Differential Quantification of Cutibacterium acnes Phylotypes IA and IB / II

ABSTRACT

Cutibacterium acnes is a common skin bacterium that inhabits sebaceous follicles and comprises multiple phylotypes. Healthy skin is colonized by a C. acnes population dominated by phylotypes IA, IB, and II. In acne, this diversity is reduced, with a predominance of phylotype IA. Quantifying C. acnes phylotypes has been challenging due to the lack of specific methods. Here, we developed a droplet digital PCR (ddPCR) assay that separately quantifies phylotype IA and phylotypes IB/II, based on a difference in the hyaluronidase gene. The method was applied to skin swabs from 14 healthy individuals and 14 acne patients. Healthy skin contained nearly equal amounts of IA and IB/II, whereas acne samples showed a 111‐fold predominance of IA over IB/II, due to a marked depletion of IB/II, instead of an increase of IA. After 4–6 months of isotretinoin treatment, C. acnes levels decreased drastically, with phylotype IA reduced by 50‐fold. Twelve to 15 months after treatment, both phylotypes rebounded, although IB/II recovered only partially. Taken together, this ddPCR method can quantitatively distinguish the acne‐dominant phylotype IA from healthy skin‐associated phylotypes IB/II, and is thus a useful tool for skin microbiome studies and specifically for assessing C. acnes dysbiosis in acne.