BMC microbiology, 2017-06, Vol.17 (1), p.133-133, Article 133
2017
Details
- Autor(en) / Beteiligte
- Titel
- Towards diagnostic metagenomics of Campylobacter in fecal samples
- Ist Teil von
- BMC microbiology, 2017-06, Vol.17 (1), p.133-133, Article 133
- Ort / Verlag
- England: BioMed Central Ltd
- Erscheinungsjahr
- 2017
- Link zum Volltext
- Quelle
- SpringerLink
- Beschreibungen/Notizen
- The development of diagnostic metagenomics is driven by the need for universal, culture-independent methods for detection and characterization of pathogens to substitute the time-consuming, organism-specific, and often culture-based laboratory procedures for epidemiological source-tracing. Some of the challenges in diagnostic metagenomics are, that it requires a great next-generation sequencing depth and unautomated data analysis. DNA from human fecal samples spiked with 7.75 × 10 -7.75 × 10 colony forming unit (CFU)/ml Campylobacter jejuni and chicken fecal samples spiked with 1 × 10 -1 × 10 CFU/g Campylobacter jejuni was sequenced and data analysis was done by the metagenomic tools Kraken and CLARK. More hits were obtained at higher spiking levels, however with no significant linear correlations (human samples p = 0.12, chicken samples p = 0.10). Therefore, no definite detection limit could be determined, but the lowest spiking levels found positive were 7.75 × 10 CFU/ml in human feces and 10 CFU/g in chicken feces. Eight human clinical fecal samples with estimated Campylobacter infection loads from 9.2 × 10 -1.0 × 10 CFU/ml were analyzed using the same methods. It was possible to detect Campylobacter in all the clinical samples. Sensitivity in diagnostic metagenomics is improving and has reached a clinically relevant level. There are still challenges to overcome before real-time diagnostic metagenomics can replace quantitative polymerase chain reaction (qPCR) or culture-based surveillance and diagnostics, but it is a promising new technology.
- Sprache
- Englisch
- Identifikatoren
- ISSN: 1471-2180eISSN: 1471-2180DOI: 10.1186/s12866-017-1041-3Titel-ID: cdi_doaj_primary_oai_doaj_org_article_d0effa69e44f4f46a215357c8d6baf65
- Format
- –
- Schlagworte
- Animals, Bacteria, Bacterial infections, Bacteriological Techniques, Campylobacter, Campylobacter Infections - diagnosis, Campylobacter jejuni - genetics, Campylobacter jejuni - growth & development, Campylobacter jejuni - isolation & purification, Chickens - microbiology, Colony-forming cells, Culture independent, Data analysis, Data processing, Deoxyribonucleic acid, Diagnosis, Diagnostic microbiology, Diagnostic software, Diagnostic systems, DNA, DNA sequencing, DNA, Bacterial - genetics, E coli, Epidemiology, Feces, Feces - microbiology, Genomes, Humans, Infections, Laboratories, Loads (forces), Metagenomics - methods, Methods, Molecular typing, New technology, Next generation sequencing, Pathogens, Polymerase chain reaction, Real time, Sensitivity and Specificity, Sequence Analysis, DNA - methods, Software, Spiking, Stool specimen analysis, Studies