ArticleBMC infectious diseases2014
Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples.
Article in BMC infectious diseases, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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Who cites it
51 citing papers in PubMed.
- A new core-genome MLST approach for Chlamydia trachomatis genomic surveillance and research.Nature communications · 2026Article
- Methods, applications, and computational challenges in bait capture enrichment.Cell reports methods · 2025Review
- Evolutionary dynamics in the genome of ocularMicrobial genomics · 2025Article
- Resistome and virulome determination inMicrobiology spectrum · 2025Article
- Homogeneity Between Cervical and Vaginal Microbiomes and the Diagnostic Limitations of 16S Sequencing for STI Pathogens at Higher Ct Values.International journal of molecular sciences · 2025Article
- Evaluating methods for genome sequencing ofMicrobial genomics · 2025Article
- Enriching the future of public health microbiology with hybridization bait capture.Clinical microbiology reviews · 2024Review
- Advances in Host Depletion and Pathogen Enrichment Methods for Rapid Sequencing-Based Diagnosis of Bloodstream Infection.The Journal of molecular diagnostics : JMD · 2024Review
- High performanceApplied and environmental microbiology · 2024Article
- A proof of concept for a targeted enrichment approach to the simultaneous detection and characterization of rickettsial pathogens from clinical specimens.Frontiers in microbiology · 2024Article
- Core genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing.BMC infectious diseases · 2023Article
- Molecular Capture ofInternational journal of molecular sciences · 2023Article
- Genome organization and genomics inFrontiers in cellular and infection microbiology · 2023Review
- Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.Pathogens (Basel, Switzerland) · 2022Review
- Target-enrichment sequencing yields valuable genomic data for challenging-to-culture bacteria of public health importance.Microbial genomics · 2022Article
- Genomics of Ocular Chlamydia trachomatis After 5 Years of SAFE Interventions for Trachoma in Amhara, Ethiopia.The Journal of infectious diseases · 2022Article
- Diagnosis of Chlamydia trachomatis genital infections in the era of genomic medicine.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2021Review
- Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs.mSphere · 2021Article
- Chlamydiae - What's New?Journal of veterinary research · 2020Article
- Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity.PLoS neglected tropical diseases · 2020Article
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Authors and funding
14 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundChlamydia trachomatis is a pathogen of worldwide importance, causing more than 100 million cases of sexually transmitted infections annually. Whole-genome sequencing is a powerful high resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography and mutations associated with antimicrobial resistance. The objective of this study was to perform whole-genome enrichment and sequencing of C. trachomatis directly from clinical samples.
methodsC. trachomatis positive samples comprising seven vaginal swabs and three urine samples were sequenced without prior in vitro culture in addition to nine cultured C. trachomatis samples, representing different serovars. A custom capture RNA bait set, that captures all known diversity amongst C. trachomatis genomes, was used in a whole-genome enrichment step during library preparation to enrich for C. trachomatis DNA. All samples were sequenced on the MiSeq platform.
resultsFull length C. trachomatis genomes (>95-100% coverage of a reference genome) were successfully generated for eight of ten clinical samples and for all cultured samples. The proportion of reads mapping to C. trachomatis and the mean read depth across each genome were strongly linked to the number of bacterial copies within the original sample. Phylogenetic analysis confirmed the known population structure and the data showed potential for identification of minority variants and mutations associated with antimicrobial resistance. The sensitivity of the method was >10-fold higher than other reported methodologies.
conclusionsThe combination of whole-genome enrichment and deep sequencing has proven to be a non-mutagenic approach, capturing all known variation found within C. trachomatis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of C. trachomatis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
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