A novel multilocus sequence typing scheme for the opportunistic pathogen Propionibacterium acnes and characterization of type I cell surface-associated antigens

Immune Activation and Glycolytic Responses to Cutibacterium acnes Cell Wall Polysaccharides

Carbohydrates are key components of many microbial cell walls and play a versatile role in immune recognition. In this study, we analyzed the carbohydrate cell wall composition of Cutibacterium acnes strains associated with healthy skin (denoted as CH) and acne-prone skin (denoted as CA) to understand their influence on host immune responses in acne. We identified glucose, mannose, and galactose as the primary monosaccharides, with minor amounts of fucose, N-acetylgalactosamine, and N-acetylglucosamine. Linkage analysis revealed structural variations between CH and CA strains: CH strains showed a balanced and diverse polysaccharide structure, whereas CA strains displayed a more rigid structure with 1→4 and branched 1→6 linkages, potentially contributing to inflammatory properties. Immunostimulatory assays revealed that C acnes carbohydrates induced IL-6 and IL-17 but not IL-1β, highlighting the role of carbohydrate structures in influencing cytokine responses. Treatment with sodium meta-periodate impaired this immunostimulatory activity, indicating that carbohydrate integrity is crucial for immune activation. In addition, analysis of single-cell RNA-sequencing data from acne lesions revealed elevated glycolytic activity in acne lesions in comparison with that in nonlesional skin, suggesting a Warburg-like effect that promotes inflammation. Our findings highlight the role of C acnes polysaccharides in immune modulation and inflammation, suggesting their potential as therapeutic targets for acne treatment.

Antibacterial activity and impact on keratinocyte cell growth of Cutibacterium acnes bacteriophages in a Cutibacterium acnes IA1- colonized keratinocyte model

Acne is an inflammatory disease in which microbial disbalance is represented by an augmented population of phylotype IA1 of Cutibacterium acnes. Various treatments for acne can cause side effects, and it has been reported that C. acnes is resistant to prescribed antibiotics. Phage therapy has been proposed as an alternative treatment for acne, given its species-specificity to kill bacteria, its relative innocuity, and its potential to manage antibiotic-resistant pathogens. Moreover, bacteriophages (phages) may modulate the microbiota and immune responses. Some studies have shown the potential use of phages in the treatment of acne. Nevertheless, the capacity to specifically reduce phylotype IA1 and the effect of phage treatment on skin cells are poorly understood. We assessed the capacity of phages to clear C. acnes IA1 and their effects on cell cytotoxicity and growth in HEKa cells- C. acnes IA1 co-culture. Phylotypes IA1 and IB had similar effects on HEKa cells, causing cytotoxicity and diminishing cell growth. Nevertheless, IA1 caused a higher impact on cell doubling time by increasing it 1.8 times more than cell growth control group. Even though there are no phages IA1-specific, we found phages that have a diminished effect on other phylotypes not related to acne. Phage treatment in general reduced IA1-caused cytotoxicity, with differences in efficacy among phages. In addition, phage purification was necessary to restore metabolic activity and growth of HEKa. Overall, phage evaluation as a therapeutic alternative should include phage-bacteria interactions and their impact on skin cells because of the differences that each phage can exhibit.

Cutibacterium adaptation to life on humans provides a novel biomarker of C. acnes infections

The domestication of cattle provided Propionibacteriaceae the opportunity to adapt to human skin. These bacteria constitute a distinct genus ( Cutibacterium ), and a single species within that genus ( C. acnes ) dominates 25% of human skin. C. acnes protects humans from pathogen colonization, but it can also infect indwelling medical devices inserted through human skin. Proteins that help Cutibacteria live on our skin may also act as virulence factors during an opportunistic infection, like a shoulder periprosthetic joint infection (PJI). To better understand the evolution of this commensal and opportunistic pathogen, we sought to extensively characterize one of these proteins, RoxP. This secreted protein is only found in the Cutibacterium genus, helps C. acnes grow in oxic environments, and is required for C. acnes to colonize human skin. Structure-based sequence analysis of twenty-one RoxP orthologs (71-100% identity to C. acnes strain KPA171202 RoxP_1) revealed a high-degree of molecular surface conservation and helped identify a potential heme-binding interface. Biophysical evaluation of a subset of seven RoxP orthologs (71-100% identity) demonstrated that heme-binding is conserved. Computational modeling of these orthologs suggests that RoxP heme-binding is mediated by an invariant molecular surface composed of a surface-exposed tryptophan (W66), adjacent cationic pocket, and nearby potential heme axial ligands. Further, these orthologs were found to undergo heme-dependent oligomerization. To further probe the role of this protein in C. acnes biology, we developed four monoclonal anti-RoxP antibodies, assessed the binding of those antibodies to a subset of ten RoxP orthologs (71-100% identity), developed an anti-RoxP sandwich ELISA (sELISA) with sub-nanogram sensitivity, and adapted that sELISA to quantitate RoxP in human biofluids that can be infected by C. acnes (serum, synovial fluid, cerebrospinal fluid). This study expands our understanding of how an environmental bacterium evolved to live on humans, and the assays developed in this work can now be used to identify this organism when it gains access to sterile sites to cause opportunistic infections.

Author Summary

The longer humans live, the more they require internal "replacement parts," like prosthetic joints. Increased placement of these and other medical devices has increased their complications, which frequently are infections caused by microbes that live on humans. One of these microbes is Cutibacterium acnes , which dominates 25% of human skin. It appears that when humans domesticated cattle, a C. acnes ancestor adapted from living in cows to living on people. One of these adaptations was RoxP, a protein only found in Cutibacterium and carried by all C. acnes . Here, we describe our extensive characterization of RoxP. We found that distantly related RoxP conserve high stability at the low pH found on human skin. They also conserve the ability to bind heme, a source of iron used by microbes when they infect humans. As a part of this work, we developed tests that measure RoxP to identify C. acnes growth. In a clinic or hospital, these tests could allow a doctor to rapidly identify C. acnes infections, which would improve patient outcomes and lower healthcare costs. This work has helped us better understand how C. acnes adapted to live on humans and to identify C. acnes infections of medical devices.

Association of different cell types and inflammation in early acne vulgaris

Acne vulgaris, one of the most common skin diseases, is a chronic cutaneous inflammation of the upper pilosebaceous unit (PSU) with complex pathogenesis. Inflammation plays a central role in the pathogenesis of acne vulgaris. During the inflammatory process, the innate and adaptive immune systems are coordinately activated to induce immune responses. Understanding the infiltration and cytokine secretion of differential cells in acne lesions, especially in the early stages of inflammation, will provide an insight into the pathogenesis of acne. The purpose of this review is to synthesize the association of different cell types with inflammation in early acne vulgaris and provide a comprehensive understanding of skin inflammation and immune responses.

The Microbiome and Acne: Perspectives for Treatment

The skin microbiome consists of the microorganisms populating the human skin. Cutibacterium acnes (C. acnes, formerly named Propionibacterium acnes) is recognized as a key factor in acne development, regulating inflammatory and immune pathways. Dysbiosis has been described as the imbalance in skin microbiome homeostasis and may play a role in acne pathogenesis. Microbial interference has been shown to be a contributor to healthy skin homeostasis and staphylococcal strains may exclude acne-associated C. acnes phylotypes. In this review we present an update on the skin microbiome in acne and discuss how current acne treatments such as benzoyl peroxide, orally administered isotretinoin, and antibiotics may affect the skin microbiome homeostasis. We highlight the collateral damage of acne antibiotics on the skin microbiome, including the risk of antimicrobial resistance and the dysregulation of the microbiome equilibrium that may occur even with short-term antibiotic courses. Consequently, the interest is shifting towards new non-antibiotic pharmacological acne treatments. Orally administered spironolactone is an emerging off-label treatment for adult female patients and topical peroxisome proliferator-activated receptor gamma (PPARγ) modulation is being studied for patients with acne. The potential application of topical or oral probiotics, bacteriotherapy, and phage therapy for acne are further promising areas of future research.

Phenotypic and Genotypic Characterization of Cutibacterium acnes Isolated from Shoulder Surgery Reveals Insights into Genetic Diversity

Specific virulence factors that likely influence C. acnes invasion into deep tissues remain to be elucidated. Herein, we describe the frequency of C. acnes identification in deep tissue specimens of patients undergoing clean shoulder surgery and assess its phenotypic and genetic traits associated with virulence and antibiotic resistance patterns, compared with isolates from the skin of healthy volunteers. Multiple deep tissue specimens from the bone fragments, tendons, and bursa of 84 otherwise healthy patients undergoing primary clean-open and arthroscopic shoulder surgeries were aseptically collected. The overall yield of tissue sample cultures was 21.5% (55/255), with 11.8% (30/255) identified as C. acnes in 27.3% (23/84) of patients. Antibiotic resistance rates were low, with most strains expressing susceptibility to first-line antibiotics, while a few were resistant to penicillin and rifampicin. Phylotypes IB (73.3%) and II (23.3%) were predominant in deep tissue samples. Genomic analysis demonstrated differences in the pangenome of the isolates from the same clade. Even though strains displayed a range of pathogenic markers, such as biofilm formation, patients did not evolve to infection during the 1-year follow-up. This suggests that the presence of polyclonal C. acnes in multiple deep tissue samples does not necessarily indicate infection.

Human skin bacterial microbiota homeostasis: A delicate balance between health and disease

As the largest organ of the body, the skin acts as a barrier to prevent diseases and harbors a variety of beneficial bacteria. Furthermore, the skin bacterial microbiota plays a vital role in health and disease. Disruption of the barrier or an imbalance between symbionts and pathogens can lead to skin disorders or even systemic diseases. In this review, we first provide an overview of research on skin bacterial microbiota and human health, including the composition of skin bacteria in a healthy state, as well as skin bacterial microbiota educating the immune system and preventing the invasion of pathogens. We then discuss the diseases that result from skin microbial dysbiosis, including atopic dermatitis, common acne, chronic wounds, psoriasis, viral transmission, cutaneous lupus, cutaneous lymphoma, and hidradenitis suppurativa. Finally, we highlight the progress that utilizes skin microorganisms for disease therapeutics, such as bacteriotherapy and skin microbiome transplantation. A deeper knowledge of the interaction between human health and disease and the homeostasis of the skin bacterial microbiota will lead to new insights and strategies for exploiting skin bacteria as a novel therapeutic target.

The role of biofilm formation in the pathogenesis and antimicrobial susceptibility of Cutibacterium acnes

Cutibacterium acnes (previously known as Propionibacterium acnes) is frequently found on lipid-rich parts of the human skin. While C. acnes is most known for its role in the development and progression of the skin disease acne, it is also involved in many other types of infections, often involving implanted medical devices. C. acnes readily forms biofilms in vitro and there is growing evidence that biofilm formation by this Gram-positive, facultative anaerobic micro-organism plays an important role in vivo and is also involved in treatment failure. In this brief review we present an overview on what is known about C. acnes biofilms (including their role in pathogenesis and reduced susceptibility to antibiotics), discuss model systems that can be used to study these biofilms in vitro and in vivo and give an overview of interspecies interactions occurring in polymicrobial communities containing C. acnes.

Interference and co-existence of staphylococci and Cutibacterium acnes within the healthy human skin microbiome

Human skin is populated by trillions of microbes collectively called the skin microbiome. Staphylococcus epidermidis and Cutibacterium acnes are among the most abundant members of this ecosystem, with described roles in skin health and disease. However, knowledge regarding the health beneficial effects of these ubiquitous skin residents is still limited. Here, we profiled the staphylococcal and C. acnes landscape across four different skin sites of 30 individuals (120 skin samples) using amplicon-based next-generation sequencing. Relative abundance profiles obtained indicated the existence of phylotype-specific co-existence and exclusion scenarios. Co-culture experiments with 557 staphylococcal strains identified 30 strains exhibiting anti-C. acnes activities. Notably, staphylococcal strains were found to selectively exclude acne-associated C. acnes and co-exist with healthy skin-associated phylotypes, through regulation of the antimicrobial activity. Overall, these findings highlight the importance of skin-resident staphylococci and suggest that selective microbial interference is a contributor to healthy skin homeostasis.

The dynamic interaction between the common resident skin microbes Staphylococcus epidermidis and Cutibacterium acnes is uncovered, showing that S. epidermidis can selectively exclude acne-associated C. acnes strains from the human skin.

Hsu JE, Bumgarner RE, Bourassa LA, Budge MD, Duquin TR, Garrigues GE, Green A, Iannotti JP, Khazzam MS, Koh JL, Matsen FA, Namdari S, Nicholson TA, Richter SS, Sabesan VJ, Virk MS, Whitson AJ, Yian EH, Ricchetti ET. What do positive and negative Cutibacterium culture results in periprosthetic shoulder infection mean? A multi-institutional control study

BACKGROUND

Deep tissue culture specimens obtained at the time of revision shoulder arthroplasty are commonly positive for Cutibacterium. Clinical interpretation of positive cultures can be difficult. This was a multi-institutional study evaluating the accuracy of cultures for Cutibacterium using positive control (PC) and negative control (NC) samples. The relationship between time to culture positivity and strength of culture positivity was also studied.

METHODS

Eleven different institutions were each sent 12 blinded samples (10 PC and 2 NC samples). The 10 PC samples included 2 sets of 5 different dilutions of a Cutibacterium isolate from a failed total shoulder arthroplasty with a probable periprosthetic infection. At each institution, the samples were handled as if they were received from the operating room. Specimen growth, time to culture positivity, and strength of culture positivity (based on semiquantitative assessment) were reported.

RESULTS

A total of 110 PC samples and 22 NC samples were tested. One hundred percent of specimens at the 4 highest dilutions were positive for Cutibacterium. At the lowest dilution, 91% of samples showed positive findings. Cutibacterium grew in 14% of NC samples. Cutibacterium grew in PC samples at an average of 4.0 ± 1.3 days, and all of these samples showed growth within 7 days. The time to positivity was significantly shorter (P < .001) and the strength of positivity was significantly higher (P < .001) in true-positive cultures compared with false-positive cultures.

CONCLUSIONS

This multi-institutional study suggests that different institutions may report highly consistent rates of culture positivity for revision shoulder arthroplasty samples with higher bacterial loads. In contrast, with lower bacterial loads, the results are somewhat less consistent. Clinicians should consider using a shorter time to positivity and a higher strength of positivity as adjuncts in determining whether a tissue culture sample is a true positive.

T Cell Extracellular Traps: Tipping the Balance Between Skin Health and Disease

The role of extracellular traps (ETs) in the innate immune response against pathogens is well established. ETs were first identified in neutrophils and have since been identified in several other immune cells. Although the mechanistic details are not yet fully understood, recent reports have described antigen-specific T cells producing T cell extracellular traps (TETs). Depending on their location within the cutaneous environment, TETs may be beneficial to the host by their ability to limit the spread of pathogens and provide protection against damage to body tissues, and promote early wound healing and degradation of inflammatory mediators, leading to the resolution of inflammatory responses within the skin. However, ETs have also been associated with worse disease outcomes. Here, we consider host-microbe ET interactions by highlighting how cutaneous T cell-derived ETs aid in orchestrating host immune responses against Cutibacterium acnes (C. acnes), a commensal skin bacterium that contributes to skin health, but is also associated with acne vulgaris and surgical infections following joint-replacement procedures. Insights on the role of the skin microbes in regulating T cell ET formation have broad implications not only in novel probiotic design for acne treatment, but also in the treatment for other chronic inflammatory skin disorders and autoimmune diseases.

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris. The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes strains. To investigate the activity of these putative R-M and their relevance in host protective mechanisms, we analyzed the methylome of six representative C. acnes strains by Oxford Nanopore Technologies (ONT) sequencing. We detected the presence of a 6-methyladenine modification at a defined DNA consensus sequence in strain KPA171202 and recombinant expression of this R-M system confirmed its methylation activity. Additionally, a R-M knockout mutant verified the loss of methylation properties of the strain. We studied the potential of one C. acnes bacteriophage (PAD20) in killing various C. acnes strains and linked an increase in its specificity to phage DNA methylation acquired upon infection of a methylation competent strain. We demonstrate a therapeutic application of this mechanism where phages propagated in R-M deficient strains selectively kill R-M deficient acne-prone clades while probiotic ones remain resistant to phage infection.

Multidrug-resistant Cutibacterium avidum isolated from patients with acne vulgaris and other infections

OBJECTIVES

Cutibacterium avidum, a human skin bacterium, rarely causes infectious diseases. It has been recently shown that C. acnes, another member of the genus Cutibacterium, acts as an opportunistic pathogen in surgical site infections. However, the antimicrobial susceptibility and pathogenicity of C. avidum remain unknown. Here, we investigated the epidemiological features of C. avidum.

RESULTS

C. avidum strains were isolated from patients with acne vulgaris (29 strains) and patients with other infections (12 strains). Antimicrobial susceptibility testing showed clarithromycin and clindamycin resistance in 65.9% of the tested strains (27/41). In addition, ciprofloxacin resistance was found in 34.1% of the strains (14/41), and 13 of those strains additionally exhibited resistance to both macrolides and clindamycin. Notably, the macrolides-clindamycin resistance gene erm(X) was found on the chromosomes of 92.6% (25/27) of the clindamycin-resistant strains and may be prevalent owing to transmission among C. avidum strains. Ciprofloxacin-resistant strains developed amino acid substitutions in GyrA owing to the use of antimicrobial agents. Pulsed-field gel electrophoresis (PFGE) analysis revealed that only a few strains exhibited 100% similarity. Additionally, no clustering associated with antimicrobial resistance, biofilm-forming ability, and type of infection was observed.

CONCLUSIONS

Our study revealed that erm(X) may be frequently disseminated in C. avidum, and multidrug-resistant C. avidum strains may colonize the skin of patients with acne vulgaris and patients with other infections. Therefore, the prevalence of multidrug-resistant C. avidum and the use of antimicrobial agents for the treatment of acne vulgaris and other infections associated with C. avidum should be monitored.

Human skin microbiota in health and disease: The cutaneous communities' interplay in equilibrium and dysbiosis: The cutaneous communities' interplay in equilibrium and dysbiosis

Cutaneous microbial composition is driven by the microenvironment of the skin, as well as by internal and external factors. Local changes in the microenvironment can affect the configuration of the community, which may lead toward an imbalance of microbiota. Alterations in the microbial profile are common in both inflammatory skin diseases and chronic infections. A shift in balance within the microbiota, toward limited variation and a greater abundance of specific pathogens, may further worsen the pathogenicity of the diseases. These alterations may be prevented by topical treatment of probiotic solutions stimulating a balanced multispecies community. Compositional variations may further constitute potential biomarkers to predict flares or monitor efficacy during therapy. New approaches such as machine learning may contribute to this prediction of microbial alterations prior to the development of chronic infections and flares. This review provides insight into the composition and distribution of a healthy community of microorganisms in the skin and draws parallels with the community in chronic infections and chronic inflammatory skin diseases such acne vulgaris and Hidradenitis Suppurativa. We discuss the potential role of specific species in the pathogenesis and the possible prevention of disease exacerbation.

Metagenomic Sequencing Analysis for Acne Using Machine Learning Methods Adapted to Single or Multiple Data

The human health status can be assessed by the means of research and analysis of the human microbiome. Acne is a common skin disease whose morbidity increases year by year. The lipids which influence acne to a large extent are studied by metagenomic methods in recent years. In this paper, machine learning methods are used to analyze metagenomic sequencing data of acne, i.e., all kinds of lipids in the face skin. Firstly, lipids data of the diseased skin (DS) samples and the healthy skin (HS) samples of acne patients and the normal control (NC) samples of healthy person are, respectively, analyzed by using principal component analysis (PCA) and kernel principal component analysis (KPCA). Then, the lipids which have main influence on each kind of sample are obtained. In addition, a multiset canonical correlation analysis (MCCA) is utilized to get lipids which can differentiate the face skins of the above three samples. The experimental results show the machine learning methods can effectively analyze metagenomic sequencing data of acne. According to the results, lipids which only influence one of the three samples or the lipids which simultaneously have different degree of influence on these three samples can be used as indicators to judge skin statuses.

Common Features and Intra-Species Variation of Cutibacterium modestum Strains, and Emended Description of the Species

Cutibacterium modestum is a new species coined in 2020 as the fifth species of genus Cutibacterium, which includes Cutibacterium acnes. The species is predicted as a minor but common member of skin microbiome and includes a group tentatively named as “Propionibacterium humerusii”. The description of the species has been provided only with a single strain. To establish the characteristics of C. modestum and search for possible disease-related subtypes, we investigated the biochemical characteristics of eight live strains and performed in silico comparison of nine genomes. The common features, which included the morphology of Gram-stain positive short rods, the negativity of phenylalanine arylamidase, and several unique MALDI-TOF MS spectral peaks, were considered useful in laboratory identification. Pairwise comparisons of the genomes by in silico DNA–DNA hybridization showed similarity values of 98.1% or larger, which were far higher than the subspecies cutoff of 79–80%. The 16S rRNA gene sequences of thirteen isolates and genomes were identical. Their recA gene sequences were identical except for two strains, HM-510 (HL037PA2) and Marseille-P5998, which showed unique one-nucleotide polymorphisms. The biochemical features using API kits were slightly different among the isolates but far closer than those of the nearest other species, C. acnes and Cutibacterium namnetense. Spectra of MALDI-TOF mass spectrometry showed slight differences in the presence of m/z 10,512 (10 kD chaperonin GroS) and three other peaks, further clustering the eight isolates into three subtypes. These results indicated that these isolates did not separate to form subspecies-level clusters, but subtyping is possible by using recA gene sequences or MALDI-TOF mass spectrometry spectra. Moreover, this work has confirmed that a group “P. humerusii” is included in C. modestum.

Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications

Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.

Nonpathogenic Cutibacterium acnes Confers Host Resistance against Staphylococcus aureus

Cutibacterium acnes is a human skin-resident bacterium. Although C. acnes maintains skin health by inhibiting invasion from pathogens like Staphylococcus aureus, it also contributes to several diseases, including acne. Studies suggest that differences in genetic background may explain the diverse phenotypes of C. acnes strains. In this study, we investigated the effects of C. acnes strains on the Caenorhabditis elegans life span and observed that some strains shortened the life span, whereas other strains, such as strain HL110PA4, did not alter it. Next, we assessed the effects of C. acnes HL110PA4 on host resistance against S. aureus. The survival time of C. acnes HL110PA4-fed wild-type animals was significantly longer than that of Escherichia coli OP50 control bacterium-fed worms upon infection with S. aureus. Although the survival times of worms harboring mutations at the daf-16/FoxO and skn-1/Nrf2 loci were similar to those of wild-type worms after S. aureus infection, administration of C. acnes failed to improve survival times of tir-1/SARM1, nsy-1/mitogen-activated protein kinase kinase kinase (MAPKKK), sek-1/mitogen-activated protein kinase kinase (MAPKK), and pmk-1/p38 mitogen-activated protein kinase (MAPK) mutants. These results suggest that the TIR-1 and p38 MAPK pathways are involved in conferring host resistance against S. aureus in a C. acnes-mediated manner. IMPORTANCE Cutibacterium acnes is one of the most common bacterial species residing on the human skin. Although the pathogenic properties of C. acnes, such as its association with acne vulgaris, have been widely described, its beneficial aspects have not been well characterized. Our study classifies C. acnes strains based on its pathogenic potential toward the model host C. elegans and reveals that the life span of C. elegans worms fed on C. acnes was consistent with the clinical association of C. acnes ribotypes with acne or nonacne. Furthermore, nonpathogenic C. acnes confers host resistance against the opportunistic pathogen Staphylococcus aureus. Our study provides insights into the impact of C. acnes on the host immune system and its potential roles in the ecosystem of skin microbiota.

Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes

In 2016, a new species name Cutibacterium acnes was coined for the well-documented species, Propionibacterium acnes, one of the most successful and clinically important skin commensals. The nomenclatural changes were brought about through creation of the genus Cutibacterium, when a group of propionibacteria isolates from the skin were transferred from the genus Propionibacterium and placed in the phylum Actinobacteria. Almost simultaneously, the discovery of two novel species of Cutibacterium occurred and the proposal of three subspecies of C. acnes were reported. These dramatic changes that occurred in a long-established taxon made it challenging for the non-specialist to correlate the huge volume of hitherto published work with current findings. In this review, we aim to correlate the eco-specificity and pathophysiological properties of these newly circumscribed taxa. We envisage that this information will shed light on the pathogenic potential of new isolates and enable better assessment of their clinical importance in the foreseeable future. Currently, five species are recognized within the genus: Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, Cutibacterium modestum (previously, "Propionibacterium humerusii"), and Cutibacterium namnetense. These reside in different niches reflecting their uniqueness in their genetic makeup. Their pathogenicity includes acne inflammation, sarcoidosis, progressive macular hypomelanosis, prostate cancer, and infections (bone, lumbar disc, and heart). This is also the case for the three newly described subspecies of C. acnes, which are C. acnes subspecies acnes (C. acnes type I), subspecies defendens (C. acnes type II), and subspecies elongatum (C. acnes type III). C. acnes subspecies acnes is related to inflamed acne and sarcoidosis, while subspecies defendens to prostate cancer and subspecies elongatum to progressive macular hypomelanosis. Because the current nomenclature is based upon polyphasic analyses of the biochemical and pathogenic characteristics and comparative genomics, it provides a sound basis studying the pathophysiological roles of these species.

A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes

The bacterial species Cutibacterium acnes (formerly known as Propionibacterium acnes) is tightly associated with humans. It is the dominant bacterium in sebaceous regions of the human skin, where it preferentially colonizes the pilosebaceous unit. Multiple strains of C. acnes that belong to phylogenetically distinct types can co-exist. In this review we summarize and discuss the current knowledge of C. acnes regarding bacterial properties and traits that allow host colonization and play major roles in host-bacterium interactions and also regarding the host responses that C. acnes can trigger. These responses can have beneficial or detrimental consequences for the host. In the first part of the review, we highlight and critically review disease associations of C. acnes, in particular acne vulgaris, implant-associated infections and native infections. Here, we also analyse the current evidence for a direct or indirect role of a C. acnes-related dysbiosis in disease development or progression, i.e., reduced C. acnes strain diversity and/or the predominance of a certain phylotype. In the second part of the review, we highlight historical and recent findings demonstrating beneficial aspects of colonization by C. acnes such as colonization resistance, immune system interactions, and oxidant protection, and discuss the molecular mechanisms behind these effects. This new insight led to efforts in skin microbiota manipulation, such as the use of C. acnes strains as probiotic options to treat skin disorders.

Gut-Skin Axis: Current Knowledge of the Interrelationship between Microbial Dysbiosis and Skin Conditions

The microbiome plays an important role in a wide variety of skin disorders. Not only is the skin microbiome altered, but also surprisingly many skin diseases are accompanied by an altered gut microbiome. The microbiome is a key regulator for the immune system, as it aims to maintain homeostasis by communicating with tissues and organs in a bidirectional manner. Hence, dysbiosis in the skin and/or gut microbiome is associated with an altered immune response, promoting the development of skin diseases, such as atopic dermatitis, psoriasis, acne vulgaris, dandruff, and even skin cancer. Here, we focus on the associations between the microbiome, diet, metabolites, and immune responses in skin pathologies. This review describes an exhaustive list of common skin conditions with associated dysbiosis in the skin microbiome as well as the current body of evidence on gut microbiome dysbiosis, dietary links, and their interplay with skin conditions. An enhanced understanding of the local skin and gut microbiome including the underlying mechanisms is necessary to shed light on the microbial involvement in human skin diseases and to develop new therapeutic approaches.

Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors

Cutibacterium acnes is a member of the skin microbiota found predominantly in regions rich in sebaceous glands. It is involved in maintaining healthy skin and has long been considered a commensal bacterium. Its involvement in various infections has led to its emergence as an opportunist pathogen. Interactions between C. acnes and the human host, including the human skin microbiota, promote the selection of C. acnes strains capable of producing several virulence factors that increase inflammatory capability. This pathogenic property may be related to many infectious mechanisms, such as an ability to form biofilms and the expression of putative virulence factors capable of triggering host immune responses or enabling C. acnes to adapt to its environment. During the past decade, many studies have identified and characterized several putative virulence factors potentially involved in the pathogenicity of this bacterium. These virulence factors are involved in bacterial attachment to target cells, polysaccharide-based biofilm synthesis, molecular structures mediating inflammation, and the enzymatic degradation of host tissues. C. acnes, like other skin-associated bacteria, can colonize various ecological niches other than skin. It produces several proteins or glycoproteins that could be considered to be active virulence factors, enabling the bacterium to adapt to the lipophilic environment of the pilosebaceous unit of the skin, but also to the various organs it colonizes. In this review, we summarize current knowledge concerning characterized C. acnes virulence factors and their possible implication in the pathogenicity of C. acnes.

Cutibacterium subtype distribution on the skin of primary and revision shoulder arthroplasty patients

BACKGROUND

The skin of healthy shoulders is known to harbor multiple different subtypes of Cutibacterium (formerly Propionibacterium) acnes at the same time. C acnes can often be isolated from deep tissue and explant samples obtained during revision of a failed shoulder arthroplasty, presumably because the shoulder was inoculated with organisms from the patient's skin at the time of the index arthroplasty. It is possible that specific subtypes or distributions of subtypes may be associated with an increased pathogenic potential and that the skin of patients undergoing revision arthroplasty contains different distributions of the subtypes than in patients undergoing primary arthroplasty. We analyzed the subtype distribution of Cutibacterium from the skin of shoulders undergoing revision arthroplasty vs. primary arthroplasty.

METHODS

Preoperative skin swabs were collected from 25 patients who underwent primary shoulder arthroplasty and 27 patients who underwent revision shoulder arthroplasty. The results of semiquantitative cultures of the skin and deep tissues were reported as specimen Cutibacterium values, and scores from all deep tissue samples were added to report the total shoulder Cutibacterium score. Single-locus sequence typing (SLST) of C acnes from the skin swabs was used to determine the subtype distribution for each patient. The percentage of each subtype for each patient was averaged in patients undergoing revision arthroplasty and then compared with that in patients undergoing primary arthroplasty.

RESULTS

The C acnes subtype distribution on the skin of revision arthroplasty patients was different from that of primary shoulder arthroplasty patients, with a significantly higher percentage of SLST subtype A (36.9% vs. 16.0%, P = .0018). The distribution of SLST subtypes was similar between revision arthroplasty patients with strongly positive culture findings vs. those with weakly positive or negative culture findings.

CONCLUSIONS

Significant differences in the skin Cutibacterium subtype distributions were found between shoulders undergoing revision shoulder arthroplasty and those undergoing primary shoulder arthroplasty. Future studies are needed to determine whether certain Cutibacterium subtype distributions are associated with an increased risk of arthroplasty revision.

MG-MLST: Characterizing the Microbiome at the Strain Level in Metagenomic Data

The microbiome plays an important role in human physiology. The composition of the human microbiome has been described at the phylum, class, genus, and species levels, however, it is largely unknown at the strain level. The importance of strain-level differences in microbial communities has been increasingly recognized in understanding disease associations. Current methods for identifying strain populations often require deep metagenomic sequencing and a comprehensive set of reference genomes. In this study, we developed a method, metagenomic multi-locus sequence typing (MG-MLST), to determine strain-level composition in a microbial community by combining high-throughput sequencing with multi-locus sequence typing (MLST). We used a commensal bacterium, Propionibacterium acnes, as an example to test the ability of MG-MLST in identifying the strain composition. Using simulated communities, MG-MLST accurately predicted the strain populations in all samples. We further validated the method using MLST gene amplicon libraries and metagenomic shotgun sequencing data of clinical skin samples. MG-MLST yielded consistent results of the strain composition to those obtained from nearly full-length 16S rRNA clone libraries and metagenomic shotgun sequencing analysis. When comparing strain-level differences between acne and healthy skin microbiomes, we demonstrated that strains of RT2/6 were highly associated with healthy skin, consistent with previous findings. In summary, MG-MLST provides a quantitative analysis of the strain populations in the microbiome with diversity and richness. It can be applied to microbiome studies to reveal strain-level differences between groups, which are critical in many microorganism-related diseases.

Corynebacterium tuberculostearicum, a human skin colonizer, induces the canonical nuclear factor-κB inflammatory signaling pathway in human skin cells

INTRODUCTION

Corynebacterium tuberculostearicum (C. t.) is a ubiquitous bacterium that colonizes human skin. In contrast to other members of the genus Corynebacterium, such as toxigenic Corynebacterium diphtheriae or the opportunistic pathogen Corynebacterium jeikeium, several studies suggest that C. t. may play a role in skin health and disease. However, the mechanisms underlying these effects remain poorly understood.

METHODS

To investigate whether C. t. induces inflammatory pathways in primary human epidermal keratinocytes (HEKs) and human cutaneous squamous carcinoma cells (SCCs), cell culture, reverse transcription-polymerase chain reaction (PCR), enzyme-linked immunosorbent assay, immunofluorescence microscopy, Western blot, chromatin immunoprecipitation-PCR, small interfering RNA knockdown and luciferase reporter expression system were used.

RESULTS

Herein, we demonstrate that C. t. upregulates the messenger RNA (mRNA) and protein levels of inflammatory mediators in two human skin cell lines, HEKs and SCCs. We further show activation of the canonical nuclear factor-κB (NF-κB) pathway in response to C. t. infection, including phosphorylation of the inhibitor of κB (IκB), the nuclear translocation of NF-κB subunit (NF-κB-P65 ) and the recruitment of NF-κB-P65 and RNA polymerase to the NF-κB response elements at the promoter region of the inflammatory genes. Lastly, the data confirm that C. t.-induced tumor necrosis factor mRNA expression in HEKs is toll-like receptor 2 (TLR2 ) dependent.

CONCLUSION

Our results offer a mechanistic model for C. t.-induced inflammation in human keratinocytes via TLR2 and activation of IκB kinase and downstream signaling through the canonical NF-κB pathway. Relevance to chronic inflammatory diseases of the skin and cutaneous oncology is discussed.

The Nesting Doll of Cutibacterium acnes Clonality

In this issue of the Journal of Clinical Microbiology, R. E. Bumgarner, D. Harrison, and J. E. Hsu (J Clin Microbiol 58:e00121-19, 2020, https://doi.org/10.1128/JCM.00121-19) address in a retrospective analysis that clonality of Cutibacterium acnes isolates from deep tissue specimens obtained from patients during revision shoulder arthroplasty cannot be assumed. Given that multiple subtypes of C. acnes isolates are present on and around the skin pilosebaceous follicles, the finding of multiple subtypes in deep tissues around a single patient's infected joint is not entirely surprising. However, the authors also challenge laboratorians to consider whether further assessment of C. acnes isolates from the same joint should be performed and, if so, what testing should be undertaken.

Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification

Cutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.

The human skin surface harbors huge numbers of microbes. The skin microbiota interacts with its host and forms a skin microbiome profile that is specific for each individual. It has been reported that the skin microbiota that is left on an individual’s possessions can act as a sort of “fingerprint” and be used for owner identification. However, this approach needs to be improved to take into account any long-term instability of skin microbiota and contamination from nonspecific bacteria. Here, we took advantage of single-nucleotide polymorphisms (SNPs) in the 16S-encoding rRNA gene of Cutibacterium acnes, the most common and abundant bacterium on human skin, to perform owner identification. We first developed a high-throughput genotyping method based on next-generation sequencing to characterize the SNPs of the C. acnes 16S rRNA gene and found that the genotype composition of C. acnes 16S rRNA is individual specific. Owner identification accuracy of around 90% based on random forest machine learning was achieved by using a combination of C. acnes 16S rRNA genotype and skin microbiome profile data. Furthermore, our study showed that the C. acnes 16S rRNA genotype remained more stable over time than the skin microbiome profile. This characteristic of C. acnes was further confirmed by the analysis of publicly available human skin metagenome data. Our approach, with its high precision, good reproducibility, and low costs, thus provides new possibilities in the field of microbiome-based owner identification and forensics in general.

IMPORTANCECutibacterium acnes is the most common and abundant bacterial species on human skin, and the gene that encodes its 16S rRNA has multiple single-nucleotide polymorphisms. In this study, we developed a method to efficiently determine the C. acnes 16S rRNA genotype composition from microbial samples taken from the hands of participants and from their possessions. Using the C. acnes 16S rRNA genotype composition, we could predict the owner of a possession with around 90% accuracy when the 16S rRNA gene-based microbiome profile was included. We also showed that the C. acnes 16S rRNA genotype composition was more stable over time than the skin microbiome profile and thus is more suitable for owner identification.

Antimicrobial Susceptibility, Biotypes and Phylotypes of Clinical Cutibacterium (Formerly Propionibacterium) acnes Strains Isolated from Acne Patients: An Observational Study

INTRODUCTION

The aim of this study was to investigate the distribution of antimicrobial susceptibility, biotypes and phylotypes of clinical Cutibacterium acnes (C. acnes, formerly Propionibacterium acnes) isolates as well as the relationship among demographic factors, C. acnes biotypes and phylotypes.

METHODS

Cutibacterium acnes was collected from the skin lesions of acne patients who visited the dermatologic department of Huashan Hospital in Shanghai from October 2016 to March 2017. The agar dilution method was conducted to determine the minimum inhibitory concentrations (MICs) of C. acnes, the fermentation test to identify biotypes and then multiplex touchdown polymerase chain reaction (PCR) to identify phylotypes.

RESULTS

Of the 63 C. acnes strains we isolated, 18 (28.6%), 31 (49.2%) and 4 (6.3%) strains were resistant to clindamycin, erythromycin and moxifloxacin, respectively; no strains were resistant to tetracycline, minocycline, fusidic acid or β-lactam, while metronidazole was completely resisted; 3 strains showed multidrug resistance (MDR). Biotype III (BIII) was the major biotype (50.8%) followed by BI and BV (both 15.9%), BII (12.7%) and lastly BIV (4.8%). IA₁ was the predominant phylotype (71.4%) followed by IA₂ (19.0%), II (4.8%), IB (3.2%) and IC (1.6%), while III was not detected. Significant differences were observed in the severity of disease: different degrees of acne severity reflected different biotype and phylotype distributions, and the biotype distribution of mild acne was different from that of moderate acne; the phylotype distribution of moderate acne varies from that of severe acne, too. Additionally, there was no significant difference in the distribution of biotypes or phylotypes between resistant and susceptible strains.

CONCLUSION

Erythromycin and clindamycin resistances are the most common in clinical C. acnes strains; BIII is the predominant biotype and IA₁ is the major phylotype of C. acnes, which are mainly related to disease severity.

Age and Mothers: Potent Influences of Children's Skin Microbiota

The evolution of a child's skin microbiome is associated with the development of the immune system and skin environment. As only few studies have analyzed the microbiota in young children, we investigated changes in the skin microbiota of children (158 subjects; ≤10 years old) and compared the microbiota structures between children and their mothers using 16S rRNA gene amplicon sequencing. Sample location and age were the primary factors determining a child's skin bacterial composition, which differed significantly among the face, ventral forearm, and calf. Relative abundances of Streptococcus and Granulicatella were negatively correlated with age, and the alpha diversity at all body sites examined increased during the first 10 years of life, especially on the face. The facial bacterial composition of 10-year-old children was strongly associated with delivery mode at birth. Among mother-child pairs (50 pairs), the relative abundances of most bacterial genera in children were more similar to those of their own mothers than those of unrelated women. The data indicated that age and site were significantly associated with microbial composition and that maternal factors determine the child's microbiome. Further research is needed to characterize the effects of maturation of the infant microbiome on health in adulthood.

The role of the skin microbiota in acne pathophysiology

BACKGROUND

The role of skin microbiota in acne remains to be fully elucidated. Initial culture-based investigations were hampered by growth rate and selective media bias. Even with less biased genomic methods, sampling, lysis and methodology, the task of describing acne pathophysiology remains challenging. Acne occurs in sites dominated by Cutibacterium acnes (formerly Propionibacterium acnes) and Malassezia species, both of which can function either as commensal or pathogen.

OBJECTIVES

This article aims to review the current state of the art of the microbiome and acne.

METHODS

The literature regarding the microbiome and acne was reviewed.

RESULTS

It remains unclear whether there is a quantitative difference in microbial community distribution, making it challenging to understand any community shift from commensal to pathogenic nature. It is plausible that acne involves (i) change in the distribution of species/strains, (ii) stable distribution with pathogenic alteration in response to internal (intermicrobe) or external stimuli (host physiology or environmental) or (iii) a combination of these factors.

CONCLUSIONS

Understanding physiological changes in bacterial species and strains will be required to define their specific roles, and identify any potential intervention points, in acne pathogenesis and treatment. It will also be necessary to determine whether any fungal species are involved, and establish whether they play a significant role. Further investigation using robust, modern analytic tools in longitudinal studies with a large number of participants, may make it possible to determine whether the microbiota plays a causal role, is primarily involved in exacerbation, or is merely a bystander. It is likely that the final outcome will show that acne is the result of complex microbe-microbe and community-host interplay.

Propionibacterium acnes and Acne Vulgaris: New Insights from the Integration of Population Genetic, Multi-Omic, Biochemical and Host-Microbe Studies

The anaerobic bacterium Propionibacterium acnes is believed to play an important role in the pathophysiology of the common skin disease acne vulgaris. Over the last 10 years our understanding of the taxonomic and intraspecies diversity of this bacterium has increased tremendously, and with it the realisation that particular strains are associated with skin health while others appear related to disease. This extensive review will cover our current knowledge regarding the association of P. acnes phylogroups, clonal complexes and sequence types with acne vulgaris based on multilocus sequence typing of isolates, and direct ribotyping of the P. acnes strain population in skin microbiome samples based on 16S rDNA metagenomic data. We will also consider how multi-omic and biochemical studies have facilitated our understanding of P. acnes pathogenicity and interactions with the host, thus providing insights into why certain lineages appear to have a heightened capacity to contribute to acne vulgaris development, while others are positively associated with skin health. We conclude with a discussion of new therapeutic strategies that are currently under investigation for acne vulgaris, including vaccination, and consider the potential of these treatments to also perturb beneficial lineages of P. acnes on the skin.

Draft Genome Sequence of Propionibacterium acnes subsp. elongatum Strain Asn12

Propionibacterium acnes, a non-spore-forming anaerobic Gram-positive bacterium, has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris. Here, we present the draft genome sequence of P. acnes subsp.

Propionibacterium acnes, a non-spore-forming anaerobic Gram-positive bacterium, has been linked to a wide range of opportunistic human infections and conditions, most notably acne vulgaris. Here, we present the draft genome sequence of P. acnes subsp. elongatum strain Asn12, isolated from spinal disc tissue (in the United Kingdom).

The impact of Cymbopogon martinii essential oil on Cutibacterium (formerly Propionibacterium) acnes strains and its interaction with keratinocytes

OBJECTIVES

The human skin microbiota is mainly composed of bacteria belonging to the genera Staphylococcus, Cutibacterium, Micrococcus and Corynebacterium, but on the skin of the face and back, ca. 50% of the total microbiota is represented by the bacterium Cutibacterium acnes. The aim of this research was to evaluate the impact of C. martini EO and its major compound, geraniol, on C. acnes.

METHODS

The minimum inhibitory concentration against C. acnes strains, phenotypic changes and responses of the proteome was determined. In addition, was assessed the effect of compounds in RNA-binding assay, on C. acnes-exposed keratinocytes and on the C. acnes type distribution on shoulder skin.

KEY FINDINGS

The range of the MIC was 0.7 to 1.6 mg/ml for the three main C. acnes types. There were no cytotoxic effects of compounds in the absence or presence of C. acnes; after 7 days of exposure to C. martini EO, we could not detect a major shift of the C. acnes types on shoulder skin that was found to be dominated by C. acnes strains of types II and IA2.

CONCLUSIONS

Our work gives novel insight into the skin microbiota-interacting properties of C. martini EO.

Host-microbiome interactions and recent progress into understanding the biology of acne vulgaris

Acne is one of the most common skin diseases worldwide and results in major health care costs and significant morbidity to severely affected individuals. However, the pathophysiology of this disorder is not well understood. Host-microbiome interactions that affect both innate and adaptive immune homeostasis appear to be a central factor in this disease, with recent observations suggesting that the composition and activities of the microbiota in acne is perturbed. Staphylococcus epidermidis and Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes) are two major inhabitants of the skin that are thought to contribute to the disease but are also known to promote health by inhibiting the growth and invasion of pathogens. Because C. acnes is ubiquitous in sebaceous-rich skin, it is typically labeled as the etiological agent of acne yet it fails to fulfill all of Koch's postulates. The outdated model of acne progression proposes that increased sebum production promotes over-proliferation of C. acnes in a plugged hair follicle, thereby driving inflammation. In contrast, growing evidence indicates that C. acnes is equally abundant in both unaffected and acne-affected follicles. Moreover, recent advances in metagenomic sequencing of the acne microbiome have revealed a diverse population structure distinct from healthy individuals, uncovering new lineage-specific virulence determinants. In this article, we review recent developments in the interactions of skin microbes with host immunity, discussing the contribution of dysbiosis to the immunobiology of acne and newly emerging skin microbiome-based therapeutics to treat acne.

Clinical and Biological Features of Cutibacterium (Formerly Propionibacterium) avidum, an Underrecognized Microorganism

The recent description of the genus Cutibacterium has altered the taxonomy of Propionibacterium species. These organisms still belong to the genera of the skin coryneform group, and the most-studied species remains Cutibacterium acnes. Cutibacterium avidum is also a known skin commensal. This underrecognized microorganism can, however, act as a pathogen after bacterial seeding and can be considered opportunistic, causing either superficial or deep/invasive infections. It can cause numerous infections, including but not limited to breast infections, skin abscesses, infective endocarditis, and device-related infections. The ecological niche of C. avidum is clearly different from that of other members of the genus: it is found in the axillary region or at wet sites rather than in dry, exposed areas, and the number of microorganisms increases during puberty. Historically, it has been used for its ability to modulate the immune response and for its antitumor properties. Conventional microbial culture methods and identification processes allow for its accurate identification and characterization. Thanks to the modern omics tools used for phylogenomic approaches, understanding C. avidum pathogenesis (including host-bacterium interactions and virulence factor characterization) is becoming easier, allowing for more thorough molecular characterization. These analyses have revealed that C. avidum causes diverse diseases mediated by multiple virulence factors. The recent genome approach has revealed specific genomic regions within this species that are involved in adherence and biofilm formation as well as fitness, survival, and defense functions. Numerous regions show the presence of phages and horizontal gene transfer. C. avidum remains highly sensitive to a broad spectrum of antibiotics, such as β-lactams, fluoroquinolones, macrolides, and rifampin, although erythromycin and clindamycin resistance has been described. A long-term treatment regimen with a combination of antibiotics is required to successfully eliminate the remaining adherent bacteria, particularly in the case of deep infections after debridement surgery.

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.

Prevalence of Flp Pili-Encoding Plasmids in Cutibacterium acnes Isolates Obtained from Prostatic Tissue

Inflammation is one of the hallmarks of prostate cancer. The origin of inflammation is unknown, but microbial infections are suspected to play a role. In previous studies, the Gram-positive, low virulent bacterium Cutibacterium (formerly Propionibacterium) acnes was frequently isolated from prostatic tissue. It is unclear if the presence of the bacterium represents a true infection or a contamination. Here we investigated Cutibacterium acnes type II, also called subspecies defendens, which is the most prevalent type among prostatic C. acnes isolates. Genome sequencing of type II isolates identified large plasmids in several genomes. The plasmids are highly similar to previously identified linear plasmids of type I C. acnes strains associated with acne vulgaris. A PCR-based analysis revealed that 28.4% (21 out of 74) of all type II strains isolated from cancerous prostates carry a plasmid. The plasmid shows signatures for conjugative transfer. In addition, it contains a gene locus for tight adherence (tad) that is predicted to encode adhesive Flp (fimbrial low-molecular weight protein) pili. In subsequent experiments a tad locus-encoded putative pilin subunit was identified in the surface-exposed protein fraction of plasmid-positive C. acnes type II strains by mass spectrometry, indicating that the tad locus is functional. Additional plasmid-encoded proteins were detected in the secreted protein fraction, including two signal peptide-harboring proteins; the corresponding genes are specific for type II C. acnes, thus lacking from plasmid-positive type I C. acnes strains. Further support for the presence of Flp pili in C. acnes type II was provided by electron microscopy, revealing cell appendages in tad locus-positive strains. Our study provides new insight in the most prevalent prostatic subspecies of C. acnes, subsp. defendens, and indicates the existence of Flp pili in plasmid-positive strains. Such pili may support colonization and persistent infection of human prostates by C. acnes.

The Skin Bacterium Propionibacterium acnes Employs Two Variants of Hyaluronate Lyase with Distinct Properties

Hyaluronic acid (HA) and other glycosaminoglycans are extracellular matrix components in the human epidermis and dermis. One of the most prevalent skin microorganisms, Propionibacterium acnes, possesses HA-degrading activity, possibly conferred by the enzyme hyaluronate lyase (HYL). In this study, we identified the HYL of P. acnes and investigated the genotypic and phenotypic characteristics. Investigations include the generation of a P. acneshyl knockout mutant and HYL activity assays to determine the substrate range and formed products. We found that P. acnes employs two distinct variants of HYL. One variant, HYL-IB/II, is highly active, resulting in complete HA degradation; it is present in strains of the phylotypes IB and II. The other variant, HYL-IA, has low activity, resulting in incomplete HA degradation; it is present in type IA strains. Our findings could explain some of the observed differences between P. acnes phylotype IA and IB/II strains. Whereas type IA strains are primarily found on the skin surface and associated with acne vulgaris, type IB/II strains are more often associated with soft and deep tissue infections, which would require elaborate tissue invasion strategies, possibly accomplished by a highly active HYL-IB/II.

Phenotype and Antimicrobial Activity of Th17 Cells Induced by Propionibacterium acnes Strains Associated with Healthy and Acne Skin

Studies of the human skin microbiome suggest that Propionibacterium acnes strains may contribute differently to skin health and disease. However, the immune phenotype and functions of T helper type 17 (Th17) cells induced by healthy (P_H) versus acne (P_A) skin-associated P. acnes strains are currently unknown. We stimulated peripheral blood mononuclear cells from healthy donors and observed that P_A strains induce higher IL-17 levels than P_H strains. We next generated P_H and P_A strain-specific Th17 clones and show that P. acnes strains induce Th17 cells of varied phenotype and function that are stable in the presence of IL-2 and IL-23. Although P_H- and P_A-specific clones expressed similar levels of LL-37 and DEFB4, only P_H-specific clones secreted molecules sufficient to kill P. acnes. Furthermore, electron microscopic studies showed that supernatants derived from activated P_H and not P_A-specific clones exhibited robust bactericidal activity against P. acnes, and complete breaches in the bacterial cell envelope were observed. This antimicrobial activity was independent of IL-26, because both natural IL-26 released by Th17 clones and rhIL-26 lacked antimicrobial potency against P. acnes. Overall, our data suggest that P. acnes strains may differentially modulate the CD4⁺ T-cell responses, leading to the generation of Th17 cells that may contribute to either homeostasis or acne pathogenesis.

Characterization of a Propionibacterium acnes Surface Protein as a Fibrinogen-Binding Protein

Propionibacterium acnes (P. acnes) is a major skin-associated bacterium that was long considered commensal, until several studies revealed it to be an opportunistic pathogen. We investigated the ability of P. acnes surface proteins to recognize ECM proteins and showed that a 58 kDa P. acnes surface protein was specifically recognized by human fibrinogen (hFg). The 58 kDa protein was further characterized by two-dimensional (2-D) electrophoresis and MALDI-ToF as a P. acnes host cell-surface attachment protein, PA25957, recognizing dermatan sulfate (DsA1). This protein sequence contains 432 amino acids with the presence of three structurally different domains: an N-terminal signal peptide, a C-terminal LPXTG motif, and a PT repeat region. DsA1 is mostly produced during stationary phase. It appears to be highly glycosylated, containing GalNAc residues. Purified DsA1 strongly recognizes the Aα and Bβ subunits of hFg, and specific enzymatic deglycosylation of hFg demonstrated the involvement of the protein backbone in the recognition process. The Bβ subunit of hFg was cloned in four peptide fractions (Fg1-Fg4). The N-terminal Fg1 peptide of hFg was recognized by DsA1, and priming DsA1 with Fg1 inhibited DsA1/hFg recognition. We describe here for the first time, the characterization of a P. acnes surface glycoprotein recognizing human fibrinogen.

Optimization of genotypic and biochemical methods to profile P. acnes isolates from a patient population

Propionibacterium acnes is a key factor in the pathogenesis of acne vulgaris, although currently it is also being associated with medical-device infections. The aim of this work was to validate a safe and quick identification and typing of 24 clinical isolates of Propionibacterium acnes, applying a range of biochemical as well as genetic methods, and investigating the pathogenic potential to associate the different types with human health. RAPD-PCRs revealed the existence of two discernible clusters in correspondence with the phylogroups I and II, according to the PAtig gene polymorphism, leading them to be assigned as P. acnes subsp. acnes subsp. nov. Biotyping according to the pattern of sugar fermentation evidenced that all the isolates from acne and the majority from opportunistic infections fit the biotype I-B3. Consistent with the multiplex touchdown analysis, nearly all the isolates included in this biotype belonged to the subgroups IA1 (the exception being four strains classified as IB). The remaining ones were assigned to phylogroup II, considered to be part of the normal cutaneous microbiota. The susceptibility to three antibiotics was also investigated to explore the relations with the virulence, although no clear trend was identified.

Host Inflammatory Response During Periprosthetic Infection Is Joint Specific

BACKGROUND

Propionibacterium acnes (P. acnes) has become increasingly recognized as a cause of periprosthetic joint infection (PJI).

QUESTIONS/PURPOSES

It is not currently known if the clinical presentation of P. acnes varies depending on the joint being infected.

METHODS

We retrospectively reviewed patients infected with P. acnes after total hip, knee, and shoulder arthroplasty from two institutions. Patients were classified as having a PJI based on the Musculoskeletal Infection Society criteria and were excluded if they had a polymicrobial culture. Patient demographics, preoperative laboratory values, and microbiology data were analyzed.

RESULTS

Eighteen knees, 12 hips, and 35 shoulders with a P. acnes PJI were identified. Median ESR was significantly higher in the knee (38.0 mm/h, IQR 18.0-58.0) and hip (33.5 mm/h, IQR 15.3-60.0) groups compared to the shoulder group (11.0 mm/h, IQR 4.5-30.5). C-reactive protein levels were higher in the knee (2.0 mg/dl, IQR 1.3-8.9) and hip (2.4 mg/dl, IQR 0.8-4.9) groups compared to the shoulder group (0.7 mg/dl, IQR 0.6-1.5). Median synovial fluid WBC was significantly higher in the knee group than shoulder group (19,950 cells/mm³, IQR 482-60,063 vs 750 cells/mm³, IQR 0-2825, respectively). Peripheral blood WBC levels were similar between groups, as was mean time of P. acnes growth in culture. Clindamycin resistance was present in all groups.

CONCLUSION

The manner in which a patient with P. acnes PJI presents is joint specific. Inflammatory markers were significantly higher in the knee and hip groups compared to the hip and shoulder groups, and long hold anaerobic cultures up to 14 days are necessary to accurately identify this organism.

Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis

Psoriasis is an immune-mediated inflammatory skin disease that has been associated with cutaneous microbial dysbiosis by culture-dependent investigations and rRNA community profiling. We applied, for the first time, high-resolution shotgun metagenomics to characterise the microbiome of psoriatic and unaffected skin from 28 individuals. We demonstrate psoriatic ear sites have a decreased diversity and psoriasis is associated with an increase in Staphylococcus, but overall the microbiomes of psoriatic and unaffected sites display few discriminative features at the species level. Finer strain-level analysis reveals strain heterogeneity colonisation and functional variability providing the intriguing hypothesis of psoriatic niche-specific strain adaptation or selection. Furthermore, we accessed the poorly characterised, but abundant, clades with limited sequence information in public databases, including uncharacterised Malassezia spp. These results highlight the skins hidden diversity and suggests strain-level variations could be key determinants of the psoriatic microbiome. This illustrates the need for high-resolution analyses, particularly when identifying therapeutic targets. This work provides a baseline for microbiome studies in relation to the pathogenesis of psoriasis.

The role of microbiota, and probiotics and prebiotics in skin health

During the past decade, scientists have made great strides in understanding the microbiome's role in human health. Today, the microbiome has become key in scientific research, therapeutic development, medical treatment, and as a news feature in the media. Most studies have focused on the microbiome of our gut, but recently researchers have turned their attention to other microbiomes, including that of the skin. These studies of gut and skin microbiomes are yielding very informative results, new treatment strategies, and the development of new prebiotic and probiotic products for the treatment of many skin conditions.

Tropism and virulence of Cutibacterium (formerly Propionibacterium) acnes involved in implant-associated infection

The recognition of the pathogenicity of Cutibacterium acnes in implant-associated infection is not always obvious. In this paper, we aimed to distinguish pathogenic and non-pathogenic C. acnes isolates. To reach this goal, we investigated the clonal complex (CC) of a large collection of C. acnes clinical isolates through Multi-Locus Sequence Typing (MLST), we established a Caenorhabditis elegans model to assess C. acnes virulence and we investigated the presence of virulence factors in our collection. Ours results showed that CC36 and CC53 C. acnes isolates were more frequently observed in prosthetic joint infections (PJI) than CC18 and CC28 C. acnes isolates (p = 0.021). The C. elegans model developed here showed two distinct virulence groups of C. acnes (p < 0.05). These groups were not correlated to CC or clinical origin. Whole genome sequencing allowed us to identify a putative gene linked to low virulent strains. In conclusion, MLST remains a good method to screen pathogenic C. acnes isolates according to their clinical context but mechanisms of C. acnes virulence need to be assess thought transcriptomic analysis to investigate regulatory process.

A comparative study of Cutibacterium (Propionibacterium) acnes clones from acne patients and healthy controls

BACKGROUND

Cutibacterium (Propionibacterium) acnes is assumed to play an important role in the pathogenesis of acne.

OBJECTIVES

To examine if clones with distinct virulence properties are associated with acne.

METHODS

Multiple C. acnes isolates from follicles and surface skin of patients with moderate to severe acne and healthy controls were characterized by multilocus sequence typing. To determine if CC18 isolates from acne patients differ from those of controls in the possession of virulence genes or lack of genes conducive to a harmonious coexistence the full genomes of dominating CC18 follicular clones from six patients and five controls were sequenced.

RESULTS

Individuals carried one to ten clones simultaneously. The dominating C. acnes clones in follicles from acne patients were exclusively from the phylogenetic clade I-1a and all belonged to clonal complex CC18 with the exception of one patient dominated by the worldwide-disseminated and often antibiotic resistant clone ST3. The clonal composition of healthy follicles showed a more heterogeneous pattern with follicles dominated by clones representing the phylogenetic clades I-1a, I-1b, I-2 and II. Comparison of follicular CC18 gene contents, allelic versions of putative virulence genes and their promoter regions, and 54 variable-length intragenic and inter-genic homopolymeric tracts showed extensive conservation and no difference associated with the clinical origin of isolates.

CONCLUSIONS

The study supports that C. acnes strains from clonal complex CC18 and the often antibiotic resistant clone ST3 are associated with acne and suggests that susceptibility of the host rather than differences within these clones may determine the clinical outcome of colonization.

Propionibacterium acnes is developing gradual increase in resistance to oral tetracyclines

Propionibacterium acnes is an anaerobic bacterium that causes deep infection in organs and prosthetic joints, in addition to acne vulgaris. Many tetracycline-resistant P. acnes strains have been isolated because oral tetracyclines are frequently used as an acne treatment against P. acnes. In this study, we found a novel tetracycline resistance mechanism in P. acnes. Three doxycycline-resistant (MIC: 16 µg ml-1) strains were isolated from 69 strains in acne patients in Japan between 2010 and 2011. Additionally, six insusceptible strains (MIC: 1-2 µg ml-1) that had reduced susceptibility compared to susceptible strains (MIC: ≤0.5 µg ml-1) were identified. All doxycycline-resistant strains had a G1036C mutation in the 16S rRNA gene in addition to an amino acid substitution in the ribosomal S10 protein encoded by rpsJ. By contrast, insusceptible strains had an amino acid substitution in the S10 protein but no mutation in the 16S rRNA. When the mutant with decreased susceptibility to doxycycline was obtained in vitro, only the mutated S10 protein was found (MIC: 4 µg ml-1), not the mutated 16S rRNA gene. This result shows that the S10 protein amino acid substitution contributes to reduced doxycycline susceptibility in P. acnes and suggests that tetracycline resistance is acquired through a 16S rRNA mutation after the S10 protein amino acid substitution causes reduced susceptibility.