Exploring the role of metagenomic deep sequencing for trachoma

PROJECT SUMMARY Trachoma, still the world’s leading infectious cause of blindness, has been slated for elimination by 2030 by the World Health Organization (WHO). The elimination strategy, which relies to a large extent on annual mass azithromycin distributions, has been tremendously effective. But in some parts of the world with hyperendemic trachoma, elimination has not occurred despite more than a decade of annual mass azithromycin distributions. It is unclear why trachoma has remained stubbornly high in these places. It is possible that mass antibiotic treatments are simply not reaching enough people, but other theories have also been introduced, including the possibility of (i) antimicrobial resistance in the causative organism, Chlamydia trachomatis; (ii) extraocular reservoirs of chlamydia transmission such as the rectum; and (iii) non-chlamydial organisms that may cause a follicular conjunctivitis resembling trachoma. These theories have largely gone untested. This grant proposal seeks to leverage swabs already collected as part of other NIH-funded studies, performing metagenomic deep sequencing (MDS) to explore theories for persistent trachoma. MDS can identify all DNA and RNA sequences of a specimen in an unbiased way, and is thus useful for pathogen discovery and for assessment of gene expression. We will use MDS to assess the temporal stability of DNA and RNA sequences of chlamydia over a 4-week period, providing benchmarks on the amount of variability that could be expected. Such information will be extremely helpful when planning and interpreting future studies. We will also compare MDS results from children who did and did not clear their chlamydia infection after azithromycin treatment, providing clues about possible antimicrobial resistance genes. We will use MDS in children with chlamydia recovered from both their conjunctival and rectum in order to determine if each site has the same strain of chlamydia. Finally, we will use MDS in a group of children without chlamydia infection but with the clinical signs of trachoma to see if some unknown pathogen is responsible for causing clinical features consistent with trachoma. These exploratory analyses will be useful for providing benchmarks for future studies of MDS for ocular chlamydia, while at the same time furthering our knowledge about the potential role of antimicrobial resistance, extraocular chlamydial reservoirs, and non-chlamydial infections for trachoma.