Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.

ABSTRACT: Sequencing bacterial genomes from DNA isolated directly from clinical samples offers the promise of rapid and precise acquisition of informative genetic information. In the case of Chlamydia trachomatis, direct sequencing is particularly desirable because it obviates the requirement for culture in mammalian cells, saving time, cost and the possibility of missing low abundance strains. In this proof of concept study, we developed methodology that would allow genome-scale direct sequencing, using a multiplexed microdroplet PCR enrichment technology to amplify a 100 kb region of the C. trachomatis genome with 500 1.1-1.3 kb overlapping amplicons (5-fold amplicon redundancy). We integrated comparative genomic data into a pipeline to preferentially select conserved sites for amplicon design. Th

SUBMITTER: Joseph SJ 

PROVIDER: S-EPMC4074039 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature