Identification of novel single nucleotide polymorphisms in inflammatory genes as risk factors associated with trachomatous trichiasis

Exploring multi-level risk factors and post-war burdens of trachomatous trichiasis among displaced population in Raya Kobo districts, implication for urgent action

AIM

To estimate post-war burdens of trachomatous trichiasis (TT) and multi-level risk factors among displaced population in Raya Kobo districts, implication for urgent action.

METHODS

A community-based cross-sectional study was conducted among 603 participants from randomly selected 14 displaced slums in the Raya Kobo district. The data was collected from February 16th to March 30th, 2023. Study participants were selected using the multistage sampling technique. A structured questionnaire and ophthalmic loupe with ×2.5 magnificence were used to collect from participants. Multi-level binary logistic regression was used to determine associated factors with TT infection. Adjusted odds ratio (AOR) with 95% confidence interval (CI) were claimed for the strength of association at P<0.05.

RESULTS

We recruited 602 (99.9%) participants for the final analysis. From the total, 126 (20.9%) and 98 (16.3%, 95%CI: 13.5%-19.4%) participants were diagnosed with active trachoma & TT infection, respectively. Being age ≥45y (AOR=7.9, 95%CI: 2.4-25.3), having multiple eye infections (AOR=2.73, 95%CI: 1.47-5.29), poor wealth index (AOR=9.2; 95%CI: 2.7-23.7) and twice face washing per day (AOR=0.082, 95%CI: 0.03-0.21) has identified as individual as factors for TT infection. Whereas, distance between clean water source ≥10 km (AOR=6.5, 95%CI: 3.9-31.3), and latrine availability (AOR=0.35, 95%CI: 0.21-0.58) were the two community-level factors associated with TT infections.

CONCLUSION

The high prevalence of TT infection post-war throughout the study districts indicates a need for urgent clinical intervention in addition to rapid scaling up surgery, antibiotics, facial cleanliness, and environmental improvement (SAFE) strategies, strategy for high-risk population. Age≥45y, distance from the clean water source, poor wealth indexes, and eye infection are identified to be risk factors for TT infection. Furthermore, community-level preventative factors for TT infection are found as latrine availability and face washing practice.

Prevalence of active trachoma infection and associated factors post-war resettled population in raya kobo districts, North East Ethiopia: A community-based cross-sectional study in 2022

Background

Active trachoma infection poses a serious threat to public health, particularly for those who live in an unprivileged area and has practiced open-field defecation. This study aimed to estimate the prevalence of active trachoma infection and associated factors in the post-war resettled population in Raya Kobo district, North East Ethiopia: a community-based cross-sectional study in 2022.

Methods

A community-based cross-sectional study was conducted among 602 participants randomly selected in 14 slum villages in Raya Kobo from February 16th to March 30th, 2023. After the data was collected using a semi-structured questionnaire and entered into Epi-data version 3.2. The study participants were chosen using a two-stage sampling process. Binary logistic regression was used to identify factors for active trachoma infection. Adjusted odds ratios (AORs) with 95% confidence intervals (CIs) were claimed for the strength of association at p < 0.05.

Results

Overall, 602 (99.9%) study participants were included in the final analysis. At the end of the study period, 126 (20.9) participants developed active trachoma infection. On multivariable analysis, were aged ≥45 years (AOR = 7.9, 95% CI = 2.4-25.3), history of eye infection (AOR = 3.7, 95% CI = 2.4-10.4, p = 0.001), were poor wealth index (AOR = 9.2, 95% CI = 2.7-23.7), having separated kitchen (AOR = 4.05, 95% CI = 1.86-8.86), living with animals (AOR = 5.92, 95% CI = 2.31-14.7) and having got administration of mass-drug (AOR = 8.9, 95% CI = 2.36-33.6) were significant risk factors for active trachoma infection. Whereas, face washing practice regularly (AOR = 0.23, 95% CI = 0.127-0.43), and toilet availability (AOR = 0.35, 95% CI = 0.20-0.97) were preventive factors for active trachoma infection.

Conclusion

A significant prevalence of active trachoma infection was reported in the area as compared with previous findings and urgent clinical intervention, and the WHO critical SAFE strategies (surgery, antibiotics, facial cleanliness, and environmental improvement) implementation is highly needed in the area. In addition, healthcare providers should focus on information dissemination on proper latrine utilization, and washing the face regularly to prevent active trachoma infection is highly recommended.

Genetic association analysis between IL9 and coronary artery disease in a Chinese Han population

Interleukin-9 (IL-9) plays important role in coronary artery disease (CAD). However, the exact relationship between them is not explored yet. Here, four tag SNPs covering IL9 (rs31563, rs2069868, rs2069870 and rs31564) were selected to conduct case-control association analyses in a total of 3704 individuals from Chinese Han population (1863 CAD vs 1841 control). Results showed that: first, rs2069868 was associated with CAD combined with hypertension (P_adj = 0.027); second, IL9 haplotype (CGAT) was associated with CAD (P_adj = 0.035), and the combination genotype of "rs31563_CC/rs31564_TT" would remarkably decrease the risk of CAD (P_adj = 0.001); third, significant associations were found between rs2069870 and decreased LDL-c levels and decreased total cholesterol levels, and between rs31563 and increased HDL-c levels (P_adj < 0.05). Therefore, we conclude that IL9 might play a causal role in CAD by interacted with CAD traditional risk factors, which might confer a new way to improve the prevention and treatment of CAD.

A Review on Methods for Detecting SNP Interactions in High-Dimensional Genomic Data

In this era of genome-wide association studies (GWAS), the quest for understanding the genetic architecture of complex diseases is rapidly increasing more than ever before. The development of high throughput genotyping and next generation sequencing technologies enables genetic epidemiological analysis of large scale data. These advances have led to the identification of a number of single nucleotide polymorphisms (SNPs) responsible for disease susceptibility. The interactions between SNPs associated with complex diseases are increasingly being explored in the current literature. These interaction studies are mathematically challenging and computationally complex. These challenges have been addressed by a number of data mining and machine learning approaches. This paper reviews the current methods and the related software packages to detect the SNP interactions that contribute to diseases. The issues that need to be considered when developing these models are addressed in this review. The paper also reviews the achievements in data simulation to evaluate the performance of these models. Further, it discusses the future of SNP interaction analysis.

Conjunctival fibrosis and the innate barriers to Chlamydia trachomatis intracellular infection: a genome wide association study

Chlamydia trachomatis causes both trachoma and sexually transmitted infections. These diseases have similar pathology and potentially similar genetic predisposing factors. We aimed to identify polymorphisms and pathways associated with pathological sequelae of ocular Chlamydia trachomatis infections in The Gambia. We report a discovery phase genome-wide association study (GWAS) of scarring trachoma (1090 cases, 1531 controls) that identified 27 SNPs with strong, but not genome-wide significant, association with disease (5 × 10⁻⁶ > P > 5 × 10⁻⁸). The most strongly associated SNP (rs111513399, P = 5.38 × 10⁻⁷) fell within a gene (PREX2) with homology to factors known to facilitate chlamydial entry to the host cell. Pathway analysis of GWAS data was significantly enriched for mitotic cell cycle processes (P = 0.001), the immune response (P = 0.00001) and for multiple cell surface receptor signalling pathways. New analyses of published transcriptome data sets from Gambia, Tanzania and Ethiopia also revealed that the same cell cycle and immune response pathways were enriched at the transcriptional level in various disease states. Although unconfirmed, the data suggest that genetic associations with chlamydial scarring disease may be focussed on processes relating to the immune response, the host cell cycle and cell surface receptor signalling.

Trachoma and Ocular Chlamydial Infection in the Era of Genomics

Trachoma is a blinding disease usually caused by infection with Chlamydia trachomatis (Ct) serovars A, B, and C in the upper tarsal conjunctiva. Individuals in endemic regions are repeatedly infected with Ct throughout childhood. A proportion of individuals experience prolonged or severe inflammatory episodes that are known to be significant risk factors for ocular scarring in later life. Continued scarring often leads to trichiasis and in-turning of the eyelashes, which causes pain and can eventually cause blindness. The mechanisms driving the chronic immunopathology in the conjunctiva, which largely progresses in the absence of detectable Ct infection in adults, are likely to be multifactorial. Socioeconomic status, education, and behavior have been identified as contributing to the risk of scarring and inflammation. We focus on the contribution of host and pathogen genetic variation, bacterial ecology of the conjunctiva, and host epigenetic imprinting including small RNA regulation by both host and pathogen in the development of ocular pathology. Each of these factors or processes contributes to pathogenic outcomes in other inflammatory diseases and we outline their potential role in trachoma.

TRAIL-R1 is a negative regulator of pro-inflammatory responses and modulates long-term sequelae resulting from Chlamydia trachomatis infections in humans

The immune system eliminates Chlamydia trachomatis infection through inflammation. However, uncontrolled inflammation can enhance pathology. In mice, TNF-related apoptosis-inducing ligand receptor (TRAIL-R), known for its effects on apoptosis, also regulates inflammation. In humans, the four homologues of TRAIL-R had never been investigated for effects on inflammation. Here, we examined whether TRAIL-R regulates inflammation during chlamydial infection. We examined TRAIL-R1 single nucleotide polymorphisms (SNPs) in an Ecuadorian cohort with and without C. trachomatis infections. There was a highly significant association for the TRAIL+626 homozygous mutant GG for infection vs no infection in this population. To confirm the results observed in the human population, primary lung fibroblasts and bone marrow-derived macrophages (BMDMs) were isolated from wildtype (WT) and TRAIL-R-deficient mice, and TRAIL-R1 levels in human cervical epithelial cells were depleted by RNA interference. Infection of BMDMs and primary lung fibroblasts with C. trachomatis strain L₂, or the murine pathogen C. muridarum, led to higher levels of MIP2 mRNA expression or IL-1β secretion from TRAIL-R-deficient cells than WT cells. Similarly, depletion of TRAIL-R1 expression in human epithelial cells resulted in a higher level of IL-8 mRNA expression and protein secretion during C. trachomatis infection. We conclude that human TRAIL-R1 SNPs and murine TRAIL-R modulate the innate immune response against chlamydial infection. This is the first evidence that human TRAIL-R1 is a negative regulator of inflammation and plays a role in modulating Chlamydia pathogenesis.

Towards a safe and effective chlamydial vaccine: lessons from the eye

As well as being the most common bacterial sexually transmitted infection, Chlamydia trachomatis (Ct) is the leading infectious cause of blindness. The pathogenesis of ocular chlamydial infection (trachoma) is similar to that of genital infection. In the 1960s the efficacy of Ct vaccines against ocular infection was evaluated in major field trials in Saudi Arabia, Taiwan, The Gambia, India and Ethiopia. These trials showed that it was possible to induce short term immunity to ocular infection, and to reduce the incidence of inflammatory trachoma, by parenteral immunisation with killed or live whole organism vaccines. In one study, it was also shown that the incidence of scarring sequelae was reduced in vaccinated children. Detailed studies in non-human primates conducted at this time suggested that vaccination could lead to more severe inflammatory disease on subsequent challenge. Since that time there have been many studies on the immunological correlates of protective immunity and immunopathology in ocular Ct infection in humans and non-human primates, and on host genetic polymorphisms associated with protection from adverse sequelae. These have provided important information to guide the development and evaluation of a human Ct vaccine.

Genetic variation in Chlamydia trachomatis and their hosts: impact on disease severity and tissue tropism

Chlamydia trachomatis infections are a global health problem. This obligate intracellular bacterial pathogen comprises lymphogranuloma venereum (L1-L3), ocular (A-C) and genital (D-K) serovars. Although genetically similar, each serovar group differs in disease severity and tissue tropism through mechanisms that are not well understood. It is clear that host genetic differences also play a role in chlamydial disease outcome and key host polymorphisms are beginning to emerge from both human and experimental animal studies. In this review, we will highlight pathogen and host genes that link genetic diversity, disease severity and tissue tropism. We will also use this information to provide new insights that may be helpful in developing improved management strategies for these important pathogens.

Chlamydia trachomatis infections and subfertility: opportunities to translate host pathogen genomic data into public health

Chlamydia trachomatis (CT) infections in women can result in tubal pathology (TP). Worldwide 10-15% of all couples are subfertile, meaning they did not get pregnant after 1 year. Part of the routine subfertility diagnostics is the Chlamydia Antibody Test (CAT) to decide for laparoscopy or not in order to diagnose TP. The CAT positive and negative predictive value is such that many unneeded laparoscopies are done and many TP cases are missed. Addition of host genetic markers related to infection susceptibility and severity could potentially improve the clinical management of couples who suffer from subfertility. In the present study, the potential translational and clinical value of adding diagnostic host genetic marker profiles on the basis of infection and inflammation to the current clinical management of subfertility was investigated. This review provides an overview of the current state of the art of host genetic markers in relation to CT infection, proposes a new clinical diagnostic approach, and investigates how the Learning-Adapting-Leveling model (LAL, a public health genomic (PHG) model) can be of value and provide insight to see whether these host genetic markers can be translated into public health. This review shows that the preliminary basis of adding host genetic marker profiles to the current diagnostic procedures of subfertility is present but has to be further developed before implementation into health care can be achieved. CT infection is an example in the field of PHG with potential diagnostic to be taken up in the future in the field of subfertility diagnosis with a time line for integration to be dependent on enhanced participation of many stakeholders in the field of PHG which could be advanced through the LAL model.

Trachoma: protective and pathogenic ocular immune responses to Chlamydia trachomatis

Trachoma, caused by Chlamydia trachomatis (Ct), is the leading infectious blinding disease worldwide. Chronic conjunctival inflammation develops in childhood and leads to eyelid scarring and blindness in adulthood. The immune response to Ct provides only partial protection against re-infection, which can be frequent. Moreover, the immune response is central to the development of scarring pathology, leading to loss of vision. Here we review the current literature on both protective and pathological immune responses in trachoma. The resolution of Ct infection in animal models is IFNγ-dependent, involving Th1 cells, but whether this is the case in human ocular infection still needs to be confirmed. An increasing number of studies indicate that innate immune responses arising from the epithelium and other innate immune cells, along with changes in matrix metalloproteinase activity, are important in the development of tissue damage and scarring. Current trachoma control measures, which are centred on repeated mass antibiotic treatment of populations, are logistically challenging and have the potential to drive antimicrobial resistance. A trachoma vaccine would offer significant advantages. However, limited understanding of the mechanisms of both protective immunity and immunopathology to Ct remain barriers to vaccine development.

Polymorphisms of innate immunity receptors in infection by parasites

The innate immune system is the first line of defence against infection by pathogenic bacteria, virus and parasites and is also responsible for initiating an adaptive immune response. In contrast to the receptors of adaptive immunity (TCRs and antibodies) which are generated by gene recombination, receptors of the innate immune system are encoded in the germline and are thus inherited from generation to generation. Although evolutionarily selected, the genes encoding the innate recognition receptors show variations among individuals, and these polymorphisms may have an impact on the ability of an individual to deal with an infection. In recent years, several polymorphisms have been identified in innate recognition receptors, and efforts are being made to determine whether these polymorphisms are associated with a higher or lower susceptibility to infectious diseases. These studies will allow a better understanding of the role of innate receptors in specific diseases and are valuable in the design of preventive or therapeutic interventions to fight the disease. In this review, we summarize studies aimed at determining the influence of polymorphisms in innate recognition receptors on the susceptibility to diseases caused by parasites.

Methods for identifying SNP interactions: a review on variations of Logic Regression, Random Forest and Bayesian logistic regression

Due to advancements in computational ability, enhanced technology and a reduction in the price of genotyping, more data are being generated for understanding genetic associations with diseases and disorders. However, with the availability of large data sets comes the inherent challenges of new methods of statistical analysis and modeling. Considering a complex phenotype may be the effect of a combination of multiple loci, various statistical methods have been developed for identifying genetic epistasis effects. Among these methods, logic regression (LR) is an intriguing approach incorporating tree-like structures. Various methods have built on the original LR to improve different aspects of the model. In this study, we review four variations of LR, namely Logic Feature Selection, Monte Carlo Logic Regression, Genetic Programming for Association Studies, and Modified Logic Regression-Gene Expression Programming, and investigate the performance of each method using simulated and real genotype data. We contrast these with another tree-like approach, namely Random Forests, and a Bayesian logistic regression with stochastic search variable selection.

Rates and risk factors for unfavorable outcomes 6 weeks after trichiasis surgery

PURPOSE

Several studies of trichiasis recurrence suggest an association between surgical factors and long-term recurrence, yet data on short-term risk factors are limited. This study was conducted to evaluate risk factors for early trichiasis recurrence and other unfavorable short-term outcomes.

METHODS

Trichiasis patients presenting for surgery were evaluated for presence of active trachoma and signs of cicatricial outcomes of trachoma, including number of trichiatic lashes, epilation, and entropion. Surgical factors recorded included incision length, surgery duration, and the surgeon performing the operation. Participants were followed up for 6 weeks after surgery and evaluated for eyelid closure defect and trichiasis recurrence; in addition, in two thirds of the patients, eyelid contour abnormality and granuloma formation were evaluated.

RESULTS

First-time trichiasis surgery was performed on 2615 eyelids. Of these, 2601 eyelids without surgical failure were followed up 6 weeks after surgery. Of the eyelids treated, 2.3% had recurrent trichiasis and 1.3% had an eyelid closure defect. Data on eyelid contour abnormalities and granuloma formation were recorded for 1881 eyes, with rates of 1.2% and 10.5%, respectively. Associated risk factors differed by outcome. Surgeon was predictive of eyelid closure defect and granuloma formation. Eyelids with short incisions were nearly four times more likely to have recurrent trichiasis (95% confidence interval, 1.7-9.3). Baseline trichiasis severity was predictive of eyelid contour abnormalities and recurrent trichiasis. Epilation was associated with granuloma formation, but was protective against eyelid closure defect.

CONCLUSIONS

Surgical factors are important predictors of unfavorable outcomes in the weeks immediately after surgery. Although the overall rate of serious uncorrectable unfavorable outcomes was very low, the high rate of granuloma formation, which can be treated by removal, highlights the need for follow-up of patients after trichiasis surgery. (ClinicalTrials.gov number, NCT00347776.).

Haptoglobin and sickle cell polymorphisms and risk of active trachoma in Gambian children

Background

Susceptibility and resistance to trachoma, the leading infectious cause of blindness, have been associated with a range of host genetic factors. In vitro studies of the causative organism, Chlamydia trachomatis, demonstrate that iron availability regulates its growth, suggesting that host genes involved in regulating iron status and/or availability may modulate the risk of trachoma. The objective was to investigate whether haptoglobin (Hp) haplotypes constructed from the functional polymorphism (Hp1/Hp2) plus the functional promoter SNPs -61A-C (rs5471) and -101C-G (rs5470), or sickle cell trait (HbAS, rs334) were associated with risk of active trachoma when stratified by age and sex, in rural Gambian children.

Methodology and Principal Findings

In two cross sectional surveys of children aged 6–78 months (n = 836), the prevalence of the clinical signs of active trachoma was 21.4%. Within boys, haplotype E (-101G, -61A, Hp1), containing the variant allele of the -101C-G promoter SNP, was associated with a two-fold increased risk of active trachoma (OR = 2.0 [1.17–3.44]). Within girls, an opposite association was non-significant (OR = 0.58 [0.32–1.04]; P = 0.07) and the interaction by sex was statistically significant (P = 0.001). There was no association between trachoma and HbAS.

Conclusions

These data indicate that genetic variation in Hp may affect susceptibility to active trachoma differentially by sex in The Gambia.

Chlamydia trachomatis today: treatment, detection, immunogenetics and the need for a greater global understanding of chlamydial disease pathogenesis

Chlamydia trachomatis is an important human pathogen causing a myriad of severe and debilitating diseases. While antibiotics have been a mainstay of treatment, there is increasing evidence for potential drug resistance, reinfection and persistent infections that require a reevaluation of treatment strategies. A critical need to address these issues will be a rapid, sensitive and cost-effective diagnostic that can be used for global screening, treatment and test-of-cure of infected individuals instead of empirical therapy that not only drives drug resistance but is not costeffective. This type of diagnostic would allow clinicians and researchers to evaluate the true incidence and prevalence of chlamydial infections in both developed and developing countries. There are extremely limited data on chlamydial sexually transmitted diseases (STDs) in many developing countries, including those in Central and South America. In addition, advancing our understanding of chlamydial disease pathogenesis will require an evaluation of host genetic susceptibility to infection and sequelae. We provide preliminary data on rates of chlamydial STDs and host genetic factors that predispose to infection among adolescent pregnant and nonpregnant commercial sex worker populations residing in Quito, Ecuador.