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Wagner TM, Pöntinen AK, Fenzel CK, Engi D, Janice J, Almeida-Santos AC, Tedim AP, Freitas AR, Peixe L, van Schaik W, Johannessen M, Hegstad K. Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium. FEMS Microbes 2024; 5:xtae009. [PMID: 38606354 PMCID: PMC11008740 DOI: 10.1093/femsmc/xtae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.
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Affiliation(s)
- Theresa Maria Wagner
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Carolin Kornelia Fenzel
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Daniel Engi
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Ana C Almeida-Santos
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CiberES CB22/06/00035), 28029 Madrid, Spain
| | - Ana R Freitas
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H- TOXRUN – One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, 4584-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mona Johannessen
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
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Roer L, Kaya H, Tedim AP, Novais C, Coque TM, Aarestrup FM, Peixe L, Hasman H, Hammerum AM, Freitas AR. VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data. Microbiol Spectr 2024; 12:e0372423. [PMID: 38329344 PMCID: PMC10913372 DOI: 10.1128/spectrum.03724-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Luísa Peixe
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana R. Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - On behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
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Tedim AP, Merino I, Ortega A, Domínguez-Gil M, Eiros JM, Bermejo-Martín JF. Quantification of bacterial DNA in blood using droplet digital PCR: a pilot study. Diagn Microbiol Infect Dis 2024; 108:116075. [PMID: 37837915 DOI: 10.1016/j.diagmicrobio.2023.116075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/16/2023] [Accepted: 08/28/2023] [Indexed: 10/16/2023]
Abstract
We used droplet digital PCR (ddPCR) assays to detect/quantify DNA from Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Enterococcus spp. in blood samples. Bacterial DNA from clinical strains (4 < n < 12) was extracted, quantified and diluted (10-0.0001 ng/µL) and ddPCR assays were performed in triplicate. These ddPCR assays showed low replication variability, low detection limit (1-0.1 pg/µL), and genus/species specificity. ddPCR assays were also used to quantify bacterial DNA obtained from spiked blood (1 × 104-1 CFU/mL) of each bacterial genus/species. Comparison between ddPCR assays and bacterial culture was performed by Pearson correlation. There was an almost perfect correlation (r ≥ 0.997, P ≤ 0.001) between the number of CFU/mL from bacterial culture and the number of gene copies/mL detected by ddPCR. The time from sample preparation to results was determined to be 3.5 to 4 hours. The results demonstrated the quantification capacity and specificity of the ddPCR assays to detect/quantify 4 of the most important bloodstream infection (BSI) bacterial pathogens directly from blood. SIGNIFICANCE AND IMPACT: This pilot study results support the potential of ddPCR for the diagnosis and/or severity stratification of BSI. Applied to patients' blood samples it can improve diagnosis and diminish sample-to-results time, improving patient care.
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Affiliation(s)
- Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain; Hospital Universitario Río Hortega, Valladolid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CiberES), CB22/06/00035, Instituto de Salud Carlos III, Madrid, Spain.
| | - Irene Merino
- Microbiology Department, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain; Hospital Universitario Río Hortega, Valladolid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CiberES), CB22/06/00035, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Valladolid, Spain
| | - José Maria Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Valladolid, Spain
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Salamanca, Spain; Hospital Universitario Río Hortega, Valladolid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CiberES), CB22/06/00035, Instituto de Salud Carlos III, Madrid, Spain
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4
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Almansa R, Eiros JM, de Gonzalo-Calvo D, Postigo T, Ortega A, Lopez-Izquierdo R, Moncusí-Moix A, Gort-Paniello C, Dominguez-Gil M, Fuente ADL, González-González L, Luis-García T, García-Mateo N, Tedim AP, Rodríguez-Jara F, Jorge N, González J, Torres G, Gutiérrez-Pérez ON, Villegas MJ, Campo S, Ayllon E, Albi TR, de Frutos Arribas J, Domingo AA, Abadia-Otero J, Barquero JG, Trapiello W, Garcia Frade LJ, Inglada L, Campo FD, Bermejo-Martin JF, Barbé F, Torres A. N-antigenemia detection by a rapid lateral flow test predicts 90-day mortality in COVID-19: a prospective cohort study. Clin Microbiol Infect 2022; 28:1391.e1-1391.e5. [PMID: 35654316 PMCID: PMC9150910 DOI: 10.1016/j.cmi.2022.05.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 05/03/2022] [Accepted: 05/14/2022] [Indexed: 11/28/2022]
Abstract
Objectives To evaluate if the detection of N antigen of SARS-CoV-2 in plasma by a rapid lateral flow test predicts 90-day mortality in COVID-19 patients hospitalized at the wards. Methods The presence of N-antigenemia was evaluated in the first 36 hours after hospitalization in 600 unvaccinated COVID-19 patients, by using the Panbio COVID-19 Ag Rapid Test Device from Abbott (Abbott Laboratories Inc., Chicago, IL, USA). The impact of N-antigenemia on 90-day mortality was assessed by multivariable Cox regression analysis. Results Prevalence of N-antigenemia at hospitalization was higher in nonsurvivors (69% (82/118) vs. 52% (250/482); p < 0.001). The patients with N-antigenemia showed more frequently RNAemia (45.7% (148/324) vs. 19.8% (51/257); p < 0.001), absence of anti-SARS-CoV-2 N antibodies (80.7% (264/327) vs. 26.6% (69/259); p < 0.001) and absence of S1 antibodies (73.4% (240/327) vs. 23.6% (61/259); p < 0.001). The patients with antigenemia showed more frequently acute respiratory distress syndrome (30.1% (100/332) vs. 18.7% (50/268); p = 0.001) and nosocomial infections (13.6% (45/331) vs. 7.9% (21/267); p = 0.026). N-antigenemia was a risk factor for increased 90-day mortality in the multivariable analysis (HR, 1.99 (95% CI,1.09–3.61), whereas the presence of anti-SARS-CoV-2 N-antibodies represented a protective factor (HR, 0.47 (95% CI, 0.26–0.85). Discussion The presence of N-antigenemia or the absence of anti-SARS-CoV-2 N-antibodies after hospitalization is associated to increased 90-day mortality in unvaccinated COVID-19 patients. Detection of N-antigenemia by using lateral flow tests is a quick, widely available tool that could contribute to early identify those COVID-19 patients at risk of deterioration.
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Affiliation(s)
- Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Department of Cellular Biology, Hystology and Pharmacology. University of Valladolid, Av. Ramón y Cajal, 7, 47005 Valladolid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Jose María Eiros
- Microbiology Service, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - David de Gonzalo-Calvo
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Tamara Postigo
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Raul Lopez-Izquierdo
- Emergency Department, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Anna Moncusí-Moix
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Clara Gort-Paniello
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Marta Dominguez-Gil
- Microbiology Service, Hospital Universitario Rio Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Laura González-González
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Tania Luis-García
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Nadia García-Mateo
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Fátima Rodríguez-Jara
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Gerard Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Oliver Norberto Gutiérrez-Pérez
- Hematology Service. Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Maria José Villegas
- Hematology Service. Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Sonia Campo
- Hematology Service. Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Eva Ayllon
- Hematology Service. Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Tomás Ruiz Albi
- Pneumology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Julio de Frutos Arribas
- Pneumology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain; Deparment of Medicine, Dermatology and Toxicology, School of Medicine, University of Valladolid, Av. Ramón y Cajal, 7, 47005 Valladolid, Spain
| | - Ainhoa Arroyo Domingo
- Pneumology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Jesica Abadia-Otero
- Internal Medicine Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Julia Gómez Barquero
- Internal Medicine Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Wysali Trapiello
- Clinical Analysis Service. Hospital Clínico Universitario de Valladolid, Gerencia Regional de Salud de Castilla y León, Av. Ramón y Cajal, 3, 47003 Valladolid, Spain
| | - Luis Javier Garcia Frade
- Hematology Service. Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Luis Inglada
- Internal Medicine Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain
| | - Felix Del Campo
- Pneumology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain; Deparment of Medicine, Dermatology and Toxicology, School of Medicine, University of Valladolid, Av. Ramón y Cajal, 7, 47005 Valladolid, Spain; Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain
| | - Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de Salud de Castilla y León, Paseo de San Vicente, 58-182, 37007 Salamanca, Spain; Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Hospital Universitario Río Hortega, Gerencia Regional de Salud de Castilla y León, Calle Dulzaina, 2, 47012 Valladolid, Spain.
| | - Ferran Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRB Lleida, Av. Alcalde Rovira Roure, 80, 25198 Lleida Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029 Madrid, Spain; Department of Pulmonology, Hospital Clinic de Barcelona, Universidad de Barcelona, Institut D investigacions August Pi I Sunyer (IDIBAPS), Carrer del Rosselló, 149, 08036 Barcelona, Spain; Catalan Institution for Research and Advanced Studies, Passeig de Lluís Companys, 23, 08010 Barcelona, Spain
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5
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García-Hidalgo MC, González J, Benítez ID, Carmona P, Santisteve S, Moncusí-Moix A, Gort-Paniello C, Rodríguez-Jara F, Molinero M, Perez-Pons M, Torres G, Caballero J, Barberà C, Tedim AP, Almansa R, Ceccato A, Fernández-Barat L, Ferrer R, Garcia-Gasulla D, Menéndez R, Motos A, Peñuelas O, Riera J, Bermejo-Martin JF, Torres A, Barbé F, de Gonzalo-Calvo D. Proteomic profiling of lung diffusion impairment in the recovery stage of SARS-CoV-2-induced ARDS. Clin Transl Med 2022; 12:e838. [PMID: 35538880 PMCID: PMC9091985 DOI: 10.1002/ctm2.838] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 12/19/2022] Open
Affiliation(s)
- María C García-Hidalgo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Jessica González
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Iván D Benítez
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Paola Carmona
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Sally Santisteve
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Anna Moncusí-Moix
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Clara Gort-Paniello
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Fátima Rodríguez-Jara
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Marta Molinero
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain
| | - Manel Perez-Pons
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Gerard Torres
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Jesús Caballero
- Intensive Care Department, University Hospital Arnau de Vilanova, IRBLleida, Lleida, Spain
| | - Carme Barberà
- Intensive Care Department, University Hospital Santa María, IRBLleida, Lleida, Spain
| | - Ana P Tedim
- Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Raquel Almansa
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Adrián Ceccato
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - Laia Fernández-Barat
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ricard Ferrer
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | | | - Rosario Menéndez
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Ana Motos
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Oscar Peñuelas
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario de Getafe, Madrid, Spain
| | - Jordi Riera
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca (VHIR), Spain
| | - Jesús F Bermejo-Martin
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Hospital Universitario Río Hortega de Valladolid, Valladolid, Spain.,Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain
| | - Antoni Torres
- CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain.,Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, Barcelona, Spain
| | - Ferran Barbé
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
| | - David de Gonzalo-Calvo
- Translational Research in Respiratory Medicine, University Hospital Arnau de Vilanova and Santa Maria, IRBLleida, Lleida, Spain.,CIBER of Respiratory Diseases (CIBERES), Institute of Health Carlos III, Madrid, Spain
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6
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Merino I, de la Fuente A, Domínguez-Gil M, Eiros JM, Tedim AP, Bermejo-Martín JF. Digital PCR applications for the diagnosis and management of infection in critical care medicine. Crit Care 2022; 26:63. [PMID: 35313934 PMCID: PMC8935253 DOI: 10.1186/s13054-022-03948-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/11/2022] [Indexed: 12/15/2022] Open
Abstract
Infection (either community acquired or nosocomial) is a major cause of morbidity and mortality in critical care medicine. Sepsis is present in up to 30% of all ICU patients. A large fraction of sepsis cases is driven by severe community acquired pneumonia (sCAP), which incidence has dramatically increased during COVID-19 pandemics. A frequent complication of ICU patients is ventilator associated pneumonia (VAP), which affects 10–25% of all ventilated patients, and bloodstream infections (BSIs), affecting about 10% of patients. Management of these severe infections poses several challenges, including early diagnosis, severity stratification, prognosis assessment or treatment guidance. Digital PCR (dPCR) is a next-generation PCR method that offers a number of technical advantages to face these challenges: it is less affected than real time PCR by the presence of PCR inhibitors leading to higher sensitivity. In addition, dPCR offers high reproducibility, and provides absolute quantification without the need for a standard curve. In this article we reviewed the existing evidence on the applications of dPCR to the management of infection in critical care medicine. We included thirty-two articles involving critically ill patients. Twenty-three articles focused on the amplification of microbial genes: (1) four articles approached bacterial identification in blood or plasma; (2) one article used dPCR for fungal identification in blood; (3) another article focused on bacterial and fungal identification in other clinical samples; (4) three articles used dPCR for viral identification; (5) twelve articles quantified microbial burden by dPCR to assess severity, prognosis and treatment guidance; (6) two articles used dPCR to determine microbial ecology in ICU patients. The remaining nine articles used dPCR to profile host responses to infection, two of them for severity stratification in sepsis, four focused to improve diagnosis of this disease, one for detecting sCAP, one for detecting VAP, and finally one aimed to predict progression of COVID-19. This review evidences the potential of dPCR as a useful tool that could contribute to improve the detection and clinical management of infection in critical care medicine.
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Affiliation(s)
- Irene Merino
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José María Eiros
- Microbiology Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain. .,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.
| | - Jesús F Bermejo-Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain.,Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Martin‐Vicente M, Almansa R, Martínez I, Tedim AP, Bustamante E, Tamayo L, Aldecoa C, Gómez JM, Renedo G, Berezo JÁ, Cedeño JA, Mamolar N, García Olivares P, Herrán‐Monge R, Cicuendez R, Enríquez P, Ortega A, Jorge N, Doncel C, de la Fuente A, Bustamante‐Munguira J, Muñoz‐Gómez MJ, González‐Rivera M, Puertas C, Más V, Vázquez M, Pérez‐García F, Rico‐Feijoo J, Martín S, Motos A, Fernandez‐Barat L, Eiros JM, Dominguez‐Gil M, Ferrer R, Barbé F, Trapiello W, Kelvin DJ, Bermejo‐Martin JF, Resino S, Torres A. Low anti-SARS-CoV-2 S antibody levels predict increased mortality and dissemination of viral components in the blood of critical COVID-19 patients. J Intern Med 2022; 291:232-240. [PMID: 34611927 PMCID: PMC8661581 DOI: 10.1111/joim.13386] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Anti-SARS-CoV-2 S antibodies prevent viral replication. Critically ill COVID-19 patients show viral material in plasma, associated with a dysregulated host response. If these antibodies influence survival and viral dissemination in ICU-COVID patients is unknown. PATIENTS/METHODS We studied the impact of anti-SARS-CoV-2 S antibodies levels on survival, viral RNA-load in plasma, and N-antigenaemia in 92 COVID-19 patients over ICU admission. RESULTS Frequency of N-antigenaemia was >2.5-fold higher in absence of antibodies. Antibodies correlated inversely with viral RNA-load in plasma, representing a protective factor against mortality (adjusted HR [CI 95%], p): (S IgM [AUC ≥ 60]: 0.44 [0.22; 0.88], 0.020); (S IgG [AUC ≥ 237]: 0.31 [0.16; 0.61], <0.001). Viral RNA-load in plasma and N-antigenaemia predicted increased mortality: (N1-viral load [≥2.156 copies/ml]: 2.25 [1.16; 4.36], 0.016); (N-antigenaemia: 2.45 [1.27; 4.69], 0.007). CONCLUSIONS Low anti-SARS-CoV-2 S antibody levels predict mortality in critical COVID-19. Our findings support that these antibodies contribute to prevent systemic dissemination of SARS-CoV-2.
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Affiliation(s)
- María Martin‐Vicente
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Isidoro Martínez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Elena Bustamante
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Department of AnesthesiologyFacultad de Medicina de ValladolidValladolidSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Gloria Renedo
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Jamil Antonio Cedeño
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Nuria Mamolar
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pablo García Olivares
- Intensive Care Unit. Hospital General Universitario Gregorio Marañón, Calle del Dr. EsquerdoMadridSpain
| | - Rubén Herrán‐Monge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ramón Cicuendez
- Intensive Care UnitHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - Pedro Enríquez
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Intensive Care UnitHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
| | - Juan Bustamante‐Munguira
- Department of Cardiovascular SurgeryHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - María José Muñoz‐Gómez
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | | | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Vicente Más
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Mónica Vázquez
- Unidad de Biología ViralCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMadridSpain
| | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Jesús Rico‐Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Anesthesiology and Reanimation ServiceHospital Universitario Rio Hortega, Gerencia Regional de SaludValladolidSpain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Laia Fernandez‐Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
| | - Jose María Eiros
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Marta Dominguez‐Gil
- Microbiology ServiceHospital Universitario Río Hortega, Gerencia Regional de SaludValladolidSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Intensive Care DepartmentVall d'Hebron Hospital Universitari, SODIR Research GroupVall d'Hebron Institut de RecercaBarcelonaSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaLleidaSpain
| | - Wysali Trapiello
- Clinical Analysis ServiceHospital Clínico Universitario de Valladolid, Gerencia Regional de SaludValladolidSpain
| | - David J. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeShantouGuangdongChina
| | - Jesús F. Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de Salamanca, (IBSAL), Gerencia Regional de SaludSalamancaSpain
- Hospital Universitario Río HortegaGerencia Regional de SaludValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
| | - Salvador Resino
- Unidad de Infección Viral e InmunidadCentro Nacional de MicrobiologíaInstituto de Salud Carlos IIIMajadahondaSpain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIMadridSpain
- Department of PulmonologyHospital Clinic de BarcelonaUniversidad de BarcelonaInstitut D investigacions August Pi I Sunyer (IDIBAPS)BarcelonaSpain
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Tedim AP, Lanza VF, Rodríguez CM, Freitas AR, Novais C, Peixe L, Baquero F, Coque TM. Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks. J Antimicrob Chemother 2021; 76:2757-2764. [PMID: 34450635 DOI: 10.1093/jac/dkab249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study's aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds. METHODS Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison. RESULTS All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (-2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%-49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness. CONCLUSIONS The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.
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Affiliation(s)
- Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Val F Lanza
- Unit of Bioinformatics, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain.,Centres for Biomedical Research in the Epidemiology and Public Health Network (CIBER-ESP), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
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10
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Freitas AR, Finisterra L, Tedim AP, Duarte B, Novais C, Peixe L. Linezolid- and Multidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020. Emerg Infect Dis 2021; 27:2221-2224. [PMID: 34287135 PMCID: PMC8314808 DOI: 10.3201/eid2708.204933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We describe enterococci in raw-frozen dog food commercialized in Europe as a source of genes encoding resistance to the antibiotic drug linezolid and of strains and plasmids enriched in antibiotic-resistance and virulence genes in hospitalized patients. Whole-genome sequencing was fundamental to linking isolates from dog food to human cases across Europe.
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11
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Freitas AR, Tedim AP, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Read A, Alves V, Novais C, Peixe L. Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link. J Antimicrob Chemother 2021; 75:2416-2423. [PMID: 32607549 DOI: 10.1093/jac/dkaa227] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts. METHODS poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives. RESULTS poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30-100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment. CONCLUSIONS poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Antónia Read
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Valquíria Alves
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Page AJ, Mather AE, Le-Viet T, Meader EJ, Alikhan NF, Kay GL, de Oliveira Martins L, Aydin A, Baker DJ, Trotter AJ, Rudder S, Tedim AP, Kolyva A, Stanley R, Yasir M, Diaz M, Potter W, Stuart C, Meadows L, Bell A, Gutierrez AV, Thomson NM, Adriaenssens EM, Swingler T, Gilroy RAJ, Griffith L, Sethi DK, Aggarwal D, Brown CS, Davidson RK, Kingsley RA, Bedford L, Coupland LJ, Charles IG, Elumogo N, Wain J, Prakash R, Webber MA, Smith SJL, Chand M, Dervisevic S, O’Grady J. Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microb Genom 2021; 7:000589. [PMID: 34184982 PMCID: PMC8461472 DOI: 10.1099/mgen.0.000589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/19/2021] [Indexed: 01/28/2023] Open
Abstract
The COVID-19 pandemic has spread rapidly throughout the world. In the UK, the initial peak was in April 2020; in the county of Norfolk (UK) and surrounding areas, which has a stable, low-density population, over 3200 cases were reported between March and August 2020. As part of the activities of the national COVID-19 Genomics Consortium (COG-UK) we undertook whole genome sequencing of the SARS-CoV-2 genomes present in positive clinical samples from the Norfolk region. These samples were collected by four major hospitals, multiple minor hospitals, care facilities and community organizations within Norfolk and surrounding areas. We combined clinical metadata with the sequencing data from regional SARS-CoV-2 genomes to understand the origins, genetic variation, transmission and expansion (spread) of the virus within the region and provide context nationally. Data were fed back into the national effort for pandemic management, whilst simultaneously being used to assist local outbreak analyses. Overall, 1565 positive samples (172 per 100 000 population) from 1376 cases were evaluated; for 140 cases between two and six samples were available providing longitudinal data. This represented 42.6 % of all positive samples identified by hospital testing in the region and encompassed those with clinical need, and health and care workers and their families. In total, 1035 cases had genome sequences of sufficient quality to provide phylogenetic lineages. These genomes belonged to 26 distinct global lineages, indicating that there were multiple separate introductions into the region. Furthermore, 100 genetically distinct UK lineages were detected demonstrating local evolution, at a rate of ~2 SNPs per month, and multiple co-occurring lineages as the pandemic progressed. Our analysis: identified a discrete sublineage associated with six care facilities; found no evidence of reinfection in longitudinal samples; ruled out a nosocomial outbreak; identified 16 lineages in key workers which were not in patients, indicating infection control measures were effective; and found the D614G spike protein mutation which is linked to increased transmissibility dominates the samples and rapidly confirmed relatedness of cases in an outbreak at a food processing facility. The large-scale genome sequencing of SARS-CoV-2-positive samples has provided valuable additional data for public health epidemiology in the Norfolk region, and will continue to help identify and untangle hidden transmission chains as the pandemic evolves.
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Affiliation(s)
- Andrew J. Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alison E. Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Emma J. Meader
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | | | - Gemma L. Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - David J. Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alexander J. Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Ana P. Tedim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Anastasia Kolyva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Rachael Stanley
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Maria Diaz
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Will Potter
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Claire Stuart
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Lizzie Meadows
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Andrew Bell
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | | | | | - Tracey Swingler
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Luke Griffith
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Dheeraj K. Sethi
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Dinesh Aggarwal
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Colin S. Brown
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
| | - Rose K. Davidson
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Robert A. Kingsley
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Luke Bedford
- Ipswich Hospital, Heath Road, Ipswich, IP4 5PD, UK
| | | | - Ian G. Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Reenesh Prakash
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Mark A. Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Meera Chand
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
| | - Samir Dervisevic
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Justin O’Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - The COVID-19 Genomics UK (COG-UK) Consortium
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
- Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
- Public Health England, 61 Colindale Ave., London, NW9 5EQ, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Ipswich Hospital, Heath Road, Ipswich, IP4 5PD, UK
- Public Health, County Hall, Martineau Lane, Norwich, NR1 2DH, UK
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Tedim AP, Almansa R, Domínguez‐Gil M, González‐Rivera M, Micheloud D, Ryan P, Méndez R, Blanca‐López N, Pérez‐García F, Bustamante E, Gómez JM, Doncel C, Trapiello W, Kelvin AA, Booth R, Ostadgavahi AT, Oneizat R, Puertas C, Barbé F, Ferrer R, Menéndez R, Bermejo‐Martin JF, Eiros JM, Kelvin DJ, Torres A. Comparison of real-time and droplet digital PCR to detect and quantify SARS-CoV-2 RNA in plasma. Eur J Clin Invest 2021; 51:e13501. [PMID: 33512013 PMCID: PMC7995030 DOI: 10.1111/eci.13501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/13/2021] [Accepted: 01/25/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND The presence of SARS-CoV-2 RNA in plasma has been linked to disease severity and mortality. We compared RT-qPCR to droplet digital PCR (ddPCR) to detect SARS-CoV-2 RNA in plasma from COVID-19 patients (mild, moderate, and critical disease). METHODS The presence/concentration of SARS-CoV-2 RNA in plasma was compared in three groups of COVID-19 patients (30 outpatients, 30 ward patients and 30 ICU patients) using both RT-qPCR and ddPCR. Plasma was obtained in the first 24h following admission, and RNA was extracted using eMAG. ddPCR was performed using Bio-Rad SARS-CoV-2 detection kit, and RT-qPCR was performed using GeneFinder™ COVID-19 Plus RealAmp Kit. Statistical analysis was performed using Statistical Package for the Social Science. RESULTS SARS-CoV-2 RNA was detected, using ddPCR and RT-qPCR, in 91% and 87% of ICU patients, 27% and 23% of ward patients and 3% and 3% of outpatients. The concordance of the results obtained by both methods was excellent (Cohen's kappa index = 0.953). RT-qPCR was able to detect 34/36 (94.4%) patients positive for viral RNA in plasma by ddPCR. Viral RNA load was higher in ICU patients compared with the other groups (P < .001), by both ddPCR and RT-qPCR. AUC analysis revealed Ct values (RT-qPCR) and viral RNA load values (ddPCR) can similarly differentiate between patients admitted to wards and to the ICU (AUC of 0.90 and 0.89, respectively). CONCLUSION Both methods yielded similar prevalence of RNAemia between groups, with ICU patients showing the highest (>85%). RT-qPCR was as useful as ddPCR to detect and quantify SARS-CoV-2 RNAemia in plasma.
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Affiliation(s)
- Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | | | | | - Dariela Micheloud
- Emergency DepartmentHospital General Universitario Gregorio MarañónMadridSpain
| | - Pablo Ryan
- Hospital Universitario Infanta LeonorMadridSpain
| | - Raúl Méndez
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | | | - Felipe Pérez‐García
- Servicio de Microbiología ClínicaHospital Universitario Príncipe de AsturiasMadridSpain
| | - Elena Bustamante
- Intensive Care UnitHospital Clínico Universitario de Valladolid. Av. Ramón y CajalValladolidSpain
| | - José Manuel Gómez
- Intensive Care Unit. Hospital General Universitario Gregorio MarañónMadridSpain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - Wysali Trapiello
- Clinical Analysis Service. HospitalClínico Universitario de ValladolidAv. Ramón y CajalValladolidSpain
| | - Alyson A. Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ryan Booth
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Ruth Oneizat
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - Carolina Puertas
- Department of Laboratory MedicineHospital General Universitario Gregorio MarañónMadridSpain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Respiratory DepartmentInstitut Ricerca Biomedica de LleidaAv. Alcalde Rovira RoureLleidaSpain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Intensive Care DepartmentSODIR Research GroupVall d’Hebron Hospital UniversitariVall d’Hebron Institut de RecercaBarcelonaSpain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Pulmonology ServiceHospital Universitario y Politécnico de La FeAvinguda de Fernando Abril MartorellSpain
| | - Jesús F Bermejo‐Martin
- Group for Biomedical Research in Sepsis (BioSepsis)Instituto de Investigación Biomédica de SalamancaSalamancaSpain
- Hospital Universitario Río HortegaValladolidSpain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
| | - José María Eiros
- Microbiology ServiceHospital Universitario Rio HortegaValladolidSpain
| | - David J Kelvin
- Department of Microbiology and ImmunologyFaculty of MedicineCanadian Center for Vaccinology CCfVDalhousie UniversityHalifaxNova ScotiaCanada
- Laboratory of ImmunityShantou University Medical CollegeJinping, ShantouChina
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES)Instituto de Salud Carlos IIIAv. de Monforte de LemosMadridSpain
- Department of PulmonologyInstitut D investigacions August Pi I Sunyer (IDIBAPS)Hospital Clinic de BarcelonaUniversidad de BarcelonaBarcelonaSpain
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Almansa R, Tedim AP, de la Fuente A, Eiros JM, Kelvin DJ, Torres A, Bermejo-Martin JF. Combining immunomodulators and antivirals for COVID-19 - Authors' reply. Lancet Microbe 2021; 2:e234. [PMID: 34100005 PMCID: PMC8172165 DOI: 10.1016/s2666-5247(21)00115-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Raquel Almansa
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - Jose María Eiros
- Microbiology Service, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
- Research Unit, Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Jinping, Shantou, Guangdong, China
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Universidad de Barcelona, Institut D investigacions August Pi I Sunyer, Barcelona, Spain
| | - Jesus F Bermejo-Martin
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Paseo de San Vicente, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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Bermejo-Martin JF, Almansa R, Tedim AP, de la Fuente A, Eiros JM, Torres A, Kelvin DJ. Mounting evidence of impaired viral control in severe COVID-19. Lancet Microbe 2021; 2:e228-e229. [PMID: 33880456 PMCID: PMC8049594 DOI: 10.1016/s2666-5247(21)00084-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Jesus F Bermejo-Martin
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis, Instituto de Investigación Biomédica de Salamanca, Gerencia Regional de Salud, Salamanca 37007, Spain
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Jose María Eiros
- Hospital Universitario Río Hortega, Gerencia Regional de Salud, Valladolid 47012, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid 28029, Spain
- Department of Pulmonology, Institut D investigacions August Pi I Sunyer, Hospital Clinic de Barcelona, Universidad de Barcelona, Barcelona, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology, Dalhousie University, Halifax, NS, Canada
- Laboratory of Immunity, Shantou University Medical College, Guangdong, China
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16
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Elghaieb H, Tedim AP, Abbassi MS, Novais C, Duarte B, Hassen A, Peixe L, Freitas AR. From farm to fork: identical clones and Tn6674-like elements in linezolid-resistant Enterococcus faecalis from food-producing animals and retail meat. J Antimicrob Chemother 2021; 75:30-35. [PMID: 31605129 DOI: 10.1093/jac/dkz419] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Increasing numbers of linezolid-resistant Enterococcus carrying optrA are being reported across different niches worldwide. We aimed to characterize the first optrA-carrying Enterococcus faecalis obtained from food-producing animals and retail meat samples in Tunisia. METHODS Seven optrA-carrying E. faecalis obtained from chicken faeces (n=3, August 2017) and retail chicken meat (n=4, August 2017) in Tunisia were analysed. Antimicrobial susceptibility was determined by disc diffusion, broth microdilution and Etest against 13 antibiotics, linezolid and tedizolid, respectively (EUCAST/CLSI). optrA stability (∼600 bacterial generations), transfer (filter mating) and location (S1-PFGE/hybridization) were characterized. WGS (Illumina-HiSeq) was done for four representatives that were analysed through in silico and genomic mapping tools. RESULTS Four MDR clones carrying different virulence genes were identified in chicken faeces (ST476) and retail meat (the same ST476 clone plus ST21 and ST859) samples. MICs of linezolid and tedizolid were stably maintained at 8 and 1-2 mg/L, respectively. optrA was located in the same transferable chromosomal Tn6674-like element in ST476 and ST21 clones, similar to isolates from pigs in Malaysia and humans in China. ST859 carried a non-conjugative plasmid of ∼40 kb with an impB-fexA-optrA segment, similar to plasmids from pigs and humans in China. CONCLUSIONS The same chromosomal and transferable Tn6674-like element was identified in different E. faecalis clones from humans and animals. The finding of retail meat contaminated with the same linezolid-resistant E. faecalis strain obtained from a food-producing animal highlights the potential role of the food chain in the worrisome dissemination of optrA that can be stably maintained without selective pressure over generations.
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Affiliation(s)
- Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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17
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Baker DJ, Aydin A, Le-Viet T, Kay GL, Rudder S, de Oliveira Martins L, Tedim AP, Kolyva A, Diaz M, Alikhan NF, Meadows L, Bell A, Gutierrez AV, Trotter AJ, Thomson NM, Gilroy R, Griffith L, Adriaenssens EM, Stanley R, Charles IG, Elumogo N, Wain J, Prakash R, Meader E, Mather AE, Webber MA, Dervisevic S, Page AJ, O'Grady J. CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes. Genome Med 2021; 13:21. [PMID: 33563320 PMCID: PMC7871948 DOI: 10.1186/s13073-021-00839-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 01/26/2021] [Indexed: 01/15/2023] Open
Abstract
We present CoronaHiT, a platform and throughput flexible method for sequencing SARS-CoV-2 genomes (≤ 96 on MinION or > 96 on Illumina NextSeq) depending on changing requirements experienced during the pandemic. CoronaHiT uses transposase-based library preparation of ARTIC PCR products. Method performance was demonstrated by sequencing 2 plates containing 95 and 59 SARS-CoV-2 genomes on nanopore and Illumina platforms and comparing to the ARTIC LoCost nanopore method. Of the 154 samples sequenced using all 3 methods, ≥ 90% genome coverage was obtained for 64.3% using ARTIC LoCost, 71.4% using CoronaHiT-ONT and 76.6% using CoronaHiT-Illumina, with almost identical clustering on a maximum likelihood tree. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally.
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Affiliation(s)
- Dave J Baker
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Alp Aydin
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Thanh Le-Viet
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Gemma L Kay
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Steven Rudder
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | - Ana P Tedim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Grupo de Investigación Biomédica en Sepsis - BioSepsis. Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Anastasia Kolyva
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Maria Diaz
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | - Lizzie Meadows
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Andrew Bell
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | | | - Alexander J Trotter
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Nicholas M Thomson
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Rachel Gilroy
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
| | - Luke Griffith
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Rachael Stanley
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Ngozi Elumogo
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Reenesh Prakash
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Emma Meader
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Samir Dervisevic
- Norfolk and Norwich University Hospital, Colney Lane, Norwich, NR4 7UY, UK
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK.
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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18
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Bermejo-Martin JF, González-Rivera M, Almansa R, Micheloud D, Tedim AP, Domínguez-Gil M, Resino S, Martín-Fernández M, Ryan Murua P, Pérez-García F, Tamayo L, Lopez-Izquierdo R, Bustamante E, Aldecoa C, Gómez JM, Rico-Feijoo J, Orduña A, Méndez R, Fernández Natal I, Megías G, González-Estecha M, Carriedo D, Doncel C, Jorge N, Ortega A, de la Fuente A, Del Campo F, Fernández-Ratero JA, Trapiello W, González-Jiménez P, Ruiz G, Kelvin AA, Ostadgavahi AT, Oneizat R, Ruiz LM, Miguéns I, Gargallo E, Muñoz I, Pelegrin S, Martín S, García Olivares P, Cedeño JA, Ruiz Albi T, Puertas C, Berezo JÁ, Renedo G, Herrán R, Bustamante-Munguira J, Enríquez P, Cicuendez R, Blanco J, Abadia J, Gómez Barquero J, Mamolar N, Blanca-López N, Valdivia LJ, Fernández Caso B, Mantecón MÁ, Motos A, Fernandez-Barat L, Ferrer R, Barbé F, Torres A, Menéndez R, Eiros JM, Kelvin DJ. Viral RNA load in plasma is associated with critical illness and a dysregulated host response in COVID-19. Crit Care 2020; 24:691. [PMID: 33317616 PMCID: PMC7734467 DOI: 10.1186/s13054-020-03398-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND COVID-19 can course with respiratory and extrapulmonary disease. SARS-CoV-2 RNA is detected in respiratory samples but also in blood, stool and urine. Severe COVID-19 is characterized by a dysregulated host response to this virus. We studied whether viral RNAemia or viral RNA load in plasma is associated with severe COVID-19 and also to this dysregulated response. METHODS A total of 250 patients with COVID-19 were recruited (50 outpatients, 100 hospitalized ward patients and 100 critically ill). Viral RNA detection and quantification in plasma was performed using droplet digital PCR, targeting the N1 and N2 regions of the SARS-CoV-2 nucleoprotein gene. The association between SARS-CoV-2 RNAemia and viral RNA load in plasma with severity was evaluated by multivariate logistic regression. Correlations between viral RNA load and biomarkers evidencing dysregulation of host response were evaluated by calculating the Spearman correlation coefficients. RESULTS The frequency of viral RNAemia was higher in the critically ill patients (78%) compared to ward patients (27%) and outpatients (2%) (p < 0.001). Critical patients had higher viral RNA loads in plasma than non-critically ill patients, with non-survivors showing the highest values. When outpatients and ward patients were compared, viral RNAemia did not show significant associations in the multivariate analysis. In contrast, when ward patients were compared with ICU patients, both viral RNAemia and viral RNA load in plasma were associated with critical illness (OR [CI 95%], p): RNAemia (3.92 [1.183-12.968], 0.025), viral RNA load (N1) (1.962 [1.244-3.096], 0.004); viral RNA load (N2) (2.229 [1.382-3.595], 0.001). Viral RNA load in plasma correlated with higher levels of chemokines (CXCL10, CCL2), biomarkers indicative of a systemic inflammatory response (IL-6, CRP, ferritin), activation of NK cells (IL-15), endothelial dysfunction (VCAM-1, angiopoietin-2, ICAM-1), coagulation activation (D-Dimer and INR), tissue damage (LDH, GPT), neutrophil response (neutrophils counts, myeloperoxidase, GM-CSF) and immunodepression (PD-L1, IL-10, lymphopenia and monocytopenia). CONCLUSIONS SARS-CoV-2 RNAemia and viral RNA load in plasma are associated with critical illness in COVID-19. Viral RNA load in plasma correlates with key signatures of dysregulated host responses, suggesting a major role of uncontrolled viral replication in the pathogenesis of this disease.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Milagros González-Rivera
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Dariela Micheloud
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Salvador Resino
- Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, 28222, Majadahonda, Spain
| | - Marta Martín-Fernández
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo Ryan Murua
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Carr. de Alcalá, s/n, 28805, Madrid, Spain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Raúl Lopez-Izquierdo
- Emergency Department, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Elena Bustamante
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Department of Anesthesiology, Facultad de Medicina de Valladolid, Av. Ramón y Cajal, 47005, Valladolid, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José Manuel Gómez
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jesús Rico-Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Antonio Orduña
- Microbiology Service, Hospital Clinico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Raúl Méndez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Isabel Fernández Natal
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - Gregoria Megías
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Montserrat González-Estecha
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Félix Del Campo
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | | | - Wysali Trapiello
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Paula González-Jiménez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Guadalupe Ruiz
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Alyson A Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ruth Oneizat
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Luz María Ruiz
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Iria Miguéns
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Esther Gargallo
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ioana Muñoz
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Sara Pelegrin
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo García Olivares
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jamil Antonio Cedeño
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Tomás Ruiz Albi
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Carolina Puertas
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Gloria Renedo
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Rubén Herrán
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Juan Bustamante-Munguira
- Department of Cardiovascular Surgery, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Pedro Enríquez
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ramón Cicuendez
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Jesús Blanco
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Jesica Abadia
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Julia Gómez Barquero
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Nuria Mamolar
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Natalia Blanca-López
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Luis Jorge Valdivia
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Belén Fernández Caso
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - María Ángeles Mantecón
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Laia Fernandez-Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca, Passeig de la Vall d'Hebron, 119, 08035, Barcelona, Spain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Respiratory Department, Institut Ricerca Biomedica de Lleida, Av. Alcalde Rovira Roure, 80, 25198, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - José María Eiros
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China.
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Bermejo-Martin JF, González-Rivera M, Almansa R, Micheloud D, Tedim AP, Domínguez-Gil M, Resino S, Martín-Fernández M, Ryan Murua P, Pérez-García F, Tamayo L, Lopez-Izquierdo R, Bustamante E, Aldecoa C, Gómez JM, Rico-Feijoo J, Orduña A, Méndez R, Fernández Natal I, Megías G, González-Estecha M, Carriedo D, Doncel C, Jorge N, Ortega A, de la Fuente A, Del Campo F, Fernández-Ratero JA, Trapiello W, González-Jiménez P, Ruiz G, Kelvin AA, Ostadgavahi AT, Oneizat R, Ruiz LM, Miguéns I, Gargallo E, Muñoz I, Pelegrin S, Martín S, García Olivares P, Cedeño JA, Ruiz Albi T, Puertas C, Berezo JÁ, Renedo G, Herrán R, Bustamante-Munguira J, Enríquez P, Cicuendez R, Blanco J, Abadia J, Gómez Barquero J, Mamolar N, Blanca-López N, Valdivia LJ, Fernández Caso B, Mantecón MÁ, Motos A, Fernandez-Barat L, Ferrer R, Barbé F, Torres A, Menéndez R, Eiros JM, Kelvin DJ. Viral RNA load in plasma is associated with critical illness and a dysregulated host response in COVID-19. Crit Care 2020; 24:691. [PMID: 33317616 DOI: 10.1186/s13054‐020‐03398‐0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/18/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND COVID-19 can course with respiratory and extrapulmonary disease. SARS-CoV-2 RNA is detected in respiratory samples but also in blood, stool and urine. Severe COVID-19 is characterized by a dysregulated host response to this virus. We studied whether viral RNAemia or viral RNA load in plasma is associated with severe COVID-19 and also to this dysregulated response. METHODS A total of 250 patients with COVID-19 were recruited (50 outpatients, 100 hospitalized ward patients and 100 critically ill). Viral RNA detection and quantification in plasma was performed using droplet digital PCR, targeting the N1 and N2 regions of the SARS-CoV-2 nucleoprotein gene. The association between SARS-CoV-2 RNAemia and viral RNA load in plasma with severity was evaluated by multivariate logistic regression. Correlations between viral RNA load and biomarkers evidencing dysregulation of host response were evaluated by calculating the Spearman correlation coefficients. RESULTS The frequency of viral RNAemia was higher in the critically ill patients (78%) compared to ward patients (27%) and outpatients (2%) (p < 0.001). Critical patients had higher viral RNA loads in plasma than non-critically ill patients, with non-survivors showing the highest values. When outpatients and ward patients were compared, viral RNAemia did not show significant associations in the multivariate analysis. In contrast, when ward patients were compared with ICU patients, both viral RNAemia and viral RNA load in plasma were associated with critical illness (OR [CI 95%], p): RNAemia (3.92 [1.183-12.968], 0.025), viral RNA load (N1) (1.962 [1.244-3.096], 0.004); viral RNA load (N2) (2.229 [1.382-3.595], 0.001). Viral RNA load in plasma correlated with higher levels of chemokines (CXCL10, CCL2), biomarkers indicative of a systemic inflammatory response (IL-6, CRP, ferritin), activation of NK cells (IL-15), endothelial dysfunction (VCAM-1, angiopoietin-2, ICAM-1), coagulation activation (D-Dimer and INR), tissue damage (LDH, GPT), neutrophil response (neutrophils counts, myeloperoxidase, GM-CSF) and immunodepression (PD-L1, IL-10, lymphopenia and monocytopenia). CONCLUSIONS SARS-CoV-2 RNAemia and viral RNA load in plasma are associated with critical illness in COVID-19. Viral RNA load in plasma correlates with key signatures of dysregulated host responses, suggesting a major role of uncontrolled viral replication in the pathogenesis of this disease.
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Affiliation(s)
- Jesús F Bermejo-Martin
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Milagros González-Rivera
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Raquel Almansa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Dariela Micheloud
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Marta Domínguez-Gil
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Salvador Resino
- Viral Infection and Immunity Unit, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, 28222, Majadahonda, Spain
| | - Marta Martín-Fernández
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo Ryan Murua
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Felipe Pérez-García
- Servicio de Microbiología Clínica, Hospital Universitario Príncipe de Asturias, Carr. de Alcalá, s/n, 28805, Madrid, Spain
| | - Luis Tamayo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Raúl Lopez-Izquierdo
- Emergency Department, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Elena Bustamante
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - César Aldecoa
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Department of Anesthesiology, Facultad de Medicina de Valladolid, Av. Ramón y Cajal, 47005, Valladolid, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - José Manuel Gómez
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jesús Rico-Feijoo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Antonio Orduña
- Microbiology Service, Hospital Clinico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Raúl Méndez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Isabel Fernández Natal
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - Gregoria Megías
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Montserrat González-Estecha
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Plaza de Ramón y Cajal, s/n, 28040, Madrid, Spain
| | - Demetrio Carriedo
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Cristina Doncel
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Noelia Jorge
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Alicia Ortega
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Amanda de la Fuente
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
| | - Félix Del Campo
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | | | - Wysali Trapiello
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Paula González-Jiménez
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Guadalupe Ruiz
- Clinical Analysis Service. Hospital, Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Alyson A Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ali Toloue Ostadgavahi
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China
| | - Ruth Oneizat
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Luz María Ruiz
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Iria Miguéns
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Esther Gargallo
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Ioana Muñoz
- Emergency Department, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Sara Pelegrin
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Silvia Martín
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Pablo García Olivares
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jamil Antonio Cedeño
- Intensive Care Unit, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Tomás Ruiz Albi
- Pneumology Service, Hospital Universitario Río Hortega/Biomedical Engineering Group, Universidad de Valladolid, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Carolina Puertas
- Department of Laboratory Medicine, Hospital General Universitario Gregorio Marañón, Calle del Dr. Esquerdo, 46, 28007, Madrid, Spain
| | - Jose Ángel Berezo
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Gloria Renedo
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Rubén Herrán
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, (IBSAL), Paseo de San Vicente, 58-182, 37007, Salamanca, Spain
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Juan Bustamante-Munguira
- Department of Cardiovascular Surgery, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Pedro Enríquez
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Ramón Cicuendez
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Jesús Blanco
- Intensive Care Unit, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Jesica Abadia
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Julia Gómez Barquero
- Infectious Diseases Clinic, Internal Medicine Department, Hospital Universitario Río Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - Nuria Mamolar
- Intensive Care Unit, Hospital Clínico Universitario de Valladolid, Av. Ramón y Cajal, 47003, Valladolid, Spain
| | - Natalia Blanca-López
- Hospital Universitario Infanta Leonor, Av. Gran Vía del Este, 80, 28031, Madrid, Spain
| | - Luis Jorge Valdivia
- Intensive Care Unit, Complejo Asistencial Universitario de León, Calle Altos de nava, s/n, 24001, León, Spain
| | - Belén Fernández Caso
- Clinical Microbiology Department, Complejo Asistencial Universitario de León, Calle Altos de Nava, s/n, 24001, León, Spain
| | - María Ángeles Mantecón
- Microbiology Service, Hospital Universitario de Burgos, Av. Islas Baleares, 3, 09006, Burgos, Spain
| | - Anna Motos
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Laia Fernandez-Barat
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Ricard Ferrer
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Intensive Care Department, Vall d'Hebron Hospital Universitari, SODIR Research Group, Vall d'Hebron Institut de Recerca, Passeig de la Vall d'Hebron, 119, 08035, Barcelona, Spain
| | - Ferrán Barbé
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Respiratory Department, Institut Ricerca Biomedica de Lleida, Av. Alcalde Rovira Roure, 80, 25198, Lleida, Spain
| | - Antoni Torres
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Department of Pulmonology, Hospital Clinic de Barcelona, Institut D Investigacions August Pi I Sunyer (IDIBAPS), Universidad de Barcelona, Carrer del Rosselló, 149, 08036, Barcelona, Spain
| | - Rosario Menéndez
- Centro de Investigación Biomédica en Red en Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Av. de Monforte de Lemos, 3-5, 28029, Madrid, Spain
- Pulmonology Service, Hospital Universitario y Politécnico de La Fe, Avinguda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - José María Eiros
- Microbiology Service, Hospital Universitario Rio Hortega, Calle Dulzaina, 2, 47012, Valladolid, Spain
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Canadian Center for Vaccinology CCfV, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
- Laboratory of Immunity, Shantou University Medical College, 22 Xinling Rd., Jinping, Shantou, Guangdong, China.
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20
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Freitas AR, Tedim AP, Novais C, Lanza VF, Peixe L. Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes. Microb Genom 2020; 6. [PMID: 32149599 PMCID: PMC7371108 DOI: 10.1099/mgen.0.000350] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Ana P Tedim
- Grupo de Investigación Biomédica en Sepsis - BioSepsis. Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Val F Lanza
- Departamento de Bioinformática. Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
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21
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Schell CM, Tedim AP, Rodríguez-Baños M, Sparo MD, Lissarrague S, Basualdo JA, Coque TM. Detection of β-Lactamase-Producing Enterococcus faecalis and Vancomycin-Resistant Enterococcus faecium Isolates in Human Invasive Infections in the Public Hospital of Tandil, Argentina. Pathogens 2020; 9:pathogens9020142. [PMID: 32093230 PMCID: PMC7168638 DOI: 10.3390/pathogens9020142] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/27/2022] Open
Abstract
The study’s aim was to analyze the population structure of enterococci causing human invasive infections in a medium-sized Argentinian Hospital coincidental with a 5 year-period of increased recovery of antibiotic resistant enterococci (2010–2014). Species identification (biochemical testing/MALDI-TOF-MS), antimicrobial susceptibility (disk-diffusion) and clonal relatedness (PFGE/MLST/BAPS) were determined according to standard guidelines. β-lactamase production was determined by a nitrocefin test and confirmed by PCR/sequencing. The isolates were identified as Enterococcus faecalis and Enterococcus faecium at a 2:1 ratio. Most of the E. faecalis isolates, grouped in 25 PFGE-types (ST9/ST179/ST236/ST281/ST388/ST604/ST720), were resistant to high-levels (HLR) of gentamicin/streptomycin. A ST9 clone (bla+/HLR-gentamicin) was detected in patients of different wards during 2014. E. faecium isolates were grouped in 10 PFGE-types (ST25/ST18/ST19/ST52/ST792), with a low rate of ampicillin resistance. Five vancomycin-resistant E. faecium, three vanA (ST792/ST25) and two vanB (ST25) were detected. The ST25 clone carried either vanA or vanB. The recovery of a bla+-ST9-E. faecalis clone similar to that described in the late 1980s in Argentina suggests the possibility of a local hidden reservoir. These results reflect the relevance of local epidemiology in understanding the population structure of enterococci as well as the emergence and spread of antimicrobial resistance in predominant enterococcal clonal lineages.
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Affiliation(s)
- Celia M. Schell
- Centro Universitario de Estudios Microbiológicos y Parasitológicos (CUDEMyP), Centro Universidad Nacional de La Plata asociado a Comisión de Investigaciones Científicas (CIC), Facultad de Ciencias Médicas, Universidad Nacional de La Plata. Av. 60 y 120 s/n, 3er piso, CP 1900 La Plata, Buenos Aires, Argentina or (M.D.S.); (J.A.B.)
| | - Ana P. Tedim
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar, km. 9.1, Planta -1IZQ, 28034 Madrid, Spain or (A.P.T.); (M.R.-B.)
- Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, 28029 Madrid, Spain
| | - Mercedes Rodríguez-Baños
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar, km. 9.1, Planta -1IZQ, 28034 Madrid, Spain or (A.P.T.); (M.R.-B.)
| | - Mónica D. Sparo
- Centro Universitario de Estudios Microbiológicos y Parasitológicos (CUDEMyP), Centro Universidad Nacional de La Plata asociado a Comisión de Investigaciones Científicas (CIC), Facultad de Ciencias Médicas, Universidad Nacional de La Plata. Av. 60 y 120 s/n, 3er piso, CP 1900 La Plata, Buenos Aires, Argentina or (M.D.S.); (J.A.B.)
- Laboratorio de Microbiología Clínica, Hospital Municipal Ramón Santamarina, Gral. Paz 1406, B7000 Tandil, Buenos Aires, Argentina
| | - Sabina Lissarrague
- Laboratorio de Microbiología Clínica, Hospital Municipal Ramón Santamarina, Gral. Paz 1406, B7000 Tandil, Buenos Aires, Argentina
| | - Juan A. Basualdo
- Centro Universitario de Estudios Microbiológicos y Parasitológicos (CUDEMyP), Centro Universidad Nacional de La Plata asociado a Comisión de Investigaciones Científicas (CIC), Facultad de Ciencias Médicas, Universidad Nacional de La Plata. Av. 60 y 120 s/n, 3er piso, CP 1900 La Plata, Buenos Aires, Argentina or (M.D.S.); (J.A.B.)
| | - Teresa M. Coque
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar, km. 9.1, Planta -1IZQ, 28034 Madrid, Spain or (A.P.T.); (M.R.-B.)
- Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Av. Monforte de Lemos, 3-5. Pabellón 11. Planta 0, 28029 Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), 28006 Madrid, Spain
- Correspondence: or ; Tel.: +34-913-368-330
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22
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León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019; 21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.
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Affiliation(s)
- Ricardo León-Sampedro
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain
| | - Mercedes Rodriguez-Baños
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - María José Pozuelo
- Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain
| | - Carlos Francés-Cuesta
- Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Fernando González Candelas
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
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23
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Barragán-Prada H, Ruiz-Hueso P, Tedim AP, González-Candelas F, Galán JC, Cantón R, Morosini MI. Emergence and dissemination of colistin-resistant Klebsiella pneumoniae isolates expressing OXA-48 plus CTX-M-15 in patients not previously treated with colistin in a Spanish university hospital. Diagn Microbiol Infect Dis 2018; 93:147-153. [PMID: 30266401 DOI: 10.1016/j.diagmicrobio.2018.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/28/2018] [Accepted: 08/31/2018] [Indexed: 10/28/2022]
Abstract
Dissemination of multidrug-resistant Klebsiella pneumoniae in the hospital environment represents a primary target of resistance containment and stewardship programs. At present, polymyxins, mostly in combination, exemplify a last-resort alternative. Colistin-resistant K. pneumoniae isolates harboring OXA-48 plus CTX-M-15 (n = 21) with the simultaneous colistin-susceptible counterparts (n = 9) were recovered from 14 hospitalized patients (January 2014-January 2015) admitted in different wards. In most cases, patients had not previously received colistin. Genetic relatedness experiments demonstrated that 93% (28/30) of isolates belonged to the ST11 high-risk clone. Heteroresistance and the fitness cost of colistin resistance were addressed in susceptible and resistant isolates as well as in in vitro-obtained stable mutants, and results appeared to be strain dependent. Whole genome sequencing demonstrated molecular changes in pmrA, pmrB, and mgrB genes. Plasmid-mediated colistin resistance genes were not found. Colistin resistance in multidrug-resistant K. pneumoniae isolates should be continuously monitored to detect its potential emergence, even in patients not previously exposed to colistin.
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Affiliation(s)
- Hugo Barragán-Prada
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Paula Ruiz-Hueso
- Unidad Mixta "Infección y Salud Pública" FISABIO-Instituto de Biología Integrativa de Sistemas (I2SysBio), Universitat de València, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana P Tedim
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando González-Candelas
- Unidad Mixta "Infección y Salud Pública" FISABIO-Instituto de Biología Integrativa de Sistemas (I2SysBio), Universitat de València, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; CIBER en Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos los III, Madrid, Spain.
| | - María-Isabel Morosini
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Instituto de Salud Carlos los III, Madrid, Spain
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24
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Freitas AR, Tedim AP, Novais C, Coque TM, Peixe L. Distribution of putative virulence markers in Enterococcus faecium: towards a safety profile review. J Antimicrob Chemother 2017; 73:306-319. [DOI: 10.1093/jac/dkx387] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/22/2017] [Indexed: 12/14/2022] Open
Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana P Tedim
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Teresa M Coque
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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25
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Novais C, Tedim AP, Lanza VF, Freitas AR, Silveira E, Escada R, Roberts AP, Al-Haroni M, Baquero F, Peixe L, Coque TM. Co-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer. Front Microbiol 2016; 7:1581. [PMID: 27766095 PMCID: PMC5053079 DOI: 10.3389/fmicb.2016.01581] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/21/2016] [Indexed: 12/17/2022] Open
Abstract
Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180–280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E. faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.
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Affiliation(s)
- Carla Novais
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade Farmácia, Universidade do Porto Porto, Portugal
| | - Ana P Tedim
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaBarcelona, Spain
| | - Val F Lanza
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaBarcelona, Spain
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade Farmácia, Universidade do PortoPorto, Portugal; Servicio de Microbiología, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
| | - Eduarda Silveira
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade Farmácia, Universidade do Porto Porto, Portugal
| | - Ricardo Escada
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade Farmácia, Universidade do PortoPorto, Portugal; Faculdade de Ciências da Saúde, Universidade Fernando PessoaPorto, Portugal
| | - Adam P Roberts
- Division of Microbial Diseases, UCL Eastman Dental Institute, University College London London, UK
| | - Mohammed Al-Haroni
- Division of Microbial Diseases, UCL Eastman Dental Institute, University College London London, UK
| | - Fernando Baquero
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaBarcelona, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC)Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Departamento de Ciências Biológicas, Faculdade Farmácia, Universidade do Porto Porto, Portugal
| | - Teresa M Coque
- Servicio de Microbiología, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud PúblicaBarcelona, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC)Madrid, Spain
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26
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Tedim AP, Ruíz-Garbajosa P, Rodríguez MC, Rodríguez-Baños M, Lanza VF, Derdoy L, Cárdenas Zurita G, Loza E, Cantón R, Baquero F, Coque TM. Long-term clonal dynamics of Enterococcus faecium strains causing bloodstream infections (1995-2015) in Spain. J Antimicrob Chemother 2016; 72:48-55. [PMID: 27655856 DOI: 10.1093/jac/dkw366] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 07/26/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES To investigate the population structure of Enterococcus faecium causing bloodstream infections (BSIs) in a tertiary Spanish hospital with low glycopeptide resistance, and to enhance our knowledge of the dynamics of emergence and spread of high-risk clonal complexes. METHODS All available E. faecium causing BSIs (n = 413) in our hospital (January 1995-May 2015) were analysed for antibiotic susceptibility (CLSI), putative virulence traits (PCR, esp, hylEfm) and clonal relationship (SmaI-PFGE, MLST evaluated by goeBURST and BAPS). RESULTS The increased incidence of BSIs caused by enterococci [2.3‰ of attended patients (inpatients and outpatients) in 1996 to 3.0‰ in 2014] significantly correlated with the increase in BSIs caused by E. faecium (0.33‰ of attended patients in 1996 to 1.3‰ in 2014). The BSIs Enterococcus faecalis:E. faecium ratio changed from 5:1 in 1996 to 1:1 in 2014. During the last decade an increase in E. faecium BSIs episodes in cancer patients (10.9% in 1995-2005 and 37.1% in 2006-15) was detected. Ampicillin-susceptible E. faecium (ASEfm; different STs/BAPS) and ampicillin-resistant E. faecium (AREfm; ST18/ST17-BAPS 3.3a) isolates were recovered throughout the study. Successive waves of BAPS 2.1a-AREfm (ST117, ST203 and ST80) partially replaced ASEfm and ST18-AREfm since 2006. CONCLUSIONS Different AREfm clones (belonging to BAPS 2.1a and BAPS 3.3a) consistently isolated during the last decade from BSIs might be explained by a continuous and dense colonization (favouring both invasion and cross-transmission) of hospitalized patients. High-density colonization by these clones is probably enhanced in elderly patients by heavy and prolonged antibiotic exposure, particularly in oncological patients.
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Affiliation(s)
- Ana P Tedim
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
| | - Patricia Ruíz-Garbajosa
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Seville, Spain
| | - Maria Concepción Rodríguez
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Mercedes Rodríguez-Baños
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
| | - Laura Derdoy
- Microbiology Department, Laboratory Division, Hospital General de Agudos Ramos Mejía, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gonzalo Cárdenas Zurita
- Clinical Laboratory, Microbiology and Infectious Diseases Department, Clinica San Francisco, Quito, Ecuador
| | - Elena Loza
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Rafael Cantón
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Seville, Spain
| | - Fernando Baquero
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
| | - Teresa M Coque
- Microbiology Department, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain .,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain.,Centros de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Barcelona, Spain
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27
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Freitas AR, Tedim AP, Francia MV, Jensen LB, Novais C, Peixe L, Sánchez-Valenzuela A, Sundsfjord A, Hegstad K, Werner G, Sadowy E, Hammerum AM, Garcia-Migura L, Willems RJ, Baquero F, Coque TM. Multilevel population genetic analysis ofvanAandvanB Enterococcus faeciumcausing nosocomial outbreaks in 27 countries (1986–2012). J Antimicrob Chemother 2016; 71:3351-3366. [DOI: 10.1093/jac/dkw312] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/11/2016] [Accepted: 07/05/2016] [Indexed: 01/17/2023] Open
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28
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Sánchez-Díaz AM, Cuartero C, Rodríguez JD, Lozano S, Alonso JM, Rodríguez-Domínguez M, Tedim AP, Del Campo R, López J, Cantón R, Ruiz-Garbajosa P. The rise of ampicillin-resistant Enterococcus faecium high-risk clones as a frequent intestinal colonizer in oncohaematological neutropenic patients on levofloxacin prophylaxis: a risk for bacteraemia? Clin Microbiol Infect 2015; 22:59.e1-59.e8. [PMID: 26321668 DOI: 10.1016/j.cmi.2015.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/08/2015] [Accepted: 08/19/2015] [Indexed: 01/02/2023]
Abstract
Levofloxacin extended prophylaxis (LEP), recommended in oncohaematological neutropenic patients to reduce infections, might select resistant bacteria in the intestine acting as a source of endogenous infection. In a prospective observational study we evaluated intestinal emergence and persistence of ampicillin-resistant Enterococcus faecium (AREfm), a marker of hospital adapted high-risk clones. AREfm was recovered from the faeces of 52 patients with prolonged neutropenia after chemotherapy, at admission (Basal), during LEP, and twice weekly until discharge (Pos-LEP). Antibiotic susceptibility, virulence traits and population structure (pulsed-field gel electrophoresis and multilocus sequence typing) were determined and compared with bacteraemic isolates. Gut enterococcal population was monitored using a quantitative PCR quantification approach. AREfm colonized 61.4% of patients (194/482 faecal samples). Sequential AREfm acquisition (25% Basal, 36.5% LEP, 50% Pos-LEP) and high persistent colonization rates (76.9-89.5%) associated with a decrease in clonal diversity were demonstrated. Isolates were clustered into 24 PFGE-patterns within 13 sequence types, 95.8% of them belonging to hospital-associated Bayesian analysis of population structure subgroups 2.1a and 3.3a. Levofloxacin resistance and high-level streptomycin resistance were a common trait of these high-risk clones. AREfm-ST117, the most persistent clone, was dominant (60.0% isolates, 32.6% patients). It presented esp gene and caused 18.2% of all bacteraemia episodes in 21% of patients previously colonized by this clone. In AREfm-colonized patients, intestinal enrichment in the E. faecium population with a decline in total bacterial load was observed. AREfm intestinal colonization increases during hospital stay and coincides with enterococci population enrichment in the gut. Dominance and intestinal persistence of the ST117 clone might increase the risk of bacteraemia.
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Affiliation(s)
- A M Sánchez-Díaz
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - C Cuartero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - J D Rodríguez
- Servicio de Hematología, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - S Lozano
- Servicio de Hematología, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - J M Alonso
- Servicio de Hematología, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - M Rodríguez-Domínguez
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - A P Tedim
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - R Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - J López
- Servicio de Hematología, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - R Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain.
| | - P Ruiz-Garbajosa
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain; Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
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29
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Freitas AR, Novais C, Tedim AP, Francia MV, Baquero F, Peixe L, Coque TM. Microevolutionary events involving narrow host plasmids influences local fixation of vancomycin-resistance in Enterococcus populations. PLoS One 2013; 8:e60589. [PMID: 23555993 PMCID: PMC3612099 DOI: 10.1371/journal.pone.0060589] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 02/28/2013] [Indexed: 12/28/2022] Open
Abstract
Vancomycin-resistance in enterococci (VRE) is associated with isolates within ST18, ST17, ST78 Enterococcus faecium (Efm) and ST6 Enterococcus faecalis (Efs) human adapted lineages. Despite of its global spread, vancomycin resistance rates in enterococcal populations greatly vary temporally and geographically. Portugal is one of the European countries where Tn1546 (vanA) is consistently found in a variety of environments. A comprehensive multi-hierarchical analysis of VRE isolates (75 Efm and 29 Efs) from Portuguese hospitals and aquatic surroundings (1996–2008) was performed to clarify the local dynamics of VRE. Clonal relatedness was established by PFGE and MLST while plasmid characterization comprised the analysis of known relaxases, rep initiator proteins and toxin-antitoxin systems (TA) by PCR-based typing schemes, RFLP comparison, hybridization and sequencing. Tn1546 variants were characterized by PCR overlapping/sequencing. Intra- and inter-hospital dissemination of Efm ST18, ST132 and ST280 and Efs ST6 clones, carrying rolling-circle (pEFNP1/pRI1) and theta-replicating (pCIZ2-like, Inc18, pHTβ-like, two pRUM-variants, pLG1-like, and pheromone-responsive) plasmids was documented. Tn1546 variants, mostly containing ISEf1 or IS1216, were located on plasmids (30–150 kb) with a high degree of mosaicism and heterogeneous RFLP patterns that seem to have resulted from the interplay between broad host Inc18 plasmids (pIP501, pRE25, pEF1), and narrow host RepA_N plasmids (pRUM, pAD1-like). TAs of Inc18 (ω-ε-ζ) and pRUM (Axe-Txe) plasmids were infrequently detected. Some plasmid chimeras were persistently recovered over years from different clonal lineages. This work represents the first multi-hierarchical analysis of VRE, revealing a frequent recombinatorial diversification of a limited number of interacting clonal backgrounds, plasmids and transposons at local scale. These interactions provide a continuous process of parapatric clonalization driving a full exploration of the local adaptive landscape, which might assure long-term maintenance of resistant clones and eventually fixation of Tn1546 in particular geographic areas.
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Affiliation(s)
- Ana R. Freitas
- REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Carla Novais
- REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana P. Tedim
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - María Victoria Francia
- Servicio de Microbiologia, Hospital Universitario Marqués de Valdecilla e Instituto de Formación e Investigación Marqués de Valdecilla (IFIMAV), Santander, Spain
| | - Fernando Baquero
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luísa Peixe
- REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Teresa M. Coque
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- CIBER en Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- * E-mail:
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30
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Abstract
Antibiotics have natural functions, mostly involving cell-to-cell signaling networks. The anthropogenic production of antibiotics, and its release in the microbiosphere results in a disturbance of these networks, antibiotic resistance tending to preserve its integrity. The cost of such adaptation is the emergence and dissemination of antibiotic resistance genes, and of all genetic and cellular vehicles in which these genes are located. Selection of the combinations of the different evolutionary units (genes, integrons, transposons, plasmids, cells, communities and microbiomes, hosts) is highly asymmetrical. Each unit of selection is a self-interested entity, exploiting the higher hierarchical unit for its own benefit, but in doing so the higher hierarchical unit might acquire critical traits for its spread because of the exploitation of the lower hierarchical unit. This interactive trade-off shapes the population biology of antibiotic resistance, a composed-complex array of the independent "population biologies." Antibiotics modify the abundance and the interactive field of each of these units. Antibiotics increase the number and evolvability of "clinical" antibiotic resistance genes, but probably also many other genes with different primary functions but with a resistance phenotype present in the environmental resistome. Antibiotics influence the abundance, modularity, and spread of integrons, transposons, and plasmids, mostly acting on structures present before the antibiotic era. Antibiotics enrich particular bacterial lineages and clones and contribute to local clonalization processes. Antibiotics amplify particular genetic exchange communities sharing antibiotic resistance genes and platforms within microbiomes. In particular human or animal hosts, the microbiomic composition might facilitate the interactions between evolutionary units involved in antibiotic resistance. The understanding of antibiotic resistance implies expanding our knowledge on multi-level population biology of bacteria.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
| | - Ana P. Tedim
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación SanitariaMadrid, Spain
- Centros de Investigación Biomédica en Red de Epidemiología y Salud PúblicaMadrid, Spain
- Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones CientíficasMadrid, Spain
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