551
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Cleary JL, Condren AR, Zink KE, Sanchez LM. Calling all hosts: Bacterial communication in situ. Chem 2017; 2:334-358. [PMID: 28948238 DOI: 10.1016/j.chempr.2017.02.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Bacteria are cosmopolitan organisms that in recent years have demonstrated many roles in maintaining host equilibrium. In this review, we discuss three roles bacteria can occupy in a host: pathogenic, symbiotic, and transient, with a specific focus on how bacterial small molecules contribute to homeostasis or dysbiosis. First, we will dissect how small molecules produced by pathogenic bacteria can be used as a source for communication during colonization and as protection against host immune responses. The ability to achieve a higher level of organization through small molecule communication gives pathogenic bacteria an opportunity for increased virulence and fitness. Conversely, in symbiotic relationships with hosts, small molecules are used in the initial acquisition, colonization, and maintenance of this beneficial population. Chemical signals can come from both the host and symbiont, and it is often observed that these interKingdom symbioses result in coevolution of both species involved. Furthermore, the transition from transient to commensal or opportunistic likely relies on molecular mechanisms. The small molecules utilized and produced by transient bacteria are desirable for both the immune and nutritional benefits they provide to the host. Finally, the advantages and disadvantages of modern analytical techniques that are available to researchers in order to study small molecules in situ is an important aspect of this review. It is our opinion that small molecules produced by bacteria are central to many biological processes and a larger focus on uncovering the function and identity of these small molecules is required to gain a deeper understanding of host-microbe associations.
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Affiliation(s)
- Jessica L Cleary
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Alanna R Condren
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Katherine E Zink
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
| | - Laura M Sanchez
- Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago IL 60612, USA
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552
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Pierre JF. Gastrointestinal immune and microbiome changes during parenteral nutrition. Am J Physiol Gastrointest Liver Physiol 2017; 312:G246-G256. [PMID: 28154012 PMCID: PMC5401992 DOI: 10.1152/ajpgi.00321.2016] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 01/19/2017] [Accepted: 01/29/2017] [Indexed: 01/31/2023]
Abstract
Parenteral nutrition (PN) is a lifesaving therapy that provides intravenous nutrition support to patients who cannot, or should not, feed via the gastrointestinal (GI) tract. Unfortunately, PN also carries certain risks related to infection and metabolic complications compared with enteral nutrition. In this review, an overview of PN and GI immune and microbiome changes is provided. PN impacts the gut-associated lymphoid tissue functions, especially adaptive immune cells, changes the intestinal epithelium and chemical secretions, and significantly alters the intestinal microbiome. Collectively, these changes functionally result in increased susceptibility to infectious and injurious challenge. Since PN remains necessary in large numbers of patients, the search to improve outcomes by stimulating GI immune function during PN remains of interest. This review closes by describing recent advances in using enteric nervous system neuropeptides or microbially derived products during PN, which may improve GI parameters by maintaining immunity and physiology.
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Affiliation(s)
- Joseph F. Pierre
- Section of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, University of Chicago, Chicago, Illinois
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553
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Roles of the intestinal microbiota in pathogen protection. Clin Transl Immunology 2017; 6:e128. [PMID: 28243438 PMCID: PMC5311919 DOI: 10.1038/cti.2017.2] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 01/02/2017] [Accepted: 01/03/2017] [Indexed: 02/08/2023] Open
Abstract
Hundreds of commensal bacterial species inhabit the gastrointestinal tract. This diverse microbial ecosystem plays a crucial role in the prevention and resolution of infectious diseases. In this review we will describe the major mechanisms by which the intestinal microbiota confers protection against infections, focusing on those caused by intestinal bacterial pathogens. These mechanisms include both non-immune- and immune-cell-mediated pathways, notably through bacterial production of inhibitory molecules and nutrient deprivation by the former and innate lymphoid cell-, myeloid cell- or lymphocyte-dependent stimulation by the latter. Finally, we will discuss novel therapeutic approaches based on commensal microbes and their products, which could potentially be used to combat infections.
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554
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Garg N, Luzzatto-Knaan T, Melnik AV, Caraballo-Rodríguez AM, Floros DJ, Petras D, Gregor R, Dorrestein PC, Phelan VV. Natural products as mediators of disease. Nat Prod Rep 2017; 34:194-219. [PMID: 27874907 PMCID: PMC5299058 DOI: 10.1039/c6np00063k] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Covering: up to 2016Humans are walking microbial ecosystems, each harboring a complex microbiome with the genetic potential to produce a vast array of natural products. Recent sequencing data suggest that our microbial inhabitants are critical for maintaining overall health. Shifts in microbial communities have been correlated to a number of diseases including infections, inflammation, cancer, and neurological disorders. Some of these clinically and diagnostically relevant phenotypes are a result of the presence of small molecules, yet we know remarkably little about their contributions to the health of individuals. Here, we review microbe-derived natural products as mediators of human disease.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | | | - Dimitrios J. Floros
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093
| | - Daniel Petras
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Rachel Gregor
- Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be’er Sheva 84105, Israel
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Vanessa V. Phelan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of Colorado Anschutz Medical Campus, Aurora, CO 80045
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555
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556
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Liu Y, Ding S, Dietrich R, Märtlbauer E, Zhu K. A Biosurfactant‐Inspired Heptapeptide with Improved Specificity to Kill MRSA. Angew Chem Int Ed Engl 2017; 56:1486-1490. [PMID: 28106348 DOI: 10.1002/anie.201609277] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/16/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthNational Center for Veterinary Drug Safety EvaluationCollege of Veterinary MedicineChina Agricultural University Yuanmingyuan West Road No.2 Beijing 100193 China
| | - Shuangyang Ding
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthNational Center for Veterinary Drug Safety EvaluationCollege of Veterinary MedicineChina Agricultural University Yuanmingyuan West Road No.2 Beijing 100193 China
| | - Richard Dietrich
- Institute of Food SafetyDepartment of Veterinary SciencesLudwig-Maximilians-University Munich 85764 Oberschleißheim Germany
| | - Erwin Märtlbauer
- Institute of Food SafetyDepartment of Veterinary SciencesLudwig-Maximilians-University Munich 85764 Oberschleißheim Germany
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthNational Center for Veterinary Drug Safety EvaluationCollege of Veterinary MedicineChina Agricultural University Yuanmingyuan West Road No.2 Beijing 100193 China
- Department of Biomedical EngineeringDuke University Durham NC 27708 USA
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557
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Vila-Farres X, Chu J, Inoyama D, Ternei MA, Lemetre C, Cohen LJ, Cho W, Reddy BVB, Zebroski HA, Freundlich JS, Perlin DS, Brady SF. Antimicrobials Inspired by Nonribosomal Peptide Synthetase Gene Clusters. J Am Chem Soc 2017; 139:1404-1407. [PMID: 28055186 DOI: 10.1021/jacs.6b11861] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial culture broth extracts have been the starting point for the development of numerous therapeutics. However, only a small fraction of bacterial biosynthetic diversity is accessible using this strategy. Here, we apply a discovery approach that bypasses the culturing step entirely by bioinformatically predicting small molecule structures from the primary sequences of the biosynthetic gene clusters. These structures are then chemically synthesized to give synthetic-bioinformatic natural products (syn-BNPs). Using this approach, we screened syn-BNPs inspired by nonribosomal peptide synthetases against microbial pathogens, and discovered an antibiotic for which no resistance could be identified and an antifungal agent with activity against diverse fungal pathogens.
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Affiliation(s)
- Xavier Vila-Farres
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - John Chu
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Daigo Inoyama
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Melinda A Ternei
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Christophe Lemetre
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Louis J Cohen
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Wooyoung Cho
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Boojala Vijay B Reddy
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Henry A Zebroski
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Joel S Freundlich
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - David S Perlin
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
| | - Sean F Brady
- Laboratory of Genetically Encoded Small Molecules and ‡Proteomics Resource Center, The Rockefeller University , New York, New York 10065, United States.,Department of Pharmacology, Physiology, and Neuroscience and ∥Public Health Research Institute, Rutgers University , Newark, New Jersey 07103, United States
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558
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Liu Y, Ding S, Dietrich R, Märtlbauer E, Zhu K. A Biosurfactant-Inspired Heptapeptide with Improved Specificity to Kill MRSA. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609277] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health; National Center for Veterinary Drug Safety Evaluation; College of Veterinary Medicine; China Agricultural University; Yuanmingyuan West Road No.2 Beijing 100193 China
| | - Shuangyang Ding
- Beijing Advanced Innovation Center for Food Nutrition and Human Health; National Center for Veterinary Drug Safety Evaluation; College of Veterinary Medicine; China Agricultural University; Yuanmingyuan West Road No.2 Beijing 100193 China
| | - Richard Dietrich
- Institute of Food Safety; Department of Veterinary Sciences; Ludwig-Maximilians-University Munich; 85764 Oberschleißheim Germany
| | - Erwin Märtlbauer
- Institute of Food Safety; Department of Veterinary Sciences; Ludwig-Maximilians-University Munich; 85764 Oberschleißheim Germany
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health; National Center for Veterinary Drug Safety Evaluation; College of Veterinary Medicine; China Agricultural University; Yuanmingyuan West Road No.2 Beijing 100193 China
- Department of Biomedical Engineering; Duke University; Durham NC 27708 USA
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559
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Mousa WK, Athar B, Merwin NJ, Magarvey NA. Antibiotics and specialized metabolites from the human microbiota. Nat Prod Rep 2017; 34:1302-1331. [DOI: 10.1039/c7np00021a] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human microbiota associated with each body site produce specialized molecules to kill human pathogens. Advanced bioinformatics tools will help to discover unique microbiome chemistry.
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Affiliation(s)
- Walaa K. Mousa
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Bilal Athar
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nishanth J. Merwin
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
| | - Nathan A. Magarvey
- Departments of Biochemistry and Biomedical Sciences & Chemistry and Chemical Biology
- M. G. DeGroote Institute for Infectious Disease Research
- McMaster University
- Hamilton
- Canada L8S 4K1
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560
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Gilbert JA. How do we make indoor environments and healthcare settings healthier? Microb Biotechnol 2017; 10:11-13. [PMID: 27748568 PMCID: PMC5270734 DOI: 10.1111/1751-7915.12430] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 09/24/2016] [Indexed: 11/28/2022] Open
Abstract
It is now well accepted that our modern lifestyle has certain implications for our health (Schaub et al., ), mainly as a result of our willingness to remove ourselves from the biological diversity of our natural environments (Roduit et al., ), while still being drawn inextricably to interact with it (Kellert and Wilson, ). Much of our interaction with the biological world is shaped by our interaction with the microbiological world. The bacteria, fungi, viruses, archaea and protists that comprise the microbiome of this planet, are also key to the development and normal functioning of our bodies. Our immune system is built to shepherd our microbial exposure, ensuring that microbial organisms that we need are kept close (but not too close), and that less-desirable organisms are expelled or killed before they can do too much damage. By moving from a life interacting with nature on a regular basis, to a life in which we isolate ourselves physically from natural microbial exposure, we may have instigated one of the great plagues of the 21st century; chronic immune disorders.
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Affiliation(s)
- Jack A. Gilbert
- The Microbiome CenterDepartment of SurgeryUniversity of ChicagoChicagoIL60637USA
- The Division of BioscienceArgonne National LaboratoryLemontIL60439USA
- The Marine Biological LaboratoryWoods HoleMA02543USA
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561
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Park KD, Pak SC, Park KK. The Pathogenetic Effect of Natural and Bacterial Toxins on Atopic Dermatitis. Toxins (Basel) 2016; 9:toxins9010003. [PMID: 28025545 PMCID: PMC5299398 DOI: 10.3390/toxins9010003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 12/15/2016] [Accepted: 12/19/2016] [Indexed: 12/18/2022] Open
Abstract
Atopic dermatitis (AD) is a common allergic skin disease that is associated with chronic, recurrent eczematous and pruritic lesions at the flexural folds caused by interacting factors related to environmental and immune system changes. AD results in dry skin, and immunoglobulin E-mediated allergic reactions to foods and environmental allergens. While steroids and anti-histamines temporarily relieve the symptoms of AD, the possibility of side effects from pharmacological interventions remains. Despite intensive research, the underlying mechanisms for AD have not been clarified. A study of Staphylococcus aureus (S. aureus) established the role of its toxins in the pathogenesis of AD. Approximately 90% of patients with AD experience S. aureus colonization and up to 50%–60% of the colonizing S. aureus is toxin-producing. Any damage to the protective skin barrier allows for the entry of invading allergens and pathogens that further drive the pathogenesis of AD. Some natural toxins (or their components) that have therapeutic effects on AD have been studied. In addition, recent studies on inflammasomes as one component of the innate immune system have been carried out. Additionally, studies on the close relationship between the activation of inflammasomes and toxins in AD have been reported. This review highlights the literature that discusses the pathogenesis of AD, the role of toxins in AD, and the positive and negative effects of toxins on AD. Lastly, suggestions are made regarding the role of inflammasomes in AD.
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Affiliation(s)
- Kyung-Duck Park
- Department of Dermatology, College of Medicine, Catholic University of Daegu, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Korea.
| | - Sok Cheon Pak
- School of Biomedical Sciences, Charles Sturt University, Panorama Avenue, Bathurst NSW 2795, Australia.
| | - Kwan-Kyu Park
- Department of Pathology, College of Medicine, Catholic University of Daegu, 33, Duryugongwon-ro 17-gil, Nam-gu, Daegu 42472, Korea.
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562
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Sullivan SB, Kamath S, McConville TH, Gray BT, Lowy FD, Gordon PG, Uhlemann AC. Staphylococcus epidermidis Protection Against Staphylococcus aureus Colonization in People Living With Human Immunodeficiency Virus in an Inner-City Outpatient Population: A Cross-Sectional Study. Open Forum Infect Dis 2016; 3:ofw234. [PMID: 28018932 PMCID: PMC5170490 DOI: 10.1093/ofid/ofw234] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/26/2016] [Indexed: 01/22/2023] Open
Abstract
Background. People living with human immunodeficiency virus (PLWH) have been disproportionally affected by methicillin-resistant Staphylococcus aureus (MRSA) colonization and infection, in particular by clones USA300 and USA500. However, the contribution of epidemiological, bacterial, and immunological risk factors to the excess of S aureus in PLWH remain incompletely understood. Methods. In this cross-sectional study, we determined the prevalence and molecular epidemiology of S aureus colonization in 93 PLWH attending an urban human immunodeficiency virus (HIV) clinic. Participants completed a structured interview assessing demographic information and risk factors for MRSA. Swabs were obtained from the nose, throat, and groin and cultured for S aureus and Staphylococcus epidermidis. Results. Most participants had well controlled HIV infection (89, 96% CD4 >200). Thirty-six (39%) individuals were colonized with S aureus at 1 or more body sites, including 6 (6%) with MRSA. Regular gym use was a risk factor for S aureus but not MRSA carriage. In contrast, S epidermidis was present in almost all individuals (n = 84, 90%), predominantly in the nares (n = 66, 71%). Using generalized estimating equation models, we observed that the odds of S aureus colonization were significantly and drastically reduced when S epidermidis was detected (P = .0001). After controlling for site, gender, and age, we identified that the odds of S aureus colonization were 80% less if S epidermidis was present (adjusted odds ratio, 0.20; 95% confidence interval, .09–.45; P < .0001). Conclusions. Taken together, we observed a lower prevalence of S aureus and MRSA colonization than has been previously reported in PLWH. In this cohort, colonization with S epidermidis was protective against S aureus colonization.
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Affiliation(s)
| | - Suneel Kamath
- Departments ofMedicine and; Northwestern Memorial Hospital, Chicago, Illinois
| | | | | | - Franklin D Lowy
- Departments ofMedicine and; Pathology, Columbia University Medical Center, New York
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563
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Liu L, Hao T, Xie Z, Horsman GP, Chen Y. Genome mining unveils widespread natural product biosynthetic capacity in human oral microbe Streptococcus mutans. Sci Rep 2016; 6:37479. [PMID: 27869143 PMCID: PMC5116633 DOI: 10.1038/srep37479] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 10/28/2016] [Indexed: 11/09/2022] Open
Abstract
Streptococcus mutans is a major pathogen causing human dental caries. As a Gram-positive bacterium with a small genome (about 2 Mb) it is considered a poor source of natural products. Due to a recent explosion in genomic data available for S. mutans strains, we were motivated to explore the natural product production potential of this organism. Bioinformatic characterization of 169 publically available genomes of S. mutans from human dental caries revealed a surprisingly rich source of natural product biosynthetic gene clusters. Anti-SMASH analysis identified one nonribosomal peptide synthetase (NRPS) gene cluster, seven polyketide synthase (PKS) gene clusters and 136 hybrid PKS/NRPS gene clusters. In addition, 211 ribosomally synthesized and post-translationally modified peptides (RiPPs) clusters and 615 bacteriocin precursors were identified by a combined analysis using BAGEL and anti-SMASH. S. mutans harbors a rich and diverse natural product genetic capacity, which underscores the importance of probing the human microbiome and revisiting species that have traditionally been overlooked as "poor" sources of natural products.
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Affiliation(s)
- Liwei Liu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Hao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhoujie Xie
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Geoff P Horsman
- Department of Chemistry and Biochemistry, Wilfrid Laurier University, Waterloo, ON, N2L3C5, Canada
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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564
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Canovas J, Baldry M, Bojer MS, Andersen PS, Grzeskowiak PK, Stegger M, Damborg P, Olsen CA, Ingmer H. Cross-Talk between Staphylococcus aureus and Other Staphylococcal Species via the agr Quorum Sensing System. Front Microbiol 2016; 7:1733. [PMID: 27877157 PMCID: PMC5099252 DOI: 10.3389/fmicb.2016.01733] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 10/17/2016] [Indexed: 11/13/2022] Open
Abstract
Staphylococci are associated with both humans and animals. While most are non-pathogenic colonizers, Staphylococcus aureus is an opportunistic pathogen capable of causing severe infections. S. aureus virulence is controlled by the agr quorum sensing system responding to secreted auto-inducing peptides (AIPs) sensed by AgrC, a two component histidine kinase. agr loci are found also in other staphylococcal species and for Staphylococcus epidermidis, the encoded AIP represses expression of agr regulated virulence genes in S. aureus. In this study we aimed to better understand the interaction between staphylococci and S. aureus, and show that this interaction may eventually lead to the identification of new anti-virulence candidates to target S. aureus infections. Here we show that culture supernatants of 37 out of 52 staphylococcal isolates representing 17 different species inhibit S. aureus agr. The dog pathogen, Staphylococcus schleiferi, expressed the most potent inhibitory activity and was active against all four agr classes found in S. aureus. By employing a S. aureus strain encoding a constitutively active AIP receptor we show that the activity is mediated via agr. Subsequent cloning and heterologous expression of the S. schleiferi AIP in S. aureus demonstrated that this molecule was likely responsible for the inhibitory activity, and further proof was provided when pure synthetic S. schleiferi AIP was able to completely abolish agr induction of an S. aureus reporter strain. To assess impact on S. aureus virulence, we co-inoculated S. aureus and S. schleiferi in vivo in the Galleria mellonella wax moth larva, and found that expression of key S. aureus virulence factors was abrogated. Our data show that the S. aureus agr locus is highly responsive to other staphylococcal species suggesting that agr is an inter-species communication system. Based on these results we speculate that interactions between S. aureus and other colonizing staphylococci will significantly influence the ability of S. aureus to cause infection, and we propose that other staphylococci are potential sources of compounds that can be applied as anti-virulence therapy for combating S. aureus infections.
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Affiliation(s)
- Jaime Canovas
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Mara Baldry
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Martin S Bojer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Paal S Andersen
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of CopenhagenFrederiksberg, Denmark; Department of Microbiology and Infection Control, Statens Serum InstitutCopenhagen, Denmark
| | - Piotr K Grzeskowiak
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Marc Stegger
- Department of Microbiology and Infection Control, Statens Serum Institut Copenhagen, Denmark
| | - Peter Damborg
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
| | - Christian A Olsen
- Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Faculty of Health and Medical Sciences, University of Copenhagen Frederiksberg, Denmark
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565
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Jorge AM, Schneider J, Unsleber S, Göhring N, Mayer C, Peschel A. Utilization of glycerophosphodiesters by Staphylococcus aureus. Mol Microbiol 2016; 103:229-241. [PMID: 27726204 DOI: 10.1111/mmi.13552] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2016] [Indexed: 01/02/2023]
Abstract
The facultative pathogen Staphylococcus aureus colonizes the human anterior nares and causes infections of various organ systems. Which carbon, energy, and phosphate sources can be utilized by S. aureus in nutrient-poor habitats has remained largely unknown. We describe that S. aureus secretes a glycerophosphodiesterase (glycerophosphodiester phosphodiesterase, EC 3.1.4.46), GlpQ, degrading the glycerophosphodiester (GPD) head groups of phospholipids such as human phosphatidylcholine (GroPC). Deletion of glpQ completely abolished the GroPC-degrading activity in S. aureus culture supernatants. GroPC has been detected in human tissues and body fluids probably as a result of phospholipid remodelling and degradation. Notably, GroPC promoted S. aureus growth under carbon- and phosphate-limiting conditions in a GlpQ-dependent manner indicating that GlpQ permits S. aureus to utilize GPD-derived glycerol-3-phosphate as a carbon and phosphate sources. Thus, S. aureus can use a broader spectrum of nutrients than previously thought which underscores its capacity to adapt to the highly variable and nutrient-poor surroundings.
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Affiliation(s)
- Ana Maria Jorge
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Germany
| | - Jonathan Schneider
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Germany
| | - Sandra Unsleber
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology Department, University of Tübingen, Germany
| | - Nadine Göhring
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Germany
| | - Christoph Mayer
- Interfaculty Institute of Microbiology and Infection Medicine, Microbiology/Biotechnology Department, University of Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Infection Biology Department, University of Tübingen, Germany
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566
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Patients as Patches: Ecology and Epidemiology in Healthcare Environments. Infect Control Hosp Epidemiol 2016; 37:1507-1512. [PMID: 27760571 DOI: 10.1017/ice.2016.224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The modern healthcare system involves complex interactions among microbes, patients, providers, and the built environment. It represents a unique and challenging setting for control of the emergence and spread of infectious diseases. We examine an extension of the perspectives and methods from ecology (and especially urban ecology) to address these unique issues, and we outline 3 examples: (1) viewing patients as individual microbial ecosystems; (2) the altered ecology of infectious diseases specifically within hospitals; and (3) ecosystem management perspectives for infection surveillance and control. In each of these cases, we explore the accuracy and relevance of analogies to existing urban ecological perspectives, and we demonstrate a few of the potential direct uses of this perspective for altering research into the control of healthcare-associated infections. Infect Control Hosp Epidemiol. 2016;1507-1512.
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567
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Tapping into our own resources. Nat Rev Microbiol 2016; 14:604-5. [DOI: 10.1038/nrmicro.2016.126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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568
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Fernandes P, Martens E. Antibiotics in late clinical development. Biochem Pharmacol 2016; 133:152-163. [PMID: 27687641 DOI: 10.1016/j.bcp.2016.09.025] [Citation(s) in RCA: 156] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/23/2016] [Indexed: 01/30/2023]
Abstract
Most pharmaceutical companies have stopped or have severely limited investments to discover and develop new antibiotics to treat the increasing prevalence of infections caused by multi-drug resistant bacteria, because the return on investment has been mostly negative for antibiotics that received marketing approved in the last few decades. In contrast, a few small companies have taken on this challenge and are developing new antibiotics. This review describes those antibiotics in late-stage clinical development. Most of them belong to existing antibiotic classes and a few with a narrow spectrum of activity are novel compounds directed against novel targets. The reasons for some of the past failures to find new molecules and a path forward to help attract investments to fund discovery of new antibiotics are described.
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Affiliation(s)
| | - Evan Martens
- Cempra, Inc., 6320 Quadrangle Dr. Bldg 2, Chapel Hill, NC 27517, USA
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569
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Advances in the Microbiome: Applications to Clostridium difficile Infection. J Clin Med 2016; 5:jcm5090083. [PMID: 27657145 PMCID: PMC5039486 DOI: 10.3390/jcm5090083] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/02/2016] [Accepted: 09/13/2016] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.
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570
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Chaves-Moreno D, Wos-Oxley ML, Jáuregui R, Medina E, Oxley AP, Pieper DH. Exploring the transcriptome of Staphylococcus aureus in its natural niche. Sci Rep 2016; 6:33174. [PMID: 27641137 PMCID: PMC5027550 DOI: 10.1038/srep33174] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 08/23/2016] [Indexed: 02/07/2023] Open
Abstract
Staphylococcus aureus is an important human pathogen and commensal, where the human nose is the predominant reservoir. To better understand its behavior in this environmental niche, RNA was extracted from the anterior nares of three documented S. aureus carriers and the metatranscriptome analyzed by RNAseq. In addition, the in vivo transcriptomes were compared to previously published transcriptomes of two in vitro grown S. aureus strains. None of the in vitro conditions, even growth in medium resembling the anterior nares environment, mimicked in vivo conditions. Survival in the nose was strongly controlled by the limitation of iron and evident by the expression of iron acquisition systems. S. aureus populations in different individuals clearly experience different environmental stresses, which they attempt to overcome by the expression of compatible solute biosynthetic pathways, changes in their cell wall composition and synthesis of general stress proteins. Moreover, the expression of adhesins was also important for colonization of the anterior nares. However, different S. aureus strains also showed different in vivo behavior. The assessment of general in vivo expression patterns and commonalities between different S. aureus strains will in the future result in new knowledge based strategies for controlling colonization.
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Affiliation(s)
- Diego Chaves-Moreno
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Melissa L Wos-Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Ruy Jáuregui
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Eva Medina
- Infection and Immunology Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Andrew Pa Oxley
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
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571
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Zipperer A, Konnerth MC, Laux C, Berscheid A, Janek D, Weidenmaier C, Burian M, Schilling NA, Slavetinsky C, Marschal M, Willmann M, Kalbacher H, Schittek B, Brötz-Oesterhelt H, Grond S, Peschel A, Krismer B. Erratum: Corrigendum: Human commensals producing a novel antibiotic impair pathogen colonization. Nature 2016; 539:314. [DOI: 10.1038/nature19781] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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572
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573
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574
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Német Z, Albert E, Nagy K, Csuka E, Dán Á, Szenci O, Hermans K, Balka G, Biksi I. Virulence type and tissue tropism of Staphylococcus strains originating from Hungarian rabbit farms. Vet Microbiol 2016; 193:1-6. [PMID: 27599923 DOI: 10.1016/j.vetmic.2016.08.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 08/03/2016] [Accepted: 08/04/2016] [Indexed: 02/04/2023]
Abstract
Staphylococcosis has a major economic impact on rabbit farming worldwide. Previous studies described a highly virulent variant, which is disseminated across Europe. Such strains are reported to be capable of inducing uncontrollable outbreaks. The authors describe a survey conducted on 374 Staphylococcus strains isolated from rabbit farms, mostly from Hungary, between 2009 and 2014, from a variety of pathological processes. The virulence type of the strains was determined using a multiplex PCR system. 84.2% of the strains belonged to a previously rarely isolated atypical highly virulent type. Only 6.1% belonged to the typical highly virulent genotype. Even low virulent strains were present at a higher percentage (6.4%). For a small group of strains (3.2%) the detection of the femA gene failed, indicating that these strains probably do not belong to the Staphylococcus aureus species. The results reveal the possibility of the asymptomatic presence of highly virulent strains on rabbit farms. "Non-aureus" Staphylococcus sp. can also have a notable role in the etiology of rabbit staphylococcosis. An association with the lesions and the virulence type was demonstrated. Statistical analysis of data on organotropism showed a significant correlation between septicaemia and the highly virulent genotype.
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Affiliation(s)
- Zoltán Német
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary.
| | - Ervin Albert
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary; MTA-SZIE Large Animal Clinical Research Group, H-2225 Dóra major, Üllő, Hungary
| | - Krisztina Nagy
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary
| | - Edit Csuka
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary
| | - Ádám Dán
- Veterinary Diagnostic Directorate, National Food Chain Safety Office (NFCSO), H-1143, 2 Tábornok street, Budapest, Hungary
| | - Ottó Szenci
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary; MTA-SZIE Large Animal Clinical Research Group, H-2225 Dóra major, Üllő, Hungary
| | - Katleen Hermans
- Ghent University, Department of Pathology, Bacteriology and Avian Diseases, Salisburylaan 133 B-9820 Merelbeke, Belgium
| | - Gyula Balka
- University of Veterinary Medicine Budapest, Department of Pathology, H-1078 István street 2, Budapest, Hungary
| | - Imre Biksi
- University of Veterinary Medicine Budapest, Department and Clinic for Production Animals, H-2225 Dóra major, Üllő, Hungary
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575
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Nowogrodzki A. The nose knows how to kill MRSA. Nature 2016. [DOI: 10.1038/nature.2016.20339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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