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McLaughlin J, Burnham CAD, McDowell A. MALDI-TOF mass spectrometry misidentification of Cutibacterium namnetense and Cutibacterium modestum: Implications for multiplex PCR phylotyping of Cutibacterium acnes. Anaerobe 2024; 88:102874. [PMID: 38848934 DOI: 10.1016/j.anaerobe.2024.102874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) can misidentify Cutibacterium namnetense and Cutibacterium modestum as Cutibacterium acnes. We now describe how such MALDI-TOF MS misidentification explains previous reports of C. acnes isolates that could not be characterised using a multiplex PCR phylotyping assay.
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Affiliation(s)
- Joseph McLaughlin
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry, UK
| | - Carey-Ann D Burnham
- Division of Laboratory and Genomic Medicine, Department of Pathology, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew McDowell
- Personalised Medicine Centre, School of Medicine, Ulster University, Londonderry, UK; Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, UK.
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Both A, Huang J, Hentschke M, Tobys D, Christner M, Klatte TO, Seifert H, Aepfelbacher M, Rohde H. Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections. Microbiol Spectr 2023; 11:e0474022. [PMID: 36976006 PMCID: PMC10100948 DOI: 10.1128/spectrum.04740-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023] Open
Abstract
Cutibacterium acnes, formerly known as Propionibacterium acnes, is a commensal of the human pilosebaceous unit but also causes deep-seated infection, especially in the context of orthopedic and neurosurgical foreign materials. Interestingly, little is known about the role of specific pathogenicity factors for infection establishment. Here, 86 infection-associated and 103 commensalism-associated isolates of C. acnes were collected from three independent microbiology laboratories. We sequenced the whole genomes of the isolates for genotyping and a genome-wide association study (GWAS). We found that C. acnes subsp. acnes IA1 was the most significant phylotype among the infection isolates (48.3% of all infection isolates; odds ratio [OR] = 1.98 for infection). Among the commensal isolates, C. acnes subsp. acnes IB was the most significant phylotype (40.8% of all commensal isolates; OR = 0.5 for infection). Interestingly, C. acnes subsp. elongatum (III) was rare overall and did not occur at all in infection. The open reading frame-based GWAS (ORF-GWAS) did not show any loci with a strong signal for infection association (no P values of ≤0.05 after adjustment for multiple testing; no logarithmic OR [logOR] of ≥|2|). We concluded that all subspecies and phylotypes of C. acnes, possibly with the exception of C. acnes subsp. elongatum, are able to cause deep-seated infection given favorable conditions, most importantly related to inserted foreign material. Genetic content appears to have a small effect on the likelihood of infection establishment, and functional studies are needed to understand the individual factors contributing to deep-seated infections caused by C. acnes. IMPORTANCE Opportunistic infections emerging from human skin microbiota are of ever-increasing importance. Cutibacterium acnes, being abundant on the human skin, may cause deep-seated infections (e.g., device-associated infections). Differentiation between invasive (i.e., clinically significant) C. acnes isolates and sole contaminants is often difficult. Identification of genetic markers associated with invasiveness not only would strengthen our knowledge related to pathogenesis but also could open ways to selectively categorize invasive and contaminating isolates in the clinical microbiology lab. We show that in contrast to other opportunistic pathogens (e.g., Staphylococcus epidermidis), invasiveness is apparently a broadly distributed ability across almost all C. acnes subspecies and phylotypes. Thus, our work strongly supports an approach in which clinical significance is judged from clinical context rather than by detecting specific genetic traits.
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Affiliation(s)
- Anna Both
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jiabin Huang
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - David Tobys
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Martin Christner
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Till Orla Klatte
- Department for Trauma Surgery and Orthopedics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Martin Aepfelbacher
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Holger Rohde
- Institute for Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Brüggemann H, Salar-Vidal L, Gollnick HPM, Lood R. A Janus-Faced Bacterium: Host-Beneficial and -Detrimental Roles of Cutibacterium acnes. Front Microbiol 2021; 12:673845. [PMID: 34135880 PMCID: PMC8200545 DOI: 10.3389/fmicb.2021.673845] [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: 02/28/2021] [Accepted: 04/29/2021] [Indexed: 12/18/2022] Open
Abstract
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.
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Affiliation(s)
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Fundacion Jimenez Diaz University Hospital, Madrid, Spain
| | - Harald P. M. Gollnick
- Department of Dermatology and Venerology, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Rolf Lood
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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Mayslich C, Grange PA, Dupin N. Cutibacterium acnes as an Opportunistic Pathogen: An Update of Its Virulence-Associated Factors. Microorganisms 2021; 9:303. [PMID: 33540667 PMCID: PMC7913060 DOI: 10.3390/microorganisms9020303] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 02/06/2023] Open
Abstract
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.
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Affiliation(s)
- Constance Mayslich
- NSERM Institut Cochin, INSERM U1016-CNRS UMR8104, Equipe de Biologie Cutanée, Université de Paris, 75014 Paris, France; (C.M.); (P.A.G.)
| | - Philippe Alain Grange
- NSERM Institut Cochin, INSERM U1016-CNRS UMR8104, Equipe de Biologie Cutanée, Université de Paris, 75014 Paris, France; (C.M.); (P.A.G.)
- Service de Dermatologie-Vénéréologie, Groupe Hospitalier APHP.5, CNR IST Bactériennes—Laboratoire Associé Syphilis, 75014 Paris, France
| | - Nicolas Dupin
- NSERM Institut Cochin, INSERM U1016-CNRS UMR8104, Equipe de Biologie Cutanée, Université de Paris, 75014 Paris, France; (C.M.); (P.A.G.)
- Service de Dermatologie-Vénéréologie, Groupe Hospitalier APHP.5, CNR IST Bactériennes—Laboratoire Associé Syphilis, 75014 Paris, France
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Cutibacterium acnes Isolates from Deep Tissue Specimens Retrieved during Revision Shoulder Arthroplasty: Similar Colony Morphology Does Not Indicate Clonality. J Clin Microbiol 2020; 58:JCM.00121-19. [PMID: 31645372 DOI: 10.1128/jcm.00121-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 09/28/2019] [Indexed: 01/10/2023] Open
Abstract
Cutibacterium acnes is the most common bacterium associated with periprosthetic shoulder infections. Sequencing of C. acnes has been proposed as a potential rapid diagnostic tool and a method of determining subtypes associated with pathogenicity and antibiotic resistance patterns. When multiple deep samples from the same surgery are culture positive for the same species and the isolates show the same culture phenotype, it is typically assumed that these isolates are clonal. However, it is well-known that C. acnes is not clonal on the skin of most individuals. We hypothesized that the C. acnes bacteria recovered at the time of revision shoulder arthroplasty would often represent more than one subtype, and we tested this hypothesis in this work. For patients undergoing revision shoulder arthroplasty, multiple samples from the surgical field were taken. For those patients with multiple samples that were culture positive for C. acnes, isolates from each sample were subjected to full genome sequencing. Of 11 patients, 5 (45%) had different subtypes of C. acnes within the deep tissues even though the colony morphology was similar. One patient had four subtypes in the deep tissues, while four patients had two different subtypes. Up to four different subtypes of C. acnes were observed in the deep tissues of a single patient. Clonality of C. acnes isolates from deep specimens from a potential periprosthetic shoulder infection cannot be assumed. Sequence-based characterization of virulence and antibiotic resistance may require testing of multiple deep specimens.
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Rao AJ, MacLean IS, Naylor AJ, Garrigues GE, Verma NN, Nicholson GP. Next-generation sequencing for diagnosis of infection: is more sensitive really better? J Shoulder Elbow Surg 2020; 29:20-26. [PMID: 31619355 DOI: 10.1016/j.jse.2019.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 02/01/2023]
Abstract
BACKGROUND The utility of next-generation sequencing (NGS) in differentiating between active infection and contaminant or baseline flora remains unclear. The purpose of this study is to compare NGS with culture-based methods in primary shoulder arthroplasty. METHODS A prospective series of primary shoulder arthroplasty patients with no history of infection or antibiotic use within 60 days of surgery was enrolled. All patients received standard perioperative antibiotics. After skin incision, a 10 × 3-mm sample of the medial skin edge was excised. A 2 × 2-cm synovial tissue biopsy was taken from the rotator interval after subscapularis takedown. Each sample set was halved and sent for NGS and standard cultures. RESULTS Samples from 25 patients were analyzed. Standard aerobic/anaerobic cultures were positive in 10 skin samples (40%, 95% confidence interval [CI] 20%-60%) and 3 deep tissue samples (12%, 90% CI 1%-23%]). NGS detected ≥1 bacterial species in 17 of the skin samples (68%, 95% CI 49%-87%) and 7 deep tissue samples (28%, 95% CI 9%-47%). There was a significant difference (P < .03) in the mean number of bacterial species detected with NGS between the positive standard culture (1.6 species) and the negative standard culture groups (5.7 species). CONCLUSION NGS identified bacteria at higher rates in skin and deep tissue samples than standard culture did in native, uninfected patients undergoing primary procedures. Further research is needed to determine which NGS results are clinically relevant and which are false positives before NGS can be reliably used in orthopedic cases.
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Affiliation(s)
- Allison J Rao
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Ian S MacLean
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Amanda J Naylor
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Grant E Garrigues
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Nikhil N Verma
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA
| | - Gregory P Nicholson
- Department of Orthopaedic Surgery, Rush University Medical Center, Chicago, IL, USA.
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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: 3.3] [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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McDowell A. Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt? Microorganisms 2017; 6:microorganisms6010001. [PMID: 29267255 PMCID: PMC5874615 DOI: 10.3390/microorganisms6010001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 11/16/2022] Open
Abstract
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.
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Affiliation(s)
- Andrew McDowell
- Northern Ireland Centre for Stratified Medicine, School of Biomedical Sciences, Ulster University, Londonderry BT47 6SB, UK.
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