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Verani JR, Massora S, Acácio S, dos Santos RT, Vubil D, Pimenta F, Moura I, Whitney CG, Costa MH, Macete E, Matsinhe MB, Carvalho MDG, Sigaúque B. Nasopharyngeal carriage of Streptococcus pneumoniae among HIV-infected and -uninfected children <5 years of age before introduction of pneumococcal conjugate vaccine in Mozambique. PLoS One 2018; 13:e0191113. [PMID: 29447196 PMCID: PMC5813901 DOI: 10.1371/journal.pone.0191113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [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: 09/18/2017] [Accepted: 12/28/2017] [Indexed: 12/03/2022] Open
Abstract
Nasopharyngeal carriage is a precursor for pneumococcal disease and can be useful for evaluating pneumococcal conjugate vaccine (PCV) impact. We studied pre-PCV pneumococcal carriage among HIV-infected and -uninfected children in Mozambique. Between October 2012 and March 2013, we enrolled HIV-infected children age <5 years presenting for routine care at seven HIV clinics in 3 sites, including Maputo (urban-south), Nampula (urban-north), and Manhiça (rural-south). We also enrolled a random sample of HIV-uninfected children <5 years old from a demographic surveillance site in Manhiça. A single nasopharyngeal swab was obtained and cultured following enrichment in Todd Hewitt broth with yeast extract and rabbit serum. Pneumococcal isolates were serotyped by Quellung reaction and multiplex polymerase chain reaction. Factors associated with pneumococcal carriage were examined using logistic regression. Overall pneumococcal carriage prevalence was 80.5% (585/727), with similar prevalences among HIV-infected (81.5%, 339/416) and HIV-uninfected (79.1%, 246/311) children, and across age strata. Among HIV-infected, after adjusting for recent antibiotic use and hospitalization, there was no significant association between study site and colonization: Maputo (74.8%, 92/123), Nampula (83.7%, 82/98), Manhiça (84.6%, 165/195). Among HIV-uninfected, report of having been born to an HIV-infected mother was not associated with colonization. Among 601 pneumococcal isolates from 585 children, serotypes 19F (13.5%), 23F (13.1%), 6A (9.2%), 6B (6.2%) and 19A (5.2%) were most common. The proportion of serotypes included in the 10- and 13-valent vaccines was 44.9% and 61.7%, respectively, with no significant differences by HIV status or age group. Overall 36.9% (n = 268) of children were colonized with a PCV10 serotype and 49.7% (n = 361) with a PCV13 serotype. Pneumococcal carriage was common, with little variation by geographic region, age, or HIV status. PCV10 was introduced in April 2013; ongoing carriage studies will examine the benefits of PCV10 among HIV-infected and–uninfected children.
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Affiliation(s)
- Jennifer R. Verani
- Respiratory Diseases Branch, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
- * E-mail: (JRV); (BS)
| | - Sérgio Massora
- Centro de Investigação em Saúde de Manhiça / Fundação Manhiça, Manhiça, Moçambique
| | - Sozinho Acácio
- Centro de Investigação em Saúde de Manhiça / Fundação Manhiça, Manhiça, Moçambique
- Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Moçambique
| | | | - Delfino Vubil
- Centro de Investigação em Saúde de Manhiça / Fundação Manhiça, Manhiça, Moçambique
| | - Fabiana Pimenta
- Respiratory Diseases Branch, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Iaci Moura
- Respiratory Diseases Branch, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Cynthia G. Whitney
- Respiratory Diseases Branch, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | | | - Eusébio Macete
- Centro de Investigação em Saúde de Manhiça / Fundação Manhiça, Manhiça, Moçambique
| | | | - Maria da Gloria Carvalho
- Respiratory Diseases Branch, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Betuel Sigaúque
- Centro de Investigação em Saúde de Manhiça / Fundação Manhiça, Manhiça, Moçambique
- Instituto Nacional de Saúde, Ministério de Saúde, Maputo, Moçambique
- * E-mail: (JRV); (BS)
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Egüez KE, Alonso-Padilla J, Terán C, Chipana Z, García W, Torrico F, Gascon J, Lozano-Beltran DF, Pinazo MJ. Rapid diagnostic tests duo as alternative to conventional serological assays for conclusive Chagas disease diagnosis. PLoS Negl Trop Dis 2017; 11:e0005501. [PMID: 28369081 PMCID: PMC5391121 DOI: 10.1371/journal.pntd.0005501] [Citation(s) in RCA: 40] [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: 12/01/2016] [Revised: 04/13/2017] [Accepted: 03/17/2017] [Indexed: 11/24/2022] Open
Abstract
Chagas disease is caused by the parasite Trypanosoma cruzi. It affects several million people, mainly in Latin America, and severe cardiac and/or digestive complications occur in ~30% of the chronically infected patients. Disease acute stage is mostly asymptomatic and infection goes undiagnosed. In the chronic phase direct parasite detection is hampered due to its concealed presence and diagnosis is achieved by serological methods, like ELISA or indirect hemagglutination assays. Agreement in at least two tests must be obtained due to parasite wide antigenic variability. These techniques require equipped labs and trained personnel and are not available in distant regions. As a result, many infected people often remain undiagnosed until it is too late, as the two available chemotherapies show diminished efficacy in the advanced chronic stage. Easy-to-use rapid diagnostic tests have been developed to be implemented in remote areas as an alternative to conventional tests. They do not need electricity, nor cold chain, they can return results within an hour and some even work with whole blood as sample, like Chagas Stat-Pak (ChemBio Inc.) and Chagas Detect Plus (InBIOS Inc.). Nonetheless, in order to qualify a rapidly diagnosed positive patient for treatment, conventional serological confirmation is obligatory, which might risk its start. In this study two rapid tests based on distinct antigen sets were used in parallel as a way to obtain a fast and conclusive Chagas disease diagnosis using whole blood samples. Chagas Stat-Pak and Chagas Detect Plus were validated by comparison with three conventional tests yielding 100% sensitivity and 99.3% specificity over 342 patients seeking Chagas disease diagnosis in a reference centre in Sucre (Bolivia). Combined used of RDTs in distant regions could substitute laborious conventional serology, allowing immediate treatment and favouring better adhesion to it. Chagas disease is a neglected tropical disease caused by the parasite Trypanosoma cruzi. It affects 6–7 million people, mainly in Latin America. An initial asymptomatic phase make the infection go undiagnosed and untreated, silently progressing into its chronic stage. About 30% of the chronically infected patients end up developing life-threatening disruption of the heart and/or gut tissues. Two drugs are available but their efficacy diminishes the longer a person has been infected. Therefore, it is of paramount importance to achieve an early diagnosis to start treatment before symptoms advance. In the chronic stage parasite presence is intermittent and diagnosis is made by serological assays that detect parasite-specific immunoglobulins. Problem is that conventional serological techniques are laborious and require equipment and trained personnel unavailable in remote regions with high disease prevalence. To circumvent those inconveniences easy-to-use rapid diagnostic tests were developed. They return results within an hour and some work with whole blood as sample allowing diagnosis out of digital puncture. We propose that conventional assays could be substituted by whole blood-friendly rapid tests in order to achieve a conclusive Chagas disease diagnosis in remote regions. This would ease access to treatment increasing adherence rates to it.
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Affiliation(s)
- Karina E. Egüez
- Departmental Reference Laboratory, Chuquisaca Departmental Health Service (SEDES-Chuquisaca), Sucre, Bolivia
| | - Julio Alonso-Padilla
- Barcelona Institute for Global Health (ISGlobal), Centre for Research in International Health (CRESIB), Hospital Clinic-University of Barcelona, Barcelona, Spain
| | - Carolina Terán
- School of Medicine, University of San Francisco Xavier of Chuquisaca, Sucre, Bolivia; and Health Area, Simón Bolívar Andean University, Sucre, Bolivia
| | - Zenobia Chipana
- Departmental Reference Laboratory, Chuquisaca Departmental Health Service (SEDES-Chuquisaca), Sucre, Bolivia
| | | | | | - Joaquim Gascon
- Barcelona Institute for Global Health (ISGlobal), Centre for Research in International Health (CRESIB), Hospital Clinic-University of Barcelona, Barcelona, Spain
| | | | - María-Jesús Pinazo
- Barcelona Institute for Global Health (ISGlobal), Centre for Research in International Health (CRESIB), Hospital Clinic-University of Barcelona, Barcelona, Spain
- * E-mail:
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Gonzalez S, Clavijo B, Rivarola M, Moreno P, Fernandez P, Dopazo J, Paniego N. ATGC transcriptomics: a web-based application to integrate, explore and analyze de novo transcriptomic data. BMC Bioinformatics 2017; 18:121. [PMID: 28222698 PMCID: PMC5320735 DOI: 10.1186/s12859-017-1494-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 10/21/2016] [Accepted: 01/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In the last years, applications based on massively parallelized RNA sequencing (RNA-seq) have become valuable approaches for studying non-model species, e.g., without a fully sequenced genome. RNA-seq is a useful tool for detecting novel transcripts and genetic variations and for evaluating differential gene expression by digital measurements. The large and complex datasets resulting from functional genomic experiments represent a challenge in data processing, management, and analysis. This problem is especially significant for small research groups working with non-model species. RESULTS We developed a web-based application, called ATGC transcriptomics, with a flexible and adaptable interface that allows users to work with new generation sequencing (NGS) transcriptomic analysis results using an ontology-driven database. This new application simplifies data exploration, visualization, and integration for a better comprehension of the results. CONCLUSIONS ATGC transcriptomics provides access to non-expert computer users and small research groups to a scalable storage option and simple data integration, including database administration and management. The software is freely available under the terms of GNU public license at http://atgcinta.sourceforge.net .
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Affiliation(s)
- Sergio Gonzalez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
| | | | - Máximo Rivarola
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
| | - Patricio Moreno
- Instituto de Ingeniería Biomédica, Facultad de Ingeniería, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Paula Fernandez
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
- Escuela de Ciencia y Tecnología, Universidad Nacional de San Martín, San Martín, Buenos Aires Argentina
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Norma Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA) INTA, Hurlingham, Buenos Aires Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2290, Buenos Aires, C1425FQB Argentina
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