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09:03
Forward Genetic Approaches in Chlamydia trachomatis
Published on: October 23, 2013
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Whole-Genome Sequencing of Chlamydia trachomatis Directly from Human Samples
Amanda Claire Brown1,2, Mette T Christiansen3
1Oxford Gene Technology, Oxford, UK. amanda.brown@cornell.edu.
Methods in Molecular Biology (Clifton, N.J.)
|August 7, 2019
Summary
Whole-genome sequencing of Chlamydia trachomatis from clinical samples is now feasible. A novel enrichment and deep sequencing method overcomes low pathogen DNA levels for rapid bacterial genome analysis.
Area of Science:
- Microbiology
- Genomics
- Infectious Diseases
Background:
- Whole-genome sequencing provides high-resolution data on bacterial populations, phylogeography, and antimicrobial resistance mutations.
- Sequencing pathogen genomes directly from clinical samples offers time and labor savings, particularly for difficult-to-culture organisms like Chlamydia trachomatis.
- Low pathogen nucleic acid levels and high host/microbiota DNA/RNA in clinical samples currently limit direct whole-genome sequencing.
Purpose of the Study:
- To develop a method for rapid whole-genome sequencing of Chlamydia trachomatis directly from clinical specimens.
- To overcome the challenge of low pathogen nucleic acid concentration in clinical samples.
- To enable accurate analysis of bacterial population structure and antimicrobial resistance.
Main Methods:
- Utilized a combination of whole-genome enrichment and deep sequencing techniques.
- The approach was confirmed to be nonmutagenic.
- Applied the method to capture all known variations within Chlamydia trachomatis genomes.
Main Results:
- Demonstrated a consistent and sensitive method for whole-genome sequencing of Chlamydia trachomatis.
- Enabled rapid sequencing directly from clinical samples, bypassing the need for in vitro culturing.
- Successfully captured comprehensive genomic variation.
Conclusions:
- The developed method facilitates efficient whole-genome sequencing of Chlamydia trachomatis from clinical samples.
- This approach offers significant advantages for studying bacterial pathogens, especially those that are slow-growing or obligate intracellular.
- The technique has potential for adaptation to other clonal pathogens.
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