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2.
PLoS One ; 15(9): e0239060, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32941511

RESUMO

Quokkas (Setonix brachyurus) are small macropodid marsupials from Western Australia, which are identified as of conservation concern. Studies on their blood analytes exist but involve small sample sizes and are associated with very little information concerning the health of the animals. Blood was collected from free-ranging quokkas from Rottnest Island (n = 113) and mainland (n = 37) Western Australia, between September 2010 and December 2011, to establish haematology and blood chemistry reference intervals. Differences in haematology and blood chemistry between sites (Rottnest Island v mainland) were significant for haematology (HMT, p = 0.003), blood chemistry (BLC, p = 0.001) and peripheral blood cell morphology (PBCM, p = 0.001). Except for alkaline phosphatase, all blood chemistry analytes were higher in mainland animals. There were also differences with time of year in HMT (p = 0.001), BLC (p = 0.001) and PBCM (p = 0.001) for Rottnest Island quokkas. A small sample of captive animals (n = 8) were opportunistically sampled for plasma concentrations of vitamin E and were found to be deficient compared with wild-caught animals. Fifty-eight of the 150 quokkas were also tested for the presence of Salmonella, microfilariae, Macropodid herpesvirus-6, Theileria spp., Babesia spp., trypanosomes, Cryptococcus spp. and other saprophytic fungi. All eight infectious agents were detected in this study. Infectious agents were detected in 24 of these 58 quokkas (41%), with more than one infectious agent detected for all 24 individuals. Salmonella were detected concurrently with microfilariae in 8 of these 24 quokkas, and this mixed infection was associated with lower values across all haematological analytes, with Salmonella having the greater involvement in the decreased haematological values (p < 0.05). There was no evidence for an effect of sex on HMT, BLC and PBCM. Our data provide important haematological and blood chemistry reference intervals for free-ranging quokkas. We applied novel methods of analyses to HMT and BLC that can be used more broadly, aiding identification of potential disease in wildlife.


Assuntos
Macropodidae/sangue , Fosfatase Alcalina/sangue , Animais , Animais Selvagens/sangue , Animais Selvagens/microbiologia , Animais Selvagens/virologia , Análise Química do Sangue , Doenças Transmissíveis/sangue , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/veterinária , Doenças Transmissíveis/virologia , Feminino , Testes Hematológicos , Macropodidae/microbiologia , Macropodidae/virologia , Masculino , Estações do Ano , Vitamina E/sangue , Austrália Ocidental
3.
BMC Bioinformatics ; 21(1): 400, 2020 Sep 10.
Artigo em Inglês | MEDLINE | ID: mdl-32912135

RESUMO

BACKGROUND: Infectious diseases are a cruel assassin with millions of victims around the world each year. Understanding infectious mechanism of viruses is indispensable for their inhibition. One of the best ways of unveiling this mechanism is to investigate the host-pathogen protein-protein interaction network. In this paper we try to disclose many properties of this network. We focus on human as host and integrate experimentally 32,859 interaction between human proteins and virus proteins from several databases. We investigate different properties of human proteins targeted by virus proteins and find that most of them have a considerable high centrality scores in human intra protein-protein interaction network. Investigating human proteins network properties which are targeted by different virus proteins can help us to design multipurpose drugs. RESULTS: As host-pathogen protein-protein interaction network is a bipartite network and centrality measures for this type of networks are scarce, we proposed seven new centrality measures for analyzing bipartite networks. Applying them to different virus strains reveals unrandomness of attack strategies of virus proteins which could help us in drug design hence elevating the quality of life. They could also be used in detecting host essential proteins. Essential proteins are those whose functions are critical for survival of its host. One of the proposed centralities named diversity of predators, outperforms the other existing centralities in terms of detecting essential proteins and could be used as an optimal essential proteins' marker. CONCLUSIONS: Different centralities were applied to analyze human protein-protein interaction network and to detect characteristics of human proteins targeted by virus proteins. Moreover, seven new centralities were proposed to analyze host-pathogen protein-protein interaction network and to detect pathogens' favorite host protein victims. Comparing different centralities in detecting essential proteins reveals that diversity of predator (one of the proposed centralities) is the best essential protein marker.


Assuntos
Interações Hospedeiro-Patógeno , Mapas de Interação de Proteínas , Proteínas/metabolismo , Doenças Transmissíveis/metabolismo , Doenças Transmissíveis/patologia , Doenças Transmissíveis/virologia , Bases de Dados de Proteínas , Humanos , Interface Usuário-Computador , Vírus/patogenicidade
4.
PLoS One ; 15(9): e0239234, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32931509

RESUMO

Effective and culturally appropriate hand-hygiene education is essential to promote health-related practices to control and prevent diseases such as Diarrhoea, Ebola and COVID-19. In this paper we outline and evaluate the Co-Creation processes underpinning a handwashing intervention for young children (A Germ's Journey) developed and delivered in India, Sierra Leone and the UK, and consider the implications surrounding Imperialist/Colonial discourse and the White Saviour Complex. The paper focuses both on the ways Co-Creation was conceptualised by our collaborators in all three countries and the catalysts and challenges encountered. Qualitative data have been drawn from in-depth interviews with five key stakeholders, focus group data from 37 teachers in Sierra Leone and responses to open-ended questionnaires completed by teachers in India (N = 66) and UK (N = 63). Data were analysed using thematic analysis and three themes, each with three constituent subthemes are presented. In the theme 'Representations of and Unique Approaches to Co-Creation' we explore the ways in which Co-Creation was constructed in relation to teamwork, innovative practice and more continuous models of evaluation. In 'Advantages of Co-Creation' we consider issues around shared ownership, improved outcomes and more meaningful insights alongside the mitigation of risks and short-circuiting of problems. In 'Challenges of Co-Creation' we discuss issues around timing and organisation, attracting and working with appropriate partners and understanding the importance of local context with inherent social, economic and structural barriers, especially in low-and-middle-income countries. We consider how theoretical elements of Co-Creation can inform effective international public health interventions; crucial during a global pandemic in which handwashing is the most effective method to control the transmission of COVID-19. Finally we reflect on some of the methodological challenges of our own work and in managing the potentially conflicting goals of the ethical and participatory values of Co-Creation with pragmatic considerations about ensuring an effective final 'product'.


Assuntos
Controle de Doenças Transmissíveis/métodos , Higiene das Mãos , Betacoronavirus , Criança , Doenças Transmissíveis/patologia , Doenças Transmissíveis/transmissão , Doenças Transmissíveis/virologia , Infecções por Coronavirus/prevenção & controle , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Grupos Focais , Humanos , Índia , Entrevistas como Assunto , Pandemias/prevenção & controle , Pneumonia Viral/prevenção & controle , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Professores Escolares/psicologia , Serra Leoa , Inquéritos e Questionários , Reino Unido
5.
Biosens Bioelectron ; 169: 112592, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-32942143

RESUMO

Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.


Assuntos
Doenças Transmissíveis/diagnóstico , Dispositivos Lab-On-A-Chip , Ácidos Nucleicos/isolamento & purificação , Doenças das Plantas , Sistemas Automatizados de Assistência Junto ao Leito , Betacoronavirus/isolamento & purificação , Fracionamento Químico/instrumentação , Fracionamento Químico/métodos , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/parasitologia , Doenças Transmissíveis/virologia , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/virologia , Desenho de Equipamento , Humanos , Técnicas de Amplificação de Ácido Nucleico/instrumentação , Técnicas de Amplificação de Ácido Nucleico/métodos , Ácidos Nucleicos/sangue , Ácidos Nucleicos/urina , Pandemias , Doenças das Plantas/microbiologia , Doenças das Plantas/parasitologia , Doenças das Plantas/virologia , Pneumonia Viral/diagnóstico , Pneumonia Viral/virologia
6.
BMJ Open ; 10(8): e039856, 2020 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-32759252

RESUMO

OBJECTIVES: Our objective was to review the literature on the inferred duration of the infectious period of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, and provide an overview of the variation depending on the methodological approach. DESIGN: Rapid scoping review. Literature review with fixed search terms, up to 1 April 2020. Central tendency and variation of the parameter estimates for infectious period in (A) asymptomatic and (B) symptomatic cases from (1) virological studies (repeated testing), (2) tracing studies and (3) modelling studies were gathered. Narrative review of viral dynamics. INFORMATION SOURCES: Search strategies developed and the following searched: PubMed, Google Scholar, MedRxiv and BioRxiv. Additionally, the Health Information Quality Authority (Ireland) viral load synthesis was used, which screened literature from PubMed, Embase, ScienceDirect, NHS evidence, Cochrane, medRxiv and bioRxiv, and HRB open databases. RESULTS: There was substantial variation in the estimates, and how infectious period was inferred. One study provided approximate median infectious period for asymptomatic cases of 6.5-9.5 days. Median presymptomatic infectious period across studies varied over <1-4 days. Estimated mean time from symptom onset to two negative RT-PCR tests was 13.4 days (95% CI 10.9 to 15.8) but was shorter when studies included children or less severe cases. Estimated mean duration from symptom onset to hospital discharge or death (potential maximal infectious period) was 18.1 days (95% CI 15.1 to 21.0); time to discharge was on average 4 days shorter than time to death. Viral dynamic data and model infectious parameters were often shorter than repeated diagnostic data. CONCLUSIONS: There are limitations of inferring infectiousness from repeated diagnosis, viral loads and viral replication data alone and also potential patient recall bias relevant to estimating exposure and symptom onset times. Despite this, available data provide a preliminary evidence base to inform models of central tendency for key parameters and variation for exploring parameter space and sensitivity analysis.


Assuntos
Betacoronavirus , Doenças Transmissíveis/transmissão , Infecções por Coronavirus/transmissão , Pneumonia Viral/transmissão , Adulto , Criança , Doenças Transmissíveis/complicações , Doenças Transmissíveis/mortalidade , Doenças Transmissíveis/virologia , Infecções por Coronavirus/complicações , Infecções por Coronavirus/mortalidade , Infecções por Coronavirus/virologia , Saúde Global , Hospitalização , Humanos , Pandemias , Pneumonia Viral/complicações , Pneumonia Viral/mortalidade , Pneumonia Viral/virologia , Reação em Cadeia da Polimerase , Carga Viral
7.
Nat Commun ; 11(1): 3510, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32665616

RESUMO

We report Zika virus (ZIKV) vertical transmission in 130 infants born to PCR+ mothers at the time of the Rio de Janeiro epidemic of 2015-2016. Serum and urine collected from birth through the first year of life were tested by quantitative reverse transcriptase polymerase chain reaction (PCR) and/or IgM Zika MAC-ELISA. Four hundred and seven specimens are evaluated; 161 sera tested by PCR and IgM assays, 85 urines by PCR. Sixty-five percent of children (N = 84) are positive in at least one assay. Of 94 children tested within 3 months of age, 70% are positive. Positivity declines to 33% after 3 months. Five children are PCR+ beyond 200 days of life. Concordance between IgM and PCR results is 52%, sensitivity 65%, specificity 40% (positive PCR results as gold standard). IgM and serum PCR are 61% concordant; serum and urine PCR 55%. Most children (65%) are clinically normal. Equal numbers of children with abnormal findings (29 of 45, 64%) and normal findings (55 of 85, 65%) have positive results, p = 0.98. Earlier maternal trimester of infection is associated with positive results (p = 0.04) but not clinical disease (p = 0.98). ZIKV vertical transmission is frequent but laboratory confirmed infection is not necessarily associated with infant abnormalities.


Assuntos
Doenças Transmissíveis/transmissão , Doenças Transmissíveis/virologia , Infecção por Zika virus/transmissão , Infecção por Zika virus/virologia , Zika virus/patogenicidade , Feminino , Humanos , Imunoglobulina M/metabolismo , Reação em Cadeia da Polimerase , Gravidez , Viroses/virologia
8.
Nat Microbiol ; 5(5): 668-674, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32341570

RESUMO

Virus taxonomy emerged as a discipline in the middle of the twentieth century. Traditionally, classification by virus taxonomists has been focussed on the grouping of relatively closely related viruses. However, during the past few years, the International Committee on Taxonomy of Viruses (ICTV) has recognized that the taxonomy it develops can be usefully extended to include the basal evolutionary relationships among distantly related viruses. Consequently, the ICTV has changed its Code to allow a 15-rank classification hierarchy that closely aligns with the Linnaean taxonomic system and may accommodate the entire spectrum of genetic divergence in the virosphere. The current taxonomies of three human pathogens, Ebola virus, severe acute respiratory syndrome coronavirus and herpes simplex virus 1 are used to illustrate the impact of the expanded rank structure. This new rank hierarchy of virus taxonomy will stimulate further research on virus origins and evolution, and vice versa, and could promote crosstalk with the taxonomies of cellular organisms.


Assuntos
Classificação , Vírus/classificação , Vírus/genética , Doenças Transmissíveis/virologia , Ebolavirus/classificação , Ecologia , Evolução Molecular , Genes Virais , Herpesvirus Humano 1/classificação , Humanos , Vírus da SARS/classificação
10.
Immunol Cell Biol ; 98(4): 305-317, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32142167

RESUMO

Antibody-dependent complement activity is associated not only with autoimmune morbidity, but also with antitumor efficacy. In infectious disease, both recombinant monoclonal antibodies and polyclonal antibodies generated in natural adaptive responses can mediate complement activity to protective, therapeutic or disease-enhancing effect. Recent advances have contributed to the structural resolution of molecular complexes involved in antibody-mediated complement activation, defining the avid nature of participating interactions and pointing to how antibody isotype, subclass, hinge flexibility, glycosylation state, amino acid sequence and the contextual nature of the cognate antigen/epitope are all factors that can determine complement activity through impact on antibody multimerization and subsequent recruitment of complement component 1q. Beyond the efficiency of activation, complement activation products interact with various cell types that mediate immune adherence, trafficking, immune education and innate functions. Similarly, depending on the anatomical location and extent of activation, complement can support homeostatic restoration or be leveraged by pathogens or neoplasms to enhance infection or promote tumorigenic microenvironments, respectively. Advances in means to suppress complement activation by intravenous immunoglobulin (IVIG), IVIG mimetics and complement-intervening antibodies represent proven and promising exploratory therapeutic strategies, while antibody engineering has likewise offered frameworks to enhance, eliminate or isolate complement activation to interrogate in vivo mechanisms of action. Such strategies promise to support the optimization of antibody-based drugs that are able to tackle emerging and difficult-to-treat diseases by improving our understanding of the synergistic and antagonistic relationships between antibody mechanisms mediated by Fc receptors, direct binding and the products of complement activation.


Assuntos
Anticorpos Monoclonais/imunologia , Doenças Transmissíveis/imunologia , Ativação do Complemento/imunologia , Proteínas do Sistema Complemento/imunologia , Neoplasias/imunologia , Animais , Anticorpos Monoclonais/efeitos adversos , Anticorpos Monoclonais/metabolismo , Antígenos/imunologia , Antígenos/metabolismo , Autoanticorpos/efeitos adversos , Autoanticorpos/imunologia , Engenharia Biomédica , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/patologia , Doenças Transmissíveis/virologia , Complemento C1q/química , Complemento C1q/imunologia , Complemento C1q/metabolismo , Proteínas do Sistema Complemento/química , Proteínas do Sistema Complemento/metabolismo , Humanos , Fragmentos Fc das Imunoglobulinas/imunologia , Imunoglobulina G/química , Imunoglobulina G/imunologia , Imunoglobulina G/ultraestrutura , Neoplasias/patologia , Receptores Fc/imunologia , Receptores Fc/metabolismo
11.
APMIS ; 128(2): 136-149, 2020 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32003084

RESUMO

The purpose of the study was to investigate the association between infectious agents and the development of cancer in the ocular adnexa. A comprehensive literary study was carried out, reviewing and summarizing previous reports on the topic. A broad range of malignancies of the ocular adnexa are associated with infectious agents. A strong association and possible causal relationship between the infectious agent and the development of ocular adnexal cancer are seen in Merkel cell carcinoma (Merkel cell polyomavirus), Burkitt lymphoma (Epstein-Barr virus) and Kaposi sarcoma (human herpesvirus 8). Infection with Chlamydia psittaci has been associated with the development of extranodal marginal zone B-cell lymphoma in Italy. Human papillomavirus infection has been associated with the development of squamous cell carcinomas of the ocular adnexa, although with a highly variable reported prevalence. By exploring the role of infectious agents in the ocular adnexa and the mechanism by which they contribute to oncogenesis, the diagnostics, management and prevention of these malignancies may also improve. Antibiotic treatment and vaccines against infectious agents may be valuable in future treatment. Additionally, the presence of infectious agents within the tumours may have a prognostic or predictive value.


Assuntos
Doenças Transmissíveis/complicações , Neoplasias Oculares/etiologia , Antibacterianos/uso terapêutico , Carcinoma de Células Escamosas/tratamento farmacológico , Carcinoma de Células Escamosas/etiologia , Carcinoma de Células Escamosas/microbiologia , Carcinoma de Células Escamosas/virologia , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/virologia , Neoplasias Oculares/tratamento farmacológico , Neoplasias Oculares/microbiologia , Neoplasias Oculares/virologia , Humanos , Itália
12.
J Hum Genet ; 65(1): 35-40, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31582773

RESUMO

Infectious disease is still a major threat in the world today. Five decades ago, it was considered soon to be eradicated, but the adaptation of pathogens to environmental pressure, such as antimicrobials, encouraged the emergence and reemergence of infectious disease. The fight with infectious disease starts with prevention, diagnosis, and treatment. Diagnosis can be upheld by observing the cause of disease under the microscope or detecting the presence of nucleic acid and proteins of the pathogens. The molecular techniques span from classical polymerase chain reaction (PCR) to sequencing the nucleic acid composition. Here, we are reviewing the works have been undertaken to utilize a portable sequencer, MinION, in various aspects of infectious disease management.


Assuntos
Doenças Transmissíveis/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala/instrumentação , Análise de Sequência de DNA/instrumentação , Análise de Sequência de RNA/instrumentação , Doenças Transmissíveis/virologia , Epigenômica/instrumentação , Epigenômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Humanos , Técnicas de Diagnóstico Molecular , Técnicas de Amplificação de Ácido Nucleico , Reação em Cadeia da Polimerase , Análise de Sequência de DNA/métodos , Análise de Sequência de RNA/métodos
13.
PLoS Pathog ; 15(11): e1008038, 2019 11.
Artigo em Inglês | MEDLINE | ID: mdl-31725819

RESUMO

Zika virus (ZIKV) infection during human pregnancy may lead to severe fetal pathology and debilitating impairments in offspring. However, the majority of infections are subclinical and not associated with evident birth defects. Potentially detrimental life-long health outcomes in asymptomatic offspring evoke high concerns. Thus, animal models addressing sequelae in offspring may provide valuable information. To induce subclinical infection, we inoculated selected porcine fetuses at the mid-stage of development. Inoculation resulted in trans-fetal virus spread and persistent infection in the placenta and fetal membranes for two months. Offspring did not show congenital Zika syndrome (e.g., microcephaly, brain calcifications, congenital clubfoot, arthrogryposis, seizures) or other visible birth defects. However, a month after birth, a portion of offspring exhibited excessive interferon alpha (IFN-α) levels in blood plasma in a regular environment. Most affected offspring also showed dramatic IFN-α shutdown during social stress providing the first evidence for the cumulative impact of prenatal ZIKV exposure and postnatal environmental insult. Other eleven cytokines tested before and after stress were not altered suggesting the specific IFN-α pathology. While brains from offspring did not have histopathology, lesions, and ZIKV, the whole genome expression analysis of the prefrontal cortex revealed profound sex-specific transcriptional changes that most probably was the result of subclinical in utero infection. RNA-seq analysis in the placenta persistently infected with ZIKV provided independent support for the sex-specific pattern of in utero-acquired transcriptional responses. Collectively, our results provide strong evidence that two hallmarks of fetal ZIKV infection, altered type I IFN response and molecular brain pathology can persist after birth in offspring in the absence of congenital Zika syndrome.


Assuntos
Encéfalo/patologia , Doenças Fetais/epidemiologia , Feto/virologia , Interferon-alfa/metabolismo , Complicações Infecciosas na Gravidez/epidemiologia , Útero/virologia , Infecção por Zika virus/virologia , Animais , Antivirais/metabolismo , Encéfalo/metabolismo , Encéfalo/virologia , Doenças Transmissíveis/transmissão , Doenças Transmissíveis/virologia , Feminino , Doenças Fetais/metabolismo , Doenças Fetais/virologia , Feto/metabolismo , Feto/patologia , Masculino , Gravidez , Complicações Infecciosas na Gravidez/metabolismo , Complicações Infecciosas na Gravidez/virologia , Fatores Sexuais , Suínos , Útero/metabolismo , Útero/patologia , Zika virus/patogenicidade , Infecção por Zika virus/patologia , Infecção por Zika virus/transmissão , Infecção por Zika virus/veterinária
14.
Crit Rev Microbiol ; 45(5-6): 668-685, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31691607

RESUMO

Metagenomic next-generation sequencing (mNGS) is increasingly being applied in clinical laboratories for unbiased culture-independent diagnosis. Whether it can be a next routine pathogen identification tool has become a topic of concern. We review the current implementation of this new technology for infectious disease diagnostics and discuss the feasibility of transforming mNGS into a routine diagnostic test. Since 2008, numerous studies from over 20 countries have revealed the practicality of mNGS in the work-up of undiagnosed infectious diseases. mNGS performs well in identifying rare, novel, difficult-to-detect and coinfected pathogens directly from clinical samples and presents great potential in resistance prediction by sequencing the antibiotic resistance genes, providing new diagnostic evidence that can be used to guide treatment options and improve antibiotic stewardship. Many physicians recognized mNGS as a last resort method to address clinical infection problems. Although several hurdles, such as workflow validation, quality control, method standardisation, and data interpretation, remain before mNGS can be implemented routinely in clinical laboratories, they are temporary and can be overcome by rapidly evolving technologies. With more validated workflows, lower cost and turnaround time, and simplified interpretation criteria, mNGS will be widely accepted in clinical practice. Overall, mNGS is transforming the landscape of clinical microbiology laboratories, and to ensure that it is properly utilised in clinical diagnosis, both physicians and microbiologists should have a thorough understanding of the power and limitations of this method.


Assuntos
Doenças Transmissíveis/diagnóstico , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Bactérias/genética , Bactérias/isolamento & purificação , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/virologia , Testes Diagnósticos de Rotina , Humanos , Laboratórios Hospitalares , Vírus/genética , Vírus/isolamento & purificação
15.
Curr Top Microbiol Immunol ; 424: 75-83, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31650236

RESUMO

Infectious disease emergence into humans from animals or the environment occurs primarily due to genetic changes in the microbe through mutation or re-assortment making it either more transmissible or virulent or through a change in the disease "ecosystem". Research into infectious disease emergence can be grouped into different strategic approaches. One strategic approach is to study a specific or model disease system to understand the ecology of an infectious disease and how is transmitted and propagated through the environment and different hosts and then extrapolate that disease system knowledge to related pathogens. The other strategic approach follows the genomics and phylogenetics-tracking how pathogens are evolving and changing at the amino acid level. Here we argue that for understanding complex zoonotic diseases and for the purposes of preventing emergence and re-emergence into humans, that the Return on Investment be considered for the best research strategy.


Assuntos
Doenças Transmissíveis/economia , Doenças Transmissíveis/epidemiologia , Ecossistema , Monitoramento Epidemiológico , Filogenia , Vírus/classificação , Vírus/patogenicidade , Animais , Doenças Transmissíveis/classificação , Doenças Transmissíveis/virologia , Humanos , Investimentos em Saúde , Vírus/genética , Zoonoses/virologia
16.
PLoS One ; 14(10): e0222531, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31600207

RESUMO

BACKGROUND: Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate. METHOD: We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance. RESULTS: A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time. CONCLUSION: The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.


Assuntos
Bactérias/genética , Doenças Transmissíveis/genética , Metagenoma/genética , Microbiologia da Água , Animais , Bactérias/patogenicidade , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/parasitologia , Doenças Transmissíveis/virologia , Farmacorresistência Bacteriana/genética , Fezes/microbiologia , Fezes/parasitologia , Fezes/virologia , Humanos , Quênia/epidemiologia , Metagenômica/métodos , Parasitos/genética , Parasitos/patogenicidade , Aceitação pelo Paciente de Cuidados de Saúde , Esgotos/microbiologia , Esgotos/parasitologia , Esgotos/virologia , Vírus/genética , Vírus/patogenicidade , Água/análise
18.
BMC Infect Dis ; 19(1): 577, 2019 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-31272417

RESUMO

BACKGROUND: Acute undifferentiated febrile illness (AUFI) is caused by a multitude of diverse pathogens, with significant morbidity and mortality in the developing world. The objective of this review was to characterise the diversity and relative importance of common infectious aetiologies of AUFI in South and Southeast Asia. METHODS: We conducted a comprehensive literature review to identify common aetiologies of AUFI in Asian countries. Four medical and life sciences databases including PubMed, Medline, Embase and Cochrane Central, and Google Scholar were searched for articles published from January 1998 to March 2019. RESULTS: Forty-three studies met the inclusion criteria. Among AUFI cases, viral aetiologies at 18.5% (14888) were more common than bacterial aetiologies (12.9% [10384]). From 80,554 cases, dengue fever was the most common aetiology (11.8%, 9511), followed by leptospirosis (4.4%, 3549), typhoid (4.0%, 3258), scrub typhus (4.0%, 3243) and influenza other than H1N1 (3.1%, 2514). In both adults and children: dengue fever was the leading cause of AUFI with 16.6% (1928) and 18.7% (1281) of the total cases. In admitted patients, dengue fever was the main cause of AUFI at 16.4% (2377), however leptospirosis at 13.9% (2090) was the main cause of AUFI for outpatients. In South Asia, dengue fever was the main cause of AUFI, causing 12.0% (6821) of cases, whereas in Southeast Asia, leptospirosis was the main diagnosis, causing 12.1% (2861) of cases. CONCLUSIONS: In this study the most common causes of AUFI were viral, followed by bacterial and protozoal (malaria) infections. Dengue was the commonest virus that caused AUFI while leptospirosis and typhoid were important bacterial infectious causes. Therefore, it is imperative to maintain a sound epidemiological knowledge of AUFI so that evidence-based diagnostic criteria and treatment guidelines can be developed.


Assuntos
Doenças Transmissíveis/complicações , Febre/etiologia , Ásia , Ásia Sudeste , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/virologia , Hospitalização , Humanos , Pacientes Ambulatoriais
19.
Hum Vaccin Immunother ; 15(10): 2405-2415, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31158041

RESUMO

The Ninth Interactive Infectious Disease workshop TIPICO was held on November 22-23, 2018, in Santiago de Compostela, Spain. This 2-day academic experience addressed current and topical issues in the field of infectious diseases and vaccination. Summary findings of the meeting include: cervical cancer elimination will be possible in the future, thanks to the implementation of global vaccination action plans in combination with appropriate screening interventions. The introduction of appropriate immunization programs is key to maintain the success of current effective vaccines such as those against meningococcal disease or rotavirus infection. Additionally, reduced dose schedules might improve the efficiency of some vaccines (i.e., PCV13). New vaccines to improve current preventive alternatives are under development (e.g., against tuberculosis or influenza virus), while others to protect against infectious diseases with no current available vaccines (e.g., enterovirus, parechovirus and flaviviruses) need to be developed. Vaccinomics will be fundamental in this process, while infectomics will allow the application of precision medicine. Further research is also required to understand the impact of heterologous vaccine effects. Finally, vaccination requires education at all levels (individuals, community, healthcare professionals) to ensure its success by helping to overcome major barriers such as vaccine hesitancy and false contraindications.


Assuntos
Controle de Doenças Transmissíveis , Vacinas , Ensaios Clínicos como Assunto , Doenças Transmissíveis/parasitologia , Doenças Transmissíveis/virologia , Congressos como Assunto , Pessoal de Saúde , Humanos , Espanha
20.
Philos Trans R Soc Lond B Biol Sci ; 374(1775): 20180258, 2019 06 24.
Artigo em Inglês | MEDLINE | ID: mdl-31056055

RESUMO

Pathogen sequence data have been exploited to infer who infected whom, by using empirical and model-based approaches. Most of these approaches exploit one pathogen sequence per infected host (e.g. individual, household, field). However, modern sequencing techniques can reveal the polymorphic nature of within-host populations of pathogens. Thus, these techniques provide a subsample of the pathogen variants that were present in the host at the sampling time. Such data are expected to give more insight on epidemiological links than a single sequence per host. In general, a mechanistic viewpoint to transmission and micro-evolution has been followed to infer epidemiological links from these data. Here, we investigate an alternative approach grounded on statistical learning. The idea consists of learning the structure of epidemiological links with a pseudo-evolutionary model applied to training data obtained from contact tracing, for example, and using this initial stage to infer links for the whole dataset. Such an approach has the potential to be particularly valuable in the case of a risk of erroneous mechanistic assumptions, it is sufficiently parsimonious to allow the handling of big datasets in the future, and it is versatile enough to be applied to very different contexts from animal, human and plant epidemiology. This article is part of the theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: approaches and important themes'. This issue is linked with the subsequent theme issue 'Modelling infectious disease outbreaks in humans, animals and plants: epidemic forecasting and control'.


Assuntos
Doenças dos Animais/epidemiologia , Doenças Transmissíveis/epidemiologia , Doenças Transmissíveis/veterinária , Doenças das Plantas/estatística & dados numéricos , Vírus/genética , Doenças dos Animais/virologia , Animais , Doenças Transmissíveis/virologia , Bases de Dados Genéticas , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Modelos Estatísticos , Anotação de Sequência Molecular , Vírus/classificação , Vírus/isolamento & purificação
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