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de Oliveira Sant'Anna L, Dos Santos LS, Olivella JGB, da Cruz Mota M, Ramos JN, Baio PVP, da Rocha DJPG, Vieira VV, Almuzara M, Vay C, Barberis C, Castro TLDP, Seyffert N, Pacheco LGC, Mattos-Guaraldi AL. Description of Corynebacterium hiratae sp. nov. isolated from a human tissue bone a novel member of Corynebacterium Genus. Braz J Microbiol 2024:10.1007/s42770-024-01331-z. [PMID: 38598149 DOI: 10.1007/s42770-024-01331-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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 04/02/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Corynebacterium spp. are widely disseminated in the environment, and they are part of the skin and mucosal microbiota of animals and humans. Reports of human infections by Corynebacterium spp. have increased considerably in recent years and the appearance of multidrug resistant isolates around the world has drawn attention. OBJECTIVES To describe a new species of Corynebacterium from human tissue bone is described after being misidentified using available methods. METHODS For taxonomic analyses, phylogenetic analysis of 16S rRNA and rpoB genes, in silico DNA-DNA hybridization, average nucleotide and amino acid identity, multilocus sequence analysis, and phylogenetic analysis based on the complete genome were used. FINDINGS Genomic taxonomic analyzes revealed values of in silico DNA-DNA hybridization, average nucleotide and amino acids identity below the values necessary for species characterization between the analyzed isolates and the closest phylogenetic relative Corynebacterium aurimucosum DSM 44532T. MAIN CONCLUSIONS Genomic taxonomic analyzes indicate that the isolates analyzed comprise a new species of the Corynebacterium genus, which we propose to name Corynebacterium hiratae sp. nov. with isolate 332T (= CBAS 826T = CCBH 35,014T) as the type strain.
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Affiliation(s)
- Lincoln de Oliveira Sant'Anna
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil.
| | - Louisy Sanches Dos Santos
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Julianna Giordano Botelho Olivella
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Mariana da Cruz Mota
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | - Juliana Nunes Ramos
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
| | | | | | - Verônica Viana Vieira
- Faculty of Pharmacy and Biochemistry and Bacteriology, Department of Clinical Biochemistry, University of Buenos Aires, Autonomous City of Buenos Aires, Argentina
| | - Marisa Almuzara
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Carlos Vay
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Claudia Barberis
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Núbia Seyffert
- Institute of Health Sciences, Department of Biotechnology, Federal University of Bahia, Salvador, Brazil
| | | | - Ana Luíza Mattos-Guaraldi
- Laboratory of Diphtheria and Corynebacteria of Clinical Relevance, Department of Microbiology, Immunology and Parasitology, State University of Rio de Janeiro, Vinte e Oito de Setembro 87, Fundos, 3º andar. Vila Isabel, Rio de Janeiro, RJ, CEP:20551-030, Brazil
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Yin YS, Minacapelli CD, Parmar V, Catalano CC, Bhurwal A, Gupta K, Rustgi VK, Blaser MJ. Alterations of the fecal microbiota in relation to acute COVID-19 infection and recovery. Mol Biomed 2022; 3:36. [PMID: 36437420 PMCID: PMC9702442 DOI: 10.1186/s43556-022-00103-1] [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: 07/09/2022] [Accepted: 11/07/2022] [Indexed: 11/29/2022] Open
Abstract
People with acute COVID-19 due to SARS-CoV-2 infection experience a range of symptoms, but major factors contributing to severe clinical outcomes remain to be understood. Emerging evidence suggests associations between the gut microbiome and the severity and progression of COVID-19. To better understand the host-microbiota interactions in acute COVID-19, we characterized the intestinal microbiome of patients with active SARS-CoV-2 infection in comparison to recovered patients and uninfected healthy controls. We performed 16S rRNA sequencing of stool samples collected between May 2020 and January 2021 from 20 COVID-19-positive patients, 20 COVID-19-recovered subjects and 20 healthy controls. COVID-19-positive patients had altered microbiome community characteristics compared to the recovered and control subjects, as assessed by both α- and β-diversity differences. In COVID-19-positive patients, we observed depletion of Bacteroidaceae, Ruminococcaceae, and Lachnospiraceae, as well as decreased relative abundances of the genera Faecalibacterium, Adlercreutzia, and the Eubacterium brachy group. The enrichment of Prevotellaceae with COVID-19 infection continued after viral clearance; antibiotic use induced further gut microbiota perturbations in COVID-19-positive patients. In conclusion, we present evidence that acute COVID-19 induces gut microbiota dysbiosis with depletion of particular populations of commensal bacteria, a phenomenon heightened by antibiotic exposure, but the general effects do not persist post-recovery.
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Affiliation(s)
- Yue Sandra Yin
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carlos D Minacapelli
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Veenat Parmar
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA
| | - Carolyn C Catalano
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Abhishek Bhurwal
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kapil Gupta
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA.,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Vinod K Rustgi
- Division of Gastroenterology and Hepatology, Rutgers Robert Wood Johnson School of Medicine, New Brunswick, NJ, USA. .,Center for Liver Diseases and Liver Masses, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.
| | - Martin J Blaser
- Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, NJ, USA.
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Auguet OT, Niehus R, Gweon HS, Berkley JA, Waichungo J, Njim T, Edgeworth JD, Batra R, Chau K, Swann J, Walker SA, Peto TE, Crook DW, Lamble S, Turner P, Cooper BS, Stoesser N. Population-level faecal metagenomic profiling as a tool to predict antimicrobial resistance in Enterobacterales isolates causing invasive infections: An exploratory study across Cambodia, Kenya, and the UK. EClinicalMedicine 2021; 36:100910. [PMID: 34124634 PMCID: PMC8173267 DOI: 10.1016/j.eclinm.2021.100910] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/16/2021] [Accepted: 04/30/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) in Enterobacterales is a global health threat. Capacity for individual-level surveillance remains limited in many countries, whilst population-level surveillance approaches could inform empiric antibiotic treatment guidelines. METHODS In this exploratory study, a novel approach to population-level prediction of AMR in Enterobacterales clinical isolates using metagenomic (Illumina) profiling of pooled DNA extracts from human faecal samples was developed and tested. Taxonomic and AMR gene profiles were used to derive taxonomy-adjusted population-level AMR metrics. Bayesian modelling, and model comparison based on cross-validation, were used to evaluate the capacity of each metric to predict the number of resistant Enterobacterales invasive infections at a population-level, using available bloodstream/cerebrospinal fluid infection data. FINDINGS Population metagenomes comprised samples from 177, 157, and 156 individuals in Kenya, the UK, and Cambodia, respectively, collected between September 2014 and April 2016. Clinical data from independent populations included 910, 3356 and 197 bacterial isolates from blood/cerebrospinal fluid infections in Kenya, the UK and Cambodia, respectively (samples collected between January 2010 and May 2017). Enterobacterales were common colonisers and pathogens, and faecal taxonomic/AMR gene distributions and proportions of antimicrobial-resistant Enterobacterales infections differed by setting. A model including terms reflecting the metagenomic abundance of the commonest clinical Enterobacterales species, and of AMR genes known to either increase the minimum inhibitory concentration (MIC) or confer clinically-relevant resistance, had a higher predictive performance in determining population-level resistance in clinical Enterobacterales isolates compared to models considering only AMR gene information, only taxonomic information, or an intercept-only baseline model (difference in expected log predictive density compared to best model, estimated using leave-one-out cross-validation: intercept-only model = -223 [95% credible interval (CI): -330,-116]; model considering only AMR gene information = -186 [95% CI: -281,-91]; model considering only taxonomic information = -151 [95% CI: -232,-69]). INTERPRETATION Whilst our findings are exploratory and require validation, intermittent metagenomics of pooled samples could represent an effective approach for AMR surveillance and to predict population-level AMR in clinical isolates, complementary to ongoing development of laboratory infrastructures processing individual samples.
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Affiliation(s)
- Olga Tosas Auguet
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Rene Niehus
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Hyun Soon Gweon
- School of Biological Sciences, University of Reading, Reading, UK
- Centre for Ecology & Hydrology, Wallingford, UK
| | - James A. Berkley
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya
- The Childhood Acute Illness and Nutrition (CHAIN) Network, Nairobi, Kenya
| | | | - Tsi Njim
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Rahul Batra
- Centre for Clinical Infection and Diagnostics Research (CIDR), Department of Infectious Diseases, King's College London, London, UK
| | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jeremy Swann
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah A. Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Tim E.A. Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Cambodia-Oxford Medical Research Unit, Microbiology Department, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ben S. Cooper
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK
- Mahidol–Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- NIHR Health Protection Research Unit in Healthcare-associated Infections and Antimicrobial Resistance, Oxford, UK
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Kitagawa H, Ohge H, Yu L, Kayama S, Hara T, Kashiyama S, Kajihara T, Hisatsune J, Sueda T, Sugai M. Aeromonas dhakensis is not a rare cause of Aeromonas bacteremia in Hiroshima, Japan. J Infect Chemother 2019; 26:316-320. [PMID: 31570322 DOI: 10.1016/j.jiac.2019.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 08/17/2019] [Accepted: 08/30/2019] [Indexed: 10/25/2022]
Abstract
Aeromonas dhakensis, a newly recognized species, is often misidentified as A. hydrophila, A. veronii, or A. caviae by commercial phenotypic tests. Limited data about A. dhakensis are available in Japan. We retrospectively analyzed the patients with monomicrobial Aeromonas bacteremia at Hiroshima University Hospital from January 2011 to December 2017, and species re-identification was conducted using rpoD and gyrB gene sequencing and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system. Of the 19 strains from blood isolates, A. caviae (n = 9, 47.4%), A. dhakensis (n = 4, 21.1%), A. hydrophila (n = 3, 15.8%), and A. veronii (n = 3, 15.8%) were re-identified. A. dhakensis was phenotypically misidentified as A. hydrophila (n = 3, 75%) or A. sobria (n = 1, 25%). A. dhakensis was also misidentified as A. caviae (n = 2, 50%), A. hydrophila (n = 1, 25%), and A. jandaei (n = 1, 25%) in MALDI-TOF MS system. Malignancies (n = 12, 63.2%) and liver cirrhosis (n = 7, 36.8%) were common comorbidities. Biliary tract infection was the most frequent source of Aeromonas bacteremia (n = 11, 57.9%). The major source of A. dhakensis bacteremia was also biliary tract infection (n = 3, 75%), and the 14-day infection-related mortality of A. dhakensis was 25%. A. dhakensis isolates showed similar clinical characteristics, antimicrobial susceptibility, and mortality with those of other Aeromonas species isolates. This study demonstrated that A. dhakensis is not a rare cause of Aeromonas bacteremia, but is often misidentified as A. hydrophila in Hiroshima, Japan. Further studies should be conducted to identify the geographical distribution and clinical impact of A. dhakensis in Japan.
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Affiliation(s)
- Hiroki Kitagawa
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan.
| | - Hiroki Ohge
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Liansheng Yu
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan; Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Shizuo Kayama
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan; Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Toshinori Hara
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases Laboratory, Department of Clinical Practice and Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Seiya Kashiyama
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Bacteriology, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases Laboratory, Department of Clinical Practice and Support, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Toshiki Kajihara
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, 734-8551, Japan
| | - Junzo Hisatsune
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan; Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Taijiro Sueda
- Department of Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
| | - Motoyuki Sugai
- Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, 734-8551, Japan; Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, 189-0002, Japan; Department of Antimicrobial Resistance, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, 734-8551, Japan
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Loria-Cervera EN, Sosa-Bibiano EI, Van Wynsberghe NR, Saldarriaga OA, Melby PC, Andrade-Narvaez FJ. Cytokine mRNA expression in Peromyscus yucatanicus (Rodentia: Cricetidae) infected by Leishmania (Leishmania) mexicana. Cytokine 2016; 83:176-181. [PMID: 27155064 DOI: 10.1016/j.cyto.2016.04.016] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 02/04/2023]
Abstract
Peromyscus yucatanicus, the main reservoir of Leishmania (Leishmania) mexicana in the Yucatan peninsula of Mexico, reproduces clinical and histological pictures of LCL in human as well as subclinical infection. Thus, we used this rodent as a novel experimental model. In this work, we analyzed cytokine mRNA expression in P. yucatanicus infected with L. (L.) mexicana. Animals were inoculated with either 2.5×10(6) or 1×10(2) promastigotes and cytokine expressions were analyzed by real-time RT-PCR in skin at 4 and 12weeks post-infection (wpi). Independently of the parasite inoculum none of the infected rodents had clinical signs of LCL at 4wpi and all expressed high IFN-γ mRNA. All P. yucatanicus inoculated with 2.5×10(6) promastigotes developed signs of LCL at 12wpi while the mice inoculated with 1×10(2) remained subclinical. At that time, both IFN-γ and IL-10 were expressed in P. yucatanicus with clinical and subclinical infections. Expressions of TNF-α and IL-4 were significantly higher in clinical animals (2.5×10(6)) compared with subclinical ones (1×10(2)). High TGF-β expression was observed in P. yucatanicus with clinical signs when compared with healthy animals. Results suggested that the clinical course of L. (L.) mexicana infection in P. yucatanicus was associated with a specific local pattern of cytokine production at 12wpi.
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Affiliation(s)
- Elsy Nalleli Loria-Cervera
- Universidad Autonoma de Yucatan, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Laboratorio de Inmunologia, Ave. Itzaes No. 490 x 59-A, Merida, Yucatan, Mexico.
| | - Erika Ivett Sosa-Bibiano
- Universidad Autonoma de Yucatan, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Laboratorio de Inmunologia, Ave. Itzaes No. 490 x 59-A, Merida, Yucatan, Mexico.
| | - Nicole Raymonde Van Wynsberghe
- Universidad Autonoma de Yucatan, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Laboratorio de Inmunologia, Ave. Itzaes No. 490 x 59-A, Merida, Yucatan, Mexico.
| | - Omar Abdul Saldarriaga
- Center for Tropical Diseases, Department of Internal Medicine, University of Texas Medical Branch, 4.304 Marvin Graves Building, 301 University Boulevard, Galveston, TX, USA.
| | - Peter C Melby
- Center for Tropical Diseases, Department of Internal Medicine, University of Texas Medical Branch, 4.304 Marvin Graves Building, 301 University Boulevard, Galveston, TX, USA.
| | - Fernando Jose Andrade-Narvaez
- Universidad Autonoma de Yucatan, Centro de Investigaciones Regionales "Dr. Hideyo Noguchi", Laboratorio de Inmunologia, Ave. Itzaes No. 490 x 59-A, Merida, Yucatan, Mexico.
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