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Hodzhev Y, Tsafarova B, Tolchkov V, Youroukova V, Ivanova S, Kostadinov D, Yanev N, Zhelyazkova M, Tsonev S, Kalfin R, Panaiotov S. Visualization of the individual blood microbiome to study the etiology of sarcoidosis. Comput Struct Biotechnol J 2023; 22:50-57. [PMID: 37928975 PMCID: PMC10624578 DOI: 10.1016/j.csbj.2023.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/14/2023] [Accepted: 10/16/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction Single microbial pathogens or host-microbiome dysbiosis are the causes of lung diseases with suspected infectious etiology. Metagenome sequencing provides an overview of the microbiome content. Due to the rarity of most granulomatous lung diseases collecting large systematic datasets is challenging. Thus, single-patient data often can only be summarized visually. Objective To increase the information gain from a single-case metagenome analysis we suggest a quantitative and qualitative approach. Results The 16S metagenomic results of 7 patients with pulmonary sarcoidosis were compared with those of 22 healthy individuals. From lysed blood, total microbial DNA was extracted and sequenced. Cleaned data reads were identified taxonomically using Kraken 2 software. Individual metagenomic data were visualized with a Sankey diagram, Krona chart, and a heat-map. We identified five genera that were exclusively present or significantly enhanced in patients with sarcoidosis - Veillonella, Prevotella, Cutibacterium, Corynebacterium, and Streptococcus. Conclusions Our approach can characterize the blood microbiome composition and diversity in rare diseases at an individual level. Investigation of the blood microbiome in patients with granulomatous lung diseases of unknown etiology, such as sarcoidosis could enhance our comprehension of their origin and pathogenesis and potentially uncover novel personalized therapeutics.
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Affiliation(s)
- Yordan Hodzhev
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Borislava Tsafarova
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Vladimir Tolchkov
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
| | - Vania Youroukova
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Silvia Ivanova
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Dimitar Kostadinov
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Nikolay Yanev
- Department of Pulmonary Diseases, University Hospital for Pulmonary Diseases “St. Sofia”, Medical University of Sofia, Akad. Ivan Evstratiev Geshov 17 Blvd., Sofia 1431, Bulgaria
| | - Maya Zhelyazkova
- Faculti of Mathematics and Informatics, Sofia University St. Kliment Ohridski, 5 James Bourchier Blvd., 1164 Sofia, Bulgaria
| | - Stefan Tsonev
- Agrobioinstitute (ABI), 8 Dragan Tsankov, Blvd, Sofia 1164, Bulgaria
| | - Reni Kalfin
- Institute of Neurobiology, Bulgarian Academy of Sciences, Sofia 1113, Bulgaria
- Department of Health Care, South-West University “Neofit Rilski”, Blagoevgrad 2700, Bulgaria
| | - Stefan Panaiotov
- Microbiology Department, National Center of Infectious and Parasitic Diseases, Yanko Sakazov 26 Blvd., Sofia 1504, Bulgaria
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Watkins RR, Bonomo RA, Rello J. Managing sepsis in the era of precision medicine: challenges and opportunities. Expert Rev Anti Infect Ther 2022; 20:871-880. [PMID: 35133228 DOI: 10.1080/14787210.2022.2040359] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Precision medicine is a medical model in which decisions, practices, interventions and therapies are tailored to the individual patient based on their predicted response or risk of disease. Sepsis is a life-threatening condition characterized by immune system dysregulation whose pathophysiology remains incompletely understood. There is much hope that precision medicine can lead to better outcomes in patients with sepsis. AREAS COVERED In this review from a comprehensive literature search in PubMed for English-language studies conducted in adults, we highlight recent advances in the diagnosis and treatment of sepsis of bacterial origin in adults using precision medicine approaches including rapid diagnostic tests, predictive biomarkers, genomic methods, rapid antimicrobial susceptibility testing, and monitoring cell mediated immunity. Challenges and directions for future research are also discussed. EXPERT OPINION Current diagnostic testing in sepsis relies primarily on conventional cultures (e.g. blood cultures), which are time-consuming and may delay critical therapeutic decisions. Nonculture-based techniques including nucleic acid amplification technologies (NAAT), other molecular methods (biomarkers), and genomic sequencing offer promise to overcome some of the inherent limitations seen with culture-based techniques.
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Affiliation(s)
- Richard R Watkins
- Department of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, USA
| | - Robert A Bonomo
- Medicine Service, Louis Stokes Cleveland Veterans Affairs Medical Center, Cleveland, Ohio, USA.,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA.,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology, Cleveland, OH, USA
| | - Jordi Rello
- Clinical Research in Pneumonia and Sepsis, Vall d'Hebron Institute of Research, Barcelona, Spain.,Clinical Research, Centre Hospitalier Universitaire Maribeau, Nimes, France
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Abu Y, Vitari N, Yan Y, Roy S. Opioids and Sepsis: Elucidating the Role of the Microbiome and microRNA-146. Int J Mol Sci 2022; 23:1097. [PMID: 35163021 PMCID: PMC8835205 DOI: 10.3390/ijms23031097] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/14/2022] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
Sepsis has recently been defined as life-threatening organ dysfunction caused by the dysregulated host response to an ongoing or suspected infection. To date, sepsis continues to be a leading cause of morbidity and mortality amongst hospitalized patients. Many risk factors contribute to development of sepsis, including pain-relieving drugs like opioids, which are frequently prescribed post-operatively. In light of the opioid crisis, understanding the interactions between opioid use and the development of sepsis has become extremely relevant, as opioid use is associated with increased risk of infection. Given that the intestinal tract is a major site of origin of sepsis-causing microbes, there has been an increasing focus on how alterations in the gut microbiome may predispose towards sepsis and mediate immune dysregulation. MicroRNAs, in particular, have emerged as key modulators of the inflammatory response during sepsis by tempering the immune response, thereby mediating the interaction between host and microbiome. In this review, we elucidate contributing roles of microRNA 146 in modulating sepsis pathogenesis and end with a discussion of therapeutic targeting of the gut microbiome in controlling immune dysregulation in sepsis.
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Affiliation(s)
- Yaa Abu
- Medical Scientist Training Program, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Nicolas Vitari
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Yan Yan
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
| | - Sabita Roy
- Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
- Department of Surgery, Miller School of Medicine, University of Miami, Miami, FL 33136, USA;
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Lazzaro A, De Girolamo G, Filippi V, Innocenti GP, Santinelli L, Ceccarelli G, Trecarichi EM, Torti C, Mastroianni CM, d’Ettorre G, Russo A. The Interplay between Host Defense, Infection, and Clinical Status in Septic Patients: A Narrative Review. Int J Mol Sci 2022; 23:ijms23020803. [PMID: 35054993 PMCID: PMC8776148 DOI: 10.3390/ijms23020803] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/05/2022] [Accepted: 01/09/2022] [Indexed: 01/08/2023] Open
Abstract
Sepsis is a life-threatening condition that arises when the body's response to an infection injures its own tissues and organs. Despite significant morbidity and mortality throughout the world, its pathogenesis and mechanisms are not clearly understood. In this narrative review, we aimed to summarize the recent developments in our understanding of the hallmarks of sepsis pathogenesis (immune and adaptive immune response, the complement system, the endothelial disfunction, and autophagy) and highlight novel laboratory diagnostic approaches. Clinical management is also discussed with pivotal consideration for antimicrobic therapy management in particular settings, such as intensive care unit, altered renal function, obesity, and burn patients.
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Affiliation(s)
- Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Gabriella De Girolamo
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Valeria Filippi
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Giuseppe Pietro Innocenti
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Letizia Santinelli
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Enrico Maria Trecarichi
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
| | - Carlo Torti
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
| | - Claudio Maria Mastroianni
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Gabriella d’Ettorre
- Department of Public Health and Infectious Diseases, “Sapienza” University of Rome, 00161 Rome, Italy; (A.L.); (G.D.G.); (V.F.); (G.P.I.); (L.S.); (G.C.); (C.M.M.); (G.d.)
| | - Alessandro Russo
- Infectious and Tropical Disease Unit, Department of Medical and Surgical Sciences, “Magna Graecia” University of Catanzaro, 88100 Catanzaro, Italy; (E.M.T.); (C.T.)
- Correspondence:
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