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 seven 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.

Download Full-text

Propionibacterium (Cutibacterium) granulosum Extracellular DNase BmdE Targeting Propionibacterium (Cutibacterium) acnes Biofilm Matrix, a Novel Inter-Species Competition Mechanism

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.809792 ◽

2022 ◽

Vol 11 ◽

Author(s):

Vicky Bronnec ◽

Hinnerk Eilers ◽

Anika C. Jahns ◽

Hélène Omer ◽

Oleg A. Alexeyev

Keyword(s):

Extracellular Matrix ◽

Acne Vulgaris ◽

Opportunistic Pathogen ◽

Resistant Bacteria ◽

Skin Microbiome ◽

Cutibacterium Acnes ◽

Propionibacterium Granulosum ◽

Extracellular Nuclease

Acne vulgaris is the most common dermatological disorder worldwide affecting more than 80% of adolescents and young adults with a global prevalence of 231 million cases in 2019. The involvement of the skin microbiome disbalance in the pathophysiology of acne is recognized, especially regarding the relative abundance and diversity of Propionibacterium acnes a well-known dominant human skin commensal. Biofilms, where bacteria are embedded into a protective polymeric extracellular matrix, are the most prevalent life style for microorganisms. P. acnes and its biofilm-forming ability is believed to be a contributing factor in the development of acne vulgaris, the persistence of the opportunistic pathogen and antibiotic therapy failures. Degradation of the extracellular matrix is one of the strategies used by bacteria to disperse the biofilm of competitors. In this study, we report the identification of an endogenous extracellular nuclease, BmdE, secreted by Propionibacterium granulosum able to degrade P. acnes biofilm both in vivo and in vitro. This, to our knowledge, may represent a novel competitive mechanism between two closely related species in the skin. Antibiotics targeting P. acnes have been the mainstay in acne treatment. Extensive and long-term use of antibiotics has led to the selection and spread of resistant bacteria. The extracellular DNase BmdE may represent a new bio-therapeutical strategy to combat P. acnes biofilm in acne vulgaris.

Download Full-text

Circulating Antibodies to Skin Bacteria Detected by Serological Lateral Flow Immunoassays Differentially Correlated With Bacterial Abundance

Frontiers in Microbiology ◽

10.3389/fmicb.2021.709562 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ryan Yuki Huang ◽

Chuen Neng Lee ◽

Shabbir Moochhala

Keyword(s):

Acne Vulgaris ◽

Lateral Flow ◽

Sequencing Analysis ◽

Skin Microbiome ◽

Pilosebaceous Unit ◽

Skin Bacteria ◽

Cutibacterium Acnes ◽

Next Generation Sequencing Analysis ◽

Antibody Titers ◽

Circulating Antibodies

The serological lateral flow immunoassay (LFIA) was used to detect circulating antibodies to skin bacteria. Next-generation sequencing analysis of the skin microbiome revealed a high relative abundance of Cutibacterium acnes but low abundance of Staphylococcus aureus and Corynebacterium aurimucosum on human facial samples. Yet, results from both LFIA and antibody titer quantification in 96-well microplates illustrated antibody titers that were not correspondent, and instead negatively correlated, to their respective abundance with human blood containing higher concentrations of antibodies to both S. aureus and C. aurimucosum than C. acnes. Acne vulgaris develops several unique microbial and cellular features, but its correlation with circulating antibodies to bacteria in the pilosebaceous unit remains unknown. Results here revealed that antibodies to C. acnes and S. aureus were approximately 3-fold higher and 1.5-fold lower, respectively, in acne patients than in healthy subjects. Although the results can be further validated by larger sample sizes, the proof-of-concept study demonstrates a newfound discrepancy between the abundance of skin bacteria and amounts of their corresponding antibodies. And in light of acne-correlated amplified titers of specific anticommensal antibodies, we highlight that profiling these antibodies in the pilosebaceous unit by LFIAs may provide a unique signature for monitoring acne vulgaris.

Download Full-text

PEG-8 Laurate Fermentation of Staphylococcus epidermidis Reduces the Required Dose of Clindamycin Against Cutibacterium acnes

International Journal of Molecular Sciences ◽

10.3390/ijms21145103 ◽

2020 ◽

Vol 21 (14) ◽

pp. 5103

Author(s):

Shinta Marito ◽

Sunita Keshari ◽

Chun-Ming Huang

Keyword(s):

Staphylococcus Epidermidis ◽

Low Dose ◽

Acne Vulgaris ◽

Carbon Sources ◽

Skin Microbiome ◽

Adjuvant Effect ◽

Inflammatory Protein ◽

Cutibacterium Acnes ◽

First Time ◽

Macrophage Inflammatory Protein

The probiotic activity of skin Staphylococcus epidermidis (S. epidermidis) bacteria can elicit diverse biological functions via the fermentation of various carbon sources. Here, we found that polyethylene glycol (PEG)-8 Laurate, a carbon-rich molecule, can selectively induce the fermentation of S. epidermidis, not Cutibacterium acnes (C. acnes), a bacterium associated with acne vulgaris. The PEG-8 Laurate fermentation of S. epidermidis remarkably diminished the growth of C. acnes and the C. acnes-induced production of pro-inflammatory macrophage-inflammatory protein 2 (MIP-2) cytokines in mice. Fermentation media enhanced the anti-C. acnes activity of a low dose (0.1%) clindamycin, a prescription antibiotic commonly used to treat acne vulgaris, in terms of the suppression of C. acnes colonization and MIP-2 production. Furthermore, PEG-8 Laurate fermentation of S. epidermidis boosted the activity of 0.1% clindamycin to reduce the sizes of C. acnes colonies. Our results demonstrated, for the first time, that the PEG-8 Laurate fermentation of S. epidermidis displayed the adjuvant effect on promoting the efficacy of low-dose clindamycin against C. acnes. Targeting C. acnes by lowering the required doses of antibiotics may avoid the risk of creating drug-resistant C. acnes and maintain the bacterial homeostasis in the skin microbiome, leading to a novel modality for the antibiotic treatment of acne vulgaris.

Download Full-text

Microbiome and acne vulgaris

Russian Journal of Skin and Venereal Diseases ◽

10.17816/dv60039 ◽

2020 ◽

Vol 23 (6) ◽

pp. 388-394

Author(s):

Ziyuan Ma ◽

Nikolay G. Kochergin

Keyword(s):

Staphylococcus Epidermidis ◽

Acne Vulgaris ◽

Skin Microbiome ◽

Inflammatory Skin Disease ◽

Treatment Resistant ◽

Number Of Patients ◽

Cutibacterium Acnes ◽

Pathogenic Microbes ◽

The Relationship

Acne vulgaris is a highly prevalent inflammatory skin disease involving sebaceous follicle. Although the pathogensis of acne remains uncertain, skin microbes are considered to plays an essential role in acne vulgaris. Cutibacterium acnes is the most important microbe in acne pathogenesis and its several processes: colonization, over-proliferation and inflammation have long been thought to contribute to the disease. Moreover, Staphylococcus epidermidis and Malassezia also synergistically collaborate with Cutibacterium acnes. Besides, given the growing number of patients who are treatment resistant, assessments are needed on phenotypic changes in the skin microbiome with retinoids and antibacterial therapy. Further research on the role of microbes in the pathogenesis of acne and the relationship between pathogenic microbes is expected to provide a new theoretical basis for clinical treatment of acne.

Download Full-text

Characterization of Weissella viridescens UCO-SMC3 as a Potential Probiotic for the Skin: Its Beneficial Role in the Pathogenesis of Acne Vulgaris

Microorganisms ◽

10.3390/microorganisms9071486 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1486

Author(s):

Marcela Espinoza-Monje ◽

Jorge Campos ◽

Eduardo Alvarez Villamil ◽

Alonso Jerez ◽

Stefania Dentice Maidana ◽

...

Keyword(s):

Immune Response ◽

Oral Treatment ◽

Acne Vulgaris ◽

Topical Administration ◽

In Vivo Studies ◽

Mice Model ◽

Cutibacterium Acnes ◽

Snail Helix Aspersa

Previously, we isolated lactic acid bacteria from the slime of the garden snail Helix aspersa Müller and selected Weissella viridescens UCO-SMC3 because of its ability to inhibit in vitro the growth of the skin-associated pathogen Cutibacterium acnes. The present study aimed to characterize the antimicrobial and immunomodulatory properties of W. viridescens UCO-SMC3 and to demonstrate its beneficial effect in the treatment of acne vulgaris. Our in vitro studies showed that the UCO-SMC3 strain resists adverse gastrointestinal conditions, inhibits the growth of clinical isolates of C. acnes, and reduces the adhesion of the pathogen to keratinocytes. Furthermore, in vivo studies in a mice model of C. acnes infection demonstrated that W. viridescens UCO-SMC3 beneficially modulates the immune response against the skin pathogen. Both the oral and topical administration of the UCO-SCM3 strain was capable of reducing the replication of C. acnes in skin lesions and beneficially modulating the inflammatory response. Of note, orally administered W. viridescens UCO-SMC3 induced more remarkable changes in the immune response to C. acnes than the topical treatment. However, the topical administration of W. viridescens UCO-SMC3 was more efficient than the oral treatment to reduce pathogen bacterial loads in the skin, and effects probably related to its ability to inhibit and antagonize the adhesion of C. acnes. Furthermore, a pilot study in acne volunteers demonstrated the capacity of a facial cream containing the UCO-SMC3 strain to reduce acne lesions. The results presented here encourage further mechanistic and clinical investigations to characterize W. viridescens UCO-SMC3 as a probiotic for acne vulgaris treatment.

Download Full-text

Pro-Inflammatory and Neurotrophic Factor Responses of Cells Derived from Degenerative Human Intervertebral Discs to the Opportunistic Pathogen Cutibacterium acnes

International Journal of Molecular Sciences ◽

10.3390/ijms22052347 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2347

Author(s):

Manu N. Capoor ◽

Anna Konieczna ◽

Andrew McDowell ◽

Filip Ruzicka ◽

Martin Smrcka ◽

...

Keyword(s):

Neurotrophic Factor ◽

Acne Vulgaris ◽

Opportunistic Pathogen ◽

Intervertebral Discs ◽

Disc Disease ◽

Gene Target ◽

Cutibacterium Acnes ◽

Pre Treatment

Previously, we proposed the hypothesis that similarities in the inflammatory response observed in acne vulgaris and degenerative disc disease (DDD), especially the central role of interleukin (IL)-1β, may be further evidence of the role of the anaerobic bacterium Cutibacterium (previously Propionibacterium) acnes in the underlying aetiology of disc degeneration. To investigate this, we examined the upregulation of IL-1β, and other known IL-1β-induced inflammatory markers and neurotrophic factors, from nucleus-pulposus-derived disc cells infected in vitro with C. acnes for up to 48 h. Upon infection, significant upregulation of IL-1β, alongside IL-6, IL-8, chemokine (C-C motif) ligand 3 (CCL3), chemokine (C-C motif) ligand 4 (CCL4), nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), was observed with cells isolated from the degenerative discs of eight patients versus non-infected controls. Expression levels did, however, depend on gene target, multiplicity and period of infection and, notably, donor response. Pre-treatment of cells with clindamycin prior to infection significantly reduced the production of pro-inflammatory mediators. This study confirms that C. acnes can stimulate the expression of IL-1β and other host molecules previously associated with pathological changes in disc tissue, including neo-innervation. While still controversial, the role of C. acnes in DDD remains biologically credible, and its ability to cause disease likely reflects a combination of factors, particularly individualised response to infection.

Download Full-text

Association of Antimicrobial Susceptibility and Treatment Outcome in Acne Vulgaris Patients: A Pilot Study

Journal of Laboratory Physicians ◽

10.1055/s-0040-1720943 ◽

2020 ◽

Vol 12 (04) ◽

pp. 233-238

Author(s):

Ashvini K. Yadav ◽

Suneel Bhooshan ◽

Allen Johnson ◽

Dinesh P. Asati ◽

Shashwati Nema ◽

...

Keyword(s):

Treatment Outcome ◽

Antimicrobial Susceptibility ◽

Acne Vulgaris ◽

Tertiary Care ◽

Care Hospital ◽

In Vitro Susceptibility ◽

Persistent Infections ◽

Significant Difference ◽

Cutibacterium Acnes

Abstract Purpose Cutibacterium acnes (C. acnes) is an emerging pathogen that is highly resistant to antibiotics and is capable of causing persistent infections that are difficult to treat. Methods & Materials Acne vulgaris patients visiting dermatology OPD of our tertiary care hospital during the study period of 2 months were recruited. Skin swabs were collected, and the sample was processed on 5% sheep-blood agar for anaerobic culture by the GasPak method. Isolates were identified by the standard biochemical test. Antimicrobial susceptibility testing was performed for clinically relevant antibiotics by the E-strip method. The clinical response was evaluated after 1-month follow-up to the prescribed antibiotics. Results Minocycline, doxycycline, ceftriaxone, and tetracycline were the most effective antibiotics. Nonsusceptibility to clindamycin and erythromycin were observed in 11.9% and 31% isolates, respectively, with 9.5% isolates being nonsusceptible to both. For none of the antibiotics we found significant difference in the proportion of susceptible and nonsusceptible isolates between mild, moderate, and severe grades of acne vulgaris. For none of the antibiotic regimens, significant difference was observed between nonresponders and responders. Twenty-seven patients received clindamycin and among them 16 of 19 responders and 6 of 8 nonresponders yielded growth of clindamycin-susceptible isolates (p = 0.57). Conclusion We observed significant prevalence of resistant strains of C. acnes among patients with acne vulgaris. No association was observed between in vitro susceptibility results and treatment outcome.

Download Full-text

ID3024 Polymeric nanoparticles display bactericidal effect and selective fermentation for the treatment of acne vulgaris

Biomedical Research and Therapy ◽

10.15419/bmrat.v4is.244 ◽

2017 ◽

Vol 4 (S) ◽

pp. 34

Author(s):

Ming-Fa Hsieh

Keyword(s):

Human Skin ◽

Ex Vivo ◽

Polymeric Nanoparticles ◽

Acne Vulgaris ◽

Short Chain Fatty Acids ◽

Bactericidal Effect ◽

Skin Microbiome ◽

Poly Ethylene Glycol ◽

Effective Doses ◽

Poly Ethylene

The use of antibiotics in the treatment of acne in specific group (pregnant women) of patients can lead to serious complications. We have previously demonstrated that the nanoparticles made of block copolymers of poly (ethylene glycol) and poly(e-caprolactone) can inhibit the growth of Propionibacterium acnes (P. acnes), a bacterium highly associated with the progress of acne vulgaris in the human skin [Polymers 2016; 8, 321]. To reduce the amount of antibiotics used in the treatment of skin acne, we have further demonstrated that a bacterium in the human skin microbiome can utilize PEG-based polymers to produce various short-chain fatty acids (SCFAs) which suppressed the growth of P. acnes. PEG-based polymers were chosen as selective fermentation initiators which specifically induced the fermentation of the skin commensal bacterium but not P. acnes. Interestingly, PEG-based polymers can efficiently suppress the growth of P. acnes. An acne ex vivo explant was established by using acne biopsies collected from patients with acne vulgaris at the early and middle stages. The levels of pro-inflammatory interleukin (IL)-8 cytokine in early- and middle-staged acnes were significantly higher than those in healthy skins. Incubation of acne ex vivo explants with sucrose remarkably reduced the level of IL-8 and the number of P. acnes. Results from mouse studies revealed that PEG-based polymer functions as antibiotic adjuvants which can considerably reduce the effective doses of clindamycin, a clinically-used acne antibiotic

Download Full-text

Anatomy promotes neutral coexistence of strains in the human skin microbiome

10.1101/2021.05.12.443817 ◽

2021 ◽

Author(s):

Arolyn Conwill ◽

Anne C Kuan ◽

Ravalika Damerla ◽

Alexandra J Poret ◽

Jacob S Baker ◽

...

Keyword(s):

Human Skin ◽

Abundant Species ◽

Therapeutic Interventions ◽

Skin Microbiome ◽

Population Fragmentation ◽

Single Strain ◽

Independent Source ◽

Cutibacterium Acnes ◽

Resident Populations ◽

And Migration

What enables strains of the same species to coexist in a microbiome? Here, we investigate if host anatomy can explain strain co-residence of Cutibacterium acnes, the most abundant species on human skin. We reconstruct on-person evolution and migration using 947 C. acnes colony genomes acquired from 16 subjects, including from individual skin pores, and find that pores maintain diversity by limiting competition. Although strains with substantial fitness differences coexist within centimeter-scale regions, each pore is dominated by a single strain. Moreover, colonies from a pore typically have identical genomes. An absence of adaptive signatures suggests a genotype-independent source of low within-pore diversity. We therefore propose that pore anatomy imposes random single-cell bottlenecks during migration into pores and subsequently blocks new migrants; the resulting population fragmentation reduces competition and promotes coexistence. Our findings imply that therapeutic interventions involving pore-dwelling species should focus on removing resident populations over optimizing probiotic fitness.

Download Full-text