Propionibacterium acnes: disease-causing agent or common contaminant? Detection in diverse patient samples by next generation sequencing

Sarah Mollerup, Jens Friis-Nielsen, Lasse Vinner, Stine Raith Richter, Helena Fridholm, Jose Romero Herrera, Ole Lund, Søren Brunak, Jose Maria Gonzalez-Izarzugaza, Tobias Mourier, Lars Peter Nielsen, Anders Johannes Hansen

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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 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 datasets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were either subjected to microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun-sequenced.We detected high proportions of P. acnes in enriched samples, particularly skin derived and other tissue samples, with levels being higher in enriched compared to shotgun-sequenced samples. P. acnes reads were detected in most samples analysed, 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 employing molecular methods such as next generation sequencing. 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 is always accompanied by experiments validating the association between this bacterium and any clinical condition.
    Original languageEnglish
    JournalJournal of Clinical Microbiology
    Volume54
    Issue number4
    Pages (from-to)980-987
    Number of pages8
    ISSN0095-1137
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    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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