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Liu C, Jiménez-Avalos G, Zhang WS, Sheen P, Zimic M, Popp J, Cialla-May D. Prussian blue (PB) modified gold nanoparticles as a SERS-based sensing platform for capturing and detection of pyrazinoic acid (POA). Talanta 2024; 266:125038. [PMID: 37574604 DOI: 10.1016/j.talanta.2023.125038] [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: 04/18/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/15/2023]
Abstract
Pyrazinoic acid (POA) is a metabolite of the anti-tuberculosis drug pyrazinamide (PZA), and its detection can be used to assess the resistance of Mycobacterium tuberculosis in cultures, as only sensitive strains of the bacteria can metabolize PZA into POA. Prussian blue is a well-known metal-organic framework compound widely used in various sensing platforms such as electrochemical, photochemical, and magnetic sensors. In this study, we present a novel sensing platform based on Prussian blue-modified gold nanoparticles (AuNPs) designed to enhance the affinity of POA towards the sensing surface and to capture POA molecules from aqueous solutions. This SERS-based method allows for the selective enrichment of POA, which can be detected in both pure aqueous solution and in the presence of its pro-drug PZA. The limit of detection (LOD) for POA was estimated to be 1.08 μM in pure aqueous solution and 0.18 mM in the presence of PZA. Furthermore, the precision of the SERS method was verified by the relative standard deviation (RSD) of 3.34-12.02% for three parallel samples using different matrices, i.e. aqueous solution, spiked river water and spiked simulated saliva. The recoveries of the samples ranged from 92.65 to 118.51%. These all demonstrate the potential application of the proposed detection scheme in medical research.
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Affiliation(s)
- Chen Liu
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany; Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Helmholtzweg 4, 07743, Jena, Germany
| | - Gabriel Jiménez-Avalos
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Wen-Shu Zhang
- China Fire and Rescue Institute, Beijing, 102202, China
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jürgen Popp
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany; Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Helmholtzweg 4, 07743, Jena, Germany
| | - Dana Cialla-May
- Leibniz Institute of Photonic Technology, Member of Leibniz Health Technologies, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Albert-Einstein-Straße 9, 07745, Jena, Germany; Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, Member of the Leibniz Centre for Photonics in Infection Research (LPI), Helmholtzweg 4, 07743, Jena, Germany.
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Toribio L, Guzman C, Noazin S, Zimic-Sheen A, Zimic M, Gonzales I, Saavedra H, Pretell EJ, Bustos JA, Handali S, García HH. Multiantigen print immunoassay (MAPIA) for the diagnosis of neurocysticercosis: a single-center diagnostic optimization and accuracy study in Lima, Peru. J Clin Microbiol 2023; 61:e0076023. [PMID: 37966225 PMCID: PMC10729656 DOI: 10.1128/jcm.00760-23] [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: 06/14/2023] [Accepted: 09/21/2023] [Indexed: 11/16/2023] Open
Abstract
Neurocysticercosis (NCC) is the most common helminthic infection of the human central nervous system. The antibody detection assay of choice is the enzyme-linked immunoelectrotransfer blot assay using lentil-lectin purified parasite antigens (LLGP-EITB, Western blot), an immunoassay with exceptional performance in clinical samples. However, its use is mainly restricted to a few research laboratories because the assay is labor-intensive and requires sophisticated equipment, expertise, and large amounts of parasite material for preparation of reagents. We report a new immunoprint assay (MAPIA) that overcomes most of these barriers. We initially compared the performance of five different antigen combinations in a subset of defined samples in the MAPIA format. After selecting the best-performing assay format (a combination of rGP50 + rT24H + sTs14 antigens), 148 archived serum samples were tested, including 40 from individuals with parenchymal NCC, 40 with subarachnoid NCC, and 68 healthy controls with no evidence of neurologic disease. MAPIA using three antigens (rGP50 + rT24H + sTs14) was highly sensitive and specific for detecting antibodies in NCC. It detected 39 out of 40 (97.5%) parenchymal NCC cases and 40/40 (100%) subarachnoid cases and was negative in 67 out of 68 (98.53%) negative samples. MAPIA using three recombinant and synthetic antigens is a simple and economical tool with a performance equivalent to the LLGP-EITB assay for the detection of specific antibodies to NCC. The MAPIA overcomes existing barriers to adoption of the EITG LLGP and is a candidate for worldwide use.
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Affiliation(s)
- L. Toribio
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - C. Guzman
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - S. Noazin
- Department of International Health, Bloomberg School of Public Health. Johns Hopkins University, Baltimore, Maryland, USA
| | - A. Zimic-Sheen
- Bioinformatics Laboratory, Molecular Biology and Technological Developments, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
| | - M. Zimic
- Bioinformatics Laboratory, Molecular Biology and Technological Developments, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
| | - I. Gonzales
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
| | - H. Saavedra
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
| | - E. J. Pretell
- Hospital Nacional Alberto Sabogal Sologuren, ESSALUD, Callao, Peru
| | - J. A. Bustos
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - S. Handali
- Parasitic Diseases Branch, Division of Parasitic Diseases & Malaria, Center for Global Health, Centers for Disease Control & Prevention, Atlanta, Georgia, USA
| | - H. H. García
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Bloomberg School of Public Health. Johns Hopkins University, Baltimore, Maryland, USA
| | - on behalf of The Cysticercosis Working Group in Peru
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Peru
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Bloomberg School of Public Health. Johns Hopkins University, Baltimore, Maryland, USA
- Bioinformatics Laboratory, Molecular Biology and Technological Developments, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, San Martín de Porres, Peru
- Hospital Nacional Alberto Sabogal Sologuren, ESSALUD, Callao, Peru
- Parasitic Diseases Branch, Division of Parasitic Diseases & Malaria, Center for Global Health, Centers for Disease Control & Prevention, Atlanta, Georgia, USA
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Sciaudone M, Carpena R, Calderón M, Sheen P, Zimic M, Coronel J, Gilman RH, Bowman NM. Rapid detection of Mycobacterium tuberculosis using recombinase polymerase amplification: A pilot study. PLoS One 2023; 18:e0295610. [PMID: 38064441 PMCID: PMC10707601 DOI: 10.1371/journal.pone.0295610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Tuberculosis remains one of the leading causes of death worldwide, especially in low- and middle-income countries. Tuberculosis treatment and control efforts are hindered by the difficulty in making the diagnosis, as currently available diagnostic tests are too slow, too expensive, or not sufficiently sensitive. Recombinase polymerase amplification (RPA) is a novel technique that allows for the amplification of DNA rapidly, at constant temperature, and with minimal expense. We calculated and compared the limit of detection, sensitivity, and specificity of two RPA-based assays for the diagnosis of pulmonary tuberculosis, using two sets of published primers. We also calculated and compared the assays' limits of detection and compared their performance using two different DNA extraction methods prior to amplification (a commercially available DNA extraction kit vs. the chelex method). The RPA-lateral flow assay had a limit of detection of 5 fg/μL of DNA, a sensitivity of 53.2%, and a specificity of 93.3%, while the real time-RPA assay had a limit of detection of 25 fg/μL of DNA, a sensitivity of 85.1%, and a specificity of 93.3%. There was no difference in assay performance when DNA extraction was carried out using the commercial kit vs. the chelex method. The real-time RPA assay has adequate sensitivity and specificity for the diagnosis of pulmonary tuberculosis and could be a viable diagnostic tool in resource-limited settings, but the lateral flow assay did not perform as well, perhaps due to the fact we used stored sputum specimens from a biorepository. More work is needed to optimize the RPA-lateral flow assay, to get a more accurate estimate of its specificity and sensitivity using prospectively collected specimens, and to develop both assays into point-of-care tests that can be easily deployed in the field.
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Affiliation(s)
- Michael Sciaudone
- Department of Medicine, Section of Infectious Diseases, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- Center for Intelligent Molecular Diagnostics, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Renzo Carpena
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maritza Calderón
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Patricia Sheen
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Coronel
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Natalie M. Bowman
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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Tataje-Lavanda L, Málaga E, Verastegui M, Mayta Huatuco E, Icochea E, Fernández-Díaz M, Zimic M. Identification and evaluation in-vitro of conserved peptides with high affinity to MHC-I as potential protective epitopes for Newcastle disease virus vaccines. BMC Vet Res 2023; 19:196. [PMID: 37805566 PMCID: PMC10559636 DOI: 10.1186/s12917-023-03726-w] [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: 03/15/2023] [Accepted: 09/12/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Newcastle disease (ND) is a major threat to the poultry industry, leading to significant economic losses. The current ND vaccines, usually based on active or attenuated strains, are only partially effective and can cause adverse effects post-vaccination. Therefore, the development of safer and more efficient vaccines is necessary. Epitopes represent the antigenic portion of the pathogen and their identification and use for immunization could lead to safer and more effective vaccines. However, the prediction of protective epitopes for a pathogen is a major challenge, especially taking into account the immune system of the target species. RESULTS In this study, we utilized an artificial intelligence algorithm to predict ND virus (NDV) peptides that exhibit high affinity to the chicken MHC-I complex. We selected the peptides that are conserved across different NDV genotypes and absent in the chicken proteome. From the filtered peptides, we synthesized the five peptides with the highest affinities for the L, HN, and F proteins of NDV. We evaluated these peptides in-vitro for their ability to elicit cell-mediated immunity, which was measured by the lymphocyte proliferation in spleen cells of chickens previously immunized with NDV. CONCLUSIONS Our study identified five peptides with high affinity to MHC-I that have the potential to serve as protective epitopes and could be utilized for the development of multi-epitope NDV vaccines. This approach can provide a safer and more efficient method for NDV immunization.
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Affiliation(s)
- Luis Tataje-Lavanda
- Research and Development Laboratories, FARVET SAC, Chincha Alta, Ica, Peru.
- Laboratory of Clinical Molecular Virology, Faculty of Biological Sciences, National University of San Marcos, Lima, Peru.
- School of Human Medicine, Private University San Juan Bautista, Lima, Peru.
| | - Edith Málaga
- Research Laboratory On Infectious Diseases, Cayetano Heredia Peruvian University, Lima, Peru
| | - Manuela Verastegui
- Research Laboratory On Infectious Diseases, Cayetano Heredia Peruvian University, Lima, Peru
| | - Egma Mayta Huatuco
- Laboratory of Clinical Molecular Virology, Faculty of Biological Sciences, National University of San Marcos, Lima, Peru
| | - Eliana Icochea
- Avian Pathology Laboratory, Faculty of Veterinary Medicine, National University of San Marcos, Lima, Peru
| | | | - Mirko Zimic
- Research and Development Laboratories, FARVET SAC, Chincha Alta, Ica, Peru
- Bioinformatics, Molecular Biology, and Technological Developments Laboratory, Faculty of Science and Philosophy, Cayetano Heredia Peruvian University, Lima, Peru
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Jiménez-Avalos G, Soto-Obando A, Solis M, Gilman RH, Cama V, Gonzalez AE, García HH, Sheen P, Requena D, Zimic M. Assembly and phylogeographical analysis of novel Taenia solium mitochondrial genomes suggest stratification within the African-American genotype. Parasit Vectors 2023; 16:349. [PMID: 37803424 PMCID: PMC10559519 DOI: 10.1186/s13071-023-05958-z] [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: 02/14/2023] [Accepted: 08/30/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Taenia solium is a parasite of public health concern, causing human taeniasis and cysticercosis. Two main genotypes have been identified: Asian and African-American. Although characterizing T. solium genotypes is crucial to understanding the genetic epidemiology of its diseases, not much is known about the differences between T. solium mitochondrial genomes from different genotypes. Also, little is known about whether genotypes are further subdivided. Therefore, this study aimed to identify a set of point mutations distributed throughout the T. solium mitochondrial genome that differentiate the African-American from the Asian genotype. Another objective was to identify whether T. solium main genotypes are further stratified. METHODS One Mexican and two Peruvian T. solium mitochondrial genomes were assembled using reads available in the NCBI Sequence Read Archive and the reference genome from China as a template. Mutations with respect to the Chinese reference were identified by multiple genome alignment. Jensen-Shannon and Grantham scores were computed for mutations in protein-coding genes to evaluate whether they affected protein function. Phylogenies by Bayesian inference and haplotype networks were constructed using cytochrome c oxidase subunit 1 and cytochrome b from these genomes and other isolates to infer phylogeographical relationships. RESULTS A set of 31 novel non-synonymous point mutations present in all genomes of the African-American genotype were identified. These mutations were distributed across the mitochondrial genome, differentiating the African-American from the Asian genotype. All occurred in non-conserved protein positions. Furthermore, the analysis suggested a stratification of the African-American genotypes into an East African and a West African sublineage. CONCLUSIONS A novel set of 31 non-synonymous mutations differentiating the main T. solium genotypes was identified. None of these seem to be causing differences in mitochondrial protein function between parasites of the two genotypes. Furthermore, two sublineages within the African-American genotype are proposed for the first time. The presence of the East African sublineage in the Americas suggests an underestimated connection between East African and Latin American countries that might have arisen in the major slave trade between Portuguese Mozambique and the Americas. The results obtained here help to complete the molecular epidemiology of the parasite.
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Affiliation(s)
- Gabriel Jiménez-Avalos
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Alina Soto-Obando
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maria Solis
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H Gilman
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, USA
| | - Vitaliano Cama
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, USA
| | - Armando E Gonzalez
- Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Hector H García
- Departamento de Microbiología, Universidad Peruana Cayetano Heredia, Lima, Perú
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurológicas, Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - David Requena
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú.
- Laboratory of Cellular Biophysics, The Rockefeller University, New York, USA.
- Bioinformatics Group in Multi-Omics and Immunology, New York, NY, 10065, USA.
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería. Universidad Peruana Cayetano Heredia, Lima, Perú.
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Hakim JMC, Waltmann A, Tinajeros F, Kharabora O, Machaca EM, Calderon M, del Carmen Menduiña M, Wang J, Rueda D, Zimic M, Verástegui M, Juliano JJ, Gilman RH, Mugnier MR, Bowman NM. Amplicon Sequencing Reveals Complex Infection in Infants Congenitally Infected With Trypanosoma Cruzi and Informs the Dynamics of Parasite Transmission. J Infect Dis 2023; 228:769-776. [PMID: 37119236 PMCID: PMC10503952 DOI: 10.1093/infdis/jiad125] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 11/24/2022] [Revised: 02/08/2023] [Accepted: 04/26/2023] [Indexed: 05/01/2023] Open
Abstract
Congenital transmission of Trypanosoma cruzi is an important source of new Chagas infections worldwide. The mechanisms of congenital transmission remain poorly understood, but there is evidence that parasite factors are involved. Investigating changes in parasite strain diversity during transmission could provide insight into the parasite factors that influence the process. Here we use amplicon sequencing of a single copy T. cruzi gene to evaluate the diversity of infection in clinical samples from Chagas positive mothers and their infected infants. Several infants and mothers were infected with multiple parasite strains, mostly of the same TcV lineage, and parasite strain diversity was higher in infants than mothers. Two parasite haplotypes were detected exclusively in infant samples, while one haplotype was never found in infants. Together, these data suggest multiple parasites initiate a congenital infection and that parasite factors influence the probability of vertical transmission.
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Affiliation(s)
- Jill M C Hakim
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Andreea Waltmann
- Institute for Global Health and Infectious Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Oksana Kharabora
- Institute for Global Health and Infectious Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Edith Málaga Machaca
- Asociación Benéfica PRISMA, Lima, Peru
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Maritza Calderon
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Jeremy Wang
- University of North Carolina, Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Daniel Rueda
- Facultad de Ciencias, Universidad Nacional de Ingeniería, Lima, Perú
| | - Mirko Zimic
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Manuela Verástegui
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Disease, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Robert H Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Monica R Mugnier
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Natalie M Bowman
- Division of Infectious Diseases, Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
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Lopez JM, Zimic M, Vallejos K, Sevilla D, Quispe-Carbajal M, Roncal E, Rodríguez J, Rodríguez J, Antiparra R, Arteaga H, Gilman RH, Maruenda H, Sheen P. Quantitative 1H Nuclear Magnetic Resonance Assay for the Rapid Detection of Pyrazinamide Resistance in Mycobacterium tuberculosis from Sputum Samples. J Clin Microbiol 2023; 61:e0152222. [PMID: 37071032 DOI: 10.1128/jcm.01522-22] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the 10 leading killer diseases in the world. At least one-quarter of the population has been infected, and there are 1.3 million deaths annually. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains challenges TB treatments. One of the drugs widely used in first- and second-line regimens is pyrazinamide (PZA). Statistically, 50% of MDR and 90% of XDR clinical strains are resistant to PZA, and recent studies have shown that its use in patients with PZA-resistant strains is associated with higher mortality rates. Therefore, the is an urgent need for the development of an accurate and efficient PZA susceptibility assay. PZA crosses the M. tuberculosis membrane and is hydrolyzed to its active form, pyrazinoic acid (POA), by a nicotinamidase encoded by the pncA gene. Up to 99% of clinical PZA-resistant strains have mutations in this gene, suggesting that this is the most likely mechanism of resistance. However, not all pncA mutations confer PZA resistance, only the ones that lead to limited POA production. Therefore, susceptibility to PZA may be addressed simply by its ability to form, or not, POA. Here, we present a nuclear magnetic resonance method to accurately quantify POA directly in the supernatant of sputum cultures collected from TB patients. The ability of the clinical sputum culture to hydrolyze PZA was determined, and the results were correlated with the results of other biochemical and molecular PZA drug susceptibility assays. The excellent sensitivity and specificity values attained suggest that this method could become the new gold standard for the determination of PZA susceptibility.
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Affiliation(s)
- Juan M Lopez
- Departamento de Ciencias-Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Mirko Zimic
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Katherine Vallejos
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Diego Sevilla
- Departamento de Ciencias-Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | | | - Elisa Roncal
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Joseline Rodríguez
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jhojailith Rodríguez
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Ricardo Antiparra
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Héctor Arteaga
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Helena Maruenda
- Departamento de Ciencias-Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Patricia Sheen
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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Rodriguez J, Alcántara R, Rodríguez J, Vargas J, Roncal E, Antiparra R, Gilman RH, Grandjean L, Moore D, Zimic M, Sheen P. Evaluation of three alternatives cost-effective culture media for Mycobacterium tuberculosis detection and drug susceptibility determination using the microscopic observation drug susceptibility (MODS) assay. Tuberculosis (Edinb) 2022; 137:102273. [PMID: 36403561 PMCID: PMC10022417 DOI: 10.1016/j.tube.2022.102273] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/28/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Tuberculosis phenotypic detection assays are commonly used in low-resource countries. Therefore, reliable detection methods are crucial for early diagnosis and treatment. The microscopic observation drug susceptibility (MODS) assay is a culture-based test to detect Mycobacterium tuberculosis and characterize drug resistance in 7-10 days directly from sputum. The use of MODS is limited by the availability of supplies necessary for preparing the enriched culture. In this study, we evaluated three dry culture media that are easier to produce and cheaper than the standard one used in MODS [1]: an unsterilized powder-based mixed (Boldú et al., 2007) [2], a sterile-lyophilized medium, and (Sengstake et al., 2017) [3] an irradiated powder-based mixed. Mycobacterial growth and drug susceptibility were evaluated for rifampin, isoniazid, and pyrazinamide (PZA). The alternative cultures were evaluated using 282 sputum samples with positive acid-fast smears. No significant differences were observed in the positivity test rates. The positivity time showed high correlations (Rho) of 0.925, 0.889, and 0.866 between each of the three alternative media and the standard. Susceptibility testing for MDR and PZA showed an excellent concordance of 1 compared to the reference test. These results demonstrate that dry culture media are appropriate and advantageous for use in MODS in low-resource settings.
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Affiliation(s)
- Jhojailith Rodriguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Roberto Alcántara
- Laboratory of Biomolecules, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, 15023, Peru
| | - Joseline Rodríguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Johnny Vargas
- Instituto Peruano de Energía Nuclear (IPEN), Lima, 15076, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, United States
| | - Louis Grandjean
- Department of Infection, Immunity, and Inflammation, Institute of Child Health, London, WC1N 1EH, UK
| | - David Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, 15102, Peru.
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9
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Ormachea O, Villazón A, Rodriguez P, Zimic M. A Smartphone-Based Low-Cost Inverted Laser Fluorescence Microscope for Disease Diagnosis. Biosensors (Basel) 2022; 12:960. [PMID: 36354469 PMCID: PMC9688076 DOI: 10.3390/bios12110960] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Fluorescence microscopy is an important tool for disease diagnosis, often requiring costly optical components, such as fluorescence filter cubes and high-power light sources. Due to its high cost, conventional fluorescence microscopy cannot be fully exploited in low-income settings. Smartphone-based fluorescence microscopy becomes an interesting low-cost alternative, but raises challenges in the optical system. We present the development of a low-cost inverted laser fluorescence microscope that uses a smartphone to visualize the fluorescence image of biological samples. Our fluorescence microscope uses a laser-based simplified optical filter system that provides analog optical filtering capabilities of a fluorescence filter cube. Firstly, we validated our inverted optical filtering by visualizing microbeads labeled with three different fluorescent compounds or fluorophores commonly used for disease diagnosis. Secondly, we validated the disease diagnosis capabilities by comparing the results of our device with those of a commercial fluorescence microscope. We successfully detected and visualized Trypanosoma cruzi parasites, responsible for the Chagas infectious disease and the presence of Antineutrophil cytoplasmic antibodies of the ANCA non-communicable autoimmune disease. The samples were labeled with the fluorescein isothiocyanate (FITC) fluorophore, one of the most commonly used fluorophores for disease diagnosis. Our device provides a 400× magnification and is at least one order of magnitude cheaper than conventional commercial fluorescence microscopes.
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Affiliation(s)
- Omar Ormachea
- Centro de Investigaciones Opticas y Energías (CIOE), Universidad Privada Boliviana (UPB), Cochabamba, Bolivia
| | - Alex Villazón
- Centro de Investigaciones en Nuevas Tecnologías Informáticas (CINTI), Universidad Privada Boliviana (UPB), Cochabamba, Bolivia
| | - Patricia Rodriguez
- Instituto de Investigaciones Biomédicas (IIBISMED), Facultad de Medicina, Universidad Mayor de San Simón (UMSS), Cochabamba, Bolivia
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
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10
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Choque-Guevara R, Poma-Acevedo A, Montesinos-Millán R, Rios-Matos D, Gutiérrez-Manchay K, Montalvan-Avalos A, Quiñones-Garcia S, Cauti-Mendoza MDG, Agurto-Arteaga A, Ramirez-Ortiz I, Criollo-Orozco M, Huaccachi-Gonzales E, Romero YK, Perez-Martinez N, Isasi-Rivas G, Sernaque-Aguilar Y, Villanueva-Pérez D, Ygnacio F, Vallejos-Sánchez K, Fernández-Sánchez M, Guevara-Sarmiento LA, Fernández-Díaz M, Zimic M. Squalene in oil-based adjuvant improves the immunogenicity of SARS-CoV-2 RBD and confirms safety in animal models. PLoS One 2022; 17:e0269823. [PMID: 35998134 PMCID: PMC9397949 DOI: 10.1371/journal.pone.0269823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
COVID-19 pandemic has accelerated the development of vaccines against its etiologic agent, SARS-CoV-2. However, the emergence of new variants of the virus lead to the generation of new alternatives to improve the current sub-unit vaccines in development. In the present report, the immunogenicity of the Spike RBD of SARS-CoV-2 formulated with an oil-in-water emulsion and a water-in-oil emulsion with squalene was evaluated in mice and hamsters. The RBD protein was expressed in insect cells and purified by chromatography until >95% purity. The protein was shown to have the appropriate folding as determined by ELISA and flow cytometry binding assays to its receptor, as well as by its detection by hamster immune anti-S1 sera under non-reducing conditions. In immunization assays, although the cellular immune response elicited by both adjuvants were similar, the formulation based in water-in-oil emulsion and squalene generated an earlier humoral response as determined by ELISA. Similarly, this formulation was able to stimulate neutralizing antibodies in hamsters. The vaccine candidate was shown to be safe, as demonstrated by the histopathological analysis in lungs, liver and kidney. These results have shown the potential of this formulation vaccine to be evaluated in a challenge against SARS-CoV-2 and determine its ability to confer protection.
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Affiliation(s)
| | | | | | - Dora Rios-Matos
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
| | | | | | - Stefany Quiñones-Garcia
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Maria de Grecia Cauti-Mendoza
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | | | - Yomara K. Romero
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Gisela Isasi-Rivas
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
| | | | | | - Freddy Ygnacio
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
| | - Katherine Vallejos-Sánchez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - Mirko Zimic
- Laboratorios de investigación y desarrollo, FARVET SAC, Chincha, Ica, Perú
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail:
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11
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Sheen P, Rodriguez J, Alcántara R, Vargas J, Grandjean L, Moore DAJ, Gilman RH, Zimic M. Alternative cost-effective media to facilitate MODS culture for diagnostics of tuberculosis. Tuberculosis (Edinb) 2022; 135:102225. [PMID: 35728429 DOI: 10.1016/j.tube.2022.102225] [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] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 12/30/2022]
Abstract
Most culture-based methods for tuberculosis diagnosis remain low-cost options for low- and mid-income countries. The MODS culture is a rapid and low-cost assay to diagnose tuberculosis and determine drug susceptibility. However, its implementation is limited due to the low accessibility to supplies required for the enriched medium. In this study, we evaluate two alternative culture media: A powder-based mixed (PM) and a lyophilized media (LM). Catalase, PANTA, and gamma irradiation were evaluated as additions to PM and LM. The culture performance of the alternative media was compared with the standard MODS medium (MM) using Mycobacterium tuberculosis isolates and positive acid-fast smear sputum samples. Overall, no significant difference was observed in the bacterial growth between PM and LM with MM. However, PANTA and gamma irradiation combined reduced bacterial growth significantly in all media variants. A median positivity day of 6 ± 5 days was observed for sputum samples, regardless of the culture medium. The preliminary results show that the two variants culture media have a similar performance to the standard MODS medium. The powder-based media with PANTA (PM_P) showed a time-to-positivity and sensitivity similar to the standard MODS medium. It is the simplest to prepare and does not require any sterilization process.
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Affiliation(s)
- Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru.
| | - Joseline Rodriguez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
| | - Roberto Alcántara
- Biomolecules Laboratory, Faculty of Health Sciences, Universidad Peruana de Ciencias Aplicadas (UPC), Lima, 15023, Peru
| | - Johnny Vargas
- Instituto Peruano de Energía Nuclear (IPEN), Lima, 15076, Peru
| | - Louis Grandjean
- Department of Infection, Immunity, and Inflammation, Institute of Child Health, WC1N 1EH, London, UK
| | - David A J Moore
- TB Centre, London School of Hygiene and Tropical Medicine, WC1E 7HT, London, UK
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, United States
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, 15102, Peru
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12
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Arica-Sosa A, Alcántara R, Jiménez-Avalos G, Zimic M, Milón P, Quiliano M. Identifying RO9021 as a Potential Inhibitor of PknG from Mycobacterium tuberculosis: Combinative Computational and In Vitro Studies. ACS Omega 2022; 7:20204-20218. [PMID: 35721990 PMCID: PMC9201901 DOI: 10.1021/acsomega.2c02093] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 06/07/2023]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). Despite being considered curable and preventable, the increase of antibiotic resistance is becoming a serious public health problem. Mtb is a pathogen capable of surviving in macrophages, causing long-term latent infection where the mycobacterial serine/threonine protein kinase G (PknG) plays a protective role. Therefore, PknG is an important inhibitory target to prevent Mtb from entering the latency stage. In this study, we use a pharmacophore-based virtual screening and biochemical assays to identify the compound RO9021 (CHEMBL3237561) as a PknG inhibitor. In detail, 1.5 million molecules were screened using a scalable cloud-based setup, identifying 689 candidates, which were further subjected to additional screening employing molecular docking. Molecular docking spotted 62 compounds with estimated binding affinities of -7.54 kcal/mol (s.d. = 0.77 kcal/mol). Finally, 14 compounds were selected for in vitro experiments considering previously reported biological activities and commercial availability. In vitro assays of PknG activity showed that RO9021 inhibits the kinase activity similarly to AX20017, a known inhibitor. The inhibitory effect was found to be dose dependent with a relative IC50 value of 4.4 ± 1.1 μM. Molecular dynamics simulations predicted that the PknG-RO9021 complex is stable along the tested timescale. Altogether, our study indicates that RO9021 is a noteworthy drug candidate for further developing new anti-TB drugs that hold excellent reported pharmacokinetic parameters.
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Affiliation(s)
- Alicia Arica-Sosa
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Roberto Alcántara
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
- Applied
Biophysics and Biochemistry Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Gabriel Jiménez-Avalos
- Laboratorio
de Bioinformática, Biología Molecular y Desarrollos
Tecnológicos, Facultad de Ciencias y Filosofía, Departamento
de Ciencias Celulares y Moleculares, Universidad
Peruana Cayetano Heredia (UPCH), 15102 Lima, Peru
| | - Mirko Zimic
- Laboratorio
de Bioinformática, Biología Molecular y Desarrollos
Tecnológicos, Facultad de Ciencias y Filosofía, Departamento
de Ciencias Celulares y Moleculares, Universidad
Peruana Cayetano Heredia (UPCH), 15102 Lima, Peru
| | - Pohl Milón
- Applied
Biophysics and Biochemistry Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Miguel Quiliano
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
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13
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Agurto-Arteaga A, Poma-Acevedo A, Rios-Matos D, Choque-Guevara R, Montesinos-Millán R, Montalván Á, Isasi-Rivas G, Cauna-Orocollo Y, Cauti-Mendoza MDG, Pérez-Martínez N, Gutierrez-Manchay K, Ramirez-Ortiz I, Núñez-Fernández D, Salguedo-Bohorquez MI, Quiñones-Garcia S, Fernández Díaz M, Guevara Sarmiento LA, Zimic M. Preclinical Assessment of IgY Antibodies Against Recombinant SARS-CoV-2 RBD Protein for Prophylaxis and Post-Infection Treatment of COVID-19. Front Immunol 2022; 13:881604. [PMID: 35664008 PMCID: PMC9157249 DOI: 10.3389/fimmu.2022.881604] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 02/22/2022] [Accepted: 04/04/2022] [Indexed: 12/21/2022] Open
Abstract
Within the framework of the current COVID-19 pandemic, there is a race against time to find therapies for the outbreak to be controlled. Since vaccines are still tedious to develop and partially available for low-income countries, passive immunity based on egg-yolk antibodies (IgY) is presented as a suitable approach to preclude potential death of infected patients, based on its high specificity/avidity/production yield, cost-effective manufacture, and ease of administration. In the present study, IgY antibodies against a recombinant RBD protein of SARS-CoV-2 were produced in specific-pathogen-free chickens and purified from eggs using a biocompatible method. In vitro immunoreactivity was tested, finding high recognition and neutralization values. Safety was also demonstrated prior to efficacy evaluation, in which body weight, kinematics, and histopathological assessments of hamsters challenged with SARS-CoV-2 were performed, showing a protective effect administering IgY intranasally both as a prophylactic treatment or a post-infection treatment. The results of this study showed that intranasally delivered IgY has the potential to both aid in prevention and in overcoming COVID-19 infection, which should be very useful to control the advance of the current pandemic and the associated mortality.
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Affiliation(s)
- Andres Agurto-Arteaga
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Astrid Poma-Acevedo
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Dora Rios-Matos
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Ricardo Choque-Guevara
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Ricardo Montesinos-Millán
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Ángela Montalván
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Gisela Isasi-Rivas
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Yudith Cauna-Orocollo
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - María de Grecia Cauti-Mendoza
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Norma Pérez-Martínez
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Kristel Gutierrez-Manchay
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Ingrid Ramirez-Ortiz
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Dennis Núñez-Fernández
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mario I Salguedo-Bohorquez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stefany Quiñones-Garcia
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Manolo Fernández Díaz
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Luis A Guevara Sarmiento
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru
| | - Mirko Zimic
- Laboratorio de Biotecnología Molecular y Genómica, Laboratorios de Investigación y Desarrollo, Farmacológicos Veterinarios SAC (FARVET SAC), Chincha, Peru.,Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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14
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León-Janampa N, Shinkaruk S, Gilman RH, Kirwan DE, Fouquet E, Szlosek M, Sheen P, Zimic M. Biorecognition and detection of antigens from Mycobacterium tuberculosis using a sandwich ELISA associated with magnetic nanoparticles. J Pharm Biomed Anal 2022; 215:114749. [PMID: 35447489 DOI: 10.1016/j.jpba.2022.114749] [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: 12/05/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 10/18/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is one of the 10 leading causes of death worldwide, especially in low-income areas. A rapid, low-cost diagnostic assay for TB with high sensitivity and specificity is not currently available. Bio-functionalized magnetic nanoparticles (MNPs) which are able to efficiently detect and concentrate biomolecules from complex biological samples, allows improving the diagnostic immunoassays. In this way, a proof-of-concept of MNP-based sandwich immunoassay was developed to detect various MTB protein antigens. The superficial and secretory antigenic proteins considered in this research were: CFP10, ESAT6, MTC28, MPT64, 38 kDa protein, Ag85B, and MoeX. The proteins were cloned and expressed in an E. coli system. Polyclonal antibodies (ab) against the recombinant antigens were elicited in rabbits and mice. Antibodies were immobilized on the surface of amine-silanized nanoparticles (MNP@Si). The functionalized MNP@Si@ab were tested in a colorimetric sandwich enzyme-linked immunosorbent assay (sELISA-MNP@Si@ab) to recognize the selected antigens in sputum samples. The selected MTB antigens were successfully detected in sputum from TB patients in a shorter time (~ 4 h) using the sELISA-MNP@Si@ab, compared to the conventional sELISA (~15 h) standardized in home. Moreover, the sELISA-MNP@Si@ab showed the higher sensitivity in the real biological samples from infected patients.
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Affiliation(s)
- Nancy León-Janampa
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 33400 Talence, France.
| | - Svitlana Shinkaruk
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 33400 Talence, France.
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | - Daniela E Kirwan
- Institute for Infection & Immunity, St. George's, University of London, London, United Kingdom.
| | - Eric Fouquet
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 33400 Talence, France.
| | - Magali Szlosek
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255, 33400 Talence, France.
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
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15
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Paula Vargas Ruiz A, Jiménez Avalos G, Delgado NE, Olivos Ramírez G, Sheen P, Quiliano M, Zimic M. Comprehensive virtual screening of 4.8k flavonoids reveals novel insights into the allosteric inhibition of SARS-CoV-2 MPRO. Biophys J 2022. [PMCID: PMC8833054 DOI: 10.1016/j.bpj.2021.11.1075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Salguedo M, Zarate G, Coronel J, Comina G, Gilman RH, Sheen P, Oberhelman R, Zimic M. Low-cost 3D-printed inverted microscope to detect Mycobacterium tuberculosis in a MODS culture. Tuberculosis (Edinb) 2022; 132:102158. [PMID: 34864388 PMCID: PMC8818028 DOI: 10.1016/j.tube.2021.102158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 10/05/2021] [Revised: 11/26/2021] [Accepted: 11/27/2021] [Indexed: 01/03/2023]
Abstract
MODS, an assay for diagnosis of tuberculosis and drug-susceptibility, is based in the microscopic observation of the characteristic cords of Mycobacterium tuberculosis colonies grown in liquid media. An inverted optical microscope (100× magnification) is required to observe and interpret MODS cultures. Unfortunately, the cost of commercial inverted microscopes is not affordable in low resource settings. To perform a diagnosis of tuberculosis using the MODS assay, images with modest quality are enough for proper interpretation. Therefore, the use of a high cost commercial inverted optical microscope is not indispensable. In this study, we designed a prototype of an optical inverted microscope created by 3D-printing and based on a smartphone. The system was evaluated with 226 MODS TB positive and 207 MODS TB negative digital images. These images were obtained from 10 sputum samples MODS positive and 10 sputum samples MODS negative. The quality of all images was assessed by a qualified technician, in terms of adequacy to interpret and classify them as positive or negative for tuberculosis. The quality of the images was considered appropriate for MODS interpretation. All the 20 samples were correctly classified (as TB positive/negative) by reading with the prototype 3D-printed inverted microscope.
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Affiliation(s)
- Mario Salguedo
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Guillermo Zarate
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Jorge Coronel
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Germán Comina
- Laboratorio de Ingeniería Física.Facultad de Ciencias. Universidad Nacional de Ingeniería. Av. Tupac Amaru 210, Rimac. Lima 25, Peru
| | - Robert H Gilman
- Department of International Health, School of Public Health, Johns Hopkins University. Baltimore, USA
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Lima, Peru
| | - Richard Oberhelman
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia. Lima, Peru.
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17
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Tohma K, Saito M, Pajuelo MJ, Mayta H, Zimic M, Lepore CJ, Ford-Siltz LA, Gilman RH, Parra GI. Viral intra-host evolution in immunocompetent children contributes to human norovirus diversification at the global scale. Emerg Microbes Infect 2021; 10:1717-1730. [PMID: 34376124 PMCID: PMC8425682 DOI: 10.1080/22221751.2021.1967706] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 06/07/2021] [Revised: 07/30/2021] [Accepted: 08/08/2021] [Indexed: 11/03/2022]
Abstract
Norovirus is a major cause of acute gastroenteritis. Human noroviruses present >30 different genotypes, with a single genotype (GII.4) predominating worldwide. Concurrent outbreaks of norovirus are often associated with the emergence of new viruses. While different hypotheses have been presented, the source of new mutations in noroviruses is still unknown. In this study, we applied high-resolution sequencing to determine the intra-host viral diversity presented by noroviruses during the acute and shedding phase of infection in children. Profiling viral intra-host diversification at nearly full genome level indicated that GII.4 viruses presented dynamic intra-host variation, while non-GII.4 viruses presented minimal variation throughout the infection. Notably, the intra-host genetic variation during the shedding phase recapitulates the genetic diversity observed at the global level, particularly those mapping at the VP1 antigenic sites. Thus the intra-host evolution in healthy children explains the source of norovirus mutations that results in diversification at the global scale.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Monica J. Pajuelo
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cara J Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, MD, USA
| | | | - Robert H. Gilman
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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18
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Rabanal J, Zimic M. Statistical analysis of 484 Mycobacterium tuberculosis genomes reveals an association between single nucleotide polymorphisms on ponA1 gene and LAM and Haarlem lineages. Infect 2021. [DOI: 10.22354/in.v26i2.1017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Objectives: Evaluate the association between rifampicin resistance and the presence of at least one SNP in the rpoB and ponA1 genes and the spoligotype defined lineages. Material and Methods: This study analyzed two databases of 484 genomes of M. tuberculosis from strains isolated from patients in the cities of Lima and Callao, for which the odds ratio (OR) was calculated considering belonging to a certain spoligotype defined lineages as an exposure factor. Results: No statistically significant association (? value> 0.05) was found between the presence of at least one SNP in the rpoB gene and the lineages included in the study (LAM, Haarlem, T and Beijing). However, a statistically significant association was found between the presence of at least one SNP in the ponA1 gene and the LAM and Haarlem lineages (? value <0.05). An association was found between the P631S SNP in the ponA1 gene and the LAM and Haarlem lineages; and the A516T SNP, of this same gene, presented an association with the LAM lineage. Likewise, an association was found between rifampicin resistance and the LAM lineage. Conclusions: The presence of SNPs in the ponA1 gene is associated with the LAM and Haarlem lineages.
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19
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Schiaffino F, Ferradas C, Jara LM, Salvatierra G, Dávila-Barclay A, Sanchez-Carrion C, Ulloa A, Mascaro L, Pajuelo MJ, Guevara Sarmiento L, Fernandez M, Zimic M. First Detection and Genome Sequencing of SARS-CoV-2 Lambda (C.37) Variant in Symptomatic Domestic Cats in Lima, Peru. Front Vet Sci 2021; 8:737350. [PMID: 34604373 PMCID: PMC8484519 DOI: 10.3389/fvets.2021.737350] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/23/2021] [Indexed: 01/10/2023] Open
Abstract
The role of domestic cats in the dynamics of SARS-CoV-2 remains poorly characterized, especially in epidemiologic contexts of countries with high viral transmission. Here, we report the first evidence of SARS-CoV-2 Lambda variant of interest in symptomatic domestic cats whose owners were diagnosed with COVID-19 in Lima, Peru, providing evidence that transmission of this new variant in domestic cats is occurring. More epidemiological studies are required to further characterize the role of domestic animals in the transmission dynamics of SARS-CoV-2.
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Affiliation(s)
- Francesca Schiaffino
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cusi Ferradas
- Unidad de Investigación en Enfermedades Emergentes y Cambio Climático (Emerge), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luis M. Jara
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Guillermo Salvatierra
- Unidad de Investigación en Enfermedades Emergentes y Cambio Climático (Emerge), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | - Lucero Mascaro
- Laboratorio de Microbiología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Monica J. Pajuelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - Mirko Zimic
- Farmacologicos Veterinarios (FARVET), Chincha, Peru
- Laboratorio de Bioinformatica, Biologia Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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20
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Jara LM, Ferradas C, Schiaffino F, Sánchez-Carrión C, Martínez-Vela A, Ulloa A, Isasi-Rivas G, Montalván A, Sarmiento LG, Fernández M, Zimic M. Evidence of neutralizing antibodies against SARS-CoV-2 in domestic cats living with owners with a history of COVID-19 in Lima - Peru. One Health 2021; 13:100318. [PMID: 34462726 PMCID: PMC8388143 DOI: 10.1016/j.onehlt.2021.100318] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/26/2022] Open
Abstract
SARS-CoV-2 can infect a variety of wild and domestic animals worldwide. Of these, domestic cats are highly susceptible species and potential viral reservoirs. As such, it is important to investigate disease exposure in domestic cats in areas with active community transmission and high disease prevalence. In this report we demonstrate the presence of serum neutralizing antibodies against the receptor binding-domain (RBD) of the SARS-CoV-2 in cats whose owners had been infected with SARS-CoV-2 in Lima, Peru, using a commercial competitive ELISA SARS-CoV-2 Surrogate Virus Neutralization Test. Out of 41 samples, 17.1% (7/41) and 31.7% (13/41) were positive, using the cut-off inhibition value of 30% and 20%, respectively. Not all cats living in a single house had detectable neutralizing antibodies showing heterogenous exposure and immunity among cohabiting animals. This is the first report of SARS-COV-2 exposure of domestic cats in Lima, Peru. Further studies are required to ascertain the prevalence of SARS-COV-2 exposure among domestic cats.
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Affiliation(s)
- Luis M Jara
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cusi Ferradas
- Unidad de Investigación en Enfermedades Emergentes y Cambio Climático (Emerge), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Schiaffino
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | | | | | | | | | - Mirko Zimic
- Farmacológicos Veterinarios (FARVET), Chincha, Peru.,Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Universidad Peruana Cayetano Heredia, Lima, Peru
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21
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Jiménez-Avalos G, Vargas-Ruiz AP, Delgado-Pease NE, Olivos-Ramirez GE, Sheen P, Fernández-Díaz M, Quiliano M, Zimic M. Comprehensive virtual screening of 4.8 k flavonoids reveals novel insights into allosteric inhibition of SARS-CoV-2 M PRO. Sci Rep 2021; 11:15452. [PMID: 34326429 PMCID: PMC8322093 DOI: 10.1038/s41598-021-94951-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 02/11/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 main protease is a common target for inhibition assays due to its high conservation among coronaviruses. Since flavonoids show antiviral activity, several in silico works have proposed them as potential SARS-CoV-2 main protease inhibitors. Nonetheless, there is reason to doubt certain results given the lack of consideration for flavonoid promiscuity or main protease plasticity, usage of short library sizes, absence of control molecules and/or the limitation of the methodology to a single target site. Here, we report a virtual screening study where dorsilurin E, euchrenone a11, sanggenol O and CHEMBL2171598 are proposed to inhibit main protease through different pathways. Remarkably, novel structural mechanisms were observed after sanggenol O and CHEMBL2171598 bound to experimentally proven allosteric sites. The former drastically affected the active site, while the latter triggered a hinge movement which has been previously reported for an inactive SARS-CoV main protease mutant. The use of a curated database of 4.8 k flavonoids, combining two well-known docking software (AutoDock Vina and AutoDock4.2), molecular dynamics and MMPBSA, guaranteed an adequate analysis and robust interpretation. These criteria can be considered for future screening campaigns against SARS-CoV-2 main protease.
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Affiliation(s)
- Gabriel Jiménez-Avalos
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru.
| | - A Paula Vargas-Ruiz
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Nicolás E Delgado-Pease
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Gustavo E Olivos-Ramirez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru
| | | | - Miguel Quiliano
- Faculty of Health Sciences, Centre for Research and Innovation, Universidad Peruana de Ciencias Aplicadas (UPC), 15023, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Departamento de Ciencias Celulares y Moleculares, Universidad Peruana Cayetano Heredia (UPCH), 15102, Lima, Peru.
- Farmacológicos Veterinarios - FARVET S.A.C. Chincha, Lima, Peru.
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22
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Tohma K, Lepore CJ, Martinez M, Degiuseppe JI, Khamrin P, Saito M, Mayta H, Nwaba AUA, Ford-Siltz LA, Green KY, Galeano ME, Zimic M, Stupka JA, Gilman RH, Maneekarn N, Ushijima H, Parra GI. Genome-wide analyses of human noroviruses provide insights on evolutionary dynamics and evidence of coexisting viral populations evolving under recombination constraints. PLoS Pathog 2021; 17:e1009744. [PMID: 34255807 PMCID: PMC8318288 DOI: 10.1371/journal.ppat.1009744] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/28/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
Norovirus is a major cause of acute gastroenteritis worldwide. Over 30 different genotypes, mostly from genogroup I (GI) and II (GII), have been shown to infect humans. Despite three decades of genome sequencing, our understanding of the role of genomic diversification across continents and time is incomplete. To close the spatiotemporal gap of genomic information of human noroviruses, we conducted a large-scale genome-wide analyses that included the nearly full-length sequencing of 281 archival viruses circulating since the 1970s in over 10 countries from four continents, with a major emphasis on norovirus genotypes that are currently underrepresented in public genome databases. We provided new genome information for 24 distinct genotypes, including the oldest genome information from 12 norovirus genotypes. Analyses of this new genomic information, together with those publicly available, showed that (i) noroviruses evolve at similar rates across genomic regions and genotypes; (ii) emerging viruses evolved from transiently-circulating intermediate viruses; (iii) diversifying selection on the VP1 protein was recorded in genotypes with multiple variants; (iv) non-structural proteins showed a similar branching on their phylogenetic trees; and (v) contrary to the current understanding, there are restrictions on the ability to recombine different genomic regions, which results in co-circulating populations of viruses evolving independently in human communities. This study provides a comprehensive genetic analysis of diverse norovirus genotypes and the role of non-structural proteins on viral diversification, shedding new light on the mechanisms of norovirus evolution and transmission. Norovirus is a highly diverse enteric pathogen. The large genomic database accumulated in the last three decades advanced our understanding of norovirus diversity; however, this information is limited by geographical bias, sporadic times of collection, and missing or incomplete genome sequences. In this multinational collaborative study, we mined archival samples collected since the 1970s and sequenced nearly full-length new genomes from 281 historical noroviruses, including the first full-length genomic sequences for three genotypes. Using this novel dataset, we found evidence for restrictions in the recombination of genetically disparate viruses and that diversifying selection results in new variants with different epidemiological profiles. These new insights on the diversification of noroviruses could provide baseline information for the study of future epidemics and ultimately the prevention of norovirus infections.
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Affiliation(s)
- Kentaro Tohma
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Cara J. Lepore
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Magaly Martinez
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- IICS, National University of Asuncion, Asuncion, Paraguay
| | | | - Pattara Khamrin
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Holger Mayta
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Amy U. Amanda Nwaba
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Lauren A. Ford-Siltz
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
| | - Kim Y. Green
- Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | | | - Mirko Zimic
- Department of Cellular and Molecular Sciences, Faculty of Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Robert H. Gilman
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Niwat Maneekarn
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
| | - Hiroshi Ushijima
- Division of Microbiology, Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo, Japan
| | - Gabriel I. Parra
- Division of Viral Products, CBER, FDA, Silver Spring, Maryland, United States of America
- * E-mail:
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23
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Jara LM, Ferradas C, Schiaffino F, Sánchez-Carrión C, Martinez A, Ulloa A, Isasi-Rivas G, Montalván A, Sarmiento LG, Fernández M, Zimic M. Evidence of neutralizing antibodies against SARS-CoV-2 in domestic cats living with owners with a history of COVID-19 in Lima - Peru. bioRxiv 2021:2021.05.26.445880. [PMID: 34075379 PMCID: PMC8168392 DOI: 10.1101/2021.05.26.445880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
SARS-CoV-2 can infect a variety of wild and domestic animals worldwide. Of these, domestic cats are highly susceptible species and potential viral reservoirs. As such, it is important to investigate disease exposure in areas with active community transmission and high disease prevalence. In this report we demonstrate the presence of serum neutralizing antibodies against the receptor binding-domain (RBD) of the SARS-CoV-2 in cats whose owners had been infected with SARS-CoV-2 in Lima, Peru, using a commercial competitive ELISA SARS-CoV-2 Surrogate Virus Neutralization Test. Out of 41 samples, 17.1% (7/41) and 31.7% (13/41) were positive, using the cut-off inhibition value of 30% and 20%, respectively. Not all cats living in a single house had detectable neutralizing antibodies showing that heterogenous exposure and immune among cohabiting animals. This is the first report of SARS-COV-2 exposure of domestic cats in Lima, Peru. Further studies are required to ascertain the prevalence of SARS-COV-2 exposure among domestic cats of Lima, Peru.
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Affiliation(s)
- Luis M. Jara
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cusi Ferradas
- Unidad de Investigación en Enfermedades Emergentes y Cambio Climático (Emerge), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Francesca Schiaffino
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | | | | | | | | | | | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Universidad Peruana Cayetano Heredia, Lima, Peru
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24
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Tohma K, Lepore CJ, Degiuseppe JI, Stupka JA, Saito M, Mayta H, Zimic M, Ford-Siltz LA, Gilman RH, Parra GI. Recombinant Nontypeable Genotype II Human Noroviruses in the Americas. Emerg Infect Dis 2021; 26:157-159. [PMID: 31855537 PMCID: PMC6924879 DOI: 10.3201/eid2601.190626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We report multiple nontypeable genotype II noroviruses circulating in South America; nucleotides differed by >25% from those of other genotypes. These viruses have been circulating in the Americas for ≈20 years and show recombination with other genotypes. Clues to norovirus natural history can guide development of treatment and prevention plans.
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25
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Florentini EA, Angulo N, Gilman RH, Alcántara R, Roncal E, Antiparra R, Toscano E, Vallejos K, Kirwan DE, Zimic M, Sheen P. Correction: Immunological detection of pyrazine-2-carboxylic acid for the detection of pyrazinamide resistance in Mycobacterium tuberculosis. PLoS One 2021; 16:e0259439. [PMID: 34705897 PMCID: PMC8550419 DOI: 10.1371/journal.pone.0259439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pone.0241600.].
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26
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Florentini EA, Angulo N, Gilman RH, Alcántara R, Roncal E, Antiparra R, Toscano E, Vallejos K, Kirwan D, Zimic M, Sheen P. Immunological detection of pyrazine-2-carboxylic acid for the detection of pyrazinamide resistance in Mycobacterium tuberculosis. PLoS One 2020; 15:e0241600. [PMID: 33151985 PMCID: PMC7643994 DOI: 10.1371/journal.pone.0241600] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 10/17/2020] [Indexed: 11/18/2022] Open
Abstract
Pyrazinamide (PZA) susceptibility testing in Mycobacterium tuberculosis (Mtb) is a current area of development and PZA-resistant strains are increasingly prevalent. Previous studies have demonstrated that the detection of pyrazinoic acid (POA), the metabolite produced by the deamidation of PZA, is a good predictor for PZA resistance since a resistant strain would not convert PZA into POA at a critical required rate, whereas a susceptible strain will do, expelling POA to the extracellular environment at a certain rate, and allowing for quantification of this accumulated analyte. In order to quantify POA, an indirect competitive ELISA (icELISA) test using hyperimmune polyclonal rabbit serum against POA was developed: for this purpose, pure POA was first covalently linked to the highly immunogenic Keyhole Limpet Hemocyanine, and inoculated in rabbits. A construct made of bovine serum albumin (BSA) linked to pure POA and fixed at the bottom of wells was used as a competitor against spiked samples and liquid Mtb culture supernatants. When spiked samples (commercial POA alone) were analyzed, the half maximal inhibitory concentration (IC50) was 1.16 mg/mL, the limit of detection 200 μg/mL and the assay was specific (it did not detect PZA, IC50 > 20 mg/mL). However, culture supernatants (7H9-OADC-PANTA medium) disrupted the competition and a proper icELISA curve was not obtainable. We consider that, although we have shown that it is feasible to induce antibodies against POA, matrix effects could damage its analytical usefulness; multiple, upcoming ways to solve this obstacle are suggested.
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Affiliation(s)
- Edgar A. Florentini
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Noelia Angulo
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Roberto Alcántara
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Ricardo Antiparra
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Emily Toscano
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Katherine Vallejos
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Danni Kirwan
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, San Martín de Porras, Lima, Perú
- * E-mail:
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27
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Ramos-Sono D, Laureano R, Rueda D, Gilman RH, La Rosa A, Ruiz J, León R, Sheen P, Zimic M. An electrochemical biosensor for the detection of Mycobacterium tuberculosis DNA from sputum and urine samples. PLoS One 2020; 15:e0241067. [PMID: 33112923 PMCID: PMC7592764 DOI: 10.1371/journal.pone.0241067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/08/2020] [Indexed: 11/25/2022] Open
Abstract
Tuberculosis (TB) is a major global public health problem with high mortality and morbidity. In low-middle income countries (LMIC) a large number of respiratory symptomatic cases that require TB screening per year demands more accurate, fast and affordable testing for TB diagnostics. Sputum smear is the initial screening test in LMICs, however, its sensitivity is limited in patients with low sputum bacilli load. The same limitation is observed in the currently available molecular tests. We designed, standardized and evaluated an electrochemical biosensor that detects the highly specific DNA insertion element 6110 (IS6110). A PCR amplified DNA product is hybridized on the surface of the working electrode built on FTO-Glass with immobilized specific DNA probes, after which cyclic voltammetry is performed with an Ag/AgCl reference electrode and a platinum counter electrode. The response of the sensor was measured by the ratio (cathodic peak current of the hybridized sensor) / (cathodic peak current of the non-hybridized sensor). We tested the biosensor, using positive hybridization control sequences, genomic DNA extracted from M. tuberculosis strains and sputum of TB patients, and extracted DNA from the urine of healthy controls spiked with M. tuberculosis DNA. This biosensor was effective for the detection of M. tuberculosis DNA with a detection limit of 16 fM in sputum sample and 1 fM in spiked urine samples. The low cost and the relatively brief duration of the assay make this an important TB screening tool in the fight against tuberculosis.
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Affiliation(s)
- Daniel Ramos-Sono
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Raúl Laureano
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Daniel Rueda
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Adolfo La Rosa
- Laboratorio de Electroquímica, Facultad de Ciencias, Universidad Nacional de Ingeniería, Lima, Perú
| | - Jesús Ruiz
- Laboratorio de Metalurgia y Ciencias de Materiales, NDT Innovations, Inc., Lima, Perú
| | - Raúl León
- Laboratorio de Metalurgia y Ciencias de Materiales, NDT Innovations, Inc., Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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28
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Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
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Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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29
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Lee GO, Comina G, Hernandez-Cordova G, Naik N, Gayoso O, Ticona E, Coronel J, Evans CA, Zimic M, Paz-Soldan VA, Gilman RH, Oberhelman R. Cough dynamics in adults receiving tuberculosis treatment. PLoS One 2020; 15:e0231167. [PMID: 32511248 PMCID: PMC7279573 DOI: 10.1371/journal.pone.0231167] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 03/17/2020] [Indexed: 11/19/2022] Open
Abstract
Cough is a characteristic symptom of tuberculosis, is the main cause of transmission, and is used to assess treatment response. We aimed to identify the best measure of cough severity and characterize changes during initial tuberculosis therapy. We conducted a prospective cohort of recently diagnosed ambulatory adult patients with pulmonary tuberculosis in two tertiary hospitals in Lima, Peru. Pre-treatment and five times during the first two months of treatment, a vibrometer was used to capture 4-hour recordings of involuntary cough. A total of 358 recordings from 69 participants were analyzed using a computer algorithm. Total time spent coughing (seconds per hour) was a better predictor of microbiologic indicators of disease severity and treatment response than the frequency of cough episodes or cough power. Patients with prior tuberculosis tended to cough more than patients without prior tuberculosis, and patients with tuberculosis and diabetes coughed more than patients without diabetes co-morbidity. Cough characteristics were similar regardless of HIV co-infection and for drug-susceptible versus drug-resistant tuberculosis. Tuberculosis treatment response may be meaningfully assessed by objectively monitoring the time spent coughing. This measure demonstrated that cough was increased in patients with TB recurrence or co-morbid diabetes, but not because of drug resistance or HIV co-infection.
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Affiliation(s)
- Gwenyth O. Lee
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana, United States of America
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Germán Comina
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana, United States of America
| | - Gustavo Hernandez-Cordova
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana, United States of America
| | - Nehal Naik
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Oscar Gayoso
- Pulmonology Department, Hospital Nacional Cayetano Heredia, Lima, Peru
| | - Eduardo Ticona
- Facultad de Medicina, Universidad Nacional Mayor de San Marcos, San Marcos, Peru
- Servicio de Enfermedades Infecciosas y Tropicales, Hospital Nacional Dos de Mayo Lima, Mayo, Lima, Perú
| | - Jorge Coronel
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Carlton A. Evans
- Asociación Benéfica PRISMA, Lima, Perú
- Laboratory of Research and Development, Innovation For Health And Development (IFHAD), Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Mirko Zimic
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Valerie A. Paz-Soldan
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana, United States of America
- Asociación Benéfica PRISMA, Lima, Perú
| | - Robert H. Gilman
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociación Benéfica PRISMA, Lima, Perú
- Department of International Health, Program in Global Disease Epidemiology and Control, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Richard Oberhelman
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana, United States of America
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Vallejos-Sánchez K, Lopez JM, Antiparra R, Toscano E, Saavedra H, Kirwan DE, Amzel LM, Gilman RH, Maruenda H, Sheen P, Zimic M. Mycobacterium tuberculosis ribosomal protein S1 (RpsA) and variants with truncated C-terminal end show absence of interaction with pyrazinoic acid. Sci Rep 2020; 10:8356. [PMID: 32433489 PMCID: PMC7239899 DOI: 10.1038/s41598-020-65173-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 12/23/2019] [Accepted: 04/29/2020] [Indexed: 01/31/2023] Open
Abstract
Pyrazinamide (PZA) is an antibiotic used in first- and second-line tuberculosis treatment regimens. Approximately 50% of multidrug-resistant tuberculosis and over 90% of extensively drug-resistant tuberculosis strains are also PZA resistant. Despite the key role played by PZA, its mechanisms of action are not yet fully understood. It has been postulated that pyrazinoic acid (POA), the hydrolyzed product of PZA, could inhibit trans-translation by binding to Ribosomal protein S1 (RpsA) and competing with tmRNA, the natural cofactor of RpsA. Subsequent data, however, indicate that these early findings resulted from experimental artifact. Hence, in this study we assess the capacity of POA to compete with tmRNA for RpsA. We evaluated RpsA wild type (WT), RpsA ∆A438, and RpsA ∆A438 variants with truncations towards the carboxy terminal end. Interactions were measured using Nuclear Magnetic Resonance spectroscopy (NMR), Isothermal Titration Calorimetry (ITC), Microscale Thermophoresis (MST), and Electrophoretic Mobility Shift Assay (EMSA). We found no measurable binding between POA and RpsA (WT or variants). This suggests that RpsA may not be involved in the mechanism of action of PZA in Mycobacterium tuberculosis, as previously thought. Interactions observed between tmRNA and RpsA WT, RpsA ∆A438, and each of the truncated variants of RpsA ∆A438, are reported.
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Affiliation(s)
- Katherine Vallejos-Sánchez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Juan M Lopez
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Emily Toscano
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Harry Saavedra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - Daniela E Kirwan
- Infection and Immunity Research Institute, St George's, University of London, London, England
| | - L M Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD., USA
| | - R H Gilman
- International Health Department. Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Helena Maruenda
- Pontificia Universidad Católica del Perú, Departamento de Ciencias, Sección Química, Centro de Espectroscopía de Resonancia Magnética Nuclear (CERMN), Lima, Perú
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Perú.
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31
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León-Janampa N, Zimic M, Shinkaruk S, Quispe-Marcatoma J, Gutarra A, Le Bourdon G, Gayot M, Changanaqui K, Gilman RH, Fouquet E, Sheen P, Szlosek M. Synthesis, characterization and bio-functionalization of magnetic nanoparticles to improve the diagnosis of tuberculosis. Nanotechnology 2020; 31:175101. [PMID: 31931490 DOI: 10.1088/1361-6528/ab6ab1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mycobacterium tuberculosis is the cause of one of the diseases with the highest mortality and morbidity rate in the Americas and in the world. In developing countries, the diagnosis of tuberculosis (TB) is based on baciloscopy and bacteriological cultures. The first method has a low sensitivity, and the second can take several weeks to reach a confirmatory diagnosis. The lack of a rapid diagnosis compromises the efforts to control this disease and favors the transmission of tuberculosis to the susceptible population. In this work, we present the synthesis, amine-silanization, characterization and bio-functionalization of magnetic nanoparticles (MNPs) to develop a sandwich ELISA to detect and concentrate antigens from M. tuberculosis. For this purpose, a recombinant mycobacterial heat shock protein Hsp16.3, which contributes to the persistence of TB, was cloned and expressed in the E. coli system. Polyclonal antibodies anti-Hsp16.3 were produced in a rabbit and in mice. Magnetic nanoparticles were synthesized by co-precipitation, amine-functionalized and characterized by several physical-chemical methods. The XRD, Mossbauer spectroscopy, zeta potential, TEM, and FTIR all proved the successful preparation of the MNPs showing a diffraction crystal diameter of 10.48 ± 2.56 nm, superficial net charge of [Formula: see text]: +23.57 ± 2.87 mV, characteristic patterns of magnetite and a structure similar to a sphere. Additionally, it showed a magnetization saturation of 37.06 emu.g-1. For the functionalization of nanoparticle surfaces with anti-Hsp16.3, the active ester method was used for bond formation, and parameters such as time of incubation, coupling agents ratio (EDC/NHS) and concentration as well as surface saturation level of amine-silanized MNPs (MNP@Si@NH2) were standardized. Finally, bio-functionalized MNPs were used to detect, fix and concentrate the recombinant antigen Hsp16.3 from M. tuberculosis in a sandwich ELISA-MNP assay.
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Affiliation(s)
- Nancy León-Janampa
- Laboratorio de Bioinformática y Biología Molecular. Facultad de Ciencias y Filosofía. Universidad Peruana Cayetano Heredia, Lima, Peru. Univ. Bordeaux, ISM, Institut des Sciences Moléculaires, UMR 5255 CNRS, 33405 Talence, France
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32
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Ramírez-Salinas GL, García-Machorro J, Rojas-Hernández S, Campos-Rodríguez R, de Oca ACM, Gomez MM, Luciano R, Zimic M, Correa-Basurto J. Bioinformatics design and experimental validation of influenza A virus multi-epitopes that induce neutralizing antibodies. Arch Virol 2020; 165:891-911. [PMID: 32060794 PMCID: PMC7222995 DOI: 10.1007/s00705-020-04537-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 05/28/2019] [Accepted: 12/11/2019] [Indexed: 02/01/2023]
Abstract
Pandemics caused by influenza A virus (IAV) are responsible for the deaths of millions of humans around the world. One of these pandemics occurred in Mexico in 2009. Despite the impact of IAV on human health, there is no effective vaccine. Gene mutations and translocation of genome segments of different IAV subtypes infecting a single host cell make the development of a universal vaccine difficult. The design of immunogenic peptides using bioinformatics tools could be an interesting strategy to increase the success of vaccines. In this work, we used the predicted amino acid sequences of the neuraminidase (NA) and hemagglutinin (HA) proteins of different IAV subtypes to perform multiple alignments, epitope predictions, molecular dynamics simulations, and experimental validation. Peptide selection was based on the following criteria: promiscuity, protein surface exposure, and the degree of conservation among different medically relevant IAV strains. These peptides were tested using immunological assays to test their ability to induce production of antibodies against IAV. We immunized rabbits and mice and measured the levels of IgG and IgA antibodies in serum samples and nasal washes. Rabbit antibodies against the peptides P11 and P14 (both of which are hybrids of NA and HA) recognized HA from both group 1 (H1, H2, and H5) and group 2 (H3 and H7) IAV and also recognized the purified NA protein from the viral stock (influenza A Puerto Rico/916/34). IgG antibodies from rabbits immunized with P11 and P14 were capable of recognizing viral particles and inhibited virus hemagglutination. Additionally, intranasal immunization of mice with P11 and P14 induced specific IgG and IgA antibodies in serum and nasal mucosa, respectively. Interestingly, the IgG antibodies were found to have neutralizing capability. In conclusion, the peptides designed through in silico studies were validated in experimental assays.
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Affiliation(s)
- G Lizbeth Ramírez-Salinas
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Jazmín García-Machorro
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
| | - Saúl Rojas-Hernández
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rafael Campos-Rodríguez
- Laboratorio de Bioquímica. Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Arturo Contis-Montes de Oca
- Laboratorio de Inmunología celular, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Miguel Medina Gomez
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Rocío Luciano
- Laboratorio de medicina de Conservación, Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - José Correa-Basurto
- Laboratorio de Diseño y Desarrollo de Nuevos Fármacos e Innovación Biotécnológica (Laboratory for the Design and Development of New Drugs and Biotechnological Innovation), Escuela Superior de Medicina, Instituto Politécnico Nacional, México City, 11340, México.
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Knight GM, Zimic M, Funk S, Gilman RH, Friedland JS, Grandjean L. The relative fitness of drug-resistant Mycobacterium tuberculosis: a modelling study of household transmission in Peru. J R Soc Interface 2019; 15:rsif.2018.0025. [PMID: 29950511 PMCID: PMC6030636 DOI: 10.1098/rsif.2018.0025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 01/11/2018] [Accepted: 06/05/2018] [Indexed: 12/22/2022] Open
Abstract
The relative fitness of drug-resistant versus susceptible bacteria in an environment dictates resistance prevalence. Estimates for the relative fitness of resistant Mycobacterium tuberculosis (Mtb) strains are highly heterogeneous and mostly derived from in vitro experiments. Measuring fitness in the field allows us to determine how the environment influences the spread of resistance. We designed a household structured, stochastic mathematical model to estimate the fitness costs associated with multidrug resistance (MDR) carriage in Mtb in Lima, Peru during 2010–2013. By fitting the model to data from a large prospective cohort study of TB disease in household contacts, we estimated the fitness, relative to susceptible strains with a fitness of 1, of MDR-Mtb to be 0.32 (95% credible interval: 0.15–0.62) or 0.38 (0.24–0.61), if only transmission or progression to disease, respectively, was affected. The relative fitness of MDR-Mtb increased to 0.56 (0.42–0.72) when the fitness cost influenced both transmission and progression to disease equally. We found the average relative fitness of MDR-Mtb circulating within households in Lima, Peru during 2010–2013 to be significantly lower than concurrent susceptible Mtb. If these fitness levels do not change, then existing TB control programmes are likely to keep MDR-TB prevalence at current levels in Lima, Peru.
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Affiliation(s)
- Gwenan M Knight
- National Institute of Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK .,Infectious Diseases and Immunity, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Centre for the Mathematical Modelling of Infectious Diseases, Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,TB Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru
| | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
| | - Robert H Gilman
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru.,Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe Street, Baltimore, MD 21205, USA
| | - Jon S Friedland
- Infectious Diseases and Immunity, Imperial College London, Commonwealth Building, Hammersmith Campus, Du Cane Road, London W12 0NN, UK.,Wellcome Trust Imperial College Centre for Global Health, St Mary's Hospital Campus, Imperial College London, Praed Street, London, W2 1NY, UK
| | - Louis Grandjean
- TB Centre, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.,Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, 31 Avenue Honorio Delgado 430, Distrito de Lima, Peru.,Wellcome Trust Imperial College Centre for Global Health, St Mary's Hospital Campus, Imperial College London, Praed Street, London, W2 1NY, UK
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Lopez JM, Antiparra R, Lippens G, Zimic M, Sheen P, Maruenda H. Backbone chemical shift assignment of macrophage infectivity potentiator virulence factor of Trypanosoma cruzi. Biomol NMR Assign 2019; 13:21-25. [PMID: 30229449 DOI: 10.1007/s12104-018-9844-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/14/2018] [Indexed: 06/08/2023]
Abstract
Chagas disease is a trypanosomiasis disease inflicted by Trypanosoma cruzi parasite. In Latin America, at least 10 million people are infected and annually, 10,000 casualties are deplored. Macrophage infectivity potentiator protein is one of the major virulence factors secreted by T. cruzi (TcMIP) in order to infect its host but little is known about its mechanism of action. Studies confer TcMIP an important role in the extracellular matrix transmigration and basal lamina penetration. Here, we report the backbone 1H, 13C, and 15N resonance assignment of TcMIP and the comparison of the secondary structure obtained against reported X-ray crystallography data.
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Affiliation(s)
- Juan M Lopez
- Centro de Espectroscopia de Resonancia Magnética Nuclear (CERMN), Departamento de Ciencias - Química, Pontificia Universidad Católica del Perú, Lima, Peru.
| | - Ricardo Antiparra
- Centro de Espectroscopia de Resonancia Magnética Nuclear (CERMN), Departamento de Ciencias - Química, Pontificia Universidad Católica del Perú, Lima, Peru
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Helena Maruenda
- Centro de Espectroscopia de Resonancia Magnética Nuclear (CERMN), Departamento de Ciencias - Química, Pontificia Universidad Católica del Perú, Lima, Peru
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Rueda D, Bernard C, Gandy L, Capton E, Boudjelloul R, Brossier F, Veziris N, Zimic M, Sougakoff W. Estimation of pyrazinamidase activity using a cell-free In vitro synthesis of pnca and its association with pyrazinamide susceptibility in Mycobacterium tuberculosis. Int J Mycobacteriol 2019. [PMID: 29516881 DOI: 10.4103/ijmy.ijmy_187_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background The main mechanism of resistance to PZA in Mycobacterium tuberculosis relies on mutations on its pyrazinamidase/nicotinamidase. Recently, a rapid colorimetric test relying on the PCR-based in vitro-synthesized-PZase assay has been reported for PZase activity determination from clinical M. tuberculosis isolates but the assay has not been compared with other tests to evaluate PZA susceptibility in M. tuberculosis isolates. Methods In this study, we have used the PCR-based in vitro-synthesized-PZase assay to analyze the specific pyrazinamidase (PZase) activity of PncA mutants and have correlated the results to the PZA susceptibility phenotype determined by culture in acidic agar medium at pH 6.0. A set of 23 clinical isolates displaying mutated pncA genes (11 PZA-resistant and 12 PZA-susceptible) and 55 PZA-susceptible clinical strains displaying a wild-type pncA gene were tested. Results Among the 23 mutants tested, 4 corresponded to mutations not reported before (I5T, Y99S, T142R and P77L+V131G). Of the 11 PncA mutants expressed from PZA-resistant clinical isolates, 9 were expressed in vitro at yields > 50% relative to the wild type enzyme. Among them, 6 enzymes (T47P, H51P, H51R, H57D, L85R and T142R) showed no detectable activity, while the relative activities for the 3 others, V9A (27%), G97D (10%) and A146V (28%) were low compared to the wild-type PZase. The remaining two mutants, I5T and V9G, presented very low relative expression (5%) and relative activities values of 12 and 1%, respectively. Twelve mutants were expressed from PZA-susceptible isolates. Their expression was similar to the wild type enzyme and behaved as active pyrazinamidase with specific relative activities ranging from 34 to 314%. Finally, discrepant results were observed for two mutants, V7A and P62T. Conclusion Thus, this study provides the proof of concept that the PCR-based in vitro-synthesized-PZase assay represents a promising rapid approach for the evaluation of PZA susceptibility based on the estimation of the relative PZase activity from clinical isolates.
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Affiliation(s)
- Daniel Rueda
- Sorbonne Universités, Université Pierre et Marie Curie, UPMC Univ Paris 06, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), team 13, Paris, France; Laboratorio de Bioinformatica y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Christine Bernard
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyRMA), Bactériologie-Hygiène, Paris, France
| | - Lucas Gandy
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyRMA), Bactériologie-Hygiène, Paris, France
| | - Estelle Capton
- Sorbonne Universités, Université Pierre et Marie Curie, UPMC Univ Paris 06, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), team 13, Paris, France
| | - Rachid Boudjelloul
- Sorbonne Universités, Université Pierre et Marie Curie, UPMC Univ Paris 06, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), team 13, Paris, France
| | - Florence Brossier
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyRMA), Bactériologie-Hygiène, Paris, France
| | - Nicolas Veziris
- AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyRMA), Bactériologie-Hygiène, Paris, France
| | - Mirko Zimic
- Laboratorio de Bioinformatica y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Wladimir Sougakoff
- Sorbonne Universités, Université Pierre et Marie Curie, UPMC Univ Paris 06, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), team 13; AP-HP, Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux (NRC MyRMA), Bactériologie-Hygiène, Paris, France
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León-Janampa N, Liendo R, Gilman RH, Padilla C, García HH, Gonzales A, Sheen P, Pajuelo MJ, Zimic M. Characterization of a novel cathepsin L-like protease from Taenia solium metacestodes for the immunodiagnosis of porcine cysticercosis. Vet Parasitol 2019; 267:9-16. [PMID: 30878092 PMCID: PMC7010362 DOI: 10.1016/j.vetpar.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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: 07/20/2018] [Revised: 01/12/2019] [Accepted: 01/14/2019] [Indexed: 11/19/2022]
Abstract
Porcine cysticercosis is an endemic parasitic disease caused by infection with Taenia solium that is found predominantly in developing countries. In order to aid in the development of simple diagnostic approaches, identification and characterization of potential new antigens for immunodiagnostic purposes is desired. The cysteine protease family has previously been found to have important immunodiagnostic properties. These proteases are expressed as zymogens which contain a signal peptide, pro-peptide, and an active domain. Subsequent catalytic cleavage of the pro-peptide converts these zymogens into enzymes. With the use of bioinformatic tools we identified an active domain of a novel cathepsin L-like cysteine protease (TsolCL) in the T. solium genome. The TsolCL gene includes 705 nucleotides (nt) within a single intron and a 633 nt exonic sequence encoding an active protein of 211 amino acids. Sequence alignment and phylogenetic analysis suggest that the TsolCL gene is closely related to genes found in Echinoccocus granulosus and E. multiloculars. In addition, TsolCL was found to have a 61.9%-99.0% similarity to other cathepsin L proteins found in other helminths and mammals. We cloned, expressed, purified, and characterized the recombinant active TsolCL (27 kDa) using the baculovirus-insect cell expression system. TsolCL showed cysteine protease enzymatic activity with the capacity to hydrolyze the Z-Phe-Arg-AMC substrate as well as bovine serum albumin. However, TsolCL was not able to hydrolyze human immunoglobulin. In addition, TsolCL has cathepsin L conserved amino acid residues in the catalytic site (Gln8, Cys14, His159, Asn179 and Trp181) and the motif GCNGG. Using ELISA, TsolCL was able to distinguish circulating IgG antibodies between healthy animals and naturally infected pigs with cysticercosis, showing a moderate sensitivity of 83.33% (40/48; 95% CI: [69.8%-92.5 %]), and a specificity of 83.78% (31/37; 95% CI: [67.9%-93.8%]). In conclusion, a novel cathepsin L-like cysteine protease from a T. solium metacestode was expressed successfully in Baculovirus system and was evaluated as a candidate antigen to diagnose porcine cysticercosis using the ELISA immunoassay.
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Affiliation(s)
- Nancy León-Janampa
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Ruddy Liendo
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | | | - Hector H García
- Cysticercosis Unit, Instituto de Ciencias Neurológicas, Lima, Peru.
| | - Armando Gonzales
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru.
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
| | - Mónica J Pajuelo
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
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Lopez-Garnier S, Sheen P, Zimic M. Automatic diagnostics of tuberculosis using convolutional neural networks analysis of MODS digital images. PLoS One 2019; 14:e0212094. [PMID: 30811445 PMCID: PMC6392246 DOI: 10.1371/journal.pone.0212094] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/26/2019] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis is an infectious disease that causes ill health and death in millions of people each year worldwide. Timely diagnosis and treatment is key to full patient recovery. The Microscopic Observed Drug Susceptibility (MODS) is a test to diagnose TB infection and drug susceptibility directly from a sputum sample in 7-10 days with a low cost and high sensitivity and specificity, based on the visual recognition of specific growth cording patterns of M. Tuberculosis in a broth culture. Despite its advantages, MODS is still limited in remote, low resource settings, because it requires permanent and trained technical staff for the image-based diagnostics. Hence, it is important to develop alternative solutions, based on reliable automated analysis and interpretation of MODS cultures. In this study, we trained and evaluated a convolutional neural network (CNN) for automatic interpretation of MODS cultures digital images. The CNN was trained on a dataset of 12,510 MODS positive and negative images obtained from three different laboratories, where it achieved 96.63 +/- 0.35% accuracy, and a sensitivity and specificity ranging from 91% to 99%, when validated across held-out laboratory datasets. The model's learned features resemble visual cues used by expert diagnosticians to interpret MODS cultures, suggesting that our model may have the ability to generalize and scale. It performed robustly when validated across held-out laboratory datasets and can be improved upon with data from new laboratories. This CNN can assist laboratory personnel, in low resource settings, and is a step towards facilitating automated diagnostics access to critical areas in developing countries.
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Affiliation(s)
- Santiago Lopez-Garnier
- Unidad de Bioinformática / Laboratorio de Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía—Universidad Peruana Cayetano Heredia, Lima, Peru
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, United States of America
| | - Patricia Sheen
- Unidad de Bioinformática / Laboratorio de Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía—Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Unidad de Bioinformática / Laboratorio de Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía—Universidad Peruana Cayetano Heredia, Lima, Peru
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Correa M, Zimic M, Barrientos F, Barrientos R, Román-Gonzalez A, Pajuelo MJ, Anticona C, Mayta H, Alva A, Solis-Vasquez L, Figueroa DA, Chavez MA, Lavarello R, Castañeda B, Paz-Soldán VA, Checkley W, Gilman RH, Oberhelman R. Automatic classification of pediatric pneumonia based on lung ultrasound pattern recognition. PLoS One 2018; 13:e0206410. [PMID: 30517102 PMCID: PMC6281243 DOI: 10.1371/journal.pone.0206410] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/12/2018] [Indexed: 11/19/2022] Open
Abstract
Pneumonia is one of the major causes of child mortality, yet with a timely diagnosis, it is usually curable with antibiotic therapy. In many developing regions, diagnosing pneumonia remains a challenge, due to shortages of medical resources. Lung ultrasound has proved to be a useful tool to detect lung consolidation as evidence of pneumonia. However, diagnosis of pneumonia by ultrasound has limitations: it is operator-dependent, and it needs to be carried out and interpreted by trained personnel. Pattern recognition and image analysis is a potential tool to enable automatic diagnosis of pneumonia consolidation without requiring an expert analyst. This paper presents a method for automatic classification of pneumonia using ultrasound imaging of the lungs and pattern recognition. The approach presented here is based on the analysis of brightness distribution patterns present in rectangular segments (here called “characteristic vectors“) from the ultrasound digital images. In a first step we identified and eliminated the skin and subcutaneous tissue (fat and muscle) in lung ultrasound frames, and the “characteristic vectors”were analyzed using standard neural networks using artificial intelligence methods. We analyzed 60 lung ultrasound frames corresponding to 21 children under age 5 years (15 children with confirmed pneumonia by clinical examination and X-rays, and 6 children with no pulmonary disease) from a hospital based population in Lima, Peru. Lung ultrasound images were obtained using an Ultrasonix ultrasound device. A total of 1450 positive (pneumonia) and 1605 negative (normal lung) vectors were analyzed with standard neural networks, and used to create an algorithm to differentiate lung infiltrates from healthy lung. A neural network was trained using the algorithm and it was able to correctly identify pneumonia infiltrates, with 90.9% sensitivity and 100% specificity. This approach may be used to develop operator-independent computer algorithms for pneumonia diagnosis using ultrasound in young children.
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Affiliation(s)
- Malena Correa
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
- * E-mail:
| | - Mirko Zimic
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Franklin Barrientos
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ronald Barrientos
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Avid Román-Gonzalez
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
- Research and Development Laboratory, Science and Philosophy Faculty, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mónica J. Pajuelo
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Cynthia Anticona
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Holger Mayta
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
- Infectious Diseases Research Laboratory, Department of Cellular and Molecular Sciences, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alicia Alva
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Leonardo Solis-Vasquez
- Bioinformatics and Molecular Biology Laboratory, Department of Cellular and Molecular Sciences, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
- Research and Development Laboratory, Science and Philosophy Faculty, Universidad Peruana Cayetano Heredia, Lima, Perú
| | | | - Miguel A. Chavez
- Biomedical Research Unit, Asociación Benéfica Prisma, Lima, Peru
| | - Roberto Lavarello
- Laboratorio de Imágenes Médicas, Sección Electricidad y Electrónica, Departamento de Ingeniería Pontificia Universidad Católica del Perú, San Miguel, Lima, Perú
| | - Benjamín Castañeda
- Laboratorio de Imágenes Médicas, Sección Electricidad y Electrónica, Departamento de Ingeniería Pontificia Universidad Católica del Perú, San Miguel, Lima, Perú
| | - Valerie A. Paz-Soldán
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
| | - William Checkley
- Division of Pulmonary and Critical Care, School of Medicine, Johns Hopkins University, Maryland, United States of America
- Program in Global Disease Epidemiology and Control, Bloombeg School of Public Health, Johns Hopkins University, Maryland, United States of America
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Richard Oberhelman
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana, United States of America
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Best I, Privat-Maldonado A, Cruz M, Zimic M, Bras-Gonçalves R, Lemesre JL, Arévalo J. IFN-γ Response Is Associated to Time Exposure Among Asymptomatic Immune Responders That Visited American Tegumentary Leishmaniasis Endemic Areas in Peru. Front Cell Infect Microbiol 2018; 8:289. [PMID: 30186774 PMCID: PMC6111704 DOI: 10.3389/fcimb.2018.00289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 03/30/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Clinical manifestations of American Tegumentary Leishmaniasis (ATL) include cutaneous (CL) and mucous forms (ML); however, there are asymptomatic individuals who despite being infected do not present any clinical manifestations. This study characterized the cell-mediated immunity of travelers who lived in the Andean highlands of Cusco, free of leishmaniasis transmission, which eventually visited leishmaniasis endemic in the Amazonian basin and returned home without any clinical signs of the disease. Their immune response was compared with CL and ML patients who acquired the disease during their stage in the same region. Fifty-four human subjects from the highlands of Cusco (Peru), who have visited an endemic area, were enrolled: 28 of them did not show any symptoms, 12 showed CL and 14 showed ML. Ten healthy subjects from a non-endemic area (HS) were included as controls. T-cell proliferation was evaluated using peripheral blood mononuclear cells (PBMC) stimulated for 5 days with a total soluble leishmanial antigen (TSLA) of L. (V.) braziliensis. Th1/Th2/Th17 cytokines were also quantified in the supernatants by a flow cytometry multiplex assay. T-cell proliferation was expressed as stimulation index (SI) and the cut off was fixed at SI >2.47. Fifteen out of 28 subjects did not show any signs of disease (54%); subjects with an SI above the cut off. They were defined as asymptomatic immune responders (AIR). CL and ML patients presented a higher SI than HS and AIR. Among the latter group, the exposure time to Leishmania was clearly associated with the IFN-γ response. Increased levels of this cytokine were observed in individuals who remained <90 days in an endemic area of leishmaniasis. Our results evidenced two sub-populations among asymptomatic individuals, one AIR who did not develop clinical disease manifestations when they were exposed to Leishmania in endemic areas. Exposure time to Leishmania in the wild was associated with the IFN-γ response.
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Affiliation(s)
- Ivan Best
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Angela Privat-Maldonado
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - María Cruz
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorios de Investigación y Desarrollo, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Rachel Bras-Gonçalves
- Institut de Recherche pour le Développement (IRD), UMR177-INTERTRYP, Montpellier, France
| | - Jean-Loup Lemesre
- Institut de Recherche pour le Développement (IRD), UMR177-INTERTRYP, Montpellier, France
| | - Jorge Arévalo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Laboratorios de Investigación y Desarrollo, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, Lima, Peru
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Ponce R, León-Janampa N, Gilman RH, Liendo R, Roncal E, Luis S, Quiñones-Garcia S, Silverstein Z, García HH, Gonzales A, Sheen P, Zimic M, Pajuelo MJ. A novel enolase from Taenia solium metacestodes and its evaluation as an immunodiagnostic antigen for porcine cysticercosis. Exp Parasitol 2018; 191:44-54. [PMID: 29885292 DOI: 10.1016/j.exppara.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 08/12/2017] [Revised: 12/06/2017] [Accepted: 06/05/2018] [Indexed: 11/19/2022]
Abstract
Cysticercosis is a worldwide parasitic disease of humans and pigs principally caused by infection with the larvae of the pork tapeworm Taenia solium. Through the use of the recently-made-available T. solium genome, we identified a gene within a novel 1448 bp ORF that theoretically encodes for a 433 amino acid-long protein and predicted to be an α-enolase closely related to enolases of other flatworms. Additional bioinformatic analyses revealed a putative plasminogen-binding region on this protein, suggesting a potential role for this protein in pathogenesis. On this basis, we isolated the mRNA encoding for this presumptive enolase from T. solium metacestodes and reverse-transcribed it into cDNA before subsequently cloning and expressing it in both E. coli (rEnoTs) and insect cells (rEnoTsBac), in a 6xHis tagged manner. The molecular weights of these two recombinant proteins were ∼48 and ∼50 kDa, respectively, with the differences likely attributable to differential glycosylation. We used spectrophotometric assays to confirm the enolase nature of rEnoTs as well as to measure its enzymatic activity. The resulting estimates of specific activity (60.000 U/mg) and Km (0.091 mM) are quite similar to the catalytic characteristics of enolases of other flatworms. rEnoTs also exhibited high immunogenicity, eliciting a strong polyclonal antibody response in immunized rabbits. We subsequently employed rEnoTsBac for use in an ELISA aimed at discriminating between healthy pigs and those infected with T. solium. This diagnostic assay exhibited a sensitivity of 88.4% (95% CI, 74.92%-96.11%) and a specificity of 83.7% (95% CI: 69.29%-93.19%). In conclusión, this study reports on and enzymatically characterizes a novel enolase from T. solium metacestode, and shows a potential use as an immunodiagnostic for porcine cysticercosis.
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MESH Headings
- Amino Acid Sequence
- Animals
- Antibodies, Helminth/biosynthesis
- Antigens, Helminth/chemistry
- Antigens, Helminth/genetics
- Antigens, Helminth/immunology
- Antigens, Helminth/metabolism
- Computational Biology
- Confidence Intervals
- Cysticercosis/diagnosis
- Cysticercosis/veterinary
- DNA, Complementary/genetics
- Enzyme-Linked Immunosorbent Assay/veterinary
- Female
- Genetic Vectors
- Phosphopyruvate Hydratase/chemistry
- Phosphopyruvate Hydratase/genetics
- Phosphopyruvate Hydratase/immunology
- Phosphopyruvate Hydratase/metabolism
- Phylogeny
- Protein Structure, Secondary
- Protein Structure, Tertiary
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- ROC Curve
- Rabbits
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/immunology
- Recombinant Proteins/metabolism
- Sensitivity and Specificity
- Sequence Alignment
- Sf9 Cells
- Spectrophotometry/veterinary
- Swine
- Swine Diseases/diagnosis
- Swine Diseases/parasitology
- Taenia solium/classification
- Taenia solium/enzymology
- Taenia solium/genetics
- Taenia solium/immunology
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Affiliation(s)
- Reynaldo Ponce
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nancy León-Janampa
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ruddy Liendo
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Sueline Luis
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Stefany Quiñones-Garcia
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Zach Silverstein
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Hector H García
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru; Cysticercosis Unit, Instituto de Ciencias Neurológicas, Lima, Peru
| | - Armando Gonzales
- School of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mónica J Pajuelo
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.
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Zimic M, Rueda D, Furukawa R, Fuentes P, Comina G, Castro NRD, Requena D, Gilman R, Sheen P. A novel inexpensive electrochemical sensor for pyrazinoic acid as a potential tool for the identification of pyrazinamide-resistant Mycobacterium tuberculosis. Int J Mycobacteriol 2018; 7:275-281. [DOI: 10.4103/ijmy.ijmy_63_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Grandjean L, Gilman RH, Iwamoto T, Köser CU, Coronel J, Zimic M, Török ME, Ayabina D, Kendall M, Fraser C, Harris S, Parkhill J, Peacock SJ, Moore DAJ, Colijn C. Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru. PLoS One 2017; 12:e0189838. [PMID: 29281674 PMCID: PMC5744980 DOI: 10.1371/journal.pone.0189838] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis poses a major threat to the success of tuberculosis control programs worldwide. Understanding how drug-resistant tuberculosis evolves can inform the development of new therapeutic and preventive strategies. METHODS Here, we use novel genome-wide analysis techniques to identify polymorphisms that are associated with drug resistance, adaptive evolution and the structure of the phylogenetic tree. A total of 471 samples from different patients collected between 2009 and 2013 in the Lima suburbs of Callao and Lima South were sequenced on the Illumina MiSeq platform with 150bp paired-end reads. After alignment to the reference H37Rv genome, variants were called using standardized methodology. Genome-wide analysis was undertaken using custom written scripts implemented in R software. RESULTS High quality homoplastic single nucleotide polymorphisms were observed in genes known to confer drug resistance as well as genes in the Mycobacterium tuberculosis ESX secreted protein pathway, pks12, and close to toxin/anti-toxin pairs. Correlation of homoplastic variant sites identified that many were significantly correlated, suggestive of epistasis. Variation in genes coding for ESX secreted proteins also significantly disrupted phylogenetic structure. Mutations in ESX genes in key antigenic epitope positions were also found to disrupt tree topology. CONCLUSION Variation in these genes have a biologically plausible effect on immunogenicity and virulence. This makes functional characterization warranted to determine the effects of these polymorphisms on bacterial fitness and transmission.
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Affiliation(s)
- Louis Grandjean
- University College London, Institute of Child Health, London, United Kingdom
- Academic Health Sciences Centre, Imperial College, London, United Kingdom
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Robert H. Gilman
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States of America
| | - Tomatada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Chuo-ku, Kobe, Japan
| | - Claudio U. Köser
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jorge Coronel
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - Mirko Zimic
- Universidad Peruana Cayetano Heredia, Avenida Honorio Delgado, San Martin de Porras, Lima, Peru
| | - M. Estee Török
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Diepreye Ayabina
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Michelle Kendall
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Diseases Epidemiology, Imperial College, London, United Kingdom
| | - Simon Harris
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sharon J. Peacock
- Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, United Kingdom
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - David A. J. Moore
- London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - Caroline Colijn
- Faculty of Natural Sciences, Department of Mathematics, Imperial College London, London, United Kingdom
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Vargas-Cuentas NI, Roman-Gonzalez A, Gilman RH, Barrientos F, Ting J, Hidalgo D, Jensen K, Zimic M. Developing an eye-tracking algorithm as a potential tool for early diagnosis of autism spectrum disorder in children. PLoS One 2017; 12:e0188826. [PMID: 29190703 PMCID: PMC5708820 DOI: 10.1371/journal.pone.0188826] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 11/14/2017] [Indexed: 12/27/2022] Open
Abstract
Background Autism spectrum disorder (ASD) currently affects nearly 1 in 160 children worldwide. In over two-thirds of evaluations, no validated diagnostics are used and gold standard diagnostic tools are used in less than 5% of evaluations. Currently, the diagnosis of ASD requires lengthy and expensive tests, in addition to clinical confirmation. Therefore, fast, cheap, portable, and easy-to-administer screening instruments for ASD are required. Several studies have shown that children with ASD have a lower preference for social scenes compared with children without ASD. Based on this, eye-tracking and measurement of gaze preference for social scenes has been used as a screening tool for ASD. Currently available eye-tracking software requires intensive calibration, training, or holding of the head to prevent interference with gaze recognition limiting its use in children with ASD. Methods In this study, we designed a simple eye-tracking algorithm that does not require calibration or head holding, as a platform for future validation of a cost-effective ASD potential screening instrument. This system operates on a portable and inexpensive tablet to measure gaze preference of children for social compared to abstract scenes. A child watches a one-minute stimulus video composed of a social scene projected on the left side and an abstract scene projected on the right side of the tablet’s screen. We designed five stimulus videos by changing the social/abstract scenes. Every child observed all the five videos in random order. We developed an eye-tracking algorithm that calculates the child’s gaze preference for the social and abstract scenes, estimated as the percentage of the accumulated time that the child observes the left or right side of the screen, respectively. Twenty-three children without a prior history of ASD and 8 children with a clinical diagnosis of ASD were evaluated. The recorded video of the child´s eye movement was analyzed both manually by an observer and automatically by our algorithm. Results This study demonstrates that the algorithm correctly differentiates visual preference for either the left or right side of the screen (social or abstract scenes), identifies distractions, and maintains high accuracy compared to the manual classification. The error of the algorithm was 1.52%, when compared to the gold standard of manual observation. Discussion This tablet-based gaze preference/eye-tracking algorithm can estimate gaze preference in both children with ASD and without ASD to a high degree of accuracy, without the need for calibration, training, or restraint of the children. This system can be utilized in low-resource settings as a portable and cost-effective potential screening tool for ASD.
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Affiliation(s)
- Natalia I. Vargas-Cuentas
- Bioinformatics and Molecular Biology Laboratory, Research and Development Laboratory, Science and Philosophy Faculty, University Peruana Cayetano Heredia, Lima, Peru
| | - Avid Roman-Gonzalez
- Bioinformatics and Molecular Biology Laboratory, Research and Development Laboratory, Science and Philosophy Faculty, University Peruana Cayetano Heredia, Lima, Peru
| | - Robert H. Gilman
- Department of International Health. School of Public Health. Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Franklin Barrientos
- Bioinformatics and Molecular Biology Laboratory, Research and Development Laboratory, Science and Philosophy Faculty, University Peruana Cayetano Heredia, Lima, Peru
| | - James Ting
- School of Medicine. Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Daniela Hidalgo
- Bioinformatics and Molecular Biology Laboratory, Research and Development Laboratory, Science and Philosophy Faculty, University Peruana Cayetano Heredia, Lima, Peru
- Psychology Faculty. Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kelly Jensen
- Tulane University School of Medicine, New Orleans, LA, United States of America
| | - Mirko Zimic
- Bioinformatics and Molecular Biology Laboratory, Research and Development Laboratory, Science and Philosophy Faculty, University Peruana Cayetano Heredia, Lima, Peru
- * E-mail:
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Sheen P, Requena D, Gushiken E, Gilman RH, Antiparra R, Lucero B, Lizárraga P, Cieza B, Roncal E, Grandjean L, Pain A, McNerney R, Clark TG, Moore D, Zimic M. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC Genomics 2017; 18:769. [PMID: 29020922 PMCID: PMC5637355 DOI: 10.1186/s12864-017-4146-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 02/10/2017] [Accepted: 10/02/2017] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear. RESULTS We genotyped and sequenced the complete genomes of 68 M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion. CONCLUSIONS These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.
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Affiliation(s)
- Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe St., Room 5515, Baltimore, MD 21205 USA
| | - Ricardo Antiparra
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Bryan Lucero
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Pilar Lizárraga
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Basilio Cieza
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Louis Grandjean
- Department of Infection, Immunology and Rheumatology, Institute of Child Health, University College London, 30 Guilford St, London, WC1N 1EH UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - David Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
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Cisneros-Velarde P, Correa M, Mayta H, Anticona C, Pajuelo M, Oberhelman R, Checkley W, Gilman RH, Figueroa D, Zimic M, Lavarello R, Castaneda B. Automatic pneumonia detection based on ultrasound video analysis. Annu Int Conf IEEE Eng Med Biol Soc 2017; 2016:4117-4120. [PMID: 28269188 DOI: 10.1109/embc.2016.7591632] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Pneumonia is a disease which causes high mortality in children under five years old, particularly in developing countries. This paper proposes a novel application of ultrasound video analysis for the detection of pneumonia. This application is based on the processing of small video chunks, in which an image processing algorithm analyzes each frame to get some overall video statistics. Then, based on these quantities, the likeness of presence of pneumonia in the video is determined. The algorithm exploits different geometrical properties of typical anatomical and pathological features that commonly appear in lung sonography and which are already clinically typified in the literature. Our technique has been tested on different transverse thoracic scanning protocols and probe's maneuvers, thus, under a variety of clinical and usage protocols. Then, it can be targeted towards screening applications. We present encouraging results (AUC measure between 0.7851 and 0.9177) based on the analysis of 346 videos with an average duration of eight seconds. The analyzed videos were taken from children who were between three and five years old. Finally, our algorithm can be used directly as a classifier, but we detail how its performance may be enhanced if used as a first stage of a larger pipeline of other complementary pneumonia detection processes.
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Proaño A, Bravard MA, López JW, Lee GO, Bui D, Datta S, Comina G, Zimic M, Coronel J, Caviedes L, Cabrera JL, Salas A, Ticona E, Vu NM, Kirwan DE, Loader MCI, Friedland JS, Moore DAJ, Evans CA, Tracey BH, Gilman RH. Dynamics of Cough Frequency in Adults Undergoing Treatment for Pulmonary Tuberculosis. Clin Infect Dis 2017; 64:1174-1181. [PMID: 28329268 PMCID: PMC5399950 DOI: 10.1093/cid/cix039] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 01/13/2017] [Indexed: 01/01/2023] Open
Abstract
Background Cough is the major determinant of tuberculosis transmission. Despite this, there is a paucity of information regarding characteristics of cough frequency throughout the day and in response to tuberculosis therapy. Here we evaluate the circadian cycle of cough, cough frequency risk factors, and the impact of appropriate treatment on cough and bacillary load. Methods We prospectively evaluated human immunodeficiency virus-negative adults (n = 64) with a new diagnosis of culture-proven, drug-susceptible pulmonary tuberculosis immediately prior to treatment and repeatedly until treatment day 62. At each time point, participant cough was recorded (n = 670) and analyzed using the Cayetano Cough Monitor. Consecutive coughs at least 2 seconds apart were counted as separate cough episodes. Sputum samples (n = 426) were tested with microscopic-observation drug susceptibility broth culture, and in culture-positive samples (n = 252), the time to culture positivity was used to estimate bacillary load. Results The highest cough frequency occurred from 1 pm to 2 pm, and the lowest from 1 am to 2 am (2.4 vs 1.1 cough episodes/hour, respectively). Cough frequency was higher among participants who had higher sputum bacillary load (P < .01). Pretreatment median cough episodes/hour was 2.3 (interquartile range [IQR], 1.2-4.1), which at 14 treatment days decreased to 0.48 (IQR, 0.0-1.4) and at the end of the study decreased to 0.18 (IQR, 0.0-0.59) (both reductions P < .001). By 14 treatment days, the probability of culture conversion was 29% (95% confidence interval, 19%-41%). Conclusions Coughs were most frequent during daytime. Two weeks of appropriate treatment significantly reduced cough frequency and resulted in one-third of participants achieving culture conversion. Thus, treatment by 2 weeks considerably diminishes, but does not eliminate, the potential for airborne tuberculosis transmission.
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Affiliation(s)
- Alvaro Proaño
- Escuela Profesional de Medicina, Facultad de Medicina Alberto Hurtado, Universidad Peruana Cayetano Heredia, Lima, Perú
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
| | - Marjory A Bravard
- Asociación Benéfica PRISMA, Lima, Perú
- Department of General Internal Medicine, Massachusetts General Hospital, Boston, USA
- Innovation For Health And Development, Laboratory of Research and Development,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - José W López
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
- Instituto Nacional de Salud del Niño San Borja, Lima, Perú
| | - Gwenyth O Lee
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana
| | - David Bui
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson
| | - Sumona Datta
- Innovation For Health And Development, Laboratory of Research and Development,Universidad Peruana Cayetano Heredia, Lima, Peru
- Infectious Diseases and Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - Germán Comina
- Department of Global Community Health and Behavioral Sciences, Tulane University, New Orleans, Louisiana
- Escuela Profesional de Ingeniería Física, Facultad de Ciencias, Universidad Nacional de Ingeniería
| | - Mirko Zimic
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Jorge Coronel
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
| | - Luz Caviedes
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
| | - José L Cabrera
- Servicio de Neumología, Hospital Nacional Alcides Carrión,Bellavista , Peru
| | - Antonio Salas
- Servicio de Neumología, Hospital Nacional Dos de Mayo, Lima, Peru
| | - Eduardo Ticona
- Facultad de Medicina, Univ Nacional Mayor de San Marcosersidad, Lima, Peru
- Servicio de Enfermedades Infecciosas y Tropicales, Hospital Nacional Dos de Mayo, Lima, Perú
| | - Nancy M Vu
- Department of Internal Medicine, Cleveland Clinic, Ohio, USA
| | - Daniela E Kirwan
- Infectious Diseases and Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - Maria-Cristina I Loader
- Infectious Diseases and Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - Jon S Friedland
- Infectious Diseases and Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - David A J Moore
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Asociación Benéfica PRISMA, Lima, Perú
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Carlton A Evans
- Asociación Benéfica PRISMA, Lima, Perú
- Innovation For Health And Development, Laboratory of Research and Development,Universidad Peruana Cayetano Heredia, Lima, Peru
- Infectious Diseases and Immunity and Wellcome Trust Imperial College Centre for Global Health Research, Imperial College London, United Kingdom
| | - Brian H Tracey
- Department of Electrical and Computer Engineering, Tufts University, Medford, Massachusetts, USA
| | - Robert H Gilman
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia
- Asociación Benéfica PRISMA, Lima, Perú
- Program in Global Disease Epidemiology and Control, Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
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Alva A, Cangalaya C, Quiliano M, Krebs C, Gilman RH, Sheen P, Zimic M. Mathematical algorithm for the automatic recognition of intestinal parasites. PLoS One 2017; 12:e0175646. [PMID: 28410387 PMCID: PMC5391948 DOI: 10.1371/journal.pone.0175646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 08/19/2016] [Accepted: 03/29/2017] [Indexed: 11/18/2022] Open
Abstract
Parasitic infections are generally diagnosed by professionals trained to recognize the morphological characteristics of the eggs in microscopic images of fecal smears. However, this laboratory diagnosis requires medical specialists which are lacking in many of the areas where these infections are most prevalent. In response to this public health issue, we developed a software based on pattern recognition analysis from microscopi digital images of fecal smears, capable of automatically recognizing and diagnosing common human intestinal parasites. To this end, we selected 229, 124, 217, and 229 objects from microscopic images of fecal smears positive for Taenia sp., Trichuris trichiura, Diphyllobothrium latum, and Fasciola hepatica, respectively. Representative photographs were selected by a parasitologist. We then implemented our algorithm in the open source program SCILAB. The algorithm processes the image by first converting to gray-scale, then applies a fourteen step filtering process, and produces a skeletonized and tri-colored image. The features extracted fall into two general categories: geometric characteristics and brightness descriptions. Individual characteristics were quantified and evaluated with a logistic regression to model their ability to correctly identify each parasite separately. Subsequently, all algorithms were evaluated for false positive cross reactivity with the other parasites studied, excepting Taenia sp. which shares very few morphological characteristics with the others. The principal result showed that our algorithm reached sensitivities between 99.10%-100% and specificities between 98.13%- 98.38% to detect each parasite separately. We did not find any cross-positivity in the algorithms for the three parasites evaluated. In conclusion, the results demonstrated the capacity of our computer algorithm to automatically recognize and diagnose Taenia sp., Trichuris trichiura, Diphyllobothrium latum, and Fasciola hepatica with a high sensitivity and specificity.
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Affiliation(s)
- Alicia Alva
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Carla Cangalaya
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Laboratorio de Inmunopatología en Neurocisticercosis, Laboratorio de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú.,Facultad de Medicina Humana, Universidad Nacional Mayor de San Marcos, Lima, Perú
| | - Miguel Quiliano
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Casey Krebs
- Weill Cornell Medical College in New York City, New York, United States of America
| | - Robert H Gilman
- Department of International Health, School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Patricia Sheen
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Mirko Zimic
- Unidad de Bioinformática, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
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Dudley MZ, Sheen P, Gilman RH, Ticona E, Friedland JS, Kirwan DE, Caviedes L, Rodriguez R, Cabrera LZ, Coronel J, Grandjean L, Moore DAJ, Evans CA, Huaroto L, Chávez-Pérez V, Zimic M. Detecting Mutations in the Mycobacterium tuberculosis Pyrazinamidase Gene pncA to Improve Infection Control and Decrease Drug Resistance Rates in Human Immunodeficiency Virus Coinfection. Am J Trop Med Hyg 2016; 95:1239-1246. [PMID: 27928075 PMCID: PMC5154434 DOI: 10.4269/ajtmh.15-0711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 08/24/2016] [Indexed: 11/07/2022] Open
Abstract
Hospital infection control measures are crucial to tuberculosis (TB) control strategies within settings caring for human immunodeficiency virus (HIV)-positive patients, as these patients are at heightened risk of developing TB. Pyrazinamide (PZA) is a potent drug that effectively sterilizes persistent Mycobacterium tuberculosis bacilli. However, PZA resistance associated with mutations in the nicotinamidase/pyrazinamidase coding gene, pncA, is increasing. A total of 794 patient isolates obtained from four sites in Lima, Peru, underwent spoligotyping and drug resistance testing. In one of these sites, the HIV unit of Hospital Dos de Mayo (HDM), an isolation ward for HIV/TB coinfected patients opened during the study as an infection control intervention: circulating genotypes and drug resistance pre- and postintervention were compared. All other sites cared for HIV-negative outpatients: genotypes and drug resistance rates from these sites were compared with those from HDM. HDM patients showed high concordance between multidrug resistance, PZA resistance according to the Wayne method, the two most common genotypes (spoligotype international type [SIT] 42 of the Latino American-Mediterranean (LAM)-9 clade and SIT 53 of the T1 clade), and the two most common pncA mutations (G145A and A403C). These associations were absent among community isolates. The infection control intervention was associated with 58-92% reductions in TB caused by SIT 42 or SIT 53 genotypes (odds ratio [OR] = 0.420, P = 0.003); multidrug-resistant TB (OR = 0.349, P < 0.001); and PZA-resistant TB (OR = 0.076, P < 0.001). In conclusion, pncA mutation typing, with resistance testing and spoligotyping, was useful in identifying a nosocomial TB outbreak and demonstrating its resolution after implementation of infection control measures.
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Affiliation(s)
- Matthew Z. Dudley
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociación Benéfica Proyectos en Informatica, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
| | - Eduardo Ticona
- Hospital Nacional Dos de Mayo, Lima, Peru
- Facultad de Medicina, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jon S. Friedland
- Infectious Diseases and Immunity, Wellcome Trust Centre for Global Health Research, Imperial College London, London, United Kingdom
| | - Daniela E. Kirwan
- Department of Medical Microbiology, St. George's Hospital, London, United Kingdom
- Infections Diseases and Immunity, Imperial College London, London, United Kingdom
| | - Luz Caviedes
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Lilia Z. Cabrera
- Asociación Benéfica Proyectos en Informatica, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
| | - Jorge Coronel
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Louis Grandjean
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Infectious Diseases and Immunity, Wellcome Trust Centre for Global Health Research, Imperial College London, London, United Kingdom
| | - David A. J. Moore
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Asociación Benéfica Proyectos en Informatica, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
- TB Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlton A. Evans
- Infectious Diseases and Immunity, Wellcome Trust Centre for Global Health Research, Imperial College London, London, United Kingdom
- Innovation For Health and Development (IFHAD), Laboratory of Research and Development, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Luz Huaroto
- Hospital Nacional Dos de Mayo, Lima, Peru
- Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Víctor Chávez-Pérez
- Hospital Nacional Dos de Mayo, Lima, Peru
- Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Investigación en Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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Oberhelman RA, Huaynate CA, Correa M, Malpartida HM, Pajuelo M, Paz-Soldan VA, Gilman RH, Zimic M, Murphy L, Belizan J. Interdisciplinary Postdoctoral Training in Global Health Through a Novel Joint Project for Trainees from Diverse Disciplines: Benefits, Risks, and Observations. Am J Trop Med Hyg 2016; 96:525-529. [PMID: 27821694 DOI: 10.4269/ajtmh.16-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Postdoctoral training programs are usually highly individualized arrangements between trainees and a limited number of senior mentors in their field, an approach that contrasts with current trends in public health education that promote interdisciplinary training to spur innovation. Herein, we describe an alternative model for postdoctoral training for a group of fellows from distinct disciplines. Fellows work with mentors from diverse fields to create a joint research project or a group of complementary projects, with the goal of developing a new device, intervention, or innovation to address a global health problem. The perceived benefits, challenges, and limitations of this team approach to interdisciplinary postdoctoral training are presented.
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Affiliation(s)
- Richard A Oberhelman
- Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana.,Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Cynthia Anticona Huaynate
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Malena Correa
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Holger Mayta Malpartida
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Monica Pajuelo
- Universidad Peruana Cayetano Heredia, Lima, Peru.,Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Valerie A Paz-Soldan
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana.,Office of Global Health, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Robert H Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.,Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratory of Bioinformatics and Molecular Biology, Department of Cellular and Molecular Science, Faculty of Science, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Laura Murphy
- Department of Global Community Health and Behavioral Sciences, Tulane University School of Public Health and Tropical Medicine, New Orleans, Louisiana
| | - Jose Belizan
- Instituto de Efectividad Clinica y Sanitaria, Buenos Aires, Argentina
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50
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Machicado C, Marcos LA, Zimic M. Hypothetical granulin-like molecule from Fasciola hepatica identified by bioinformatics analysis. Springerplus 2016; 5:773. [PMID: 27386259 PMCID: PMC4912509 DOI: 10.1186/s40064-016-2443-7] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/27/2016] [Indexed: 12/14/2022]
Abstract
Fasciola hepatica is considered an emergent human pathogen, causing liver fibrosis or cirrhosis, conditions that are known to be direct causes of cancer. Some parasites have been categorized by WHO as carcinogenic agents such as Opisthorchis viverrini, a relative of F. hepatica. Although these two parasites are from the same class (Trematoda), the role of F. hepatica in carcinogenesis is unclear. We hypothesized that F. hepatica might share some features with O. viverrini and to be responsible to induce proliferation of host cells. We analyzed the recently released genome of F. hepatica looking for a gene coding a granulin-like growth factor, a protein secreted by O. viverrini (Ov-GRN-1), which is a potent stimulator of proliferation of host cells. Using computational biology tools, we identified a granulin-like molecule in F. hepatica, here termed FhGLM, which has high sequence identity level to Ov-GRN-1 and human progranulin. We found evidence of an upstream promoter compatible with the expression of FhGLM. The FhGLM architecture showed to have five granulin domains, one of them, the domain 3, was homologue to Ov-GRN-1 and human GRNC. The structure of the FhGLM granulin domain 3 resulted to have the overall folding of its homologue the human GRNC. Our findings show the presence of a homologue of a potent modulator of cell growth in F. hepatica that might have, as other granulins, a proliferative action on host cells during fascioliasis. Future experimental assays to demonstrate the presence of FhGLM in F. hepatica are needed to confirm our hypothesis.
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Affiliation(s)
- Claudia Machicado
- Bioinformatics Laboratory, Department of Cellular and Molecular Sciences, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 31, Peru ; Institute for Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillo, Edificio I+D, 50018 Saragossa, Spain
| | - Luis A Marcos
- Division of Infectious Diseases, Department of Internal Medicine, Stony Brook University, Stony Brook, 100 Nicolls Road, Stony Brook, NY 11790 USA ; Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 262, Lima 31, Peru
| | - Mirko Zimic
- Bioinformatics Laboratory, Department of Cellular and Molecular Sciences, Faculty of Sciences and Philosophy, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, Lima 31, Peru
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