Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition

Research output: Contribution to journalJournal articlepeer-review

Standard

Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition. / Fritz, Blaine; Stavnsbjerg, Camilla; Markvart, Merete; Damgaard, Peter De Barros; Nielsen, Sofie Holtsmark; Bjørndal, Lars; Qvortrup, Klaus; Bjarnsholt, Thomas.

In: Pathogens and Disease, Vol. 77, No. 1, ftz013, 2019.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Fritz, B, Stavnsbjerg, C, Markvart, M, Damgaard, PDB, Nielsen, SH, Bjørndal, L, Qvortrup, K & Bjarnsholt, T 2019, 'Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition', Pathogens and Disease, vol. 77, no. 1, ftz013. https://doi.org/10.1093/femspd/ftz013

APA

Fritz, B., Stavnsbjerg, C., Markvart, M., Damgaard, P. D. B., Nielsen, S. H., Bjørndal, L., Qvortrup, K., & Bjarnsholt, T. (2019). Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition. Pathogens and Disease, 77(1), [ftz013]. https://doi.org/10.1093/femspd/ftz013

Vancouver

Fritz B, Stavnsbjerg C, Markvart M, Damgaard PDB, Nielsen SH, Bjørndal L et al. Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition. Pathogens and Disease. 2019;77(1). ftz013. https://doi.org/10.1093/femspd/ftz013

Author

Fritz, Blaine ; Stavnsbjerg, Camilla ; Markvart, Merete ; Damgaard, Peter De Barros ; Nielsen, Sofie Holtsmark ; Bjørndal, Lars ; Qvortrup, Klaus ; Bjarnsholt, Thomas. / Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition. In: Pathogens and Disease. 2019 ; Vol. 77, No. 1.

Bibtex

@article{56479c2211db4597b5c16efea125cfd6,
title = "Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition",
abstract = "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.",
keywords = "biofilm, chronic infection, implanted device, metagenomics, microbiome, SEM",
author = "Blaine Fritz and Camilla Stavnsbjerg and Merete Markvart and Damgaard, {Peter De Barros} and Nielsen, {Sofie Holtsmark} and Lars Bj{\o}rndal and Klaus Qvortrup and Thomas Bjarnsholt",
year = "2019",
doi = "10.1093/femspd/ftz013",
language = "English",
volume = "77",
journal = "FEMS Immunology and Medical Microbiology",
issn = "2049-632X",
publisher = "Oxford University Press",
number = "1",

}

RIS

TY - JOUR

T1 - Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition

AU - Fritz, Blaine

AU - Stavnsbjerg, Camilla

AU - Markvart, Merete

AU - Damgaard, Peter De Barros

AU - Nielsen, Sofie Holtsmark

AU - Bjørndal, Lars

AU - Qvortrup, Klaus

AU - Bjarnsholt, Thomas

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - biofilm

KW - chronic infection

KW - implanted device

KW - metagenomics

KW - microbiome

KW - SEM

U2 - 10.1093/femspd/ftz013

DO - 10.1093/femspd/ftz013

M3 - Journal article

C2 - 30844070

AN - SCOPUS:85064169686

VL - 77

JO - FEMS Immunology and Medical Microbiology

JF - FEMS Immunology and Medical Microbiology

SN - 2049-632X

IS - 1

M1 - ftz013

ER -

ID: 216872643