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Noshak MA, Rezaee MA, Hasani A, Mirzaii M. The Role of the Coagulase-negative Staphylococci (CoNS) in Infective Endocarditis; A Narrative Review from 2000 to 2020. Curr Pharm Biotechnol 2020; 21:1140-1153. [PMID: 32324510 DOI: 10.2174/1389201021666200423110359] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/12/2020] [Accepted: 04/02/2020] [Indexed: 12/15/2022]
Abstract
Coagulase-negative staphylococci (CoNS) are part of the microbiota of human skin and rarely linked with soft tissue infections. In recent years, CoNS species considered as one of the major nosocomial pathogens and can cause several infections such as catheter-acquired sepsis, skin infection, urinary tract infection, endophthalmitis, central nervous system shunt infection, surgical site infections, and foreign body infection. These microorganisms have a significant impact on human life and health and, as typical opportunists, cause peritonitis in individuals undergoing peritoneal dialysis. Moreover, it is revealed that these potential pathogens are mainly related to the use of indwelling or implanted in a foreign body and cause infective endocarditis (both native valve endocarditis and prosthetic valve endocarditis) in patients. In general, approximately eight percent of all cases of native valve endocarditis is associated with CoNS species, and these organisms cause death in 25% of all native valve endocarditis cases. Moreover, it is revealed that methicillin-resistant CoNS species cause 60 % of all prosthetic valve endocarditis cases. In this review, we describe the role of the CoNS species in infective endocarditis, and we explicated the reported cases of CoNS infective endocarditis in the literature from 2000 to 2020 to determine the role of CoNS in the process of infective endocarditis.
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Affiliation(s)
- Mohammad A Noshak
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad A Rezaee
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alka Hasani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran,Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Mirzaii
- Department of Microbiology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
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2
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Sun Z, Zhou D, Zhang X, Li Q, Lin H, Lu W, Liu H, Lu J, Lin X, Li K, Xu T, Bao Q, Zhang H. Determining the Genetic Characteristics of Resistance and Virulence of the "Epidermidis Cluster Group" Through Pan-Genome Analysis. Front Cell Infect Microbiol 2020; 10:274. [PMID: 32596166 PMCID: PMC7303328 DOI: 10.3389/fcimb.2020.00274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/07/2020] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus caprae, Staphylococcus capitis, and Staphylococcus epidermidis belong to the “Epidermidis Cluster Group” (ECG) and are generally opportunistic pathogens. In this work, whole genome sequencing, molecular cloning and pan-genome analysis were performed to investigate the genetic characteristics of the resistance, virulence and genome structures of 69 ECG strains, including a clinical isolate (S. caprae SY333) obtained in this work. Two resistance genes (blaZ and aadD2) encoded on the plasmids pSY333-41 and pSY333-45 of S. caprae SY333 were confirmed to be functional. The bla region in ECG exhibited three distinct structures, and these chromosome- and plasmid-encoded bla operons seemed to follow two different evolutionary paths. Pan-genome analysis revealed their pan-genomes tend to be “open.” For the virulence-related factors, the genes involved in primary attachment were observed almost exclusively in S. epidermidis, while the genes associated with intercellular aggregation were observed more frequently in S. caprae and S. capitis. The type VII secretion system was present in all strains of S. caprae and some of S. epidermidis but not in S. capitis. Moreover, the isd locus (iron regulated surface determinant) was first found to be encoded on the genomes of S. caprae and S. capitis. These findings suggested that the plasmid and chromosome encoded bla operons of ECG species underwent different evolution paths, as well as they differed in the abundance of virulence genes associated with adherence, invasion, secretion system and immune evasion. Identification of isd loci in S. caprae and S. capitis indicated their ability to acquire heme as nutrient iron during infection.
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Affiliation(s)
- Zhewei Sun
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Danying Zhou
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xueya Zhang
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Qiaoling Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailong Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Wei Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hongmao Liu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Junwan Lu
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Xi Lin
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Kewei Li
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
| | - Qiyu Bao
- Key Laboratory of Medical Genetics of Zhejiang Province, Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
| | - Hailin Zhang
- The Second Affiliated Hospital and Yuying Children's Hospital, Wenzhou Medical University, Wenzhou, China.,Institute of Biomedical Informatics, Wenzhou Medical University, Wenzhou, China
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Preda VG, Săndulescu O. Communication is the key: biofilms, quorum sensing, formation and prevention. Discoveries (Craiova) 2019; 7:e100. [PMID: 32309618 PMCID: PMC7086079 DOI: 10.15190/d.2019.13] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 09/29/2019] [Accepted: 09/29/2019] [Indexed: 12/19/2022] Open
Abstract
Antibiotic resistance is a relevant topic nowadays, representing one of the main causes of infection-related mortality and morbidity at a global level. This phenomenon is worrisome and represents an area of interest for both clinical practice and fundamental research. One important mechanism whereby bacteria acquire resistance to antibiotics and evade the immune system is by forming biofilms. It is estimated that ~80% of the bacteria producing chronic infections can form biofilms. During the process of biofilm formation microorganisms have the ability to communicate with each other through quorum sensing. Quorum sensing regulates the metabolic activity of planktonic cells, and it can induce microbial biofilm formation and increased virulence. In this review we describe the biofilm formation process, quorum sensing, quorum quenching, several key infectious bacteria producing biofilm, methods of prevention and their challenges and limitations. Although progress has been made in the prevention and treatment of biofilm-driven infections, new strategies are required and have to be further developed.
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Affiliation(s)
- Veronica G. Preda
- Department of Biochemistry and Molecular Biology, University of Bucharest, Faculty of Biology, Bucharest, Romania
- Department of Genetics and Applied Biotechnology, University of Bucharest, Faculty of Biology, Bucharest, Romania
| | - Oana Săndulescu
- Department of Infectious Diseases I, Carol Davila University of Medicine and Pharmacy, National Institute for Infectious Diseases “Prof. Dr. Matei Balș”, Bucharest, Romania
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Habib G. How do we reduce embolic risk and mortality in infective endocarditis? Measure the size of the vegetation and operate early in patients with large vegetations. Eur Heart J 2019; 40:2252-2254. [PMID: 31162542 DOI: 10.1093/eurheartj/ehz354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Gilbert Habib
- APHM, La Timone Hospital, Cardiology Department, Marseille, France.,Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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Coagulase-Negative Staphylococci Pathogenomics. Int J Mol Sci 2019; 20:ijms20051215. [PMID: 30862021 PMCID: PMC6429511 DOI: 10.3390/ijms20051215] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/28/2019] [Accepted: 03/07/2019] [Indexed: 01/16/2023] Open
Abstract
Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.
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Fournier PE, Drancourt M, Raoult D. New Laboratory Tools for Emerging Bacterial Challenges. Clin Infect Dis 2018; 65:S39-S49. [PMID: 28859351 DOI: 10.1093/cid/cix405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Since its creation, the Méditerranée-Infection foundation has aimed at optimizing the management of infectious diseases and surveying the local and global epidemiology. This pivotal role was permitted by the development of rational sampling, point-of-care tests, and extended automation as well as new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and the development of versatile and permissive culture systems. By identifying and characterizing emerging microbial pathogens, these developments provided significant breakthroughs in infectious diseases.
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Affiliation(s)
- Pierre-Edouard Fournier
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Michel Drancourt
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
| | - Didier Raoult
- URMITE, UM63, CNRS7278, IRD198, Inserm 1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, Marseille, France
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7
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Bacterial Genomes. Infect Dis (Lond) 2017. [DOI: 10.1016/b978-0-7020-6285-8.00007-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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8
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Fournier PE, Dubourg G, Raoult D. Clinical detection and characterization of bacterial pathogens in the genomics era. Genome Med 2014; 6:114. [PMID: 25593594 PMCID: PMC4295418 DOI: 10.1186/s13073-014-0114-2] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The availability of genome sequences obtained using next-generation sequencing (NGS) has revolutionized the field of infectious diseases. Indeed, more than 38,000 bacterial and 5,000 viral genomes have been sequenced to date, including representatives of all significant human pathogens. These tremendous amounts of data have not only enabled advances in fundamental biology, helping to understand the pathogenesis of microorganisms and their genomic evolution, but have also had implications for clinical microbiology. Here, we first review the current achievements of genomics in the development of improved diagnostic tools, including those that are now available in the clinic, such as the design of PCR assays for the detection of microbial pathogens, virulence factors or antibiotic-resistance determinants, or the design of optimized culture media for 'unculturable' pathogens. We then review the applications of genomics to the investigation of outbreaks, either through the design of genotyping assays or the direct sequencing of the causative strains. Finally, we discuss how genomics might change clinical microbiology in the future.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Gregory Dubourg
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, InsermU1095, Institut hospitalo-universitaire Méditerranée-Infection, Aix-Marseille University, Faculté de Medecine, 27 Blvd Jean Moulin, Marseille, 13385, cedex 5 France
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Padmanabhan R, Mishra AK, Raoult D, Fournier PE. Genomics and metagenomics in medical microbiology. J Microbiol Methods 2013; 95:415-24. [PMID: 24200711 DOI: 10.1016/j.mimet.2013.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Revised: 10/08/2013] [Accepted: 10/10/2013] [Indexed: 02/06/2023]
Abstract
Over the last two decades, sequencing tools have evolved from laborious time-consuming methodologies to real-time detection and deciphering of genomic DNA. Genome sequencing, especially using next generation sequencing (NGS) has revolutionized the landscape of microbiology and infectious disease. This deluge of sequencing data has not only enabled advances in fundamental biology but also helped improve diagnosis, typing of pathogen, virulence and antibiotic resistance detection, and development of new vaccines and culture media. In addition, NGS also enabled efficient analysis of complex human micro-floras, both commensal, and pathological, through metagenomic methods, thus helping the comprehension and management of human diseases such as obesity. This review summarizes technological advances in genomics and metagenomics relevant to the field of medical microbiology.
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Affiliation(s)
- Roshan Padmanabhan
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, Aix-Marseille Université, UM63, CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, 27 Bd. Jean Moulin, 13005 Marseille, France
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10
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Fournier PE, Drancourt M, Colson P, Rolain JM, Scola BL, Raoult D. Modern clinical microbiology: new challenges and solutions. Nat Rev Microbiol 2013; 11:574-85. [PMID: 24020074 PMCID: PMC7097238 DOI: 10.1038/nrmicro3068] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the twenty-first century, the clinical microbiology laboratory plays a central part in optimizing the management of infectious diseases and surveying local and global epidemiology. This pivotal role is made possible by the adoption of rational sampling, point-of-care tests, extended automation and new technologies, including mass spectrometry for colony identification, real-time genomics for isolate characterization, and versatile and permissive culture systems. When balanced with cost, these developments can improve the workflow and output of clinical microbiology laboratories and, by identifying and characterizing microbial pathogens, provide significant input to scientific discovery.
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Affiliation(s)
- Pierre-Edouard Fournier
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Michel Drancourt
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Jean-Marc Rolain
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 Boulevard Jean Moulin, Marseille, 13385 France
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