Genomics of Ocular Chlamydia trachomatis After 5 Years of SAFE Interventions for Trachoma in Amhara, Ethiopia.

BACKGROUND: To eliminate trachoma as a public health problem, the World Health Organization recommends the SAFE (surgery, antibiotics, facial cleanliness, and environmental improvement) strategy. As part of the SAFE strategy in the Amhara Region, Ethiopia, the Trachoma Control Program distributed >124 million doses of antibiotics between 2007 and 2015. Despite this, trachoma remained hyperendemic in many districts and a considerable level of Chlamydia trachomatis (Ct) infection was evident. METHODS: We utilized residual material from Abbott m2000 Ct diagnostic tests to sequence 99 ocular Ct samples from Amhara and investigated the role of Ct genomic variation in continued transmission of Ct. RESULTS: Sequences were typical of ocular Ct at the whole-genome level and in tissue tropism-associated genes. There was no evidence of macrolide resistance in this population. Polymorphism around the ompA gene was associated with village-level trachomatous inflammation-follicular prevalence. Greater ompA diversity at the district level was associated with increased Ct infection prevalence. CONCLUSIONS: We found no evidence for Ct genomic variation contributing to continued transmission of Ct after treatment, adding to evidence that azithromycin does not drive acquisition of macrolide resistance in Ct. Increased Ct infection in areas with more ompA variants requires longitudinal investigation to understand what impact this may have on treatment success and host immunity

Precision of the Abbott RealTime Assay in the Detection of Ocular Chlamydia trachomatis in a Trachoma-Endemic Area of Ethiopia.

Nucleic acid amplification tests are increasingly used to detect ocular chlamydia infection in trachoma research and programs. To evaluate the reliability of Chlamydia trachomatis detection by the Abbott RealTime CT/NG assay (Abbott Molecular, Inc., Des Plaines, IL) on the m2000 platform, three conjunctival samples were collected from each of 200 children aged 0-9 years in Ethiopia: two from the right eye and one from the left eye. Four aliquots were processed for each child: two from the first right eye sample, one from the second right eye sample, and one from the left eye sample. Sixty-nine swabs were processed in a U.S. laboratory and 131 in an Ethiopian laboratory. Intra-class correlation coefficients (ICCs) were high when comparing two aliquots from the same swab (ICC ranged from 0.96 to 0.99), two separate swabs from the right eye (0.89-0.91), and one right and one left eye swab (0.87-0.89), indicating reliable chlamydial load assessment across different samples and laboratory settings

Prevalence of soil-transmitted helminths and Schistosoma mansoni among a population-based sample of school-age children in Amhara region, Ethiopia

Abstract Background From 2011 to 2015, seven trachoma impact surveys in 150 districts across Amhara, Ethiopia, included in their design a nested study to estimate the zonal prevalence of intestinal parasite infections including soil-transmitted helminths (STH) and Schistosoma mansoni. Methods A multi-stage cluster random sampling approach was used to achieve a population-based sample of children between the ages of 6 and 15 years. Stool samples of approximately 1 g were collected from assenting children, preserved in 10 ml of a sodium acetate-acetic acid-formalin solution, and transported to the Amhara Public Health Research Institute for processing with the ether concentration method and microscopic identification of parasites. Bivariate logistic and negative binomial regression were used to explore associations with parasite prevalence and intensity, respectively. Results A total of 16,955 children were selected within 768 villages covering 150 districts representing all ten zones of the Amhara region. The final sample included 15,455 children of whom 52% were female and 75% reported regularly attending school. The regional prevalence among children of 6 to 15 years of age was 36.4% (95% confidence interval, CI: 34.9–38.0%) for any STH and 6.9% (95% CI: 5.9–8.1%) for S. mansoni. The zonal prevalence of any STH ranged from 12.1 to 58.3%, while S. mansoni ranged from 0.5 to 40.1%. Categories of risk defined by World Health Organization guidelines would indicate that 107 districts (71.3%) warranted preventive chemotherapy (PC) for STH and 57 districts (38.0%) warranted PC for schistosomiasis based solely on S. mansoni. No statistical differences in the prevalence of these parasites were observed among boys and girls, but age and school attendance were both associated with hookworm infection (prevalence odds ratio, POR: 1.02, P = 0.03 per 1 year, and POR: 0.81, P = 0.001, respectively) and age was associated with infection by any STH (POR: 1.02, P = 0.03). Age was also associated with reduced intensity of Ascaris lumbricoides infection (unadjusted rate ratio: 0.96, P = 0.02) and increased intensity of hookworm infection (unadjusted rate ratio: 1.07, P < 0.001). Conclusions These surveys determined that between 2011 and 2015, STH and Schistosoma mansoni were present throughout the region, and accordingly, these results were used to guide PC distribution to school-age children in Amhara

Community Hand-Dug Wells for Trachoma: A Cluster-Randomized Trial.

The WHO recommends improving access to water as part of a comprehensive strategy for elimination of trachoma as a public health problem; however, this recommendation is not based on evidence from randomized trials. In a region of Ethiopia with hyperendemic trachoma, seven communities were randomized to a hand-dug well (HDW) and seven communities to no intervention to determine the impact of HDWs on the community prevalence of ocular chlamydia infection (primary prespecified outcome). All communities continued to receive government hygiene and sanitation services and outreach. Participants were not masked, given the nature of the intervention, but laboratory personnel were masked to treatment allocation. Hand-dug wells were successfully built in six of the seven communities; five of these wells were still functional at the conclusion of the trial. At the end of the trial, an average of 74% of households reported traveling &lt; 30 minutes to collect water in the HDW arm, compared with 45% in the control arm, and the daily volume of water used for hygiene was similar (e.g., mean of 0.7 L per person in each arm). The pseudo-median prevalence of ocular chlamydia among 0- to 5-year old children at the 24-month visit was 23% in the HDW group and 13% in the control group (P &gt; 0.99). This small cluster-randomized trial provided no evidence to suggest that simply constructing HDWs, in the absence of other hygiene promotion activities, is effective for reducing transmission of ocular chlamydia

Targeted Antibiotics for Trachoma: A Cluster-Randomized Trial.

BackgroundCurrent guidelines recommend community-wide mass azithromycin for trachoma, but a targeted treatment strategy could reduce the volume of antibiotics required.MethodsIn total, 48 Ethiopian communities were randomized to mass, targeted, or delayed azithromycin distributions. In the targeted arm, only children aged 6 months to 5 years with evidence of ocular chlamydia received azithromycin, distributed thrice over the following year. The primary outcome was ocular chlamydia at months 12 and 24, comparing the targeted and delayed arms (0-5 year-olds, superiority analysis) and the targeted and mass azithromycin arms (8-12 year-olds, noninferiority analysis, 10% noninferiority margin).ResultsAt baseline, the mean prevalence of ocular chlamydia in the 3 arms ranged from 7% to 9% among 0-5 year-olds and from 3% to 9% among 8-12 year-olds. Averaged across months 12-24, the mean prevalence of ocular chlamydia among 0-5 year-olds was 16.7% (95% confidence interval [CI]: 9.0%-24.4%) in the targeted arm and 22.3% (95% CI: 11.1%-33.6%) in the delayed arm (P = .61). The final mean prevalence of ocular chlamydia among 8-12 year-olds was 13.5% (95% CI: 7.9%-19.1%) in the targeted arm and 5.5% (95% CI: 0.3%-10.7%) in the mass treatment arm (adjusted risk difference 8.5 percentage points [pp] higher in the targeted arm, 95% CI: 0.9 pp-16.1 pp higher).ConclusionsAntibiotic treatments targeted to infected preschool children did not result in significantly less ocular chlamydia infections compared with untreated communities and did not meet noninferiority criteria relative to mass azithromycin distributions. Targeted approaches may require treatment of a broader segment of the population in areas with hyperendemic trachoma

A minimum spanning tree showing the sequence-types identified in the Amhara region of Ethiopia between 2011–2017.

Each MLVA-ompA sequence-type (n = 87) is coloured by serovar. Each circle represents a different sequence-type, with the size of circle being directly proportional to the number of individuals who had that variant. Trees were generated using Phyloviz 2.0. (TIF)</p

VNTR sequence types (ST) and frequency table with Pedersen et al., [26] and Wang et al., [38] type codes for CT1335, CT1299 and CT1291. Flanking regions forward and after the repeat nucleotide regions are included.

Only sequence types found in this study are shown. Novel STs are identified with an asterisk *.</p

Ocular Chlamydia trachomatis infection and infectious load among pre-school aged children within trachoma hyperendemic districts receiving the SAFE strategy, Amhara region, Ethiopia.

BACKGROUND:After approximately 5 years of SAFE (surgery, antibiotics, facial cleanliness, environmental improvement) interventions for trachoma, hyperendemic (trachomatous inflammation-follicular (TF) ≥30%) districts remained in Amhara, Ethiopia. This study's aim was to characterize the epidemiology of Chlamydia trachomatis (Ct) infection and load among pre-school aged children living under the SAFE strategy. METHODS:Conjunctival swabs from a population-based sample of children aged 1-5 years collected between 2011 and 2015 were assayed to provide Ct infection data from 4 endemic zones (comprised of 58 districts). Ct load was determined using a calibration curve. Children were graded for TF and trachomatous inflammation-intense (TI). RESULTS:7,441 children were swabbed in 4 zones. TF and TI prevalence were 39.9% (95% confidence Interval [CI]: 37.5%, 42.4%), and 9.2% (95% CI: 8.1%, 10.3%) respectively. Ct infection prevalence was 6.0% (95% CI: 5.0%, 7.2%). Infection was highest among children aged 2 to 4 years (6.6%-7.0%). Approximately 10% of infection occurred among children aged 1 year. Ct load decreased with age (P = 0.002), with the highest loads observed in children aged 1 year (P = 0.01) vs. aged 5 years. Participants with TF (P = 0.20) and TI (P<0.01) had loads greater than individuals without active trachoma. CONCLUSIONS:In this hyperendemic setting, it appears that the youngest children may contribute in meaningful ways towards persistent active trachoma

WGS results from 99 samples vs Sanger sequencing results for the three VNTRs CT1291, CT1299 and CT1335.

WGS: Whole genome sequencing. VNTR: Variable number tandem repeat. (DOCX)</p

Map of the Amhara region of Ethiopia showing the location and proportion of <i>Chlamydia trachomatis</i> serovars A, B and Ba at the first sampling time points (2011–2015) from conjunctival eye swab samples collected after the first five rounds of mass drug administration.

The size of the pie chart is proportional to how many samples are represented, with larger pie charts indicating more samples. Maps were sourced from the Trachoma Atlas (https://atlas.trachomadata.org/) which uses Open Street Maps (Mapbox).</p