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Furugaito M, Arai Y, Uzawa Y, Kamisako T, Ogura K, Okamoto S, Kikuchi K. Antimicrobial Susceptibility to 27 Drugs and the Molecular Mechanisms of Macrolide, Tetracycline, and Quinolone Resistance in Gemella sp. Antibiotics (Basel) 2023; 12:1538. [PMID: 37887239 PMCID: PMC10604004 DOI: 10.3390/antibiotics12101538] [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: 09/20/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 10/28/2023] Open
Abstract
Gemella is a catalase-negative, facultative anaerobic, Gram-positive coccus that is commensal in humans but can become opportunistic and cause severe infectious diseases, such as infective endocarditis. Few studies have tested the antimicrobial susceptibility of Gemella. We tested its antimicrobial susceptibility to 27 drugs and defined the resistant genes using PCR in 58 Gemella strains, including 52 clinical isolates and six type strains. The type strains and clinical isolates included 22 G. morbillorum, 18 G. haemolysans (GH) group (genetically indistinguishable from G. haemolysans and G. parahaemolysans), 13 G. taiwanensis, three G. sanguinis, and two G. bergeri. No strain was resistant to beta-lactams and vancomycin. In total, 6/22 (27.3%) G. morbillorum strains were erythromycin- and clindamycin-resistant ermB-positive, whereas 4/18 (22.2%) in the GH group, 7/13 (53.8%) G. taiwanensis, and 1/3 (33.3%) of the G. sanguinis strains were erythromycin-non-susceptible mefE- or mefA-positive and clindamycin-susceptible. The MIC90 of minocycline and the ratios of tetM-positive strains varied across the different species-G. morbillorum: 2 µg/mL and 27.3% (6/22); GH group: 8 µg/mL and 27.8% (5/18); G. taiwanensis: 8 µg/mL and 46.2% (6/13), respectively. Levofloxacin resistance was significantly higher in G. taiwanensis (9/13 69.2%) than in G. morbillorum (2/22 9.1%). Levofloxacin resistance was associated with a substitution at serine 83 for leucine, phenylalanine, or tyrosine in GyrA. The mechanisms of resistance to erythromycin and clindamycin differed across Gemella species. In addition, the rate of susceptibility to levofloxacin differed across Gemella sp., and the quinolone resistance mechanism was caused by mutations in GyrA alone.
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Affiliation(s)
- Michiko Furugaito
- Department of Clinical Laboratory and Biomedical Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; (M.F.); (S.O.)
- Department of Clinical Laboratory, Kindai University Hospital, Osakasayama, Osaka 589-8511, Japan
| | - Yuko Arai
- Department of Infectious Diseases, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo 162-8666, Japan; (Y.A.); (Y.U.)
| | - Yutaka Uzawa
- Department of Infectious Diseases, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo 162-8666, Japan; (Y.A.); (Y.U.)
| | - Toshinori Kamisako
- Department of Clinical Laboratory Medicine, Faculty of Medicine, Kindai University, Osakasayama, Osaka 589-8511, Japan;
| | - Kohei Ogura
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, Kyoto 611-0011, Japan;
| | - Shigefumi Okamoto
- Department of Clinical Laboratory and Biomedical Sciences, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan; (M.F.); (S.O.)
| | - Ken Kikuchi
- Department of Infectious Diseases, Tokyo Women’s Medical University, Shinjuku-ku, Tokyo 162-8666, Japan; (Y.A.); (Y.U.)
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Bacali C, Vulturar R, Buduru S, Cozma A, Fodor A, Chiș A, Lucaciu O, Damian L, Moldovan ML. Oral Microbiome: Getting to Know and Befriend Neighbors, a Biological Approach. Biomedicines 2022; 10:biomedicines10030671. [PMID: 35327473 PMCID: PMC8945538 DOI: 10.3390/biomedicines10030671] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 02/01/2023] Open
Abstract
The oral microbiome, forming a biofilm that covers the oral structures, contains a high number of microorganisms. Biofilm formation starts from the salivary pellicle that allows bacterial adhesion–colonization–proliferation, co-aggregation and biofilm maturation in a complex microbial community. There is a constant bidirectional crosstalk between human host and its oral microbiome. The paper presents the fundamentals regarding the oral microbiome and its relationship to modulator factors, oral and systemic health. The modern studies of oral microorganisms and relationships with the host benefits are based on genomics, transcriptomics, proteomics and metabolomics. Pharmaceuticals such as antimicrobials, prebiotics, probiotics, surface active or abrasive agents and plant-derived ingredients may influence the oral microbiome. Many studies found associations between oral dysbiosis and systemic disorders, including autoimmune diseases, cardiovascular, diabetes, cancers and neurodegenerative disorders. We outline the general and individual factors influencing the host–microbial balance and the possibility to use the analysis of the oral microbiome in prevention, diagnosis and treatment in personalized medicine. Future therapies should take in account the restoration of the normal symbiotic relation with the oral microbiome.
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Affiliation(s)
- Cecilia Bacali
- Department of Prosthodontics and Dental Materials, “Iuliu Hatieganu” University of Medicine and Pharmacy, 32 Clinicilor St., 400006 Cluj-Napoca, Romania; (C.B.); (S.B.)
| | - Romana Vulturar
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 6 Pasteur St., 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Correspondence:
| | - Smaranda Buduru
- Department of Prosthodontics and Dental Materials, “Iuliu Hatieganu” University of Medicine and Pharmacy, 32 Clinicilor St., 400006 Cluj-Napoca, Romania; (C.B.); (S.B.)
| | - Angela Cozma
- 4th Medical Department, University of Medicine and Pharmacy “Iuliu Hatieganu” Cluj-Napoca, 18 Republicii St., 400015 Cluj-Napoca, Romania;
| | - Adriana Fodor
- Clinical Center of Diabetes, Nutrition and Metabolic Diseases, “Iuliu Hatieganu” University of Medicine and Pharmacy, 2-4 Clinicilor St., 400012 Cluj-Napoca, Romania;
| | - Adina Chiș
- Department of Molecular Sciences, “Iuliu Hațieganu” University of Medicine and Pharmacy Cluj-Napoca, 6 Pasteur St., 400349 Cluj-Napoca, Romania;
- Cognitive Neuroscience Laboratory, University Babes-Bolyai, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Ondine Lucaciu
- Department of Oral Health, University of Medicine and Pharmacy “Iuliu Hatieganu”, 400012 Cluj-Napoca, Romania;
| | - Laura Damian
- Department of Rheumatology, Emergency Clinical County Hospital Cluj, Centre for Rare Autoimmune and Autoinflammatory Diseases, 2-4 Clinicilor St., 400006 Cluj-Napoca, Romania;
- CMI Reumatologie Dr. Damian, 6-8 Petru Maior St., 400002 Cluj-Napoca, Romania
| | - Mirela Liliana Moldovan
- Department of Dermopharmacy and Cosmetics, Faculty of Pharmacy, “Iuliu Hatieganu” University of Medicine and Pharmacy, 12, I. Creanga St., 400010 Cluj-Napoca, Romania;
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Trevors JT. Viable but non-culturable (VBNC) bacteria: Gene expression in planktonic and biofilm cells. J Microbiol Methods 2011; 86:266-73. [PMID: 21616099 DOI: 10.1016/j.mimet.2011.04.018] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Revised: 04/21/2011] [Accepted: 04/27/2011] [Indexed: 12/24/2022]
Abstract
Viable but non-culturable (VBNC) bacteria are common in nutrient poor and/or stressed environments as planktonic cells and biofilms. This article discusses approaches to researching VBNC bacteria to obtain knowledge that is lacking on their gene expression while in the VBNC state, and when they enter into and then recover from this state, when provided with the necessary nutrients and environmental conditions to support growth and cell division. Two-dimensional gel electrophoresis of proteins, global gene expression, reverse-transcription polymerase chain reaction (PCR) analysis and sequencing by synthesis coupled with data on cell numbers, viability and species present are central to understanding the VBNC state.
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Affiliation(s)
- J T Trevors
- Laboratory of Microbiology, School of Environmental Sciences, Rm. 3320 Bovey Building, University of Guelph, 50 Stone Rd., East, Guelph, Ontario, Canada N1G 2W1.
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Shemesh M, Tam A, Aharoni R, Steinberg D. Genetic adaptation of Streptococcus mutans during biofilm formation on different types of surfaces. BMC Microbiol 2010; 10:51. [PMID: 20167085 PMCID: PMC2838874 DOI: 10.1186/1471-2180-10-51] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2009] [Accepted: 02/18/2010] [Indexed: 11/29/2022] Open
Abstract
Background Adhesion and successful colonization of bacteria onto solid surfaces play a key role in biofilm formation. The initial adhesion and the colonization of bacteria may differ between the various types of surfaces found in oral cavity. Therefore, it is conceivable that diverse biofilms are developed on those various surfaces. The aim of the study was to investigate the molecular modifications occurring during in vitro biofilm development of Streptococcus mutans UA159 on several different dental surfaces. Results Growth analysis of the immobilized bacterial populations generated on the different surfaces shows that the bacteria constructed a more confluent and thick biofilms on a hydroxyapatite surface compared to the other tested surfaces. Using DNA-microarray technology we identified the differentially expressed genes of S. mutans, reflecting the physiological state of biofilms formed on the different biomaterials tested. Eight selected genes were further analyzed by real time RT-PCR. To further determine the impact of the tested material surfaces on the physiology of the bacteria, we tested the secretion of AI-2 signal by S. mutans embedded on those biofilms. Comparative transcriptome analyses indicated on changes in the S. mutans genome in biofilms formed onto different types of surfaces and enabled us to identify genes most differentially expressed on those surfaces. In addition, the levels of autoinducer-2 in biofilms from the various tested surfaces were different. Conclusions Our results demonstrate that gene expression of S. mutans differs in biofilms formed on tested surfaces, which manifest the physiological state of bacteria influenced by the type of surface material they accumulate onto. Moreover, the stressful circumstances of adjustment to the surface may persist in the bacteria enhancing intercellular signaling and surface dependent biofilm formation.
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Affiliation(s)
- Moshe Shemesh
- Biofilm Research Laboratory, Institute of Dental Sciences, Faculty of Dental Medicine, Hebrew University-Hadassah POB 12272, Jerusalem 91120, Israel
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Affiliation(s)
- Akihiro Yoshida
- Division of Community Oral Health Science, Department of Health Promotion, Kyushu Dental College
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Hogg JS, Hu FZ, Janto B, Boissy R, Hayes J, Keefe R, Post JC, Ehrlich GD. Characterization and modeling of the Haemophilus influenzae core and supragenomes based on the complete genomic sequences of Rd and 12 clinical nontypeable strains. Genome Biol 2007; 8:R103. [PMID: 17550610 PMCID: PMC2394751 DOI: 10.1186/gb-2007-8-6-r103] [Citation(s) in RCA: 200] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Revised: 04/17/2007] [Accepted: 06/05/2007] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The distributed genome hypothesis (DGH) posits that chronic bacterial pathogens utilize polyclonal infection and reassortment of genic characters to ensure persistence in the face of adaptive host defenses. Studies based on random sequencing of multiple strain libraries suggested that free-living bacterial species possess a supragenome that is much larger than the genome of any single bacterium. RESULTS We derived high depth genomic coverage of nine nontypeable Haemophilus influenzae (NTHi) clinical isolates, bringing to 13 the number of sequenced NTHi genomes. Clustering identified 2,786 genes, of which 1,461 were common to all strains, with each of the remaining 1,328 found in a subset of strains; the number of clusters ranged from 1,686 to 1,878 per strain. Genic differences of between 96 and 585 were identified per strain pair. Comparisons of each of the NTHi strains with the Rd strain revealed between 107 and 158 insertions and 100 and 213 deletions per genome. The mean insertion and deletion sizes were 1,356 and 1,020 base-pairs, respectively, with mean maximum insertions and deletions of 26,977 and 37,299 base-pairs. This relatively large number of small rearrangements among strains is in keeping with what is known about the transformation mechanisms in this naturally competent pathogen. CONCLUSION A finite supragenome model was developed to explain the distribution of genes among strains. The model predicts that the NTHi supragenome contains between 4,425 and 6,052 genes with most uncertainty regarding the number of rare genes, those that have a frequency of <0.1 among strains; collectively, these results support the DGH.
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Affiliation(s)
- Justin S Hogg
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
- Joint Carnegie Mellon University - University of Pittsburgh Ph.D. Program in Computational Biology. 3064 Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, USA
| | - Fen Z Hu
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - Benjamin Janto
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - Robert Boissy
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - Jay Hayes
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - Randy Keefe
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - J Christopher Post
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
| | - Garth D Ehrlich
- Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania 15212, USA
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Affiliation(s)
- Adam P Roberts
- Division of Microbial Diseases, Eastman Dental Institute, University College London, University of London, London, UK
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Zhang YQ, Ren SX, Li HL, Wang YX, Fu G, Yang J, Qin ZQ, Miao YG, Wang WY, Chen RS, Shen Y, Chen Z, Yuan ZH, Zhao GP, Qu D, Danchin A, Wen YM. Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228). Mol Microbiol 2003; 49:1577-93. [PMID: 12950922 DOI: 10.1046/j.1365-2958.2003.03671.x] [Citation(s) in RCA: 283] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Staphylococcus epidermidis strains are diverse in their pathogenicity; some are invasive and cause serious nosocomial infections, whereas others are non-pathogenic commensal organisms. To analyse the implications of different virulence factors in Staphylococcus epidermidis infections, the complete genome of Staphylococcus epidermidis strain ATCC 12228, a non-biofilm forming, non-infection associated strain used for detection of residual antibiotics in food products, was sequenced. This strain showed low virulence by mouse and rat experimental infections. The genome consists of a single 2499 279 bp chromosome and six plasmids. The chromosomal G + C content is 32.1% and 2419 protein coding sequences (CDS) are predicted, among which 230 are putative novel genes. Compared to the virulence factors in Staphylococcus aureus, aside from delta-haemolysin and beta-haemolysin, other toxin genes were not found. In contrast, the majority of adhesin genes are intact in ATCC 12228. Most strikingly, the ica operon coding for the enzymes synthesizing interbacterial cellular polysaccharide is missing in ATCC 12228 and rearrangements of adjacent genes are shown. No mec genes, IS256, IS257, were found in ATCC 12228. It is suggested that the absence of the ica operon is a genetic marker in commensal Staphylococcus epidermidis strains which are less likely to become invasive.
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Affiliation(s)
- Yue-Qing Zhang
- Laboratory of Medical Molecular Virology, Shanghai Medical College, Fudan University, 138 Yi Xue Yuan Road, Shanghai, 200032, China
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Abstract
Bacteria frequently attach to medical devices such as intravascular catheters by forming sessile multicellular communities known as biofilms, which can be the source of persistent infections that are recalcitrant to systemic antibiotic therapy. As a result of this persistence, a number of technologies have been developed to prevent catheter-associated biofilm formation. Whereas the most straightforward approaches focus on impregnating catheter material with classical antimicrobial agents, these approaches are not universally effective, thereby underscoring the need for more potent and more sophisticated approaches to the prevention of catheter-related biofilm infections.
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Affiliation(s)
- Paul N Danese
- Microbia, Inc., One Kendall Square, Building 1400W, Cambridge, MA 02139, USA.
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