ArticleNature protocols2013
Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Evaluating methods for genome sequencing ofMicrobial genomics · 2025Article
- The Single-Cell Sequencing: A Dazzling Light Shining on the Dark Corner of Cancer.Frontiers in oncology · 2021Review
- Chlamydiae - What's New?Journal of veterinary research · 2020Article
- The Nature and Extent of Plasmid Variation inMicroorganisms · 2020Article
- Capturing the 'ome': the expanding molecular toolbox for RNA and DNA library construction.Nucleic acids research · 2018Review
- Culture-independent approaches to chlamydial genomics.Microbial genomics · 2018Review
- Shotgun metagenomics, from sampling to analysis.Nature biotechnology · 2017Review
- Comprehensive global genome dynamics ofGenome research · 2017Article
- Treatment efficacy of azithromycin 1 g single dose versus doxycycline 100 mg twice daily for 7 days for the treatment of rectal chlamydia among men who have sex with men - a double-blind randomised controlled trial protocol.BMC infectious diseases · 2017Article
- Culture-independent genomic characterisation of Candidatus Chlamydia sanzinia, a novel uncultivated bacterium infecting snakes.BMC genomics · 2016Article
- Selective Pressure Promotes Tetracycline Resistance of Chlamydia Suis in Fattening Pigs.PloS one · 2016Article
- Culture-independent genome sequencing of clinical samples reveals an unexpected heterogeneity of infections by Chlamydia pecorum.Journal of clinical microbiology · 2015Article
- Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission.Nature communications · 2015Article
- Genomic variant representation in a Chlamydia population is dynamic and adaptive with dependence on in vitro and in vivo passage.Pathogens and disease · 2015Article
- Whole-genome enrichment and sequencing of Chlamydia trachomatis directly from clinical samples.BMC infectious diseases · 2014Article
- Article
- Capturing and cultivating single bacterial cells in gel microdroplets to obtain near-complete genomes.Nature protocols · 2014Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The study of bacterial populations using whole-genome sequencing is of considerable scientific and clinical interest. However, obtaining bacterial genomic information is not always trivial: the target bacteria may be difficult to culture or uncultured, and they may be found within samples containing complex mixtures of other contaminating microbes and/or host cells, from which it is very difficult to derive robust sequencing data. Here we describe our procedure to generate sufficient DNA for whole-genome sequencing from clinical samples and without the need for culture, as successfully used on the difficult-to-culture, obligate intracellular pathogen Chlamydia trachomatis. Our protocol combines immunomagnetic separation (IMS) for targeted bacterial enrichment with multiple displacement amplification (MDA) for whole-genome amplification (WGA), which is followed by high-throughput sequencing. Compared with other techniques that might be used to generate such data, IMS-MDA is an inexpensive, low-technology and highly transferable process that provides amplified genomic DNA for sequencing from target bacteria in under 5 h, with little hands-on time.
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Registered trials
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