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Wei Y, Palacios Araya D, Palmer KL. Enterococcus faecium: evolution, adaptation, pathogenesis and emerging therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01058-6. [PMID: 38890478 DOI: 10.1038/s41579-024-01058-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
The opportunistic pathogen Enterococcus faecium colonizes humans and a wide range of animals, endures numerous stresses, resists antibiotic treatment and stubbornly persists in clinical environments. The widespread application of antibiotics in hospitals and agriculture has contributed to the emergence of vancomycin-resistant E. faecium, which causes many hospital-acquired infections. In this Review, we explore recent discoveries about the evolutionary history, the environmental adaptation and the colonization and dissemination mechanisms of E. faecium and vancomycin-resistant E. faecium. These studies provide critical insights necessary for developing novel preventive and therapeutic approaches against vancomycin-resistant E. faecium and also reveal the intricate interrelationships between the environment, the microorganism and the host, providing knowledge that is broadly relevant to how antibiotic-resistant pathogens emerge and endure.
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Affiliation(s)
- Yahan Wei
- School of Podiatric Medicine, The University of Texas Rio Grande Valley, Harlingen, TX, USA
| | - Dennise Palacios Araya
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA
| | - Kelli L Palmer
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX, USA.
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2
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Yan T, Li M, Wang Q, Wang M, Liu L, Ma C, Xiang X, Zhou Q, Liu Z, Gong Z. Structures, functions, and regulatory networks of universal stress proteins in clinically relevant pathogenic Bacteria. Cell Signal 2024; 116:111032. [PMID: 38185228 DOI: 10.1016/j.cellsig.2023.111032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/30/2023] [Indexed: 01/09/2024]
Abstract
Universal stress proteins are a class of proteins widely present in bacteria, archaea, plants, and invertebrates, playing essential roles in bacterial adaptation to various environmental stresses. The functions of bacterial universal stress proteins are versatile, including resistance to oxidative stress, maintenance of cell wall integrity, DNA damage repair, regulation of cell division and growth, among others. When facing stresses such as temperature changes, pH shifts, fluctuations in oxygen concentration, and exposure to toxins, these proteins can bind to specific DNA sequences and rapidly adjust bacterial metabolic pathways and gene expression patterns to adapt to the new environment. In summary, bacterial universal stress proteins play a crucial role in bacterial adaptability and survival. A comprehensive understanding of bacterial stress response mechanisms and the development of new antibacterial strategies are of great significance. This review summarizes the research progress on the structure, function, and regulatory factors of universal stress proteins in clinically relevant bacteria, aiming to facilitate deeper investigations by clinicians and researchers into universal stress proteins.
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Affiliation(s)
- Tao Yan
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Min Li
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiuyan Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meng Wang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lijuan Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Chengcheng Ma
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaohong Xiang
- School of Pharmacy, Chongqing Medical and Pharmaceutical College, Chongqing, China
| | - Qiang Zhou
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhou Liu
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
| | - Zhen Gong
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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3
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Sun S, Wang D, Dong D, Xu L, Xie M, Wang Y, Ni T, Jiang W, Zhu X, Ning N, Sun Q, Zhao S, Li M, Chen P, Yu M, Li J, Chen E, Zhao B, Peng Y, Mao E. Altered intestinal microbiome and metabolome correspond to the clinical outcome of sepsis. Crit Care 2023; 27:127. [PMID: 36978107 PMCID: PMC10044080 DOI: 10.1186/s13054-023-04412-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND The gut microbiome plays a pivotal role in the progression of sepsis. However, the specific mechanism of gut microbiota and its metabolites involved in the process of sepsis remains elusive, which limits its translational application. METHOD In this study, we used a combination of the microbiome and untargeted metabolomics to analyze stool samples from patients with sepsis enrolled at admission, then microbiota, metabolites, and potential signaling pathways that might play important roles in disease outcome were screened out. Finally, the above results were validated by the microbiome and transcriptomics analysis in an animal model of sepsis. RESULTS Patients with sepsis showed destruction of symbiotic flora and elevated abundance of Enterococcus, which were validated in animal experiments. Additionally, patients with a high burden of Bacteroides, especially B. vulgatus, had higher Acute Physiology and Chronic Health Evaluation II scores and longer stays in the intensive care unit. The intestinal transcriptome in CLP rats illustrated that Enterococcus and Bacteroides had divergent profiles of correlation with differentially expressed genes, indicating distinctly different roles for these bacteria in sepsis. Furthermore, patients with sepsis exhibited disturbances in gut amino acid metabolism compared with healthy controls; namely, tryptophan metabolism was tightly related to an altered microbiota and the severity of sepsis. CONCLUSION Alterations in microbial and metabolic features in the gut corresponded with the progression of sepsis. Our findings may help to predict the clinical outcome of patients in the early stage of sepsis and provide a translational basis for exploring new therapies.
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Affiliation(s)
- Silei Sun
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Daosheng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Danfeng Dong
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Lili Xu
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Mengqi Xie
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Yihui Wang
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Tongtian Ni
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Weisong Jiang
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Xiaojuan Zhu
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Ning Ning
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Qian Sun
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Shuyuan Zhao
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Mengjiao Li
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Peili Chen
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Meiling Yu
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Jian Li
- Clinical Research Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Erzhen Chen
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China
| | - Bing Zhao
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China.
| | - Yibing Peng
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China.
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China.
| | - Enqiang Mao
- Department of Emergency, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin ER Road, Shanghai, 200025, China.
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O'Connor A, Jurado‐Martín I, Mysior MM, Manzira AL, Drabinska J, Simpson JC, Lucey M, Schaffer K, Berisio R, McClean S. A universal stress protein upregulated by hypoxia has a role in Burkholderia cenocepacia intramacrophage survival: Implications for chronic infection in cystic fibrosis. Microbiologyopen 2022; 12:e1311. [PMID: 36825886 PMCID: PMC9733578 DOI: 10.1002/mbo3.1311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022] Open
Abstract
Universal stress proteins (USPs) are ubiquitously expressed in bacteria, archaea, and eukaryotes and play a lead role in adaptation to environmental conditions. They enable adaptation of bacterial pathogens to the conditions encountered in the human niche, including hypoxia, oxidative stress, osmotic stress, nutrient deficiency, or acid stress, thereby facilitating colonization. We previously reported that all six USP proteins encoded within a low-oxygen activated (lxa) locus in Burkholderia cenocepacia showed increased abundance during chronic colonization of the cystic fibrosis (CF) lung. However, the role of USPs in chronic cystic fibrosis infection is not well understood. Structural modeling identified surface arginines on one lxa-encoded USP, USP76, which suggested it mediated interactions with heparan sulfate. Using mutants derived from the B. cenocepacia strain, K56-2, we show that USP76 is involved in host cell attachment. Pretreatment of lung epithelial cells with heparanase reduced the binding of the wild-type and complement strains but not the Δusp76 mutant strain, indicating that USP76 is directly or indirectly involved in receptor recognition on the surface of epithelial cells. We also show that USP76 is required for growth and survival in many conditions associated with the CF lung, including acidic conditions and oxidative stress. Moreover, USP76 also has a role in survival in macrophages isolated from people with CF. Overall, while further elucidation of the exact mechanism(s) is required, we can conclude that USP76, which is upregulated during chronic infection, is involved in bacterial survival within CF macrophages, a hallmark of Burkholderia infection.
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Affiliation(s)
- Andrew O'Connor
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland
| | - Irene Jurado‐Martín
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Margaritha M. Mysior
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland,Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Anotidaishe L. Manzira
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Joanna Drabinska
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
| | - Jeremy C. Simpson
- UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland,Cell Screening Laboratory, School of Biology and Environmental ScienceUniversity College DublinBelfieldDublinIreland
| | - Mary Lucey
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Kirsten Schaffer
- Department of MicrobiologySt. Vincent's University HospitalElm ParkDublinIreland
| | - Rita Berisio
- Institute of Biostructures and BioimagingNational Research CouncilNaplesItaly
| | - Siobhán McClean
- School of Biomolecular and Biomedical SciencesUniversity College DublinBelfieldDublinIreland,UCD Conway Institute of Biomolecular and Biomedical ScienceBefieldDublinIreland
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LeBlanc N, Charles TC. Bacterial genome reductions: Tools, applications, and challenges. Front Genome Ed 2022; 4:957289. [PMID: 36120530 PMCID: PMC9473318 DOI: 10.3389/fgeed.2022.957289] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial cells are widely used to produce value-added products due to their versatility, ease of manipulation, and the abundance of genome engineering tools. However, the efficiency of producing these desired biomolecules is often hindered by the cells’ own metabolism, genetic instability, and the toxicity of the product. To overcome these challenges, genome reductions have been performed, making strains with the potential of serving as chassis for downstream applications. Here we review the current technologies that enable the design and construction of such reduced-genome bacteria as well as the challenges that limit their assembly and applicability. While genomic reductions have shown improvement of many cellular characteristics, a major challenge still exists in constructing these cells efficiently and rapidly. Computational tools have been created in attempts at minimizing the time needed to design these organisms, but gaps still exist in modelling these reductions in silico. Genomic reductions are a promising avenue for improving the production of value-added products, constructing chassis cells, and for uncovering cellular function but are currently limited by their time-consuming construction methods. With improvements to and the creation of novel genome editing tools and in silico models, these approaches could be combined to expedite this process and create more streamlined and efficient cell factories.
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Affiliation(s)
- Nicole LeBlanc
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- *Correspondence: Nicole LeBlanc,
| | - Trevor C. Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
- Metagenom Bio Life Science Inc., Waterloo, ON, Canada
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Venkateswaran P, Lakshmanan PM, Muthukrishnan S, Bhagavathi H, Vasudevan S, Neelakantan P, Solomon AP. Hidden agenda of Enterococcus faecalis lifestyle transition: planktonic to sessile state. Future Microbiol 2022; 17:1051-1069. [PMID: 35899477 DOI: 10.2217/fmb-2021-0212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Enterococcus faecalis, a human gastrointestinal tract commensal, is known to cause nosocomial infections. Interestingly, the pathogen's host colonization and persistent infections are possibly linked to its lifestyle changes from planktonic to sessile state. Also, the multidrug resistance and survival fitness acquired in the sessile stage of E. faecalis has challenged treatment regimes. This situation exists because of the critical role played by several root genes and their molecular branches, which are part of quorum sensing, aggregation substance, surface adhesions, stress-related response and sex pheromones in the sessile state. It is therefore imperative to decode the hidden agenda of E. faecalis and understand the significant factors influencing biofilm formation. This would, in turn, augment the development of novel strategies to tackle E. faecalis infections.
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Affiliation(s)
- Parvathy Venkateswaran
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Priya M Lakshmanan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Sudhiksha Muthukrishnan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Hema Bhagavathi
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Sahana Vasudevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | | | - Adline P Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical & Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
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7
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Krause AL, Stinear TP, Monk IR. Barriers to genetic manipulation of Enterococci: Current Approaches and Future Directions. FEMS Microbiol Rev 2022; 46:6650352. [PMID: 35883217 PMCID: PMC9779914 DOI: 10.1093/femsre/fuac036] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 01/09/2023] Open
Abstract
Enterococcus faecalis and Enterococcus faecium are Gram-positive commensal gut bacteria that can also cause fatal infections. To study clinically relevant multi-drug resistant E. faecalis and E. faecium strains, methods are needed to overcome physical (thick cell wall) and enzymatic barriers that limit the transfer of foreign DNA and thus prevent facile genetic manipulation. Enzymatic barriers to DNA uptake identified in E. faecalis and E. faecium include type I, II and IV restriction modification systems and CRISPR-Cas. This review examines E. faecalis and E. faecium DNA defence systems and the methods with potential to overcome these barriers. DNA defence system bypass will allow the application of innovative genetic techniques to expedite molecular-level understanding of these important, but somewhat neglected, pathogens.
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Affiliation(s)
- Alexandra L Krause
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia
| | - Ian R Monk
- Corresponding author: Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, VIC 3000 Australia. E-mail:
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8
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Freitas AR, Tedim AP, Almeida-Santos AC, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Novais C, Peixe L. High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach. Microorganisms 2022; 10:microorganisms10030632. [PMID: 35336207 PMCID: PMC8948916 DOI: 10.3390/microorganisms10030632] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10–12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.
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Affiliation(s)
- Ana R. Freitas
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
| | - Ana P. Tedim
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), 47012 Valladollid, Spain;
| | - Ana C. Almeida-Santos
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Bárbara Duarte
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Houyem Elghaieb
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Mohamed S. Abbassi
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Abdennaceur Hassen
- Laboratory of Treatment and Valorisation of Wastewater, Centre of Research and Water Technologies (CERTE), Technopark of Borj-Cédria, Soliman 8020, Tunisia;
| | - Carla Novais
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
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Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss MA. Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks. Front Microbiol 2021; 12:728356. [PMID: 34646248 PMCID: PMC8503688 DOI: 10.3389/fmicb.2021.728356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 08/27/2021] [Indexed: 12/02/2022] Open
Abstract
Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster’s closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes. Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.
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Affiliation(s)
- Paola Lisotto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
| | - Sigrid Rosema
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Mariëtte Lokate
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Xuewei Zhou
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Erik Bathoorn
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Hermie J M Harmsen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, United States.,IDbyDNA Inc., Salt Lake City, UT, United States
| | - Monika A Chlebowicz-Fliss
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
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Almeida-Santos AC, Novais C, Peixe L, Freitas AR. Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context. Antibiotics (Basel) 2021; 10:antibiotics10101215. [PMID: 34680796 PMCID: PMC8532689 DOI: 10.3390/antibiotics10101215] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/10/2023] Open
Abstract
Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.
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Affiliation(s)
- Ana C. Almeida-Santos
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
| | - Ana R. Freitas
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN–Toxicology Research Unit, Department of Sciences, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
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Hazan R, Schoemann M, Klutstein M. Endurance of extremely prolonged nutrient prevention across kingdoms of life. iScience 2021; 24:102745. [PMID: 34258566 PMCID: PMC8258982 DOI: 10.1016/j.isci.2021.102745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Numerous observations demonstrate that microorganisms can survive very long periods of nutrient deprivation and starvation. Moreover, it is evident that prolonged periods of starvation are a feature of many habitats, and many cells in all kingdoms of life are found in prolonged starvation conditions. Bacteria exhibit a range of responses to long-term starvation. These include genetic adaptations such as the long-term stationary phase and the growth advantage in stationary phase phenotypes characterized by mutations in stress-signaling genes and elevated mutation rates. Here, we suggest using the term "endurance of prolonged nutrient prevention" (EPNP phase), to describe this phase, which was also recently described in eukaryotes. Here, we review this literature and describe the current knowledge about the adaptations to very long-term starvation conditions in bacteria and eukaryotes, its conceptual and structural conservation across all kingdoms of life, and point out possible directions that merit further research.
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Affiliation(s)
- Ronen Hazan
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Miriam Schoemann
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
| | - Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, P.O.B. 12272, Ein Kerem, Jerusalem 9112001, Israel
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