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1.
Artigo em Inglês | MEDLINE | ID: mdl-33278872

RESUMO

Abstract: Strict physical distancing measures and border controls have been introduced in the Northern Territory (NT), and across Australia, to reduce the spread of coronavirus disease 2019 (COVID-19). These measures have been associated with reduced incidence of other respiratory illnesses such as influenza. It is currently unclear what effect these measures have on non-respiratory communicable diseases. The incidence of notifiable non-respiratory communicable diseases within the NT, from 15 March to 15 May 2020, the period of most restrictive physical distancing, was monitored and is here compared with two control periods: (i) the 4 months immediately prior and (ii) the same two-month period from the preceding 5 years. During the study period, there was a decline in incidence of communicable enteric illnesses, particularly in shigellosis and rotavirus where person-to-person spread is the main transmission route. There was an increase in chlamydial conjunctivitis in areas with endemic trachoma, which is under further investigation. There was no observed increase in conditions associated with crowding, such as those related to group A streptococcal infection.


Assuntos
/epidemiologia , Doenças Transmissíveis/epidemiologia , /transmissão , Doenças Transmissíveis/microbiologia , Humanos , Incidência , Northern Territory/epidemiologia , Pandemias/prevenção & controle , /isolamento & purificação
2.
Nat Commun ; 11(1): 6294, 2020 12 08.
Artigo em Inglês | MEDLINE | ID: mdl-33293537

RESUMO

Biology can be misused, and the risk of this causing widespread harm increases in step with the rapid march of technological progress. A key security challenge involves attribution: determining, in the wake of a human-caused biological event, who was responsible. Recent scientific developments have demonstrated a capability for detecting whether an organism involved in such an event has been genetically modified and, if modified, to infer from its genetic sequence its likely lab of origin. We believe this technique could be developed into powerful forensic tools to aid the attribution of outbreaks caused by genetically engineered pathogens, and thus protect against the potential misuse of synthetic biology.


Assuntos
Bioterrorismo/prevenção & controle , DNA/análise , Genética Forense/métodos , Organismos Geneticamente Modificados/genética , Medidas de Segurança , Animais , Biotecnologia , Controle de Doenças Transmissíveis/métodos , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/transmissão , Conjuntos de Dados como Assunto , Engenharia Genética , Humanos , Organismos Geneticamente Modificados/patogenicidade , Virulência/genética
3.
BMC Infect Dis ; 20(1): 819, 2020 Nov 10.
Artigo em Inglês | MEDLINE | ID: mdl-33167874

RESUMO

BACKGROUND: In Finland, the routine surveillance of Lyme borreliosis (LB) is laboratory-based. In addition, we have well established national health care registers where countrywide data from patient visits in public health care units are collected. In our previous study based on these registers, we reported an increasing incidence of both microbiologically confirmed and clinically diagnosed LB cases in Finland during the past years. Here, we evaluated our register data, refined LB incidence estimates provided in our previous study, and evaluated treatment practices considering LB in the primary health care. METHODS: Three national health care registers were used. The Register for Primary Health Care Visits (Avohilmo) and the National Hospital Discharge Register (Hilmo) collect physician-recorded data from the outpatient and inpatient health care visits, respectively, whereas the National Infectious Diseases Register (NIDR) represents positive findings in LB diagnostics notified electronically by microbiological laboratories. We used a personal identification number in register-linkage to identify LB cases on an individual level in the study year 2014. In addition, antibiotic purchase data was retrieved from the Finnish Social Insurance Institution in order to evaluate the LB treatment practices in the primary health care in Finland. RESULTS: Avohilmo was found to be useful in monitoring clinically diagnosed LB (i.e. erythema migrans (EM) infections), whereas Hilmo did not add much value next to existing laboratory-based surveillance of disseminated LB. However, Hilmo gave valuable information about uncertainties related to physician-based surveillance of disseminated LB and the total annual number of EM infections in our country. Antibiotic purchases associated with the LB-related outpatient visits in the primary health care indicated a good compliance with the recommended treatment guidelines. CONCLUSIONS: Avohilmo and laboratory-based NIDR together are useful in monitoring LB incidence in Finland. A good compliance was observed with the recommended treatment guidelines of clinically diagnosed LB in the primary health care. In 2018, Avohilmo was introduced in the routine surveillance of LB in Finland next to laboratory-based surveillance of disseminated LB.


Assuntos
Borrelia burgdorferi/imunologia , Doenças Transmissíveis/epidemiologia , Monitoramento Epidemiológico , Eritema Migrans Crônico/epidemiologia , Sistema de Registros , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Antibacterianos/uso terapêutico , Criança , Pré-Escolar , Doenças Transmissíveis/tratamento farmacológico , Doenças Transmissíveis/microbiologia , Eritema Migrans Crônico/tratamento farmacológico , Eritema Migrans Crônico/microbiologia , Feminino , Finlândia/epidemiologia , Humanos , Incidência , Lactente , Recém-Nascido , Laboratórios , Masculino , Cooperação do Paciente , Alta do Paciente , Médicos , Atenção Primária à Saúde , Estudos Retrospectivos , Testes Sorológicos , Adulto Jovem
5.
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
6.
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
7.
Yakugaku Zasshi ; 140(7): 909-912, 2020.
Artigo em Japonês | MEDLINE | ID: mdl-32612055

RESUMO

In medical care, qualified physicians, nurses, and pharmacists have come to be recognized as a team integral to a patient's success, and this team approach to medical care has become popular. In the infectious disease field, more hospitals are practicing antimicrobial stewardship as a team, in addition to the conventional infection control team (ICT). As a result, infectious disease chemotherapy pharmacists are in demand. However, this specific qualification is hard to acquire for pharmacists working in a primary care pharmacy. The problem of multidrug-resistant bacteria is of vital interest today. The National Action Plan on Antimicrobial Resistance 2016-2020, published in Japan, includes an aim to largely reduce the consumption of each oral antimicrobial agent, in order to control the emergence of resistant bacteria. Hospitals and primary care pharmacies will achieve this aim differently. For infection control by primary care pharmacies, the emergence control of a resistant bacteria is important, as is the control of outbreak in a region.


Assuntos
Controle de Doenças Transmissíveis , Serviços Comunitários de Farmácia , Farmacêuticos , Atenção Primária à Saúde , Gestão de Antimicrobianos , Doenças Transmissíveis/tratamento farmacológico , Doenças Transmissíveis/microbiologia , Resistência a Múltiplos Medicamentos , Hospitais , Humanos , Equipe de Assistência ao Paciente
8.
BMC Infect Dis ; 20(1): 384, 2020 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-32471442

RESUMO

BACKGROUND: A particular ability of the Staphylococcus aureus clonal complex 398 (CC398) to cause bone and joint infections (BJI) remains questionable, since some studies have described high prevalence of MSSA CC398 in prosthetic joint infection (PJI) and diabetic foot ostemolyelitis (DFO). Here, we described the long-term epidemiology of CC398 among S. aureus isolated from BJI and identified risk factors associated with CC398. METHODS: We included all bone and joint samples with S. aureus-positive culture in our university hospital between January 2010 and December 2017. Logistic regression was used for univariate and multivariate analysis. RESULTS: We identified 124 CC398 isolates among the 958 BJI-associated S. aureus. The proportion of CC398 among S. aureus increased steadily from 4% in 2010 to 26% in 2017. Only 4 isolates of CC398 were resistant to methicillin. The distribution of BJI types due to CC398 and non CC398 isolates was similar. In multivariate analysis, age (p = 0.034, OR = 3.9), McCabe score (p = 0.005, OR = 5) and inoculation mechanism (p = 0.020, OR = 3.7) were associated with PJI-related CC398. The year of infection (p < 0.001, OR = 1.6), Charlson's score (p = 0.001, OR = 1.5) and grade 4 (severe) of the International Working Group of the Diabetic Foot classification (p < 0.001, OR = 8.5) were associated with DFO-related CC398. CONCLUSION: We highlighted here the emergence and spread of CC398-MSSA in BJI. Patients with comorbidities are at high risk of CC398 MSSA PJI and DFO. The spread of CC398 in the community and hospital settings remains unclear and further epidemiological studies are needed to identify the determinants of its success.


Assuntos
Artrite Infecciosa/epidemiologia , Doenças Transmissíveis/epidemiologia , Pé Diabético/epidemiologia , Staphylococcus aureus Resistente à Meticilina/genética , Osteomielite/epidemiologia , Infecções Estafilocócicas/epidemiologia , Adulto , Idoso , Idoso de 80 Anos ou mais , Artrite Infecciosa/microbiologia , Doenças Transmissíveis/microbiologia , Comorbidade , Pé Diabético/microbiologia , Feminino , Hospitais Universitários , Humanos , Masculino , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Pessoa de Meia-Idade , Osteomielite/microbiologia , Reação em Cadeia da Polimerase , Prevalência , Estudos Retrospectivos , Fatores de Risco , Infecções Estafilocócicas/microbiologia
9.
J Med Microbiol ; 69(6): 844-849, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32459615

RESUMO

Introduction. Signal transducer and activator of transcription 3 (STAT3) deficiency is a rare primary immunodeficiency associated with increased susceptibility to bacterial and fungal infections, notably pulmonary aspergillosis.Aim. We describe the emergence of azole-resistant Aspergillus fumigatus infections in STAT3-deficient patients.Methodology. During a retrospective study of 13 pulmonary aspergillosis cases in STAT3-deficient patients conducted in France, we identified patients infected with azole-resistant A. fumigatus isolates.Results. Two out of the 13 STAT3-deficient patients with aspergillosis had azole-resistant A. fumigatus infection, indicating an unexpectedly high prevalence of resistance. The first patient with STAT3 deficiency presented several flares of allergic bronchopulmonary aspergillosis-like episodes. He was chronically infected with two azole-resistant A. fumigatus isolates (TR34/L98). Despite prolonged antifungal treatment, including caspofungin and amphotericin B, the patient was not able to clear the azole-resistant A. fumigatus. The second patient had chronic cavitary pulmonary aspergillosis (CCPA). The A. fumigatus isolate was initially azole susceptible but harboured three F46Y, M172V and E427K point mutations. Despite prolonged antifungal therapies, lesions worsened and the isolate became resistant to all azoles. Surgery and caspofungin treatments were then required to cure CCPA. Resistance was probably acquired from the environment (TR34/L98) in the first case whereas resistance developed under antifungal treatments in the second case. These infections required long-term antifungal treatments and surgery.Conclusions. The emergence of azole-resistant A. fumigatus infections in STAT3-deficiency dramatically impacts both curative and prophylactic antifungal strategies. Physicians following patients with primary immune-deficiencies should be aware of this emerging problem as it complicates management of the patient.


Assuntos
Antifúngicos/uso terapêutico , Aspergillus fumigatus/efeitos dos fármacos , Azóis/uso terapêutico , Farmacorresistência Fúngica/efeitos dos fármacos , Aspergilose Pulmonar/tratamento farmacológico , Aspergilose Pulmonar/genética , Fator de Transcrição STAT3/deficiência , Adulto , Anfotericina B/uso terapêutico , Caspofungina/uso terapêutico , Criança , Doenças Transmissíveis/tratamento farmacológico , Doenças Transmissíveis/genética , Doenças Transmissíveis/microbiologia , Farmacorresistência Fúngica/genética , França , Proteínas Fúngicas/genética , Genótipo , Humanos , Masculino , Testes de Sensibilidade Microbiana , Estudos Retrospectivos , Adulto Jovem
10.
Nat Microbiol ; 5(6): 787-795, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32467623

RESUMO

Antimicrobial resistance (AMR) is a growing public health challenge that is expected to disproportionately burden lower- and middle-income countries (LMICs) in the coming decades. Although the contributions of human and veterinary antibiotic misuse to this crisis are well-recognized, environmental transmission (via water, soil or food contaminated with human and animal faeces) has been given less attention as a global driver of AMR, especially in urban informal settlements in LMICs-commonly known as 'shanty towns' or 'slums'. These settlements may be unique hotspots for environmental AMR transmission given: (1) the high density of humans, livestock and vermin living in close proximity; (2) frequent antibiotic misuse; and (3) insufficient drinking water, drainage and sanitation infrastructure. Here, we highlight the need for strategies to disrupt environmental AMR transmission in urban informal settlements. We propose that water and waste infrastructure improvements tailored to these settings should be evaluated for their effectiveness in limiting environmental AMR dissemination, lowering the community-level burden of antimicrobial-resistant infections and preventing antibiotic misuse. We also suggest that additional research is directed towards developing economic and legal incentives for evaluating and implementing water and waste infrastructure in these settings. Given that almost 90% of urban population growth will occur in regions predicted to be most burdened by the AMR crisis, there is an urgent need to build effective, evidence-based policies that could influence massive investments in the built urban environment in LMICs over the next few decades.


Assuntos
Anti-Infecciosos/farmacologia , Doenças Transmissíveis/epidemiologia , Doenças Transmissíveis/transmissão , Resistência Microbiana a Medicamentos , Exposição Ambiental , Saúde da População Urbana , Reforma Urbana , Doenças Transmissíveis/tratamento farmacológico , Doenças Transmissíveis/microbiologia , Meio Ambiente , Humanos , Saneamento , Águas Residuárias
11.
Sci Rep ; 10(1): 5919, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32246023

RESUMO

Epidemics and evolution of many pathogens occur on similar timescales so that their dynamics are often entangled. Here, in a first step to study this problem theoretically, we analyze mutating pathogens spreading on simple SIR networks with grid-like connectivity. We have in mind the spatial aspect of epidemics, which often advance on transport links between hosts or groups of hosts such as cities or countries. We focus on the case of mutations that enhance an agent's infection rate. We uncover that the small-world property, i.e., the presence of long-range connections, makes the network very vulnerable, supporting frequent supercritical mutations and bringing the network from disease extinction to full blown epidemic. For very large numbers of long-range links, however, the effect reverses and we find a reduced chance for large outbreaks. We study two cases, one with discrete number of mutational steps and one with a continuous genetic variable, and we analyze various scaling regimes. For the continuous case we derive a Fokker-Planck-like equation for the probability density and solve it for small numbers of shortcuts using the WKB approximation. Our analysis supports the claims that a potentiating mutation in the transmissibility might occur during an epidemic wave and not necessarily before its initiation.


Assuntos
Doenças Transmissíveis/epidemiologia , Doenças Transmissíveis/transmissão , Epidemias , Modelos Biológicos , Taxa de Mutação , Doenças Transmissíveis/microbiologia , Humanos , Probabilidade
13.
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
14.
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
15.
Microbiome ; 8(1): 18, 2020 02 11.
Artigo em Inglês | MEDLINE | ID: mdl-32046792

RESUMO

BACKGROUND: Cell-free DNA (cfDNA) in blood, urine, and other biofluids provides a unique window into human health. A proportion of cfDNA is derived from bacteria and viruses, creating opportunities for the diagnosis of infection via metagenomic sequencing. The total biomass of microbial-derived cfDNA in clinical isolates is low, which makes metagenomic cfDNA sequencing susceptible to contamination and alignment noise. RESULTS: Here, we report low biomass background correction (LBBC), a bioinformatics noise filtering tool informed by the uniformity of the coverage of microbial genomes and the batch variation in the absolute abundance of microbial cfDNA. We demonstrate that LBBC leads to a dramatic reduction in false positive rate while minimally affecting the true positive rate for a cfDNA test to screen for urinary tract infection. We next performed high-throughput sequencing of cfDNA in amniotic fluid collected from term uncomplicated pregnancies or those complicated with clinical chorioamnionitis with and without intra-amniotic infection. CONCLUSIONS: The data provide unique insight into the properties of fetal and maternal cfDNA in amniotic fluid, demonstrate the utility of cfDNA to screen for intra-amniotic infection, support the view that the amniotic fluid is sterile during normal pregnancy, and reveal cases of intra-amniotic inflammation without infection at term. Video abstract.


Assuntos
Ácidos Nucleicos Livres/análise , Biologia Computacional/métodos , DNA Bacteriano/análise , Metagenoma , Análise de Sequência de DNA/métodos , Líquido Amniótico/microbiologia , Ácidos Nucleicos Livres/sangue , Ácidos Nucleicos Livres/urina , Corioamnionite/microbiologia , Doenças Transmissíveis/diagnóstico , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/urina , Estudos Transversais , Análise de Dados , Reações Falso-Positivas , Feminino , Feto/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Inflamação , Masculino , Gravidez , Complicações na Gravidez/diagnóstico , Complicações na Gravidez/microbiologia , Software
16.
mSphere ; 5(1)2020 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-31969481

RESUMO

Soo Chan Lee works in the field of medical mycology. In this mSphere of Influence article, he reflects on how "Interactions between commensal fungi and the C-type lectin receptor Dectin-1 influence colitis" (Science 336:1314-1317, 2012, https://doi.org/10.1126/science.1221789) by I. D. Iliev, V. A. Funari, K. D. Taylor, Q. Nguyen, et al., "CX3CR1+ mononuclear phagocytes control immunity to intestinal fungi" (Science 359:232-236, 2018, https://doi.org/10.1126/science.aao1503) by I. Leonardi, X. Li, A. Semon, D. Li, et al., and "The fungal mycobiome promotes pancreatic oncogenesis via activation of MBL" (Nature 574:264-267, 2019, https://doi.org/10.1038/s41586-019-1608-2) by B. Aykut, S. Pushalkar, R. Chen, Q. Li, et al. made an impact on him to study medically important fungi by providing a forum to understand the roles of fungal microbiota or mycobiota in human diseases and health.


Assuntos
Doenças Transmissíveis/microbiologia , Disbiose , Fungos/patogenicidade , Micobioma , Humanos , Intestinos/microbiologia , Simbiose
17.
Parasit Vectors ; 13(1): 34, 2020 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-31959217

RESUMO

BACKGROUND: Rodents are considered to contribute strongly to the risk of tick-borne diseases by feeding Ixodes ricinus larvae and by acting as amplifying hosts for pathogens. Here, we tested to what extent these two processes depend on rodent density, and for which pathogen species rodents synergistically contribute to the local disease risk, i.e. the density of infected nymphs (DIN). METHODS: In a natural woodland, we manipulated rodent densities in plots of 2500 m2 by either supplementing a critical food source (acorns) or by removing rodents during two years. Untreated plots were used as controls. Collected nymphs and rodent ear biopsies were tested for the presence of seven tick-borne microorganisms. Linear models were used to capture associations between rodents, nymphs, and pathogens. RESULTS: Investigation of data from all plots, irrespective of the treatment, revealed a strong positive association between rodent density and nymphal density, nymphal infection prevalence (NIP) with Borrelia afzelii and Neoehrlichia mikurensis, and hence DIN's of these pathogens in the following year. The NIP, but not the DIN, of the bird-associated Borrelia garinii, decreased with increasing rodent density. The NIPs of Borrelia miyamotoi and Rickettsia helvetica were independent of rodent density, and increasing rodent density moderately increased the DINs. In addition, NIPs of Babesia microti and Spiroplasma ixodetis decreased with increasing rodent density, which had a non-linear association with DINs of these microorganisms. CONCLUSIONS: A positive density dependence for all rodent- and tick-associated tick-borne pathogens was found, despite the observation that some of them decreased in prevalence. The effects on the DINs were variable among microorganisms, more than likely due to contrasts in their biology (including transmission modes, host specificity and transmission efficiency). The strongest associations were found in rodent-associated pathogens that most heavily rely on horizontal transmission. Our results draw attention to the importance of considering transmission mode of a pathogen while developing preventative measures to successfully reduce the burden of disease.


Assuntos
Vetores Aracnídeos/microbiologia , Doenças Transmissíveis/epidemiologia , Ixodes/microbiologia , Roedores/crescimento & desenvolvimento , Roedores/parasitologia , Doenças Transmitidas por Carrapatos/epidemiologia , Animais , Aves , Grupo Borrelia Burgdorferi/fisiologia , Doenças Transmissíveis/microbiologia , Doenças Transmissíveis/transmissão , DNA Bacteriano/isolamento & purificação , Ehrlichia/fisiologia , Florestas , Transmissão Vertical de Doença Infecciosa , Modelos Lineares , Países Baixos/epidemiologia , Densidade Demográfica , Prevalência , Reação em Cadeia da Polimerase em Tempo Real , Fatores de Risco , Estações do Ano , Doenças Transmitidas por Carrapatos/microbiologia , Doenças Transmitidas por Carrapatos/transmissão
18.
Abdom Radiol (NY) ; 45(2): 261-292, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31960117

RESUMO

BACKGROUND: Sonography of the gastrointestinal (GI) tract is a practical, safe, inexpensive, and reproducible diagnostic tool for the evaluation, diagnosis, and follow-up of infectious bowel disease. The modality is rapidly gaining prominence among clinicians on a global scale. In the United States, however, ultrasound of the bowel remains underutilized primarily due to insufficient experience among radiologists and sonographers in performing sonographic bowel assessment. This lack of experience and knowledge results in misinterpretations, missed diagnoses, and underutilization of this modality in patients with acute abdomen, with the majority of GI pathology on sonography discovered incidentally. OBJECTIVES: This article aims to demonstrate the characteristic sonographic findings associated with GI infectious processes as well as provide dedicated ultrasound protocols for evaluation of the GI tract. CONCLUSION: This article serves a twofold purpose, raising awareness of the utility of this imaging modality within the radiology community and also providing practical teaching points for sonographic evaluation of infectious disorders of the GI tract.


Assuntos
Doenças Transmissíveis/diagnóstico por imagem , Doenças Transmissíveis/microbiologia , Gastroenteropatias/diagnóstico por imagem , Gastroenteropatias/microbiologia , Ultrassonografia/métodos , Diagnóstico Diferencial , Humanos
19.
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
20.
Microb Pathog ; 140: 103931, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31846741

RESUMO

Although antibiotics are commonly used to treat infectious diseases, emergence of antibiotic resistant strains highlights the necessity for developing novel alternative approaches. Meanwhile, clinically, antibiotics can destroy the gut microbes balance, which is not conducive to the recovery of infectious disorders. As a result, recent studies have begun to explore potential prevention and treatment methods for infectious diseases, starting with more readily available dietary fiber and probiotics. Moreover, researches have shown the personalized nature of host responses to dietary fiber intervention, with outcomes being dependent on individual pre-treatment gut microbes. In this review, we will focus on the roles of dietary fiber and probiotics on infectious diseases, how probiotics and dietary fiber work on infectious diseases and then explore their mechanisms, so as to guide clinical consideration of new therapies for infectious diseases.


Assuntos
Doenças Transmissíveis , Fibras na Dieta/farmacologia , Probióticos/farmacologia , Antibacterianos/efeitos adversos , Antibacterianos/uso terapêutico , Doenças Transmissíveis/dietoterapia , Doenças Transmissíveis/microbiologia , Dietoterapia , Microbioma Gastrointestinal/efeitos dos fármacos , Trato Gastrointestinal/efeitos dos fármacos , Trato Gastrointestinal/microbiologia , Humanos
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