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

Abstract

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.

Abstract

Whole-genome sequencing of ocular Chlamydia trachomatis from Amhara, Ethiopia, found no evidence of macrolide resistance, despite 5 years of trachoma control interventions, including mass distribution of azithromycin. Polymorphisms in ompA were associated with prevalence of ocular infection and trachomatous disease.