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Journal of Clinical Microbiology
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Bacteriology

Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

Sarah Mollerup, Jens Friis-Nielsen, Lasse Vinner, Thomas Arn Hansen, Stine Raith Richter, Helena Fridholm, Jose Alejandro Romero Herrera, Ole Lund, Søren Brunak, Jose M. G. Izarzugaza, Tobias Mourier, Lars Peter Nielsen, Anders Johannes Hansen
C.-A. D. Burnham, Editor
Sarah Mollerup
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Jens Friis-Nielsen
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Lasse Vinner
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Thomas Arn Hansen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Stine Raith Richter
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Helena Fridholm
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Jose Alejandro Romero Herrera
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Ole Lund
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Søren Brunak
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, DenmarkDisease Systems Biology Program, Panum Institute, University of Copenhagen, Copenhagen, Denmark
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Jose M. G. Izarzugaza
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
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Tobias Mourier
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Lars Peter Nielsen
Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen S, and Aalborg University, Health Sciences, Aalborg, Denmark
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Anders Johannes Hansen
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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C.-A. D. Burnham
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DOI: 10.1128/JCM.02723-15
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ABSTRACT

Propionibacterium acnes is the most abundant bacterium on human skin, particularly in sebaceous areas. P. acnes is suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence of P. acnes DNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions of P. acnes DNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples. P. acnes reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that P. acnes can be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully when P. acnes is detected in clinical samples. We advocate that detection of P. acnes always be accompanied by experiments validating the association between this bacterium and any clinical condition.

FOOTNOTES

    • Received 15 October 2015.
    • Returned for modification 7 November 2015.
    • Accepted 16 January 2016.
    • Accepted manuscript posted online 27 January 2016.
  • Supplemental material for this article may be found at http://dx.doi.org/10.1128/JCM.02723-15.

  • Copyright © 2016 Mollerup et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing
Sarah Mollerup, Jens Friis-Nielsen, Lasse Vinner, Thomas Arn Hansen, Stine Raith Richter, Helena Fridholm, Jose Alejandro Romero Herrera, Ole Lund, Søren Brunak, Jose M. G. Izarzugaza, Tobias Mourier, Lars Peter Nielsen, Anders Johannes Hansen
Journal of Clinical Microbiology Mar 2016, 54 (4) 980-987; DOI: 10.1128/JCM.02723-15

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Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing
Sarah Mollerup, Jens Friis-Nielsen, Lasse Vinner, Thomas Arn Hansen, Stine Raith Richter, Helena Fridholm, Jose Alejandro Romero Herrera, Ole Lund, Søren Brunak, Jose M. G. Izarzugaza, Tobias Mourier, Lars Peter Nielsen, Anders Johannes Hansen
Journal of Clinical Microbiology Mar 2016, 54 (4) 980-987; DOI: 10.1128/JCM.02723-15
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