Genome-wide meta-analysis and fine-mapping prioritize potential causal variants and genes related to leprosy.

To date, genome-wide association studies (GWASs) have discovered 35 susceptible loci of leprosy; however, the cumulative effects of these loci can only partially explain the overall risk of leprosy, and the causal variants and genes within these loci remain unknown. Here, we conducted out new GWASs in two independent cohorts of 5007 cases and 4579 controls and then a meta-analysis in these newly generated and multiple previously published (2277 cases and 3159 controls) datasets were performed. Three novel and 15 previously reported risk loci were identified from these datasets, increasing the known leprosy risk loci of explained genetic heritability from 23.0 to 38.5%. A comprehensive fine-mapping analysis was conducted, and 19 causal variants and 14 causal genes were identified. Specifically, manual checking of epigenomic information from the Epimap database revealed that the causal variants were mainly located within the immune-relevant or immune-specific regulatory elements. Furthermore, by using gene-set, tissue, and cell-type enrichment analyses, we highlighted the key roles of immune-related tissues and cells and implicated the PD-1 signaling pathways in the pathogenetic mechanism of leprosy. Collectively, our study identified candidate causal variants and elucidated the potential regulatory and coding mechanisms for genes associated with leprosy.

The role of an active surveillance strategy of targeting household and neighborhood contacts related to leprosy cases released from treatment in a low-endemic area of China.

OBJECTIVE: Early diagnosis remains the primary goal for leprosy management programs. This study aims to determine whether active surveillance of patients with leprosy and their contact individuals increased identification of latent leprosy cases in the low-endemic areas. METHODS: This cross-sectional survey was carried out between October 2014 and August 2016 in 21 counties throughout Shandong Province. The survey was conducted among patients with leprosy released from treatment (RFT) and their contacts from both household and neighbors. RESULTS: A total of 2,210 RFT patients and 9,742 contacts comprising 7877 household contacts (HHCs), including 5,844 genetic related family members (GRFMs) and 2033 non-genetic related family members and 1,865 contacts living in neighboring houses (neighbor contacts, NCs), were recruited. Among identified individuals, one relapsed and 13 were newly diagnosed, giving a detection rate of 0.12%, corresponding to 120 times the passive case detection rate. Detection rates were similar for HHCs and NCs (0.114% vs. 0.214%, P = 0.287). Analysis of the family history of leprosy patients revealed clustering of newly diagnosed cases and association with residential coordinates of previously-diagnosed multibacillary leprosy cases. CONCLUSION: Active case-finding programs are feasible and contributes to early case detection by tracking HHCs and NCs in low-endemic areas.

Prevalence of genital Chlamydia trachomatis infection in the general population: a meta-analysis.

BACKGROUND: Estimating prevalence of Chlamydia trachomatis (CT) worldwide is necessary in designing control programs and allocating health resources. We performed a meta-analysis to calculate the prevalence of CT in the general population. METHODS: The Pubmed and Embase databases were searched for eligible population-based studies from its inception through June 5, 2019. Q test and I2 statistic were used to calculate the heterogeneity between studies. Random effects models were used to pool the prevalence of CT. Meta regression was performed to explore the possible sources of heterogeneity. Publication bias was evaluated using a funnel plot and "trim and fill" method. RESULTS: Twenty nine studies that reported prevalence of CT infection from 24 countries were identified, including a total population of 89,886 persons. The pooled prevalence of CT among the general population was 2.9% (95% CI, 2.4-3.5%), and females had a higher CT prevalence (3.1, 95% CI, 2.5-3.8%) than males (2.6, 95% CI, 2.0-3.2%) (χ2 = 10.38, P <  0.01). Prevalence of CT was highest in region of America (4.5, 95% CI, 3.1-5.9%), especially in Latin America (6.7, 95% CI, 5.0-8.4%), followed by females in region of Africa (3.8, 95% CI, 0.7-6.9%), while South-East Asia had a lowest CT prevalence 0.8% (95% CI, 0.3-1.3%). CONCLUSIONS: This study provided the updated prevalence of CT among general population worldwide. General population from Latin America, especially females, and women in Africa should be given priority by WHO when design and delivery CT control programs.

Comprehensive measures succeeded in improving early detection of leprosy cases in post-elimination era: Experience from Shandong province, China.

BACKGROUND: A few new leprosy cases still can be seen in Shandong province after elimination. In post-elimination era, government commitments dwindled and active case-finding activities were seldom done. Most of the cases were detected by passive modes and advanced cases with longer delay and visible disability were common. MATERIALS AND METHODS: Comprehensive measures including health promotion, personnel training, reward-offering, symptom surveillance and a powerful referral center were implemented in the past decade. The diagnosis of leprosy was mainly based on three cardinal clinical signs. Two-group classification system developed by the WHO was used and cases were classified into multibacillary (MB) type or paucibacillary (PB) type. Cases detected during period 2007-2017 were analyzed and associated factors of grade 2 disability (G2D) were explored. RESULTS: 231 new leprosy cases detected during 2007-2017 were analyzed. The mean age at diagnosis is 51.7±16.0 years and the number of males, peasants, illiterates, MB cases, G2D cases and immigrants were 130(56.3%), 221(95.7%), 73(31.6%), 184(79.7%), 92(39.8%) and 40(17.3%) respectively. 181(78.4%) cases were reported by skin clinics and 152 (65.8%) cases came from formerly high endemic counties/districts. The annual number of new cases showed a decreasing trend, from 42 cases in 2008 to 13 cases in 2017. 92 (39.8%) cases presented with G2D at diagnosis. The annual proportion of new cases with G2D declined from 50% in 2008 to 23% in 2017. PB type (OR = 2.76, 95% CI, 1.43-5.32), >12 months of patient delay (OR = 2.40, 95% CI, 1.38-4.19), >24 months of total delay (OR = 4.35, 95% CI, 2.33-8.11), detected by non skin-clinic (OR = 3.21, 95% CI, 1.68-6.14), known infectious source (OR = 1.77, 95% CI, 1.01-3.12) were associated with G2D. CONCLUSION: A few scattered cases still can be seen in post-elimination era and some kind of leprosy control program is still necessary. Government commitments including adequate financial security and strong policy support are vital. Comprehensive case-finding measures including health promotion, personnel training, reward-offering, with an emphasis on former high or middle endemic areas, are necessary to improve early presentation of suspected cases and to increase suspicion and encourage participation of all relevant medical staff. Symptom surveillance based on a powerful transfer center may play an important role in the early detection of new cases in post-elimination era.

Seroprevalence and associated factors of HSV-2 infection among general population in Shandong Province, China.

BACKGROUND: Herpes simplex virus type-2 (HSV-2) infection is the main cause of genital ulcer disease and increases the risk of HIV acquisition. Little information is available regards the epidemiological characteristics of HSV-2 among general population in China. The aim of this study was to explore seroprevalence and associated factors of HSV-2 and provide information for design of HSV-2 control strategy in Shandong, China. METHODS: In this cross-sectional study, a total of 8074 persons, 18-49 years of age, were selected using multi-stage probability sampling to represent the general population of Shandong in 2016. Demographic data were collected through face-to-face interviews. Other variables were obtained by self-administered questionnaire surveys. Blood was collected for HSV-2 IgG detection with ELISA. RESULTS: A total of 7256 sexually-active participants were included in the analysis. The weighted seroprevalence of HSV-2 infection was 4.2% (95% confidence interval [CI], 3.2-5.3) in females, which was significant higher than that in males (2.7%; 95% CI, 1.1-4.2) (P = 0.04). The seroprevalence of HSV-2 was higher in individuals from eastern region (6.4%; 95% CI, 5.9-6.9) and urban areas (4.3%; 95% CI, 2.6-6.0) of Shandong than those from other regions (P < 0.01). Associated factors for HSV-2 infection among men were being urban residents (adjusted odds ratio [AOR], 2.36; 95% CI, 1.14-4.88), having two or more sex partners in the past year (AOR, 3.22; 95% CI, 1.90-5.43) and having commercial sex (AOR, 1.51; 95% CI, 1.00-2.26). Among females, being divorced or widowed (AOR, 1.79; 95% CI, 1.08-2.97), having a tattoo (AOR, 2.89; 95% CI, 1.07-7.84), and being dissatisfied with the sex activity quality (AOR, 2.12; 95% CI, 1.24-3.63) was associated with HSV-2 infection. CONCLUSIONS: This study showed a relatively low burden of HSV-2 in Shandong province, China compared with the seroprevalence reported in many other provinces and countries. HSV-2 control programs in Shandong should focus on eastern, urban and female residents, and pay more attention to individuals with identified associated factors.

Availability of benzathine penicillin G for syphilis treatment in Shandong Province, Eastern China.

BACKGROUND: The shortage of benzathine penicillin G (BPG) worldwide presents a major challenge in the treatment of syphilis. Its availability for syphilis treatment has not been adequately evaluated in China. METHODS: Two surveys were conducted among hospitals providing sexually transmitted infection clinical services in Shandong Province in 2012 and 2018. Data on the basic information and BPG availability of the surveyed hospitals and related factors were collected and analyzed using SPSS 17.0. RESULTS: A total of 433 and 515 hospitals were surveyed in 2012 and 2018, respectively. A significant difference in BPG availability was observed among different levels and types of hospitals both in 2012 (X2 = 9.747, p = 0.008; X2 = 37.167, p = 0.000) and 2018 (X2 = 11.775, p = 0.003; X2 = 28.331, p = 0.000). The BPG availability among surveyed hospitals increased from 45.0% in 2012 to 56.4% in 2018 (X2 = 11.131, p = 0.001). The BPG availability was higher in 2018 than in 2012 among county-level hospitals (52.0% vs. 40.8%, X2 = 7.783, p = 0.005), general western medicine hospitals (62.1% vs. 50.0%, X2 = 6.742, p = 0.009), maternal and child health hospitals (57.1% vs. 26.9%, X2 = 13.906, p = 0.000), and public hospitals (56.8% vs. 45.0%, X2 = 11.361, p = 0.001). However, the county-level availability of BPG (at least one hospital has BPG in a county-level unit) has not improved between 2012 and 2018 (65.93% vs. 70.34%; X2 = 0.563, p = 0.453). The absences of clinical needs, restriction of clinical antibacterial drugs, and lack of qualifications for providing syphilis treatment were the major reasons for the low BPG availability of hospitals. CONCLUSIONS: BPG availability for syphilis treatment in Shandong Province remains low and presents disparities among different levels and types of hospitals, although it has been improved in recent years. The low availability of BPG for syphilis treatment in China is related to its clinical use by doctors rather than the market supply. Health care reforms should further improve the availability and accessibility of health services.

Evaluation of Prospective HLA-B*13:01 Screening to Prevent Dapsone Hypersensitivity Syndrome in Patients With Leprosy.

Importance: Dapsone hypersensitivity syndrome (DHS) is the most serious adverse reaction associated with dapsone administration and one of the major causes of death in patients with leprosy, whose standard treatment includes multidrug therapy (MDT) with dapsone, rifampicin, and clofazimine. Although the HLA-B*13:01 polymorphism has been identified as the genetic determinant of DHS in the Chinese population, no studies to date have been done to evaluate whether prospective HLA-B*13:01 screening could prevent DHS by identifying patients who should not receive dapsone. Objective: To evaluate the clinical use of prospective HLA-B*13:01 screening for reduction of the incidence of DHS by excluding dapsone from the treatment for patients with HLA-B*13:01-positive leprosy. Design, Setting, and Participants: A prospective cohort study was conducted from February 15, 2015, to April 30, 2018, in 21 provinces throughout China. A total of 1539 patients with newly diagnosed leprosy were enrolled who had not received dapsone previously. After excluding patients who had a history of allergy to sulfones or glucose-6-phosphate dehydrogenase deficiency, 1512 individuals underwent HLA-B*13:01 genotyping. All of the patients were followed up weekly for the first 8 weeks after treatment to monitor for adverse events. Exposures: Patients who were HLA-B*13:01 carriers were instructed to eliminate dapsone from their treatment regimens, and noncarrier patients received standard MDT. Main Outcomes and Measures: The primary outcome was the incidence of DHS. The historical incidence rate of DHS (1.0%) was used as a control. Results: Among 1512 patients (1026 [67.9%] men, 486 [32.1%] women; mean [SD] age, 43.1 [16.2] years), 261 (17.3%) were identified as carriers of the HLA-B*13:01 allele. A total of 714 adverse events in 384 patients were observed during the follow-up period. Dapsone hypersensitivity syndrome did not develop in any of the 1251 patients who were HLA-B*13:01-negative who received dapsone, while approximately 13 patients would be expected to experience DHS, based on the historical incidence rate of 1.0% per year (P = 2.05 × 10-5). No significant correlation was found between other adverse events, including dermatologic or other events, and HLA-B*13:01 status. Conclusions and Relevance: Prospective HLA-B*13:01 screening and subsequent elimination of dapsone from MDT for patients with HLA-B*13:01-positive leprosy may significantly reduce the incidence of DHS in the Chinese population.

Prevalence, risk factors, and medical costs of Chlamydia trachomatis infections in Shandong Province, China: a population-based, cross-sectional study.

BACKGROUND: A population-based study of Chlamydia trachomatis (CT) infections is essential in designing a specific control program; however, no large investigation of CT infections among the general population in mainland China has been conducted since 2000. We aimed to determine the prevalence, risk factors, and associated medical costs of CT among residents, 18-49 years of age, in Shandong, China. METHODS: From May to August 2016, a multistage probability sampling survey involving 8074 individuals was distributed. Data were collected via face-to-face interviews, followed by self-administered questionnaire surveys. First-void urines were collected and tested for CT and Neisseria gonorrhoeae (NG) using nucleic acid amplification. RESULTS: The weighted prevalence of CT infection was 2.3% (95% confidence interval [CI], 1.5-3.2) in females and 2.7% (1.6-3.8) in males. Women, 30-34 years of age, had the highest prevalence of CT infections (3.5%, 2.6-4.4), while the highest prevalence of CT infections in males was in those 18-24 years of age (4.3%, 0.0-8.8). Neisseria gonorrhoeae infection had a prevalence of 0.1% (0.0-0.3) in women and 0.03% (0.0-0.1) in men. Risk factors for CT infections among females included being unmarried, divorced, or widowed (odds ratio [OR], 95% CI 3.57, 1.54-8.24) and having two or more lifetime sex partners (3.72, 1.14-12.16). Among males, first intercourse before 20 years of age (1.83, 1.10-3.02) and having two or more lifetime sex partners (1.85, 1.14-3.02) were associated with CT infections. The estimated lifetime cost of CT infections in patients 18-49 years of age in Shandong was 273 million (range, 172-374 million) China Renminbi in 2016. CONCLUSIONS: This study demonstrated a high burden of CT infections among females < 35 years of age and males < 25 years of age in Shandong. Thus, a CT infection control program should focus on this population, as well as others with identified risk factors.

Prediction of leprosy in the Chinese population based on a weighted genetic risk score.

Genome wide association studies (GWASs) have revealed multiple genetic variants associated with leprosy in the Chinese population. The aim of our study was to utilize the genetic variants to construct a risk prediction model through a weighted genetic risk score (GRS) in a Chinese set and to further assess the performance of the model in identifying higher-risk contact individuals in an independent set. The highest prediction accuracy, with an area under the curve (AUC) of 0.743 (95% confidence interval (CI): 0.729-0.757), was achieved with a GRS encompassing 25 GWAS variants in a discovery set that included 2,144 people affected by leprosy and 2,671 controls. Individuals in the high-risk group, based on genetic factors (GRS > 28.06), have a 24.65 higher odds ratio (OR) for developing leprosy relative to those in the low-risk group (GRS≤18.17). The model was then applied to a validation set consisting of 1,385 people affected by leprosy and 7,541 individuals in contact with leprosy, which yielded a discriminatory ability with an AUC of 0.707 (95% CI: 0.691-0.723). When a GRS cut-off value of 22.38 was selected with the optimal sensitivity and specificity, it was found that 39.31% of high risk contact individuals should be screened in order to detect leprosy in 64.9% of those people affected by leprosy. In summary, we developed and validated a risk model for the prediction of leprosy that showed good discrimination capabilities, which may help physicians in the identification of patients coming into contact with leprosy and are at a higher-risk of developing this condition.

Comparison of Doxycycline and Benzathine Penicillin G for the Treatment of Early Syphilis.

Doxycycline is the preferred recommended second-line treatment for the treatment of early syphilis. Recent reports showed a declining efficacy trend of doxycycline in treatment of early syphilis. The aim of our study was to assess the serological response to the treatment for early syphilis with doxycycline compared with benzathine penicillin G and evaluate whether doxycycline is still an effective agent for the treatment of early syphilis. A record-based retrospective study was conducted. Patients were diagnosed with early syphilis in an sexually transmitted disease (STD) clinic from January 1, 2008 to December 31, 2014. They were treated with a single dose of benzathine penicillin G 2.4MU or oral doxycycline 100 mg twice daily for 14 days. Pearson's chi-squared test was used for data analysis. 601 cases were included in the final study sample: 105 (17.5%) patients received a 14-day course of doxycycline (doxycycline group), and 496 (82.5%) patients received single-dose benzathine penicillin G (BPG group). The serological responses at 6 months and 12 months after treatment were compared. No statistically significant differences were found between the two groups at 6 months (69.52% vs. 75.00%, P=0.245), and at 12 months (92.38% vs. 96.17%, P=0.115). Doxycycline is still an effective agent for the treatment of early syphilis.

Genome-Wide Analysis of Protein-Coding Variants in Leprosy.

Although genome-wide association studies have greatly advanced our understanding of the contribution of common noncoding variants to leprosy susceptibility, protein-coding variants have not been systematically investigated. We carried out a three-stage genome-wide association study of protein-coding variants in Han Chinese, of whom were 7,048 leprosy patients and 14,398 were healthy control subjects. Seven coding variants of exome-wide significance were discovered, including two rare variants: rs145562243 in NCKIPSD (P = 1.71 × 10-9, odds ratio [OR] = 4.35) and rs149308743 in CARD9 (P = 2.09 × 10-8, OR = 4.75); three low-frequency variants: rs76418789 in IL23R (P = 1.03 × 10-10, OR = 1.36), rs146466242 in FLG (P = 3.39 × 10-12, OR = 1.45), and rs55882956 in TYK2 (P = 1.04 × 10-6, OR = 1.30); and two common variants: rs780668 in SLC29A3 (P = 2.17 × 10-9, OR = 1.14) and rs181206 in IL27 (P = 1.08 × 10-7, OR = 0.83). Discovered protein-coding variants, particularly low-frequency and rare ones, showed involvement of skin barrier and endocytosis/phagocytosis/autophagy, in addition to known innate and adaptive immunity, in the pathogenesis of leprosy, highlighting the merits of protein-coding variant studies for complex diseases.

TRENDS IN THE PREVALENCE OF SYPHILIS AMONG OLDER ADULTS IN SHANDONG, CHINA.

The epidemiology of syphilis among older adults in China has not been well studied. We studied changes over time in the prevalence of syphilis among older adults in Shandong, China to inform a syphilis intervention program in order to develop management strategies. We retrospectively reviewed passive surveillance data of syphilis among older adults in Shandong, China during 2008-2013, reported by clinicians in medical facilities. The data included the stage of syphilis, age of patient and gender by year. The prevalences for first, second, latent and overall syphilis by age among adults aged ≥60 years in Shandong were 0.92, 0.70, 2.37 and 3.92 cases per 100,000 population in 2008 and 2.66, 1.99, 9.11 and 13.95 cases per 100,000 population in 2013; giving average yearly increases of 23.66%, 23.24%, 30.90% and 28.90%, respectively. The reported overall prevalence of syphilis among those aged ≥80 years was greater than the general population (8.25 vs 4.38 cases per 100,000 population in 2008; 21.99 vs 13.95 cases per 100,000 population in 2013). The prevalence of syphilis is increasing in the study population. Age appropriate interventions are needed to reduce the prevalence of syphilis in the study population.

Discovery of six new susceptibility loci and analysis of pleiotropic effects in leprosy.

Genome-wide association studies (GWAS) have led to the discovery of several susceptibility loci for leprosy with robust evidence, providing biological insight into the role of host genetic factors in mycobacterial infection. However, the identified loci only partially explain disease heritability, and additional genetic risk factors remain to be discovered. We performed a 3-stage GWAS of leprosy in the Chinese population using 8,313 cases and 16,017 controls. Besides confirming all previously published loci, we discovered six new susceptibility loci, and further gene prioritization analysis of these loci implicated BATF3, CCDC88B and CIITA-SOCS1 as new susceptibility genes for leprosy. A systematic evaluation of pleiotropic effects demonstrated a high tendency for leprosy susceptibility loci to show association with autoimmunity and inflammatory diseases. Further analysis suggests that molecular sensing of infection might have a similar pathogenic role across these diseases, whereas immune responses have discordant roles in infectious and inflammatory diseases.

An association study of TOLL and CARD with leprosy susceptibility in Chinese population.

Previous genome-wide association studies (GWASs) identified multiple susceptibility loci that have highlighted the important role of TLR (Toll-like receptor) and CARD (caspase recruitment domain) genes in leprosy. A large three-stage candidate gene-based association study of 30 TLR and 47 CARD genes was performed in the leprosy samples of Chinese Han. Of 4363 SNPs investigated, eight SNPs showed suggestive association (P < 0.01) in our previously published GWAS datasets (Stage 1). Of the eight SNPs, rs2735591 and rs4889841 showed significant association (P < 0.001) in an independent series of 1504 cases and 1502 controls (Stage 2), but only rs2735591 (next to BCL10) showed significant association in the second independent series of 938 cases and 5827 controls (Stage 3). Rs2735591 showed consistent association across the three stages (P > 0.05 for heterogeneity test), significant association in the combined validation samples (Pcorrected = 5.54 × 10(-4) after correction for 4363 SNPs tested) and genome-wide significance in the whole GWAS and validation samples (P = 1.03 × 10(-9), OR = 1.24). In addition, we demonstrated the lower expression of BCL10 in leprosy lesions than normal skins and a significant gene connection between BCL10 and the eight previously identified leprosy loci that are associated with NFκB, a major regulator of downstream inflammatory responses, which provides further biological evidence for the association. We have discovered a novel susceptibility locus on 1p22, which implicates BCL10 as a new susceptibility gene for leprosy. Our finding highlights the important role of both innate and adaptive immune responses in leprosy.

Gender difference in the characteristics of and high-risk behaviours among non-injecting heterosexual methamphetamine users in Qingdao, Shandong Province, China.

BACKGROUND: Despite the increasing risk of HIV infections, few studies concerning the characteristics of non-injecting heterosexual methamphetamine (MA) users and related risk behaviours have been conducted in China. METHODS: Gender differences in socio-demographic characteristics, perception of MA and STD/HIV, MA use practices, and sexual behaviours related to MA use were examined among 398 non-injecting heterosexual MA users (288 males, 110 females). RESULTS: Male MA users were more likely to be married, local, and self-employed; female MA users were more likely to be young, single, engaged in commercial service or unemployed. Female MA users usually start MA use at an earlier age than males (24.3 vs. 31.3 years old), with shorter abuse durations (2.6 vs. 2.9 years), higher frequency of MA use (3.6 vs. 2.4 times per week), and higher likelihood of using MA with heterosexual partners (100% vs. 78.1%). More male MA users have had multiple sex partners (96.9% vs. 77.3%) and sex exchanges (72.9% vs. 46.4%). Among 277 males who had had sex with commercial sex workers (CSW), 69.4% never used condoms, and among 77 males who had had sex with multiple partners who are commercial sex workers and always or usually used condoms, 87.0% never changed condoms when changing partners. CONCLUSION: There may be gender difference in the characteristics of high-risk behaviours among non-injecting heterosexual MA users. The findings suggest the integration of specific risk reduction strategies into intervention programs for non-injecting heterosexual MA user populations may significantly improve program goals.

Identification of IL18RAP/IL18R1 and IL12B as leprosy risk genes demonstrates shared pathogenesis between inflammation and infectious diseases.

Of eight leprosy susceptibility loci identified by genome-wide association studies, five have been implicated in Crohn disease, suggesting a common genetic fingerprint between leprosy and inflammatory bowel disease (IBD). Here, we conducted a multiple-stage genetic association study of 133 IBD susceptibility loci in multiple leprosy samples (totaling 4,971 leprosy cases and 5,503 controls) from a Chinese population and discovered two associations at rs2058660 on 2q12.1 (p = 4.57 × 10(-19); odds ratio [OR] = 1.30) and rs6871626 on 5q33.3 (p = 3.95 × 10(-18); OR = 0.75), implicating IL18RAP/IL18R1 and IL12B as susceptibility genes for leprosy. Our study reveals the important role of IL12/IL18-mediated transcriptional regulation of IFN-γ production in leprosy, and together with previous findings, it demonstrates the shared genetic susceptibility between infectious and inflammatory diseases.