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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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2
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Chudzik A, Bromke MA, Gamian A, Paściak M. Comprehensive lipidomic analysis of the genus Cutibacterium. mSphere 2024; 9:e0005424. [PMID: 38712970 PMCID: PMC11237483 DOI: 10.1128/msphere.00054-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024] Open
Abstract
Cutibacterium are part of the human skin microbiota and are opportunistic microorganisms that become pathogenic in immunodeficient states. These lipophilic bacteria willingly inhabit areas of the skin where sebaceous glands are abundant; hence, there is a need to thoroughly understand their metabolism. Lipids are no longer considered only structural elements but also serve as signaling molecules and may have antigenic properties. Lipidomics remains a major research challenge, mainly due to the diverse physicochemical properties of lipids. Therefore, this study aimed to perform a large comparative lipidomic analysis of eight representatives of the Cutibacterium genus, including four phylotypes of C. acnes and two strains of C. granulosum, C. avidum, and C. namnetense. Lipidomic analysis was performed by liquid chromatography‒mass spectrometry (LC-MS) in both positive and negative ion modes, allowing the detection of the widest range of metabolites. Fatty acid analysis by gas chromatography‒mass spectrometry (GC-MS) corroborated the lipidomic data. As a result, 128 lipids were identified, among which it was possible to select marker compounds, some of which were characteristic even of individual C. acnes phylotypes. These include phosphatidylcholine PC 30:0, sphingomyelins (SM 33:1, SM 35:1), and phosphatidylglycerol with an alkyl ether substituent PG O-32:0. Moreover, cardiolipins and fatty acid amides were identified in Cutibacterium spp. for the first time. This comparative characterization of the cutibacterial lipidome with the search for specific molecular markers reveals its diagnostic potential for clinical microbiology. IMPORTANCE Cutibacterium (previously Propionibacterium) represents an important part of the human skin microbiota, and its role in clinical microbiology is growing due to opportunistic infections. Lipidomics, apart from protein profiling, has the potential to prove to be a useful tool for defining the cellular fingerprint, allowing for precise differentiation of microorganisms. In this work, we presented a comparative analysis of lipids found in eight strains of the genus Cutibacterium, including a few C. acnes phylotypes. Our results are one of the first large-scale comprehensive studies regarding the bacterial lipidome, which also enabled the selection of C. acnes phylotype-specific lipid markers. The increased role of lipids not only as structural components but also as diagnostic markers or potential antigens has led to new lipid markers that can be used as diagnostic tools for clinical microbiology. We believe that the findings in our paper will appeal to a wide range of researchers.
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Affiliation(s)
- Anna Chudzik
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Mariusz A Bromke
- Department of Biochemistry and Immunochemistry, Wroclaw Medical University, Wroclaw, Poland
| | - Andrzej Gamian
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Mariola Paściak
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
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3
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Corvec S, Fayoux E, Tessier E, Guillouzouic A, Moraru C, Lecomte R, Bémer P, Ruffier d'Epenoux L. Cutibacterium namnetense osteosynthetic cervical spine infections: experience with two cases. Eur J Clin Microbiol Infect Dis 2024; 43:395-399. [PMID: 38093085 DOI: 10.1007/s10096-023-04731-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/28/2023] [Indexed: 01/28/2024]
Abstract
We report two uncommon cases of osteosynthetic cervical spine infection. Clinical patient features, microbiological strain characteristics, diagnostic methods, and treatment were analyzed. Both patients were male, and one had risk factors for surgical site infection. During surgery, perioperative samples were positive yielding an anaerobic microorganism identified as Cutibacterium namnetense by MALDI-TOF MS and confirmed by 16S rRNA/gyrB genes sequencing. All isolates were fully susceptible. C. namnetense osteosynthetic cervical spine infections are rare. Both cases were early surgical site infections. Bruker MALDI-TOF MS appears to be an excellent tool for rapid and accurate identification. Amoxicillin seems to be an option for the treatment.
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Affiliation(s)
- S Corvec
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France.
- Nantes Study Group Members of CRIOGO (Centre de Référence Des Infections Ostéo-Articulaires du Grand Ouest), Nantes, France.
- Université de Nantes, CHU Nantes, INSERM, INCIT, U1302 F- 44000, Nantes, France.
| | - E Fayoux
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France
| | - E Tessier
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France
| | - A Guillouzouic
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France
| | - C Moraru
- CHU Nantes, Service de Neuro-Chirurgie, Nantes, France
| | - R Lecomte
- CHU Nantes, Service Des Maladies Infectieuses, Nantes Université, Nantes, France
| | - P Bémer
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France
- Nantes Study Group Members of CRIOGO (Centre de Référence Des Infections Ostéo-Articulaires du Grand Ouest), Nantes, France
| | - L Ruffier d'Epenoux
- Institut de Biologie des Hôpitaux de Nantes, Service de Bactériologie Et Des Contrôles Microbiologiques, CHU Nantes, Nantes Université, 9 Quai Moncousu, 44093, Cedex 01, Nantes, France
- Nantes Study Group Members of CRIOGO (Centre de Référence Des Infections Ostéo-Articulaires du Grand Ouest), Nantes, France
- Université de Nantes, CHU Nantes, INSERM, INCIT, U1302 F- 44000, Nantes, France
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4
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Erbežnik A, Celar Šturm A, Strašek Smrdel K, Triglav T, Maver Vodičar P. Comparative Genomic Analysis of Cutibacterium spp. Isolates in Implant-Associated Infections. Microorganisms 2023; 11:2971. [PMID: 38138116 PMCID: PMC10745319 DOI: 10.3390/microorganisms11122971] [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: 11/15/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Bacteria of the genus Cutibacterium are Gram-positive commensals and opportunistic pathogens that represent a major challenge in the diagnosis and treatment of implant-associated infections (IAIs). This study provides insight into the distribution of different sequence types (STs) of C. acnes, and the presence of virulence factors (VFs) in 64 Cutibacterium spp. isolates from suspected or confirmed IAIs obtained during routine microbiological diagnostics. Fifty-three C. acnes, six C. avidum, four C. granulosum, and one C. namnetense isolate, collected from different anatomical sites, were included in our study. Using whole-genome sequencing and a single-locus sequencing typing scheme, we successfully characterized all C. acnes strains and revealed the substantial diversity of STs, with the discovery of six previously unidentified STs. Phylotype IA1, previously associated with both healthy skin microbiome and infections, was the most prevalent, with ST A1 being the most common. Some minor differences in STs' distribution were observed in correlation with anatomical location and association with infection. A genomic analysis of 40 investigated VFs among 64 selected strains showed no significant differences between different STs, anatomical sites, or infection-related and infection undetermined/unlikely groups of strains. Most differences in VF distribution were found between strains of different Cutibacterium spp., subspecies, and phylotypes, with CAMP factors, biofilm-related VFs, lipases, and heat shock proteins identified in all analyzed Cutibacterium spp.
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Affiliation(s)
| | | | | | | | - Polona Maver Vodičar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.E.); (A.C.Š.); (K.S.S.); (T.T.)
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5
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Sambruni G, Macandog AD, Wirbel J, Cagnina D, Catozzi C, Dallavilla T, Borgo F, Fazio N, Fumagalli-Romario U, Petz WL, Manzo T, Ravenda SP, Zeller G, Nezi L, Schaefer MH. Location and condition based reconstruction of colon cancer microbiome from human RNA sequencing data. Genome Med 2023; 15:32. [PMID: 37131219 PMCID: PMC10155404 DOI: 10.1186/s13073-023-01180-9] [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: 08/18/2022] [Accepted: 04/13/2023] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND The association between microbes and cancer has been reported repeatedly; however, it is not clear if molecular tumour properties are connected to specific microbial colonisation patterns. This is due mainly to the current technical and analytical strategy limitations to characterise tumour-associated bacteria. METHODS Here, we propose an approach to detect bacterial signals in human RNA sequencing data and associate them with the clinical and molecular properties of the tumours. The method was tested on public datasets from The Cancer Genome Atlas, and its accuracy was assessed on a new cohort of colorectal cancer patients. RESULTS Our analysis shows that intratumoural microbiome composition is correlated with survival, anatomic location, microsatellite instability, consensus molecular subtype and immune cell infiltration in colon tumours. In particular, we find Faecalibacterium prausnitzii, Coprococcus comes, Bacteroides spp., Fusobacterium spp. and Clostridium spp. to be strongly associated with tumour properties. CONCLUSIONS We implemented an approach to concurrently analyse clinical and molecular properties of the tumour as well as the composition of the associated microbiome. Our results may improve patient stratification and pave the path for mechanistic studies on microbiota-tumour crosstalk.
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Affiliation(s)
- Gaia Sambruni
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Angeli D Macandog
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Jakob Wirbel
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Danilo Cagnina
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Carlotta Catozzi
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Tiziano Dallavilla
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Francesca Borgo
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
- Center for Omics Sciences, IRCCS San Raffaele Institute, Milano, Italy
| | - Nicola Fazio
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCS, Milano, Italy
| | | | - Wanda L Petz
- Digestive Surgery, European Institute of Oncology-IRCCS, Milano, Italy
| | - Teresa Manzo
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy
| | - Simona P Ravenda
- Division of Gastrointestinal Medical Oncology and Neuroendocrine Tumors, European Institute of Oncology-IRCCS, Milano, Italy
| | - Georg Zeller
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Luigi Nezi
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy.
| | - Martin H Schaefer
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, Milano, Italy.
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6
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Larson PJ, Zhou W, Santiago A, Driscoll S, Fleming E, Voigt AY, Chun OK, Grady JJ, Kuchel GA, Robison JT, Oh J. Associations of the skin, oral and gut microbiome with aging, frailty and infection risk reservoirs in older adults. NATURE AGING 2022; 2:941-955. [PMID: 36398033 PMCID: PMC9667708 DOI: 10.1038/s43587-022-00287-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/30/2022] [Indexed: 01/25/2023]
Abstract
Older adults represent a vulnerable population with elevated risk for numerous morbidities. To explore the association of the microbiome with aging and age-related susceptibilities including frailty and infectious disease risk, we conducted a longitudinal study of the skin, oral, and gut microbiota in 47 community- or skilled nursing facility-dwelling older adults vs. younger adults. We found that microbiome changes were not associated with chronological age so much as frailty: we identified prominent changes in microbiome features associated with susceptibility to pathogen colonization and disease risk, including diversity, stability, heterogeneity, and biogeographic determinism, which were moreover associated with a loss of Cutibacterium (C.) acnes in the skin microbiome. Strikingly, the skin microbiota were also the primary reservoir for antimicrobial resistance, clinically important pathobionts, and nosocomial strains, suggesting a potential role particularly for the skin microbiome in disease risk and dissemination of multidrug resistant pathogens.
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Affiliation(s)
- Peter J. Larson
- UCONN Health (University of Connecticut), Farmington, CT
- The Jackson Laboratory, Farmington, CT
| | - Wei Zhou
- The Jackson Laboratory, Farmington, CT
| | - Alba Santiago
- UCONN Health (University of Connecticut), Farmington, CT
| | - Sarah Driscoll
- UCONN Health (University of Connecticut), Farmington, CT
| | | | | | | | - James J. Grady
- UCONN Health (University of Connecticut), Farmington, CT
| | | | | | - Julia Oh
- The Jackson Laboratory, Farmington, CT
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7
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True infection or contamination in patients with positive Cutibacterium blood cultures-a retrospective cohort study. Eur J Clin Microbiol Infect Dis 2022; 41:1029-1037. [PMID: 35612767 PMCID: PMC9250478 DOI: 10.1007/s10096-022-04458-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
Cutibacterium is a genus often considered a contaminant when present in blood cultures, but it can also cause severe infections, especially related to implanted foreign materials. We investigated the incidence and features of patients with true Cutibacterium infection. Patients with positive Cutibacterium blood cultures between the years 2015-2020 in southern Sweden were identified through microbiology records and medical records were studied retrospectively. Cutibacterium isolates were species determined using MALDI-TOF MS. Patients were classified as having true infection or contamination according to a definition considering both clinical and microbiological features and these groups were compared. A total of 313 episodes of positive Cutibacterium blood cultures were identified in 312 patients. Of these, 49 (16%, corresponding to an incidence of 6 cases per million inhabitants per year) were classified as true infections. The most common species was Cutibacterium acnes (87%), and the majority were elderly men with comorbidities. Patients with true Cutibacterium infection often had an unknown focus of infection (n = 21) or a focus in the respiratory tract (n = 18). We identified one episode of ventriculo-peritoneal shunt infection, three episodes of aortic stent-graft infection, and one episode of infective endocarditis. Two patients, where Cutibacterium was isolated at the site of infection, had only one positive blood culture. The finding of positive Cutibacterium blood cultures should not always be considered contamination. Definitions of true Cutibacterium bacteremia with a demand that more than one blood culture must be positive may miss true infections.
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8
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Rahim MA, Seo H, Kim S, Tajdozian H, Barman I, Lee Y, Lee S, Song HY. In vitro anti-tuberculosis effect of probiotic Lacticaseibacillus rhamnosus PMC203 isolated from vaginal microbiota. Sci Rep 2022; 12:8290. [PMID: 35585245 PMCID: PMC9116076 DOI: 10.1038/s41598-022-12413-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), the etiological agent of tuberculosis (TB), poses a severe challenge for public health and remains the number one cause of death as a single infectious agent. There are 10 million active cases of TB per year with 1.5 million deaths, and 2-3 billion people are estimated to harbor latent M. tb infection. Moreover, the emergence of multi-drug-resistant (MDR), extremely-drug-resistant (XDR), and the recent totally drug-resistant (TDR) M. tb is becoming a global issue that has fueled the need to find new drugs different from existing regimens. In these circumstances, probiotics can be a potential choice, so we focused on developing them as an anti-tuberculosis drug candidate. Here, we report the anti-tubercular activities of Lacticaseibacillus rhamnosus PMC203 isolated from the vaginal microbiota of healthy women. PMC203 exhibited a promising intracellular killing effect against both drug-sensitive and resistant M. tb infected murine macrophage cell line RAW 264.7 without showing any cytotoxicity. Additionally, it also inhibited the growth of M. tb under broth culture medium. PMC203 did not cause weight change or specific clinical symptoms in a 2-week repeated oral administration toxicity test in a guinea pig model. Here, we also found that PMC203 induces autophagy in a dose dependent manner by increasing the signal of well-known autophagy gene markers, suggesting a possible intracellular killing mechanism.
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Affiliation(s)
- Md Abdur Rahim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea.,Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Chungnam, Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Hanieh Tajdozian
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea.,Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Chungnam, Korea
| | - Indrajeet Barman
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea.,Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Chungnam, Korea
| | - Youngkyoung Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea.,Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Chungnam, Korea
| | - Saebim Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea
| | - Ho-Yeon Song
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Chungnam, Korea. .,Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Chungnam, Korea.
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9
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Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients. Biomedicines 2022; 10:biomedicines10050982. [PMID: 35625719 PMCID: PMC9138573 DOI: 10.3390/biomedicines10050982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/23/2022] Open
Abstract
The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited at microbiota genus level and by the lack of functional interpretation. Our study, therefore, characterized the URT bacterial microbiome at species level and their encoded pathways in patients with COVID-19 and correlated these to clinical outcomes. Whole metagenome sequencing was performed on nasopharyngeal samples from hospitalized patients with critical COVID-19 (n = 37) and SARS-CoV-2-negative individuals (n = 20). Decreased bacterial diversity, a reduction in commensal bacteria, and high abundance of pathogenic bacteria were observed in patients compared to negative controls. Several bacterial species and metabolic pathways were associated with better respiratory status and lower inflammation. Strong correlations were found between species biomarkers and metabolic pathways associated with better clinical outcome, especially Moraxella lincolnii and pathways of vitamin K2 biosynthesis. Our study demonstrates correlations between the URT microbiome and COVID-19 patient outcomes; further studies are warranted to validate these findings and to explore the causal roles of the identified microbiome biomarkers in COVID-19 pathogenesis.
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10
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Yoon Y, Seo H, Kim S, Lee Y, Rahim MDA, Lee S, Song HY. Anti-Tuberculosis Activity of Pediococcus acidilactici Isolated from Young Radish Kimchi against Mycobacterium tuberculosis. J Microbiol Biotechnol 2021; 31:1632-1642. [PMID: 34584040 PMCID: PMC9705845 DOI: 10.4014/jmb.2107.07044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 09/24/2021] [Accepted: 09/26/2021] [Indexed: 12/15/2022]
Abstract
Tuberculosis is a highly contagious disease caused by Mycobacterium tuberculosis. It affects about 10 million people each year and is still one of the leading causes of death worldwide. About 2 to 3 billion people (equivalent to 1 in 3 people in the world) are infected with latent tuberculosis. Moreover, as the number of multidrug-resistant, extensively drug-resistant, and totally drug-resistant strains of M. tuberculosis continues to increase, there is an urgent need to develop new anti-tuberculosis drugs that are different from existing drugs to combat antibiotic-resistant M. tuberculosis. Against this background, we aimed to develop new anti-tuberculosis drugs using probiotics. Here, we report the anti-tuberculosis effect of Pediococcus acidilactici PMC202 isolated from young radish kimchi, a traditional Korean fermented food. Under coculture conditions, PMC202 inhibited the growth of M. tuberculosis. In addition, PMC202 inhibited the growth of drug-sensitive and -resistant M. tuberculosis- infected macrophages at a concentration that did not show cytotoxicity and showed a synergistic effect with isoniazid. In a 2-week, repeated oral administration toxicity study using mice, PMC202 did not cause weight change or specific clinical symptoms. Furthermore, the results of 16S rRNA-based metagenomics analysis confirmed that dysbiosis was not induced in bronchoalveolar lavage fluid after oral administration of PMC202. The anti-tuberculosis effect of PMC202 was found to be related to the reduction of nitric oxide. Our findings indicate that PMC202 could be used as an anti-tuberculosis drug candidate with the potential to replace current chemicalbased drugs. However, more extensive toxicity, mechanism of action, and animal efficacy studies with clinical trials are needed.
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Affiliation(s)
- Youjin Yoon
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Youngkyoung Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - MD Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Saebim Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea,Corresponding author Phone: +82-41-570-2412 Fax : +82-41-577-2415 E-mail:
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11
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Dekio I, Okuda KI, Nishida M, Hamada-Tsutsumi S, Suzuki T, Kinoshita S, Tamura H, Ohnuma K, Murakami Y, Kinjo Y, Asahina A. Common Features and Intra-Species Variation of Cutibacterium modestum Strains, and Emended Description of the Species. Microorganisms 2021; 9:microorganisms9112343. [PMID: 34835467 PMCID: PMC8620323 DOI: 10.3390/microorganisms9112343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 11/30/2022] Open
Abstract
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.
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Affiliation(s)
- Itaru Dekio
- Department of Dermatology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan;
- Seikakai Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan;
- Correspondence: ; Tel.: +81-3-3433-1111 (ext. 3341); Fax: +81-3-5401-0125
| | - Ken-ichi Okuda
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan; (K.-i.O.); (Y.K.)
| | - Masako Nishida
- Department of Clinical Laboratory, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (M.N.); (K.O.)
| | - Susumu Hamada-Tsutsumi
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Tomo Suzuki
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Hirokoji-agaru, Kawaramachi-dori, Kamigyo-ku, Kyoto 602-0841, Japan;
- Department of Ophthalmology, Kyoto City Hospital, 1-2 Higashitakada-cho, Mibu, Nakagyo-ku, Kyoto 604-8845, Japan
| | - Shigeru Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kamigyo-ku, Kyoto 602-0841, Japan;
| | - Hiroto Tamura
- Department of Environmental Bioscience, Meijo University, 1-501 Shiogamaguchi, Tenpaku-ku, Nagoya 468-8502, Japan; (S.H.-T.); (H.T.)
| | - Kenichiro Ohnuma
- Department of Clinical Laboratory, Kobe University Hospital, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan; (M.N.); (K.O.)
| | - Yoshiyuki Murakami
- Seikakai Mildix Skin Clinic, 3rd Floor, 3-98 Senju, Adachi-ku, Tokyo 120-0034, Japan;
| | - Yuki Kinjo
- Department of Bacteriology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan; (K.-i.O.); (Y.K.)
| | - Akihiko Asahina
- Department of Dermatology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan;
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12
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Lee Y, Seo H, Kim S, Rahim MDA, Yoon Y, Jung J, Lee S, Beom Ryu C, Song HY. Activity of Lactobacillus crispatus isolated from vaginal microbiota against Mycobacterium tuberculosis. J Microbiol 2021; 59:1019-1030. [PMID: 34724180 DOI: 10.1007/s12275-021-1332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/23/2021] [Accepted: 09/29/2021] [Indexed: 10/19/2022]
Abstract
Tuberculosis, an infectious disease, is caused by Mycobacterium tuberculosis. It remains a significant public health issue around the globe, causing about 1.8 million deaths every year. Drug-resistant M. tuberculosis, including multi-drug-resistant (MDR), extremely-drug-resistant (XDR), and totally drug-resistant (TDR) M. tuberculosis, continues to be a threat to public health. In the case of antibiotic-resistant tuberculosis, the treatment effect of conventional antibiotics is low. Side effects caused by high doses over a long period are causing severe problems. To overcome these problems, there is an urgent need to develop a new anti-tuberculosis drug that is different from the existing compound-based antibiotics. Probiotics are defined as live microorganisms conferring health benefits. They can be potential therapeutic agents in this context as the effectiveness of probiotics against different infectious diseases has been well established. Here, we report that Lactobacillus crispatus PMC201 shows a promising effect on tuberculosis isolated from vaginal fluids of healthy Korean women. Lactobacillus crispatus PMC201 reduced M. tuberculosis H37Rv under co-culture conditions in broth and reduced M. tuberculosis H37Rv and XDR M. tuberculosis in macrophages. Lactobacillus crispatus PMC201 was not toxic to a guinea pig model and did not induce dysbiosis in a human intestinal microbial ecosystem simulator. Taken together, these results indicate that L. crispatus PMC201 can be a promising alternative drug candidate in the current tuberculosis drug regime. Further study is warranted to assess the in vivo efficacy and confirm the mode of action of L. crispatus PMC201.
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Affiliation(s)
- Youngkyoung Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - M D Abdur Rahim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Youjin Yoon
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Jehee Jung
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea
| | - Saebim Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea
| | - Chang Beom Ryu
- Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, 14584, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan, 31151, Republic of Korea.
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan, 31538, Republic of Korea.
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13
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Sultana OF, Lee S, Seo H, Mahmud HA, Kim S, Seo A, Kim M, Song HY. Biodegradation and Removal of PAHs by Bacillus velezensis Isolated from Fermented Food. J Microbiol Biotechnol 2021; 31:999-1010. [PMID: 34024889 PMCID: PMC9705940 DOI: 10.4014/jmb.2104.04023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/15/2022]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment. They are highly toxigenic and carcinogenic. Probiotic bacteria isolated from fermented foods were tested to check their ability to degrade and/or detoxify PAHs. Five probiotic bacteria with distinct morphologies were isolated from a mixture of 26 fermented foods co-cultured with benzo(a)pyrene (BaP) containing Bushnell Haas minimal broth. Among them, B. velezensis (PMC10) significantly reduced the abundance of BaP in the broth. PMC10 completely degraded BaP presented at a lower concentration in broth culture. B. velezensis also showed a clear zone of degradation on a BaP-coated Bushnell Haas agar plate. Gene expression profiling showed significant increases of PAH ringhydroxylating dioxygenases and 4-hydroxybenzoate 3-monooxygenase genes in B. velezensis in response to BaP treatment. In addtion, both live and heat-killed B. velezensis removed BaP and naphthalene (Nap) from phosphate buffer solution. Live B. velezensis did not show any cytotoxicity to macrophage or human dermal fibroblast cells. Live-cell and cell-free supernatant of B. velezensis showed potential anti-inflammatory effects. Cell-free supernatant and extract of B. velezensis also showed free radical scavenging effects. These results highlight the prospective ability of B. velezensis to biodegrade and remove toxic PAHs from the human body and suggest that the biodegradation of BaP might be regulated by ring-hydroxylating dioxygenase-initiated metabolic pathway.
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Affiliation(s)
- Omme Fatema Sultana
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea
| | - Saebim Lee
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Hoonhee Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Hafij Al Mahmud
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Sukyung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ahyoung Seo
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Mijung Kim
- Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Soonchunhyang University, Asan 31538, Republic of Korea,Corresponding author Phone: +82-41-570-2412 Fax: +82-41-577-2415 E-mail:
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Unravelling the eco-specificity and pathophysiological properties of Cutibacterium species in the light of recent taxonomic changes. Anaerobe 2021; 71:102411. [PMID: 34265438 DOI: 10.1016/j.anaerobe.2021.102411] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 11/22/2022]
Abstract
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.
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Goldenberger D, Søgaard KK, Cuénod A, Seth-Smith H, de Menezes D, Vandamme P, Egli A. Cutibacterium modestum and "Propionibacterium humerusii" represent the same species that is commonly misidentified as Cutibacterium acnes. Antonie van Leeuwenhoek 2021; 114:1315-1320. [PMID: 33961161 PMCID: PMC8286925 DOI: 10.1007/s10482-021-01589-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/26/2021] [Indexed: 11/30/2022]
Abstract
Cutibacterium spp. play an increasing role in soft tissue and implant-associated infections. We isolated a novel Cutibacterium spp. from an implant and investigated this isolate using multiple identification approaches. Correct identification was hampered by inconsistent reference data. The isolate was characterised using conventional methods such as Gram stain, MALDI-TOF MS, and antimicrobial susceptibility testing against multiple antimicrobials. Partial 16S rRNA gene sequencing and whole genome sequencing were also performed. In addition, we summarised the available published sequence data and compared prior data to our strain. Conventional phenotypic identification of our isolate resulted in Cutibacterium spp. After analysis of 16S rRNA gene and genome sequences, our isolate was identified as C. modestum, a very recently described species. The 16S rRNA gene analysis was hampered by three incorrect nucleotides within the 16S rRNA gene reference sequence of C. modestum M12T (accession no. LC466959). We also clearly demonstrate that this novel species is identical to tentatively named "Propionibacterium humerusii". Retrospective data analysis indicates that C. modestum is a clinically important Cutibacterium species often misidentified as C. acnes. The isolation and identification of Cutibacterium spp. is still a challenge. The correct description of very recently named C. modestum and the availability of a correct 16S rRNA sequence of the type strain may help to clarify the taxonomical uncertainty concerning "P. humerusii". The novel C. modestum is an additional, clinically important species within the genus Cutibacterium and may represent a new member of the human skin microbiome.
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Affiliation(s)
- Daniel Goldenberger
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.
| | - Kirstine K Søgaard
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Helena Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium.,BCCM/LMG Bacteria Collection, Department of Biochemistry and Biotechnology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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16
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Molecular characterization and antibacterial activity of oral antibiotics and copper nanoparticles against endodontic pathogens commonly related to health care-associated infections. Clin Oral Investig 2021; 25:6729-6741. [PMID: 33895915 DOI: 10.1007/s00784-021-03959-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVE To carry out molecular characterization and determine the antibacterial activity of oral antibiotics and copper nanoparticles (Cu-NPs) against endodontic strains isolated from persistent infections. MATERIALS AND METHODS Root canal samples from 24 teeth in different patients with persistent endodontic infections were obtained. The isolated strains were identified by biochemical tests and 16S rDNA sequencing. Genotyping was achieved by molecular methods. The antibacterial activity of antibiotics and copper nanostructures was determined by using minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) values. Furthermore, a time-kill kinetics assay was evaluated. Nonparametric tests (Kruskal-Wallis ANOVA) were performed (p value <0.05). RESULTS Twenty-one isolated strains were identified. Six isolates of Enterococcus faecalis were grouped into two clusters of three isolates each, two of which were clones. All were clarithromycin-resistant and erythromycin. Eight Pseudomonas putida presented two clusters, two Pseudomonas spp. were not clonal, and all were resistant to the tested antibiotics except tetracycline. Two of five strains of Cutibacterium acnes were clonal, and all were resistant only to metronidazole. The lowest MIC and MBC values were obtained with Cu-NPs. Time-kill kinetics using Cu-NPs showed a significant decrease in all tested species within 4 h and reached 100% in 2 h for C. acnes. CONCLUSION In this study, in relation to health care-associated infections, endodontic strains of each species isolated at least in one patient were polyclonal. In Pseudomonas spp., at least one clone was shared between patients. E. faecalis and C. acnes strains were susceptible to low Cu-NP concentrations, while Pseudomonas spp. strains were resistant. CLINICAL RELEVANCE Assessing and keeping track of the susceptibility of clinical strains to antimicrobial compounds is important for the clinical outcome. Based on our results, Cu-NPs could be an alternative for endodontic treatment, in order to avoid selection of resistant strains.
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Liver abscess caused by Cutibacterium namnetense after transarterial chemoembolization for hepatocellular carcinoma. Clin J Gastroenterol 2020; 14:246-250. [DOI: 10.1007/s12328-020-01283-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022]
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Kim S, Seo H, Mahmud HA, Islam MI, Sultana OF, Lee Y, Kim M, Song HY. Melanin Bleaching and Melanogenesis Inhibition Effects of Pediococcus acidilactici PMC48 Isolated from Korean Perilla Leaf Kimchi. J Microbiol Biotechnol 2020; 30:1051-1059. [PMID: 32238779 PMCID: PMC9728375 DOI: 10.4014/jmb.2003.03007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 03/26/2020] [Indexed: 12/15/2022]
Abstract
Overproduction and accumulation of melanin in the skin will darken the skin and cause skin disorders. So far, components that can inhibit tyrosinase, a melanin synthase of melanocytes, have been developed and used as ingredients of cosmetics or pharmaceutical products. However, most of existing substances can only inhibit the biosynthesis of melanin while melanin that is already synthesized and deposited is not directly decomposed. Thus, their effects in decreasing melanin concentration in the skin are weak. To overcome the limitation of existing therapeutic agents, we started to develop a substance that could directly biodegrade melanin. We screened traditional fermented food microorganisms for their abilities to direct biodegrade melanin. As a result, we found that a kimchi-derived Pediococcus acidilactici PMC48 had a direct melanin-degrading effect. This PMC48 strain is a new strain, different from P. acidilactici strains reported so far. It not only directly degrades melanin, but also has tyrosinase-inhibiting effect. It has a direct melanindecomposition effect. It exceeds existing melanin synthesis-inhibiting technology. It is expected to be of high value as a raw material for melanin degradation drugs and cosmetics.
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Affiliation(s)
- Sukyung Kim
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Hoonhee Seo
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Hafij Al Mahmud
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Md Imtiazul Islam
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Omme Fatema Sultana
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Youngkyoung Lee
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea
| | - Minhee Kim
- Emory university, Institute for Quantitative Theory and Methods (QuanTM), GA 30322, USA
| | - Ho-Yeon Song
- Department of Microbiology and Immunology, School of Medicine, Soonchunhyang University, Cheonan 31151, Republic of Korea,Probiotics Microbiome Convergence Center, Asan 31538, Republic of Korea,Corresponding author Phone: +82-41-570-2412 Fax: +82-41-570-2412 E-mail:
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Dekio I, Sakamoto M, Suzuki T, Yuki M, Kinoshita S, Murakami Y, Ohkuma M. Cutibacterium modestum sp. nov., isolated from meibum of human meibomian glands, and emended descriptions of Cutibacterium granulosum and Cutibacterium namnetense. Int J Syst Evol Microbiol 2020; 70:2457-2462. [PMID: 32559834 DOI: 10.1099/ijsem.0.004058] [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] [Indexed: 01/03/2023] Open
Abstract
An anaerobic and aerotolerant bacterium, strain M12T, was isolated from the meibum of inflamed human meibomian glands. Cells of the strain was Gram-stain-positive, non-spore-forming and non-motile rods. Growth on trypticase soy agar plates supplemented with 5 % sheep blood was fastest at 30-37 °C under anaerobic conditions. The 16S rRNA gene sequence of the strain revealed that it belongs to the genus Cutibacterium with a 98.0 % similarity value to the closest species, Cutibacterium acnes. Genome analysis of the strain with type strains of the other Cutibacterium species resulted in digital DNA-DNA hybridization values of 32.3-22.3% and average nucleotide identity (OrthoANI) values of 86.7-73.6 %. Biochemical and physiological analyses using API rapid ID 32A and API Coryne kits revealed relatively low reactivity of the strain compared with C. acnes and Cutibacterium namnetense. The most abundant major cellular fatty acid was iso-C15 : 0. Fermentation end-products from glucose were propionate, lactate, succinate and acetate. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. Major menaquinones were MK-9(H4), MK-9(H2) and MK-9. The major peaks of the MALDI-TOF mass spectrometry spectrum were at 3493, 3712, 6986 and 7424 Da. The DNA G+C content was 59.9 mol%. Based on these findings, we propose a novel species, Cutibacterium modestum. The type strain of C. modestum is M12T (=JCM 33380T=DSM 109769T). On the basis of further genomic analysis, we also provide emended descriptions of Cutibacterium granulosum (Prévot 1938) Scholz and Kilian 2016 and Cutibacterium namnetense (Aubin et al. 2016) Nouioui et al. 2018.
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Affiliation(s)
- Itaru Dekio
- Microbe Division / Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan.,Skin Microbe Laboratory, Mildix Skin Clinic, Tokyo, Japan
| | - Mitsuo Sakamoto
- PRIME, Japan Agency for Medical Research and Development (AMED), Tsukuba, Japan.,Microbe Division / Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Tomo Suzuki
- Department of Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan.,Department of Ophthalmology, Kyoto City Hospital Organization, Kyoto, Japan
| | - Masahiro Yuki
- Microbe Division / Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Shigeru Kinoshita
- Department of Frontier Medical Science and Technology for Ophthalmology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Moriya Ohkuma
- Microbe Division / Japan Collection of Microorganisms, RIKEN BioResource Research Center, Tsukuba, Japan
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Diop K, Cadoret F, Nguyen TT, Baudoin JP, Armstrong N, Raoult D, Bretelle F, Fournier PE, Fenollar F. Vaginimicrobium propionicum gen. nov., sp. nov., a novel propionic acid bacterium derived from human vaginal discharge. Int J Syst Evol Microbiol 2020; 70:4091-4097. [PMID: 32628103 DOI: 10.1099/ijsem.0.004106] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A Gram-stain-positive anaerobic rod-shaped bacterium, designated strain Marseille-P3275T, was isolated using culturomics from the vaginal discharge of healthy French woman. Marseille-P3275T was non-motile and did not form spores. Cells had neither catalase nor oxidase activity. The major fatty acids were C16 : 0 (29 %), C18:1ω9 (18 %), and iso-C15 : 0 (17 %). The genomic DNA G+C content was 50.64 mol%. The phylogenetic analysis based on 16S rRNA gene sequence indicated that Marseille-P3275T was related to members of the family Propionibacteriaceae (between 90.32-92.92 % sequence similarity) with formation of a clade with the monospecific genus Propionimicrobium (type species Propionimicrobium lymphophilum). On the basis of these phylogenetic and phenotypic differences, Marseille-P3275T was classified in a novel genus, Vaginimicrobium, as Vaginimicrobium propionicum gen. nov., sp. nov. The type strain is Marseille-P3275T (=CSUR P3275T=CECT 9677T).
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Affiliation(s)
- Khoudia Diop
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Frederic Cadoret
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Thi Tien Nguyen
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Jean-Pierre Baudoin
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Nicholas Armstrong
- Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Florence Bretelle
- Department of Gynecology and Obstetrics, Gynépole, Hôpital Nord, AP-HM, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, MEPHI, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
| | - Pierre-Edouard Fournier
- IHU-Méditerranée Infection, Marseille, France.,Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Florence Fenollar
- Aix-Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France.,IHU-Méditerranée Infection, Marseille, France
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Misidentification of Cutibacterium namnetense as Cutibacterium acnes among clinical isolates by MALDI-TOF VitekMS: usefulness of gyrB sequencing and new player in bone infections. Eur J Clin Microbiol Infect Dis 2020; 39:1605-1610. [PMID: 32382853 DOI: 10.1007/s10096-020-03873-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/20/2020] [Indexed: 01/03/2023]
Abstract
The taxonomy modification of Propionibacterium sp. with the description of new species, especially Cutibacterium namnetense, raises the question of species distribution in routine clinical samples. We performed a retrospective study during 3 years before the implementation of MALDI-TOF. Two hundred sixty-nine isolates were included in the study. MALDI-TOF identification, 16S rRNA, and new developed gyrB partial sequencings were performed. The most representative species was C. acnes in 88% of the cases, regardless of the origin of the clinical sample. Eventually, we identified three C. namnetense strains, representing a 1.1% prevalence over the period of time, including two bone infections. MALDI-TOF databases should be regularly updated to incorporate new species. gyrB sequencing constitutes a both easy and relevant method to identify Cutibacterium sp. especially C. namnetense, a new player in bone infections.
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22
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Propionibacterium/Cutibacterium species-related positive samples, identification, clinical and resistance features: a 10-year survey in a French hospital. Eur J Clin Microbiol Infect Dis 2020; 39:1357-1364. [PMID: 32125556 DOI: 10.1007/s10096-020-03852-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 02/16/2020] [Indexed: 02/07/2023]
Abstract
A 10-year retrospective study of Propionibacterium/Cutibacterium-positive samples gathered from hospitalized patients was conducted at Nantes University hospital. A total of 2728 Propionibacterium/Cutibacterium-positive samples analyzed between 2007 and 2016 were included. Due to the implementation of MALDI-TOF identification in 2013, most non-Cutibacterium acnes isolates were identified a second time using this technology. Over that period, Cutibacterium acnes remained the most predominant species accounting for 91.5% (2497/2728) of the isolates, followed by Cutibacterium avidum (4.2%, 115/2728) and Cutibacterium granulosum (2.4%, 64/2728). Regarding the origin of samples, the orthopaedic department was the main Cutibacterium sample provider representing 51.9% (1415/2728) of all samples followed by the dermatology department (11.5%, 315/2728). Samples were recovered from various tissue locations: 31.5% (858/2728) from surgery-related samples such as shoulder, spine or hip replacement devices and 19.1% (520/2728) from skin samples. MALDI-TOF method revealed misidentification before 2013. Cutibacterium avidum was falsely identified as C. granulosum (n = 33). Consequently, MALDI-TOF technology using up-to-date databases should be preferred to biochemical identification in order to avoid biased species identification. Regarding antibiotic resistance, 14.7% (20/136) of C. acnes was resistant to erythromycin. 4.1% (41/1005) of C. acnes strains, 17.9% (12/67) of C. avidum strains and 3.6% (1/28) of C. granulosum strains were found resistant to clindamycin.
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23
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Legaria MC, Barberis C, Camporro J, Traglia GM, Famiglietti A, Stecher D, Vay CA. Intra-peritoneal abscess after an abdominal hysterectomy involving Cutibacterium avidum (former Propionibacterium avidum) highly resistant to clindamycin. Anaerobe 2019; 59:176-183. [PMID: 31254654 DOI: 10.1016/j.anaerobe.2019.06.013] [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: 04/24/2019] [Revised: 06/20/2019] [Accepted: 06/24/2019] [Indexed: 10/26/2022]
Abstract
Cutibacterium avidum is a gram-positive anaerobic rod belonging to the cutaneous group of human bacteria with preferential colonization of sweat glands in moist areas. The microorganism rarely cause disease, generally delayed prosthetic joint infections (PJIs). We describe the second case of intraperitoneal abscess by C. avidum after an abdominal surgery in an obese female patient and the first case after a non-prosthetic abdominal surgery due to a highly clindamycin resistant strain in a patient with underling conditions. The patient was successfully treated with surgical drainage and beta-lactam antibiotics. Although rare and apparently non-pathogenic, C. avidum may be involved in infections, especially in some high-risk patients with obesity who have undergone surgical incision involving deep folder of the skin. The microorganism was identified by phenotypic methods, MALDI-TOF MS and 16S rRNA gene sequencing. Susceptibility test should be performed in C. avidum because high level resistance to clindamycin could be present. We present a literature review of C. avidum infections.
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Affiliation(s)
- M C Legaria
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina.
| | - C Barberis
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - J Camporro
- Universidad de Buenos Aires. Facultad de Medicina, Hospital de Clínicas José de San Martín, Servicio de Infectología, Buenos Aires, Argentina
| | - G M Traglia
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - A Famiglietti
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
| | - D Stecher
- Universidad de Buenos Aires. Facultad de Medicina, Hospital de Clínicas José de San Martín, Servicio de Infectología, Buenos Aires, Argentina
| | - C A Vay
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Hospital de Clínicas José de San Martín, Departamento de Bioquímica Clínica, Cátedra de Microbiología Clínica, Buenos Aires, Argentina
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24
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Vaidya JD, Hornung BVH, Smidt H, Edwards JE, Plugge CM. Propionibacterium ruminifibrarum sp. nov., isolated from cow rumen fibrous content. Int J Syst Evol Microbiol 2019; 69:2584-2590. [PMID: 31232679 DOI: 10.1099/ijsem.0.003544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel propionate producing bacterium, strain JV5T, was isolated from the rumen fibrous content of a Holstein Friesian dairy cow. Cells of strain JV5T were Gram-stain-positive, non-motile and aerotolerant. Growth occurred between 35 and 45 °C, with an optimum at 39 °C. The pH range for growth was 6.5-8, with an optimum at pH 7. The 16S rRNA gene sequence of strain JV5T was 98.4 and 96.5 % identical to those of Propionibacterium australiense DSM 15818T and Propionibacterium acidifaciens DSM 21887T, respectively. Genome wide average nucleotide identity and digital DNA-DNA hybridization values were 88.3 and 35.5 %, respectively, against P. australiense DSM 15818T. The G+C content of strain JV5T was 68.9 mol%. Strain JV5T did not produce urease and was able to metabolize glutamate, but not aspartate and glycine. Strain JV5T was able to ferment a range of substrates including certain simple and complex carbohydrates, sugar alcohols and amino acids. Chemotaxonomic analysis of strain JV5T revealed the presence of meso-diamino pimelic acid isomers similar those found in P. australiense, but different from P. acidifaciens. The observed major (>10 %) cellular fatty acids in strain JV5T (C18 : 1 ω9c, anteiso-C15 : 1, C16 : 0, C17 : 0 and C16 : 0 alcohol) were also different from those observed in P. australiense and P. acidifaciens. Based on these findings, a novel species is proposed within the genus Propionibacterium, Propionibacterium ruminifibrarum sp. nov. (type strain JV5T=DSM 106771T=TISTR 2629T).
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Affiliation(s)
- Jueeli D Vaidya
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.,Top Institute Food and Nutrition, Wageningen, The Netherlands.,Present address: DuPont, Archimedesweg 30, 2333 CN Leiden
| | - Bastian V H Hornung
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Joan E Edwards
- Top Institute Food and Nutrition, Wageningen, The Netherlands.,Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
| | - Caroline M Plugge
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
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25
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Munson E, Carroll KC. An Update on the Novel Genera and Species and Revised Taxonomic Status of Bacterial Organisms Described in 2016 and 2017. J Clin Microbiol 2019; 57:e01181-18. [PMID: 30257907 PMCID: PMC6355528 DOI: 10.1128/jcm.01181-18] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recognition and acknowledgment of novel bacterial taxonomy and nomenclature revisions can impact clinical practice, disease epidemiology, and routine clinical microbiology laboratory operations. The Journal of Clinical Microbiology (JCM) herein presents its biannual report summarizing such changes published in the years 2016 and 2017, as published and added by the International Journal of Systematic and Evolutionary Microbiology Noteworthy discussion centers around descriptions of novel Corynebacteriaceae and an anaerobic mycolic acid-producing bacterium in the suborder Corynebacterineae; revisions within the Propionibacterium, Clostridium, Borrelia, and Enterobacter genera; and a major reorganization of the family Enterobacteriaceae. JCM intends to sustain this series of reports as advancements in molecular genetics, whole-genome sequencing, and studies of the human microbiome continue to produce novel taxa and clearer understandings of bacterial relatedness.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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26
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Corvec S, Dagnelie MA, Khammari A, Dréno B. Taxonomy and phylogeny of Cutibacterium (formerly Propionibacterium) acnes in inflammatory skin diseases. Ann Dermatol Venereol 2018; 146:26-30. [PMID: 30558958 DOI: 10.1016/j.annder.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/08/2018] [Accepted: 11/14/2018] [Indexed: 01/01/2023]
Abstract
Since its discovery, Propionibacterium acnes has undergone various name changes, and has been known since 2016, as Cutibacterium acnes. Herein we set out the history and rational of these taxonomic changes together with a description of a new genus, Cutibacterium, which includes five species within the cutaneous ecosystem. Modern microbiological techniques allow finer distinction between species and subspecies while also enabling the identification of separate subtypes within the population of Cutibacterium acnes. Phylogeny and molecular typing techniques thus provide a better understanding of the subtypes involved in certain inflammatory skin diseases, including acne, folliculitis and progressive macular hypomelanosis.
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Affiliation(s)
- S Corvec
- Bacterial Department, Nantes University Hospital, CRCINA, université de Nantes, 44049 Nantes, France.
| | - M-A Dagnelie
- Dermatology Department, Nantes University Hospital, CRCINA, CIC 1413, université de Nantes, 44093 Nantes, France
| | - A Khammari
- Dermatology Department, Nantes University Hospital, CRCINA, CIC 1413, université de Nantes, 44093 Nantes, France
| | - B Dréno
- Dermatology Department, Nantes University Hospital, CRCINA, CIC 1413, université de Nantes, 44093 Nantes, France
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27
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Corvec S, Guillouzouic A, Aubin GG, Touchais S, Grossi O, Gouin F, Bémer P. Rifampin-Resistant Cutibacterium (formerly Propionibacterium) namnetense Superinfection after Staphylococcus aureus Bone Infection Treatment. J Bone Jt Infect 2018; 3:255-257. [PMID: 30533347 PMCID: PMC6284097 DOI: 10.7150/jbji.30029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 10/25/2018] [Indexed: 01/13/2023] Open
Abstract
After rifampin and levofloxacin treatment for a Staphylococcus aureus bone infection, a pyogenic granuloma due to a newly described Cutibacterium species, C. namnetense developed on the tibia former external fixator. This rifampin resistant bacterium, selected during treatment, harbored a mutation in the rpoB gene. This case illustrates the possible in vivo selection of resistant mutant most likely due to the bacterial burden and therefore the importance of adequate bone infection treatment.
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Affiliation(s)
- Stéphane Corvec
- Service de Bactériologie-Hygiène hospitalière, CHU de Nantes, Nantes, France.,CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France.,Nantes study group member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France
| | | | | | - Sophie Touchais
- Nantes study group member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France.,Clinique chirurgicale orthopédique et traumatique, CHU de Nantes, Nantes, France
| | - Olivier Grossi
- Nantes study group member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France.,Service de Maladies infectieuses, CHU de Nantes, Nantes, France - Département de Médecine Interne -Infectiologie, Nouvelles Cliniques Nantaises, Nantes, France
| | - François Gouin
- Nantes study group member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France.,Clinique chirurgicale orthopédique et traumatique, CHU de Nantes, Nantes, France
| | - Pascale Bémer
- Service de Bactériologie-Hygiène hospitalière, CHU de Nantes, Nantes, France.,Nantes study group member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France
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28
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Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Göker M. Genome-Based Taxonomic Classification of the Phylum Actinobacteria. Front Microbiol 2018; 9:2007. [PMID: 30186281 PMCID: PMC6113628 DOI: 10.3389/fmicb.2018.02007] [Citation(s) in RCA: 411] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 08/09/2018] [Indexed: 11/29/2022] Open
Abstract
The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical, and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial type strains were used to infer phylogenetic trees from genome-scale data using principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families, and genera, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families, and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognized from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Imen Nouioui
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Lorena Carro
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Rüdiger Pukall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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29
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Corvec S. Clinical and Biological Features of Cutibacterium (Formerly Propionibacterium) avidum, an Underrecognized Microorganism. Clin Microbiol Rev 2018; 31:e00064-17. [PMID: 29848774 PMCID: PMC6056840 DOI: 10.1128/cmr.00064-17] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
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.
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Affiliation(s)
- Stéphane Corvec
- CHU Nantes, Service de Bactériologie-Hygiène Hospitalière, Nantes, France
- CRCINA, INSERM, U1232, Université de Nantes, Nantes, France
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30
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Frenard C, Dagnelie MA, Khammari A, Saint-Jean M, Boisrobert A, Corvec S, Dreno B. Do Cutibacterium acnes
and Staphylococcus aureus
define two different types of folliculitis? J Eur Acad Dermatol Venereol 2018; 32:e266-e268. [DOI: 10.1111/jdv.14793] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022]
Affiliation(s)
- C. Frenard
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
| | - M-A. Dagnelie
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
| | - A. Khammari
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
| | - M. Saint-Jean
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
| | - A. Boisrobert
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
| | - S. Corvec
- Service de Bactériologie-Hygiène Hospitalière CHU de Nantes; Nantes France
- CRCINA; INSERM; Université d'Angers; Université de Nantes; Nantes France
| | - B. Dreno
- Skin Cancer Unit; Nantes University Hospital; INSERM U1232; Nantes Cedex France
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31
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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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32
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Takoudju EM, Guillouzouic A, Kambarev S, Pecorari F, Corvec S. In vitro emergence of fluoroquinolone resistance in Cutibacterium (formerly Propionibacterium) acnes and molecular characterization of mutations in the gyrA gene. Anaerobe 2017; 47:194-200. [PMID: 28602804 DOI: 10.1016/j.anaerobe.2017.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/02/2017] [Accepted: 06/07/2017] [Indexed: 12/11/2022]
Abstract
In vitro occurrence of levofloxacin (LVX) resistance in C. acnes and characterization of its molecular background were investigated. The mutation frequency was determined by inoculation of 108 cfu of C. acnes ATCC 11827 (LVX MIC = 0.25 mg/L) on LVX-containing agar plates. The progressive emergence of resistance was studied by a second exposure to increasing LVX concentrations. For mutants, the QRDR regions including the gyrA and parC genes were sequenced and compared to both C. acnes ATCC 11827 and C. acnes KPA171202 reference sequences (NC006085). The importance of the efflux pump system in resistance was investigated by using inhibitors on selected resistant mutants with no mutation in the QRDR. C. acnes growth was observed on LVX-containing plates with mutation frequencies of 3. 8 cfu × 10-8 (8 × MIC) and 1.6 cfu × 10-7 (4 × MIC). LVX resistance emerged progressively after one-step or two-step assays. In LVX-resistant isolates, the MIC ranged from 0.75 to >32 mg/L. Mutations were detected exclusively in the gyrA gene. Ten genotypes were identified: G99 C, G99 D, D100N, D100 H, D100 G, S101L, S101W, A102 P, D105 H and A105 G. Mutants S101L and S101W were always associated with a high level of resistance. Mutants with no mutation in the QRDR were more susceptible when incubated with an efflux pump inhibitor (phenyl-arginine β-naphthylamide) only, suggesting, for the first time, the expression of such a system in C. acnes LVX-resistant mutants.
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Affiliation(s)
- Eve-Marie Takoudju
- Service de Bactériologie-Hygiène Hospitalière, CHU NANTES, Nantes, France
| | | | - Stanimir Kambarev
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Frédéric Pecorari
- CRCINA, INSERM, CNRS, Université d'Angers, Université de Nantes, Nantes, France
| | - Stéphane Corvec
- Service de Bactériologie-Hygiène Hospitalière, CHU NANTES, Nantes, France; CRCINA, INSERM, Université d'Angers, Université de Nantes, Nantes, France; Nantes Study Group Member of CRIOGO (Centre de Référence des Infections Ostéo-articulaires du Grand Ouest), Nantes, France.
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33
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Janda JM. Taxonomic update on proposed nomenclature and classification changes for bacteria of medical importance, 2016. Diagn Microbiol Infect Dis 2017; 88:100-105. [PMID: 28238386 DOI: 10.1016/j.diagmicrobio.2017.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/06/2017] [Indexed: 12/22/2022]
Abstract
A key aspect of medical, public health, and diagnostic microbiology laboratories is the accurate identification and rapid reporting and communication to medical staff regarding patients with infectious agents of clinical importance. Microbial taxonomy in the age of molecular diagnostics and phylogenetics creates changes in taxonomy at a logarithmic rate further complicating this process. This update focuses on the description of new species and classification changes proposed in 2016.
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Affiliation(s)
- J Michael Janda
- Public Health Laboratory, Public Health Services Department, Kern County, Bakersfield, CA, 93306-3302.
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Draft Genome Sequence of an Erythromycin-Resistant Propionibacterium acnes Isolate Recovered from Folliculitis of the Scalp. GENOME ANNOUNCEMENTS 2017; 5:5/4/e01490-16. [PMID: 28126936 PMCID: PMC5270695 DOI: 10.1128/genomea.01490-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Propionibacterium acnes is now well-known and recognized for its implication in the pathogenesis of acne vulgaris. Here, we report the draft genome sequence of an erythromycin-resistant P. acnes strain isolated from a case of folliculitis of the scalp belonging to phylotype IA1 and sequence type 18 (ST18).
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Draft Genome Sequences of Four Propionibacterium acnes Strains Isolated from Implant-Related Infections. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01395-16. [PMID: 27979946 PMCID: PMC5159579 DOI: 10.1128/genomea.01395-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Propionibacterium acnes was previously described as a potential implant-related pathogen. Here, we report the draft genome sequence of four P. acnes strains, isolated from spine material, hip arthroplasty, and knee arthroplasty infections in France belonging to different sequence types (ST18, ST27, and ST36).
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Altieri C. Dairy propionibacteria as probiotics: recent evidences. World J Microbiol Biotechnol 2016; 32:172. [PMID: 27565782 DOI: 10.1007/s11274-016-2118-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 07/31/2016] [Indexed: 02/06/2023]
Abstract
Nowdays there is evidence that dairy propionibacteria display probiotic properties, which as yet have been underestimated. The aim of this paper is to review the recent highlights of data representing the probiotic potential of dairy propionibacteria, studied both by general selection criteria (useful for all probiotic potentials), and by more specific and innovative approach. Dairy propionibacteria show a robust nature, that makes them able to overcome technological hurdles, allowing their future use in various fermented probiotic foods. In addition to the general selection criteria for probiotics in areas such as food safety, technological and digestive stress tolerance, many potential health benefits have been recently described for dairy propionibacteria, including, production of several active molecules and adhesion capability, that can mean a steady action in modulation of microbiota and of metabolic activity in the gut; their impact on intestinal inflammation, modulation of the immune system, potential modulation of risk factors for cancer development modulation of intestinal absorption.
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Affiliation(s)
- Clelia Altieri
- Department of the Science of Agriculture, Food and Environment (SAFE), University of Foggia, via Napoli 25, 71122, Foggia, Italy.
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Draft Genome Sequence of Highly Rifampin-Resistant Propionibacterium namnetense NTS 31307302T Isolated from a Patient with a Bone Infection. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00819-16. [PMID: 27516511 PMCID: PMC4982290 DOI: 10.1128/genomea.00819-16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Propionibacterium namnetense was recently described as a potential bone pathogen, which is closely related to Propionibacterium acnes, a skin commensal microorganism. Here, we report the draft genome sequence of the highly rifampin-resistant strain NTS 31307302T isolated from a patient with a tibia infection.
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