Differential Quantification of Cutibacterium acnes Phylotypes IA and IB/II on Healthy and Acne-Prone Human Skin

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.