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

<jats:title>ABSTRACT</jats:title> <jats:p> <jats:named-content content-type="genus-species">Propionibacterium acnes</jats:named-content> is the most abundant bacterium on human skin, particularly in sebaceous areas. <jats:named-content content-type="genus-species">P. acnes</jats:named-content> 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 <jats:named-content content-type="genus-species">P. acnes</jats:named-content> 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 <jats:named-content content-type="genus-species">P. acnes</jats:named-content> 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. <jats:named-content content-type="genus-species">P. acnes</jats:named-content> reads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show that <jats:named-content content-type="genus-species">P. acnes</jats:named-content> 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 <jats:named-content content-type="genus-species">P. acnes</jats:named-content> is detected in clinical samples. We advocate that detection of <jats:named-content content-type="genus-species">P. acnes</jats:named-content> always be accompanied by experiments validating the association between this bacterium and any clinical condition. </jats:p>