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Podbielski A, Köller T, Warnke P, Barrantes I, Kreikemeyer B. Whole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates. Front Cell Infect Microbiol 2024; 14:1433783. [PMID: 39512589 PMCID: PMC11540793 DOI: 10.3389/fcimb.2024.1433783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 09/23/2024] [Indexed: 11/15/2024] Open
Abstract
Introduction Cutibacterium acnes can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are C. acnes strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results. Methods In the present study, we prospectively collected C. acnes strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality. Results Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups. Discussion Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits.
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Affiliation(s)
- Andreas Podbielski
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, Rostock, Germany
| | - Thomas Köller
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, Rostock, Germany
| | - Philipp Warnke
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, Rostock, Germany
| | - Israel Barrantes
- Research Group Translational Bioinformatics, Institute for Biostatistics and Informatics in Medicine and Aging Research, Rostock University Medical Center, Rostock, Germany
| | - Bernd Kreikemeyer
- Institute of Medical Microbiology, Virology and Hygiene, Rostock University Medical Center, Rostock, Germany
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Coenye T, Spittaels KJ, Achermann Y. The role of biofilm formation in the pathogenesis and antimicrobial susceptibility of Cutibacterium acnes. Biofilm 2022; 4:100063. [PMID: 34950868 PMCID: PMC8671523 DOI: 10.1016/j.bioflm.2021.100063] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 12/20/2022] Open
Abstract
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.
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Affiliation(s)
- Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Karl-Jan Spittaels
- Laboratory of Pharmaceutical Microbiology, Ghent University, Gent, Belgium
| | - Yvonne Achermann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Fatima N, Bjarnsholt T, Bay L. Dynamics of skin microbiota in shoulder surgery infections. APMIS 2021; 129:665-674. [PMID: 34587324 DOI: 10.1111/apm.13185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 09/25/2021] [Indexed: 01/10/2023]
Abstract
Post-surgical infections arise due to various contributing factors. Most important is the presence of potential pathogenic microorganisms in the skin complemented by the patient´s health status. Cutibacterium acnes is commonly present in the pilosebaceous glands and hair follicle funnels in human skin. After surgical intervention, these highly prevalent, slow-growing bacteria can be found in the deeper tissues and in proximity of implants. C. acnes is frequently implicated in post-surgical infections, often resulting in the need for revision surgery. This review summarizes the current understanding of microbial dynamics in shoulder surgical infections. In particular, we shed light on the contribution of C. acnes to post-surgical shoulder infections as well as their colonization and immune-modulatory potential. Despite being persistently found in post-surgical tissues, C. acnes is often underestimated as a causative organism due to its slow growth and the inefficient detection methods. We discuss the role of the skin environment constituted by microbial composition and host cellular status in influencing C. acnes recolonization potential. Future mapping of the individual skin microbiome in shoulder surgery patients using advanced molecular methods would be a useful approach for determining the risk of post-operative infections.
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Affiliation(s)
- Naireen Fatima
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
| | - Lene Bay
- Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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Abstract
Porphyrins are intermediate metabolites in the biosynthesis of vital molecules, including heme, cobalamin, and chlorophyll. Bacterial porphyrins are known to be proinflammatory, with high levels linked to inflammatory skin diseases. Propionibacterium species are dominant skin commensals and play essential roles in defending against pathogens and in triggering an inflammatory response. To better understand how the inflammatory potential of the skin microbiome may vary depending on its propionibacterial composition, we compared the production levels of porphyrins among Propionibacterium acnes, Propionibacterium granulosum, Propionibacterium avidum, and Propionibacterium humerusii strains. We found that porphyrin production varied among these species, with P. acnes type I strains producing significantly larger amounts of porphyrins than P. acnes type II and III strains and other Propionibacterium species. P. acnes strains that are highly associated with the common skin condition acne vulgaris responded to vitamin B12 supplementation with significantly higher porphyrin production. In contrast, vitamin B12 supplementation had no effect on the porphyrin production of health-associated P. acnes strains and other propionibacteria. We observed low-level porphyrin production in most Propionibacterium strains harboring the deoR repressor gene, with the exception of P. acnes strains belonging to type I clades IB-3 and IC. Our findings shed light on the proinflammatory potential of distinct phylogenetic lineages of P. acnes as well as other resident skin propionibacteria. We demonstrate that the overall species and strain composition is important in determining the metabolic output of the skin microbiome in health and disease.IMPORTANCE Porphyrins are a group of metabolites essential to the biosynthesis of heme, cobalamin, and chlorophyll in living organisms. Bacterial porphyrins can be proinflammatory, with high levels linked to human inflammatory diseases, including the common skin condition acne vulgaris. Propionibacteria are among the most abundant skin bacteria. Variations in propionibacteria composition on the skin may lead to different porphyrin levels and inflammatory potentials. This study characterized porphyrin production in all lineages of Propionibacterium acnes, the most dominant skin Propionibacterium, and other resident skin propionibacteria, including P. granulosum, P. avidum, and P. humerusii We revealed that P. acnes type I strains produced significantly more porphyrins than did type II and III strains and other Propionibacterium species. The findings from this study shed light on the proinflammatory potential of the skin microbiome and can be used to guide the development of effective acne treatments by modulating the skin microbiome and its metabolic activities.
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Dagnelie MA, Khammari A, Dréno B, Corvec S. Cutibacterium acnes molecular typing: time to standardize the method. Clin Microbiol Infect 2018; 24:1149-1155. [DOI: 10.1016/j.cmi.2018.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/01/2018] [Accepted: 03/03/2018] [Indexed: 12/11/2022]
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Draft genome sequences of three multidrug-resistant Cutibacterium (formerly Propionibacterium ) acnes strains isolated from acne patients, China. J Glob Antimicrob Resist 2017; 11:114-115. [DOI: 10.1016/j.jgar.2017.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/13/2017] [Accepted: 10/10/2017] [Indexed: 11/18/2022] Open
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Propionibacterium acnes Host Inflammatory Response During Periprosthetic Infection Is Joint Specific. HSS J 2017; 13:159-164. [PMID: 28690466 PMCID: PMC5481257 DOI: 10.1007/s11420-016-9528-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/02/2016] [Indexed: 02/07/2023]
Abstract
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.
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Yu Y, Champer J, Garbán H, Kim J. Typing of Propionibacterium acnes: a review of methods and comparative analysis. Br J Dermatol 2015; 172:1204-9. [PMID: 25600912 DOI: 10.1111/bjd.13667] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/08/2015] [Indexed: 02/06/2023]
Abstract
Propionibacterium acnes is a major commensal of the human skin. However, it is also the pathogen responsible for acne vulgaris and other diseases, such as medical-device infections. Strains of Propionibacterium acnes have long been classified into several different types. Recently, typing systems for this bacterium have taken on an increased importance as different types of P. acnes have been found to be associated with different disease states, including acne. Genetic approaches based on individual or multiple genes have classified P. acnes into types, which have been supported by the sequencing of nearly 100 P. acnes genomes. These types have distinct genetic, transcriptomic and proteomic differences. Additionally, they may have different immune response profiles. Taken together, these factors may account for the different disease associations of P. acnes types.
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Affiliation(s)
- Y Yu
- Division of Dermatology and Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, U.S.A.,Irvine School of Medicine, University of California, Irvine, CA, U.S.A
| | - J Champer
- Division of Dermatology and Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, U.S.A
| | - H Garbán
- Division of Dermatology and Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, U.S.A
| | - J Kim
- Division of Dermatology and Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, U.S.A.,Department of Dermatology, Greater Los Angeles Healthcare System Veterans Affairs, Los Angeles, CA, U.S.A
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Propionibacterium acnes: from commensal to opportunistic biofilm-associated implant pathogen. Clin Microbiol Rev 2015; 27:419-40. [PMID: 24982315 DOI: 10.1128/cmr.00092-13] [Citation(s) in RCA: 420] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Propionibacterium acnes is known primarily as a skin commensal. However, it can present as an opportunistic pathogen via bacterial seeding to cause invasive infections such as implant-associated infections. These infections have gained more attention due to improved diagnostic procedures, such as sonication of explanted foreign materials and prolonged cultivation time of up to 14 days for periprosthetic biopsy specimens, and improved molecular methods, such as broad-range 16S rRNA gene PCR. Implant-associated infections caused by P. acnes are most often described for shoulder prosthetic joint infections as well as cerebrovascular shunt infections, fibrosis of breast implants, and infections of cardiovascular devices. P. acnes causes disease through a number of virulence factors, such as biofilm formation. P. acnes is highly susceptible to a wide range of antibiotics, including beta-lactams, quinolones, clindamycin, and rifampin, although resistance to clindamycin is increasing. Treatment requires a combination of surgery and a prolonged antibiotic treatment regimen to successfully eliminate the remaining bacteria. Most authors suggest a course of 3 to 6 months of antibiotic treatment, including 2 to 6 weeks of intravenous treatment with a beta-lactam. While recently reported data showed a good efficacy of rifampin against P. acnes biofilms, prospective, randomized, controlled studies are needed to confirm evidence for combination treatment with rifampin, as has been performed for staphylococcal implant-associated infections.
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Multiplex touchdown PCR for rapid typing of the opportunistic pathogen Propionibacterium acnes. J Clin Microbiol 2015; 53:1149-55. [PMID: 25631794 DOI: 10.1128/jcm.02460-14] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The opportunistic human pathogen Propionibacterium acnes is composed of a number of distinct phylogroups, designated types IA1, IA2, IB, IC, II, and III, which vary in their production of putative virulence factors, their inflammatory potential, and their biochemical, aggregative, and morphological characteristics. Although multilocus sequence typing (MLST) currently represents the gold standard for unambiguous phylogroup classification and individual strain identification, it is a labor-intensive and time-consuming technique. As a consequence, we developed a multiplex touchdown PCR assay that in a single reaction can confirm the species identity and phylogeny of an isolate based on its pattern of reaction with six primer sets that target the 16S rRNA gene (all isolates), ATPase (types IA1, IA2, and IC), sodA (types IA2 and IB), atpD (type II), and recA (type III) housekeeping genes, as well as a Fic family toxin gene (type IC). When applied to 312 P. acnes isolates previously characterized by MLST and representing types IA1 (n=145), IA2 (n=20), IB (n=65), IC (n=7), II (n=45), and III (n=30), the multiplex displayed 100% sensitivity and 100% specificity for detecting isolates within each targeted phylogroup. No cross-reactivity with isolates from other bacterial species was observed. This multiplex assay will provide researchers with a rapid, high-throughput, and technically undemanding typing method for epidemiological and phylogenetic investigations. It will facilitate studies investigating the association of lineages with various infections and clinical conditions, and it will serve as a prescreening tool to maximize the number of genetically diverse isolates selected for downstream higher-resolution sequence-based analyses.
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Proteome analysis of human sebaceous follicle infundibula extracted from healthy and acne-affected skin. PLoS One 2014; 9:e107908. [PMID: 25238151 PMCID: PMC4169578 DOI: 10.1371/journal.pone.0107908] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 08/23/2014] [Indexed: 12/15/2022] Open
Abstract
Acne vulgaris is a very common disease of the pilosebaceous unit of the human skin. The pathological processes of acne are not fully understood. To gain further insight sebaceous follicular casts were extracted from 18 healthy and 20 acne-affected individuals by cyanoacrylate-gel biopsies and further processed for mass spectrometry analysis, aiming at a proteomic analysis of the sebaceous follicular casts. Human as well as bacterial proteins were identified. Human proteins enriched in acne and normal samples were detected, respectively. Normal follicular casts are enriched in proteins such as prohibitins and peroxiredoxins which are involved in the protection from various stresses, including reactive oxygen species. By contrast, follicular casts extracted from acne-affected skin contained proteins involved in inflammation, wound healing and tissue remodeling. Among the most distinguishing proteins were myeloperoxidase, lactotransferrin, neutrophil elastase inhibitor and surprisingly, vimentin. The most significant biological process among all acne-enriched proteins was ‘response to a bacterium’. Identified bacterial proteins were exclusively from Propionibacterium acnes. The most abundant P. acnes proteins were surface-exposed dermatan sulphate adhesins, CAMP factors, and a so far uncharacterized lipase in follicular casts extracted from normal as well as acne-affected skin. This is a first proteomic study that identified human proteins together with proteins of the skin microbiota in sebaceous follicular casts.
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McDowell A, Nagy I, Magyari M, Barnard E, Patrick S. The opportunistic pathogen Propionibacterium acnes: insights into typing, human disease, clonal diversification and CAMP factor evolution. PLoS One 2013; 8:e70897. [PMID: 24058439 PMCID: PMC3772855 DOI: 10.1371/journal.pone.0070897] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 06/26/2013] [Indexed: 12/22/2022] Open
Abstract
We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST4) that correctly predicted the phylogroup (IA1, IA2, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST4 method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated ‘virulence’ factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages.
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Affiliation(s)
- Andrew McDowell
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, United Kingdom
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Genotypic and antimicrobial characterisation of Propionibacterium acnes isolates from surgically excised lumbar disc herniations. BIOMED RESEARCH INTERNATIONAL 2013; 2013:530382. [PMID: 24066290 PMCID: PMC3771251 DOI: 10.1155/2013/530382] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2013] [Revised: 05/21/2013] [Accepted: 06/01/2013] [Indexed: 11/20/2022]
Abstract
The anaerobic skin commensal Propionibacterium acnes is an underestimated cause of human infections and clinical conditions. Previous studies have suggested a role for the bacterium in lumbar disc herniation and infection. To further investigate this, five biopsy samples were surgically excised from each of 64 patients with lumbar disc herniation. P. acnes and other bacteria were detected by anaerobic culture, followed by biochemical and PCR-based identification. In total, 24/64 (38%) patients had evidence of P. acnes in their excised herniated disc tissue. Using recA and mAb typing methods, 52% of the isolates were type II (50% of culture-positive patients), while type IA strains accounted for 28% of isolates (42% patients). Type III (11% isolates; 21% patients) and type IB strains (9% isolates; 17% patients) were detected less frequently. The MIC values for all isolates were lowest for amoxicillin, ciprofloxacin, erythromycin, rifampicin, tetracycline, and vancomycin (≤1mg/L). The MIC for fusidic acid was 1-2 mg/L. The MIC for trimethoprim and gentamicin was 2 to ≥4 mg/L. The demonstration that type II and III strains, which are not frequently recovered from skin, predominated within our isolate collection (63%) suggests that the role of P. acnes in lumbar disc herniation should not be readily dismissed.
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Jasson F, Nagy I, Knol AC, Zuliani T, Khammari A, Dréno B. Different strains ofPropionibacterium acnesmodulate differently the cutaneous innate immunity. Exp Dermatol 2013; 22:587-92. [DOI: 10.1111/exd.12206] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2013] [Indexed: 12/17/2022]
Affiliation(s)
| | - Istvan Nagy
- Institute of Biochemistry; Biological Research Centre of the Hungarian Academy of Sciences; Szeged; Hungary
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Roller M, Lucić V, Nagy I, Perica T, Vlahovicek K. Environmental shaping of codon usage and functional adaptation across microbial communities. Nucleic Acids Res 2013; 41:8842-52. [PMID: 23921637 PMCID: PMC3799439 DOI: 10.1093/nar/gkt673] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microbial communities represent the largest portion of the Earth's biomass. Metagenomics projects use high-throughput sequencing to survey these communities and shed light on genetic capabilities that enable microbes to inhabit every corner of the biosphere. Metagenome studies are generally based on (i) classifying and ranking functions of identified genes; and (ii) estimating the phyletic distribution of constituent microbial species. To understand microbial communities at the systems level, it is necessary to extend these studies beyond the species' boundaries and capture higher levels of metabolic complexity. We evaluated 11 metagenome samples and demonstrated that microbes inhabiting the same ecological niche share common preferences for synonymous codons, regardless of their phylogeny. By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for lifestyle-specific genes across the entire microbial community, effectively considering microbial communities as meta-genomes. These findings set up a 'functional metagenomics' platform for the identification of genes relevant for adaptations of entire microbial communities to environments. Our results provide valuable arguments in defining the concept of microbial species through the context of their interactions within the community.
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Affiliation(s)
- Masa Roller
- Bioinformatics Group, Department of Molecular Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Temesvári körút 62, H-6726 Szeged, Hungary, MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK and Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway
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Pan-genome and comparative genome analyses of propionibacterium acnes reveal its genomic diversity in the healthy and diseased human skin microbiome. mBio 2013; 4:e00003-13. [PMID: 23631911 PMCID: PMC3663185 DOI: 10.1128/mbio.00003-13] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Propionibacterium acnes constitutes a major part of the skin microbiome and contributes to human health. However, it has also been implicated as a pathogenic factor in several diseases, including acne, one of the most common skin diseases. Its pathogenic role, however, remains elusive. To better understand the genetic landscape and diversity of the organism and its role in human health and disease, we performed a comparative genome analysis of 82 P. acnes strains, 69 of which were sequenced by our group. This collection covers all known P. acnes lineages, including types IA, IB, II, and III. Our analysis demonstrated that although the P. acnes pan-genome is open, it is relatively small and expands slowly. The core regions, shared by all the sequenced genomes, accounted for 88% of the average genome. Comparative genome analysis showed that within each lineage, the strains isolated from the same individuals were more closely related than the ones isolated from different individuals, suggesting that clonal expansions occurred within each individual microbiome. We also identified the genetic elements specific to each lineage. Differences in harboring these elements may explain the phenotypic and functional differences of P. acnes in functioning as a commensal in healthy skin and as a pathogen in diseases. Our findings of the differences among P. acnes strains at the genome level underscore the importance of identifying the human microbiome variations at the strain level in understanding its association with diseases and provide insight into novel and personalized therapeutic approaches for P. acnes-related diseases. Propionibacterium acnes is a major human skin bacterium. It plays an important role in maintaining skin health. However, it has also been hypothesized to be a pathogenic factor in several diseases, including acne, a common skin disease affecting 85% of teenagers. To understand whether different strains have different virulent properties and thus play different roles in health and diseases, we compared the genomes of 82 P. acnes strains, most of which were isolated from acne or healthy skin. We identified lineage-specific genetic elements that may explain the phenotypic and functional differences of P. acnes as a commensal in health and as a pathogen in diseases. By analyzing a large number of sequenced strains, we provided an improved understanding of the genetic landscape and diversity of the organism at the strain level and at the molecular level that can be further applied in the development of new and personalized therapies.
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Nagy E, Urbán E, Becker S, Kostrzewa M, Vörös A, Hunyadkürti J, Nagy I. MALDI-TOF MS fingerprinting facilitates rapid discrimination of phylotypes I, II and III of Propionibacterium acnes. Anaerobe 2013; 20:20-6. [DOI: 10.1016/j.anaerobe.2013.01.007] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 01/16/2013] [Accepted: 01/29/2013] [Indexed: 01/30/2023]
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Genome sequences published outside of Standards in Genomic Sciences, May-June 2012. Stand Genomic Sci 2012. [PMCID: PMC3558956 DOI: 10.4056/sigs.3126494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
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