) were examined, 54% being female. Age-adjusted EU-level prevalence of TF in children aged 1–9 years ranged from 0.15% (95% confidence interval [CI]: 0.0–0.4) to 37.5% (95% CI: 31.1–43.7). The TF prevalence was <5% in 73/131 (56%) EUs. The EU-level age- and gender-adjusted prevalence of TT unknown to the health system among people aged ≥15 years ranged from 0.001% (95% CI: 0.00–0.02) to 2.2% (95% CI: 1.1–3.1) with 37/131 (28%) EUs having a prevalence <0.2%. Only 48% of all households surveyed had access to improved water sources for drinking. Approximately 96% of households did not have an improved latrine. Conclusion Oromia is on the path towards elimination of trachoma as a public health problem.

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Conjunctival transcriptome profiling of Solomon Islanders with active trachoma in the absence of Chlamydia trachomatis infection

Cited by 5 publications

References 36 publications

Deconvolution of Bulk Transcriptomics Data Suggests Changes in Conjunctival Immune Cell Populations in Trachoma

Deconvolution of Bulk Transcriptomics Data Suggests Changes in Conjunctival Immune Cell Populations in Trachoma

Using model-based geostatistics for assessing the elimination of trachoma

Prevalence of Trachoma after Implementation of Trachoma Elimination Interventions in Oromia Regional State, Ethiopia: Results of Impact Surveys in 131 Evaluation Units Covering 139 Districts

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