Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition
| Autor: | Blaine Gabriel Fritz, Peter de Barros Damgaard, Klaus Qvortrup, Sofie Holtsmark Nielsen, Lars Bjørndal, Thomas Bjarnsholt, Camilla Stavnsbjerg, Merete Markvart |
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| Rok vydání: | 2019 |
| Předmět: |
Microbiology (medical)
Scanning electron microscope medicine.disease_cause Microbiology 03 medical and health sciences Microscopy medicine Humans Immunology and Allergy 030304 developmental biology 0303 health sciences Bacteria General Immunology and Microbiology biology 030306 microbiology Pseudomonas aeruginosa Shotgun sequencing Biofilm Biodiversity General Medicine biology.organism_classification Infectious Diseases Community composition Metagenomics Biofilms Metagenome |
| Zdroj: | Pathogens and Disease. 77 |
| ISSN: | 2049-632X |
| Popis: | Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed by characterization of the microbial community by culturing or sequencing-based approaches. A sample, therefore, must be divided prior to analysis, often leading to inconsistent results. We demonstrate a combined approach, using scanning electron microscopy and next-generation shotgun sequencing, to visually identify a biofilm and characterize the microbial community, without dividing the sample. A clinical sample recovered from a patient following a dental root-filling procedure was prepared and visualized by scanning electron microscopy. DNA was then extracted from the sample several years later and analyzed by shotgun sequencing. The method was subsequently validated on in vitro cultures of Pseudomonas aeruginosa biofilm. Between 19 and 21 different genera and species were identified in the clinical sample with an estimated relative abundance greater than 1% by two different estimation approaches. Only eight genera identified were not associated with endodontic infections. This provides a proof-of-concept for a dual, microscopy and sequencing-based approach to identify and characterize bacterial biofilms, which could also easily be implemented in other scientific fields. |
| Databáze: | OpenAIRE |
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