ArticlePloS one2014
Direct amplification, sequencing and profiling of Chlamydia trachomatis strains in single and mixed infection clinical samples.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- Prevalence and Genetic Characterization ofThe Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale · 2025Article
- Enhancing Meningococcal Genomic Surveillance in the Meningitis Belt Using High-Resolution Culture-Free Whole-Genome Sequencing.The Journal of infectious diseases · 2022Article
- Evaluation of Urethrotropic-Clade Meningococcal Infection by Urine Metagenomic Shotgun Sequencing.Journal of clinical microbiology · 2022Article
- Whole Genome Sequencing and Comparative Genome Analyses ofPathogens (Basel, Switzerland) · 2021Article
- Chlamydiae - What's New?Journal of veterinary research · 2020Article
- High-resolution sweep metagenomics using fast probabilistic inference.Wellcome open research · 2020Article
- Comparison of reverse hybridization and ompA sequencing methods applied on Chlamydia trachomatis strains from Tunisia.MicrobiologyOpen · 2018Article
- Culture-independent approaches to chlamydial genomics.Microbial genomics · 2018Review
- Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review.European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology · 2017Review
- Demonstration of Persistent Infections and Genome Stability by Whole-Genome Sequencing of Repeat-Positive, Same-Serovar Chlamydia trachomatis Collected From the Female Genital Tract.The Journal of infectious diseases · 2017Article
- Rapid detection and strain typing of Chlamydia trachomatis using a highly multiplexed microfluidic PCR assay.PloS one · 2017Article
- Article
- Review
- Emancipating Chlamydia: Advances in the Genetic Manipulation of a Recalcitrant Intracellular Pathogen.Microbiology and molecular biology reviews : MMBR · 2016Review
- High Frequency of Chlamydia trachomatis Mixed Infections Detected by Microarray Assay in South American Samples.PloS one · 2016Article
- The single-species metagenome: subtypingPeerJ · 2016Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
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. The 100 kb target region could be amplified from clinical samples, including remnants from diagnostics tests, originating from the cervix, urethra and urine, For rapid analysis of these data, we developed a framework for whole-genome based genotyping called binstrain. We used binstrain to estimate the proportion of SNPs originating from 14 C. trachomatis reference serotype genomes in each sample. Direct DNA sequencing methods such as the one described here may have an important role in understanding the biology of C. trachomatis mixed infections and the natural genetic variation of the species within clinically relevant ecological niches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.