DNA Sequencing Helps Monitor Ocular Biome and Trachoma Potential

Chlamydia trachomatis bacteria, illustration
Chlamydia trachomatis bacteria. Computer illustration showing an inclusion composed of a group of chlamydia reticulate bodies (intracellular multiplying stage, small red spheres) near the nucleus (purple) of a cell. Chlamydia trachomatis causes a sexually transmitted infection that can go undetected causing infertility. It also causes the eye disease trachoma, which can lead to blindness.
Quarterly oral azithromycin doses reduce ocular disease-causing bacteria, but enlarge macrolide resistance after 1 year.

Macrolides, a class of antibiotics, are typically prescribed by ophthalmologists to treat eye infections, as well as by general practice physicians for illnesses such as lower respiratory tract infections. In either case, if patients develop genotypic resistance to macrolides, it can be detected in conjunctival cell samples. A report published in Cornea demonstrates DNA sequencing can help identify this antibiotic resistance, as well as monitor group microbiome changes of populations in certain geographic regions.

One such locale is the Amhara Region of northern Ethiopia, where researchers note a high prevalence of Chlamydia trachomatis. Metagenomic DNA sequencing effectively measured long-term ocular surface bacterial changes in groups of children participating in a large cluster-randomized controlled trial (Clinicaltrials.gov Identifier: NCT00322972) from May 2006 to May 2007.

Of 72 rural communities randomized to 6 treatment sets, this investigation examined 12 villages where children, average age 5 years, underwent 4 oral doses of azithromycin at 0, 3, 6, and 9 months, and 12 villages that served as a control arm. Three months after the final dose, 60 children in each community — randomly selected — were swabbed for DNA samples of the tarsal conjunctiva, right upper eyelids. Swabbed participants also underwent a clinical exam to check for signs of trachoma.

Presence of C. trachomatis was significantly decreased in treated participants, compared with the control group (P =.0003). Reduced C. trachomatis was also associated with increased ocular microbiome diversity (P =.03). For villages receiving azithromycin, differential analysis revealed Neisseria (N) meningitidis, N. lactamica,  and N. gonorrhoeae were reduced at 12 months. Further, children who underwent 4 antibiotic doses displayed “relative abundance” of bacterial species Acinetobacter, Enterobacter, and Pseudomonas. With DNA analysis, macrolide resistance genes mefA and mefE were more plentiful in the treated cohort (P =.04), but the gene ermB showed no significant difference between groups (P =.63). 

In treated villages, mean coverage with azithromycin doses comprised 80% of children. Control individuals received treatment after the study period. Because the study’s statistical assessments were calculated at a community level, and clinical data did not go further than ocular findings for individuals, this research is limited to demonstrating microbiome composition in trachoma-prone regions. 

Children may also be infected with other pathogens in the perinatal period, and azithromycin lessening of N. gonorrhoeae would add to the antibiotic’s wider spectrum benefit. “The load reduction of various pathogens seen in this study is tempered by the increase in macrolide resistance determinants on the ocular surface of children,” report investigators.


Doan T, Gebre T, Ayele B, et al. Effect of azithromycin on the ocular surface microbiome of children in a high prevalence trachoma area. Cornea. Published online September 4, 2021. doi:10.1097/ICO.0000000000002863