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Shekarkar Azgomi M, Badami GD, Lo Pizzo M, Tamburini B, Dieli C, La Manna MP, Dieli F, Caccamo N. Integrated Analysis of Single-Cell and Bulk RNA Sequencing Data Reveals Memory-like NK Cell Subset Associated with Mycobacterium tuberculosis Latency. Cells 2024; 13:293. [PMID: 38391906 PMCID: PMC10886487 DOI: 10.3390/cells13040293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/24/2024] Open
Abstract
Natural killer (NK) cells are innate-like lymphocytes that belong to the family of type-1 innate lymphoid cells and rapidly respond to virus-infected and tumor cells. In this study, we have combined scRNA-seq data and bulk RNA-seq data to define the phenotypic and molecular characteristics of peripheral blood NK cells. While the role of NK cells in immune surveillance against virus infections and tumors has been well established, their contribution to protective responses to other intracellular microorganisms, such as Mycobacterium tuberculosis (Mtb), is still poorly understood. In this study, we have combined scRNA-seq data and bulk RNA-seq data to illuminate the molecular characteristics of circulating NK cells in patients with active tuberculosis (TB) disease and subjects with latent Mtb infection (LTBI) and compared these characteristics with those of healthy donors (HDs) and patients with non-TB other pulmonary infectious diseases (ODs). We show here that the NK cell cluster was significantly increased in LTBI subjects, as compared to patients with active TB or other non-TB pulmonary diseases and HD, and this was mostly attributable to the expansion of an NK cell population expressing KLRC2, CD52, CCL5 and HLA-DRB1, which most likely corresponds to memory-like NK2.1 cells. These data were validated by flow cytometry analysis in a small cohort of samples, showing that LTBI subjects have a significant expansion of NK cells characterized by the prevalence of memory-like CD52+ NKG2C+ NK cells. Altogether, our results provide some new information on the role of NK cells in protective immune responses to Mtb.
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Affiliation(s)
- Mojtaba Shekarkar Azgomi
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Giusto Davide Badami
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Marianna Lo Pizzo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Bartolo Tamburini
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Health Promotion, Mother and Childcare, Internal Medicine and Medical Specialties, University of Palermo, 90129 Palermo, Italy
| | - Costanza Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
| | - Marco Pio La Manna
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Francesco Dieli
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
| | - Nadia Caccamo
- Central Laboratory of Advanced Diagnosis and Biomedical Research (CLADIBIOR), Azienda Ospedaliera Universitaria Policlinico (AOUP) Paolo Giaccone, University of Palermo, 90127 Palermo, Italy; (M.S.A.); (G.D.B.); (M.L.P.); (B.T.); (C.D.); (M.P.L.M.); (N.C.)
- Department of Biomedicine, Neurosciences and Advanced Diagnostic (BND), University of Palermo, 90127 Palermo, Italy
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González-Escalada A, Rebollo MJ, Barrios Payan J, Hernández-Pando R, García MJ. Detection of Mycobacterial DNA in Human Bone Marrow. Microorganisms 2023; 11:1788. [PMID: 37512960 PMCID: PMC10384717 DOI: 10.3390/microorganisms11071788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Bone marrow is a cell-rich tissue of the reticuloendothelial system essential in the homeostasis and accurate functioning of hematopoiesis and of the immune system; moreover, it is also rich in lipids because it contains marrow adipocytes. This work aimed to evaluate the detection of mycobacterial DNA in human bone marrow as a tool to understand the complex pathology caused by the main pathogen Mycobacterium tuberculosis (Mtb). Formalin-fixed paraffin-embedded human bone marrow samples were studied using both conventional PCR + hybridization and in situ PCR to figure out the cell distribution of the targeted DNA. Samples were retrospectively collected from HIV+ patients with microbiologically proved mycobacterial infection and from subjects without evidence of infection. Mycobacterium avium (Mav) as well as Mtb DNA was detected in both settings, including tissues with and without granulomas. We detected DNA from both mycobacterial species, using in situ PCR, inside bone marrow macrophages. Other cell types, including adipocytes, showed positive signals only for Mtb DNA. This result suggested, for the first time, that marrow adipocytes could constitute an ideal reservoir for the persistence of Mtb, allowing the bacilli to establish long-lasting latent infection within a suitable lipid environment. This fact might differentiate pathogenic behavior of non-specialized pathogens such as Mav from that of specialized pathogens such as Mtb.
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Affiliation(s)
- Alba González-Escalada
- Facultad de Ciencias de la Salud, Area of Medical Microbiology, Rey Juan Carlos University, 28922 Alcorcon, Spain
| | - María José Rebollo
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonoma University of Madrid, 28029 Madrid, Spain
| | - Jorge Barrios Payan
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition Salvador Zubirán, México City 14080, Mexico
| | - Rogelio Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition Salvador Zubirán, México City 14080, Mexico
| | - María Jesús García
- Department of Preventive Medicine and Public Health and Microbiology, School of Medicine, Autonoma University of Madrid, 28029 Madrid, Spain
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Kissling M, Fritschi N, Baumann P, Buettcher M, Bonhoeffer J, Naranbhai V, Ritz N. Monocyte, Lymphocyte and Neutrophil Ratios - Easy-to-Use Biomarkers for the Diagnosis of Pediatric Tuberculosis. Pediatr Infect Dis J 2023; 42:520-527. [PMID: 36977187 DOI: 10.1097/inf.0000000000003901] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
BACKGROUND The neutrophil-to-lymphocyte-ratio (NLR), neutrophil-to-monocyte-plus-lymphocyte-ratio (NMLR) and monocyte-to-lymphocyte-ratio (MLR) may have diagnostic potential for tuberculosis (TB). METHODS Data of two prospective multicenter studies in Switzerland were used, which included children <18 years with TB exposure, infection or disease or with febrile non-TB lower-respiratory-tract infection (nTB-LRTI). RESULTS Of the 389 children included 25 (6.4%) had TB disease, 12 (3.1%) TB infection, 28 (7.2%) were healthy TB exposed and 324 (83.3%) nTB-LRTI. Median (IQR) NLR was highest with 2.0 (1.2, 2.2) in children with TB disease compared to TB exposed [0.8 (0.6, 1.3); P = 0.002] and nTB-LRTI [0.3 (0.1, 1.0); P < 0.001]. Median (IQR) NMLR was highest with 1.4 (1.2, 1.7) in children with TB disease compared to healthy exposed [0.7 (0.6, 1.1); P = 0.003] and children with nTB-LRTI [0.2 (0.1, 0.6); P < 0.001). Receiver operating characteristic curves to detect TB disease compared to nTB-LRTI for NLR and NMLR had an area under the curve of 0.82 and 0.86, the sensitivity of 88% and 88%, and specificity of 71% and 76%, respectively. CONCLUSION NLR and NMLR are promising, easy-to-obtain diagnostic biomarkers to differentiate children with TB disease from other lower respiratory tract infections. These results require validation in a larger study and in settings with high and low TB endemicity.
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Affiliation(s)
- Mirjam Kissling
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
| | - Nora Fritschi
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
- University Children's Hospital Basel, Switzerland
| | - Philipp Baumann
- Department of Intensive Care Medicine and Neonatology, University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland
- Infectious Disease and Vaccinology Unit, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | - Michael Buettcher
- Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne Switzerland
- Paediatric Pharmacology and Pharmacometrics Research Center, University Children's Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Vivek Naranbhai
- Massachusetts General Hospital Cancer Center, Massachusetts General Hospital, Boston
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Center for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Nicole Ritz
- From the Department of Clinical Research, Mycobacterial and Migrant Health Research Group, University of Basel, Switzerland
- University Children's Hospital Basel, Switzerland
- Paediatric Infectious Diseases Unit, Children's Hospital, Lucerne Cantonal Hospital, Lucerne Switzerland
- Department of Pediatrics, The Royal Children's Hospital Melbourne, The University of Melbourne, Australia
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Thu VTA, Dat LD, Jayanti RP, Trinh HKT, Hung TM, Cho YS, Long NP, Shin JG. Advancing personalized medicine for tuberculosis through the application of immune profiling. Front Cell Infect Microbiol 2023; 13:1108155. [PMID: 36844400 PMCID: PMC9950414 DOI: 10.3389/fcimb.2023.1108155] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
While early and precise diagnosis is the key to eliminating tuberculosis (TB), conventional methods using culture conversion or sputum smear microscopy have failed to meet demand. This is especially true in high-epidemic developing countries and during pandemic-associated social restrictions. Suboptimal biomarkers have restricted the improvement of TB management and eradication strategies. Therefore, the research and development of new affordable and accessible methods are required. Following the emergence of many high-throughput quantification TB studies, immunomics has the advantages of directly targeting responsive immune molecules and significantly simplifying workloads. In particular, immune profiling has been demonstrated to be a versatile tool that potentially unlocks many options for application in TB management. Herein, we review the current approaches for TB control with regard to the potentials and limitations of immunomics. Multiple directions are also proposed to hopefully unleash immunomics' potential in TB research, not least in revealing representative immune biomarkers to correctly diagnose TB. The immune profiles of patients can be valuable covariates for model-informed precision dosing-based treatment monitoring, prediction of outcome, and the optimal dose prediction of anti-TB drugs.
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Affiliation(s)
- Vo Thuy Anh Thu
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Ly Da Dat
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Rannissa Puspita Jayanti
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Hoang Kim Tu Trinh
- Center for Molecular Biomedicine, University of Medicine and Pharmacy at Ho Chi Minh, Ho Chi Minh City, Vietnam
| | - Tran Minh Hung
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Nguyen Phuoc Long
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea,*Correspondence: Jae-Gook Shin, ; Nguyen Phuoc Long,
| | - Jae-Gook Shin
- Department of Pharmacology and PharmacoGenomics Research Center, Inje University College of Medicine, Busan, Republic of Korea,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea,Department of Clinical Pharmacology, Inje University Busan Paik Hospital, Busan, Republic of Korea,*Correspondence: Jae-Gook Shin, ; Nguyen Phuoc Long,
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Impact of Mycobacterium tuberculosis Infection on Human B Cell Compartment and Antibody Responses. Cells 2022; 11:cells11182906. [PMID: 36139482 PMCID: PMC9497247 DOI: 10.3390/cells11182906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important health challenges worldwide. Control of the TB epidemic has not yet been achieved because of the lack of an effective vaccine and rapid and sensitive diagnostic approaches, as well as the emergence of drug-resistant forms of M. tuberculosis. Cellular immunity has a pivotal role against M. tuberculosis infection, but the role of humoral immunity is still controversial. We analyzed the frequency, absolute counts, and phenotypic and functional subsets of B lymphocytes in the peripheral blood of patients with active TB and subjects with latent infection compared to healthy donors. Moreover, we analyzed serum levels of total Ig and their IgA, IgM, and IgG isotypes and the titers of preexisting antibodies against a pool of common viral pathogens. FlowCT and unsupervised clusterization analysis show that patients with active TB and LTBI subjects have modest non-significant reduction in the numbers of circulating B lymphocytes as compared to healthy donors. Moreover, LTBI subjects had high percentages of atypical B cell population and lower percentages of naive and switched memory B cells. These findings were supported by gene expression and GSEA analysis. Moreover, there were no differences between active TB patients, LTBI subjects and HD, either in serum levels of total Ig isotypes or in preexisting IgG antibody titers, to ten different antigens from eight common pathogenic viruses, clearly demonstrating that either active or latent M. tuberculosis infection preserves the antibody production capacity of long-lived plasma cells. Thus, our results agree with previous studies reporting unaltered B cell frequencies in the blood of active TB patients and LTBI individuals as compared to healthy controls.
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García-Morales L, Del Portillo P, Anzola JM, Ares MA, Helguera-Repetto AC, Cerna-Cortes JF, Méndez-Tenorio A, García MJ, Otal I, Martín C, Gonzalez-y-Merchand JA, Rivera-Gutiérrez S. The Lack of the TetR-Like Repressor Gene BCG_2177c (Rv2160A) May Help Mycobacteria Overcome Intracellular Redox Stress and Survive Longer Inside Macrophages When Surrounded by a Lipid Environment. Front Cell Infect Microbiol 2022; 12:907890. [PMID: 35873160 PMCID: PMC9301340 DOI: 10.3389/fcimb.2022.907890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Mycobacteria, like other microorganisms, survive under different environmental variations by expressing an efficient adaptive response, oriented by regulatory elements, such as transcriptional repressors of the TetR family. These repressors in mycobacteria also appear to be related to cholesterol metabolism. In this study, we have evaluated the effect of a fatty acid (oleic–palmitic–stearic)/cholesterol mixture on some phenotypic and genotypic characteristics of a tetR-mutant strain (BCG_2177c mutated gene) of M. bovis BCG, a homologous of Rv2160A of M. tuberculosis. In order to accomplish this, we have analyzed the global gene expression of this strain by RNA-seq and evaluated its neutral-lipid storage capacity and potential to infect macrophages. We have also determined the macrophage response by measuring some pro- and anti-inflammatory cytokine expressions. In comparison with wild-type microorganisms, we showed that the mutation in the BCG_2177c gene did not affect the growth of M. bovis BCG in the presence of lipids but it probably modified the structure/composition of its cell envelope. Compared to with dextrose, an overexpression of the transcriptome of the wild-type and mutant strains was observed when these mycobacteria were cultured in lipids, mainly at the exponential phase. Twelve putative intracellular redox balance maintenance genes and four others coding for putative transcriptional factors (including WhiB6 and three TetR-like) were the main elements repeatedly overexpressed when cultured in the presence of lipids. These genes belonged to the central part of what we called the “genetic lipid signature” for M. bovis BCG. We have also found that all these mycobacteria genotypic changes affected the outcome of BCG-infected macrophages, being the mutant strain most adapted to persist longer inside the host. This high persistence result was also confirmed when mutant-infected macrophages showed overexpression of the anti-inflammatory cytokine TGF-β versus pro-inflammatory cytokines. In summary, the lack of this TetR-like repressor expression, within a lipid environment, may help mycobacteria overcome intracellular redox stress and survive longer inside their host.
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Affiliation(s)
- Lázaro García-Morales
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Patricia Del Portillo
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá, Colombia
| | - Juan M. Anzola
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá, Colombia
- Facultad de Ingeniería y Ciencias Básicas, Universidad Central, Bogotá, D.C., Colombia
| | - Miguel A. Ares
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, Mexico
| | - Addy C. Helguera-Repetto
- Departamento de Inmuno-Bioquímica, Instituto Nacional de Perinatología Isidro Espinosa de los Reyes, Ciudad de México, Mexico
| | - Jorge F. Cerna-Cortes
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - Alfonso Méndez-Tenorio
- Laboratorio de Bioinformática y Biotecnología Genómica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
| | - María J. García
- Departamento de Medicina Preventiva, Facultad de Medicina, Universidad Autónoma de Madrid, Madrid, Spain
| | - Isabel Otal
- Grupo de Genética de Micobacterias, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- Centro de Investigación Biomédica en Red (CIBER) Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Jorge A. Gonzalez-y-Merchand
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- *Correspondence: Jorge A. Gonzalez-y-Merchand, ; Sandra Rivera-Gutiérrez,
| | - Sandra Rivera-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, Mexico
- *Correspondence: Jorge A. Gonzalez-y-Merchand, ; Sandra Rivera-Gutiérrez,
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