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1.
PLoS Negl Trop Dis ; 14(8): e0008533, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32776937

RESUMO

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and its incidence is especially high in low- and middle-income countries (LMIC). Disease epidemiology in LMICs is different compared to high income countries like the USA or in Europe. Children in LMICs commonly have repeated and chronic infections even in the absence of symptoms, which can lead to deficits in early childhood development. In this study, we sequenced and characterized C. jejuni (n = 62) from a longitudinal cohort study of children under the age of 5 with and without diarrheal symptoms, and contextualized them within a global C. jejuni genome collection. Epidemiological differences in disease presentation were reflected in the genomes, specifically by the absence of some of the most common global disease-causing lineages. As in many other countries, poultry-associated strains were likely a major source of human infection but almost half of local disease cases (15 of 31) were attributable to genotypes that are rare outside of Peru. Asymptomatic infection was not limited to a single (or few) human adapted lineages but resulted from phylogenetically divergent strains suggesting an important role for host factors in the cryptic epidemiology of campylobacteriosis in LMICs.


Assuntos
Infecções Assintomáticas , Infecções por Campylobacter/epidemiologia , Infecções por Campylobacter/microbiologia , Campylobacter jejuni/genética , Animais , Infecções por Campylobacter/diagnóstico , Infecções por Campylobacter/fisiopatologia , Campylobacter jejuni/classificação , Pré-Escolar , Estudos de Coortes , Diarreia/epidemiologia , Genômica , Genótipo , Interações Hospedeiro-Parasita , Humanos , Lactente , Recém-Nascido , Estudos Longitudinais , Tipagem Molecular , Tipagem de Sequências Multilocus , Peru/epidemiologia , Filogenia , Aves Domésticas/microbiologia
2.
PLoS One ; 15(8): e0237180, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32750094

RESUMO

BACKGROUND: Chagas disease, caused by the intracellular parasite Trypanosoma cruzi, is one of the most important parasitological infections in the Americas. It is estimated to infect approximately 6 million people from mostly low income countries in Latin America, although recent infections have been reported in southern US states. Several studies have described an extensive genetic diversity among T. cruzi isolates throughout its geographic distribution in the American continent. This diversity has been correlated with the pathology developed during an infection. However, due to a lack of a single reliable test, current diagnosis practices of the disease are not straightforward since several different tests are applied. The use of current genomic sequence data allows for the selection of molecular markers (MM) that have the ability to identify the Discrete Typing Unit (DTU) of T. cruzi in a given infection, without the need of any sequencing reaction. METHODOLOGY/PRINCIPAL FINDINGS: Applying three criteria on the genomic sequencing data of four different phylogenetic lineages of T. cruzi, we designed several molecular tests that can be used for the molecular typing of the parasite. The criteria used were: (1) single-copy orthologs of T. cruzi, (2) T. cruzi unique loci, and (3) T. cruzi polymorphic loci. All criteria combined allowed for the selection of 15 MM, 12 of which were confirmed to be functional and replicable in the laboratory with sylvatic samples. Furthermore, one MM produced distinct polymerase chain reaction (PCR) amplicon sizes among distinct T. cruzi DTUs, allowing the use of a AFLP-PCR test to distinguish DTUs I, II/IV, V and VI. Whereas two MM can differentiate DTUs I, II, IV and V/VI out of the six current DTUs with a PCR-RFLP test. CONCLUSIONS/SIGNIFICANCE: The designed molecular tests provide a practical and inexpensive molecular typing test for the majority of DTUs of T. cruzi, excluding the need to perform any sequencing reaction. This provides the scientific community with an additional specific, quick and inexpensive test that can enhance the understanding of the correlation between the DTU of T. cruzi and the pathology developed during the infection.


Assuntos
Análise do Polimorfismo de Comprimento de Fragmentos Amplificados/métodos , Doença de Chagas/diagnóstico , Polimorfismo de Fragmento de Restrição/genética , Trypanosoma cruzi/genética , Doença de Chagas/parasitologia , DNA de Protozoário/genética , Loci Gênicos , Variação Genética , Genoma de Protozoário/genética , Humanos , Tipagem Molecular/métodos , Filogenia , Polimorfismo de Nucleotídeo Único
3.
Gene ; 763: 145048, 2020 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-32805312

RESUMO

Cross-contamination of cell lines is a highly relevant and pervasive problem. The analysis of short tandem repeats (STR) is a simple and commercially available technique to authenticate cell lines for more than two decades. At present, STR multiple amplification kits have been developed up to 21 loci while the current STR databases only provide 9-loci STR profiles. Here, we compared the advantages of 21-loci STR methodology using the same algorithm as 9-loci method. The 21-loci method reduced the uncertainty ratio for authentications by 97.5% relative to the 9-loci method and exclude effectively false positive. We show that the additional 12 loci helped to greatly reduce sample-site marker specificity arising from genetic isolation and the occurrence of null alleles, suggesting that inclusion of additional loci in these databases will ultimately improve the efficiency and accuracy of authentication of cell lines. Taken together, we demonstrate the utility of a 21-loci method in human cells, providing a novel marker panel for use as a valuable alternative to 9-loci analyses to minimize cell line authentication errors and reduce costs due to erroneous experiments.


Assuntos
Autenticação de Linhagem Celular/métodos , Repetições de Microssatélites , Linhagem Celular , Autenticação de Linhagem Celular/normas , Linhagem Celular Tumoral , Loci Gênicos , Marcadores Genéticos , Humanos , Tipagem Molecular/métodos , Tipagem Molecular/normas
4.
PLoS One ; 15(8): e0237652, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32841272

RESUMO

EV-B93 is a novel serotype within the Enterovirus B species and is uncommon worldwide. Currently, only one full-length genomic sequence (the prototype strain) has been deposited in the GenBank database. In this study, three EV-B93 were identified, including one from an acute flaccid paralysis (AFP) patient (named 99052/XZ/CHN/1999, hereafter XZ99052) and two from healthy children (named 99096/XZ/CHN/1999 and 99167/XZ/CHN/1999, hereafter XZ99096 and XZ99167, respectively) from Tibet in 1999 during the polio eradication program. The identity between the nucleotide and amino acid sequences of the Tibet EV-B93 strain and the EV-B93 prototype strain is 83.2%-83.4% and 96.8%-96.9%, respectively. The Tibet EV-B93 strain was found to have greater nucleotide sequence identity in the P3 region to another enterovirus EV-B107 as per a phylogenetic tree analysis, which revealed that recombination occurred. Seroepidemiology data showed that EV-B93 has not produced an epidemic in Tibet and there may be susceptible individuals. The three Tibet EV-B93 strains are temperature-resistant with prognosticative virulence, suggesting the possibility of a potential large-scale outbreak of EV-B93. The analyzed EV-B93 strains enrich our knowledge about this serotype and provide valuable information on global EV-B93 molecular epidemiology. What is more, they permit the appraisal of the serotype's potential public health impact and aid in understanding the role of recombination events in the evolution of enteroviruses.


Assuntos
Enterovirus Humano B/genética , Infecções por Enterovirus/virologia , Genoma Viral/genética , Paralisia/virologia , Pré-Escolar , Surtos de Doenças/prevenção & controle , Enterovirus Humano B/isolamento & purificação , Enterovirus Humano B/patogenicidade , Infecções por Enterovirus/epidemiologia , Fezes/virologia , Feminino , Humanos , Lactente , Masculino , Tipagem Molecular , Paralisia/epidemiologia , Filogenia , RNA Viral/genética , Recombinação Genética , Análise de Sequência de RNA , Estudos Soroepidemiológicos , Tibet/epidemiologia
5.
Arch Virol ; 165(10): 2291-2299, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32754877

RESUMO

The multimammate mouse (Mastomys natalensis; M. natalensis) serves as the main reservoir for the zoonotic arenavirus Lassa virus (LASV), and this has led to considerable investigation into the distribution of LASV and other related arenaviruses in this host species. In contrast to the situation with arenaviruses, the presence of other viruses in M. natalensis remains largely unexplored. In this study, herpesviruses and polyomaviruses were identified and partially characterized by PCR methods, sequencing, and phylogenetic analysis. In tissues sampled from M. natalensis populations in Côte d'Ivoire and Mali, six new DNA viruses (four betaherpesviruses, one gammaherpesvirus and one polyomavirus) were identified. Phylogenetic analysis based on glycoprotein B amino acid sequences showed that the herpesviruses clustered with cytomegaloviruses and rhadinoviruses of multiple rodent species. The complete circular genome of the newly identified polyomavirus was amplified by PCR. Amino acid sequence analysis of the large T antigen or VP1 showed that this virus clustered with a known polyomavirus from a house mouse (species Mus musculus polyomavirus 1). These two polyomaviruses form a clade with other rodent polyomaviruses, and the newly identified virus represents the third known polyomavirus of M. natalensis. This study represents the first identification of herpesviruses and the discovery of a novel polyomavirus in M. natalensis. In contrast to arenaviruses, we anticipate that these newly identified viruses represent a low zoonotic risk due to the normally highly restricted specificity of members of these two DNA virus families to their individual mammalian host species.


Assuntos
Genoma Viral , Infecções por Herpesviridae/epidemiologia , Herpesviridae/genética , Filogenia , Infecções por Polyomavirus/epidemiologia , Polyomavirus/genética , Doenças dos Roedores/epidemiologia , África ao Sul do Saara/epidemiologia , Animais , Antígenos Virais de Tumores/genética , Proteínas do Capsídeo/genética , Reservatórios de Doenças/virologia , Herpesviridae/classificação , Herpesviridae/isolamento & purificação , Infecções por Herpesviridae/virologia , Especificidade de Hospedeiro , Tipagem Molecular , Murinae/virologia , Polyomavirus/classificação , Polyomavirus/isolamento & purificação , Infecções por Polyomavirus/virologia , Doenças dos Roedores/virologia , Proteínas do Envelope Viral/genética
6.
Cochrane Database Syst Rev ; 8: CD013359, 2020 08 27.
Artigo em Inglês | MEDLINE | ID: mdl-32853411

RESUMO

BACKGROUND: Every year, at least one million children become ill with tuberculosis and around 200,000 children die. Xpert MTB/RIF and Xpert Ultra are World Health Organization (WHO)-recommended rapid molecular tests that simultaneously detect tuberculosis and rifampicin resistance in adults and children with signs and symptoms of tuberculosis, at lower health system levels. To inform updated WHO guidelines on molecular assays, we performed a systematic review on the diagnostic accuracy of these tests in children presumed to have active tuberculosis. OBJECTIVES: Primary objectives • To determine the diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for (a) pulmonary tuberculosis in children presumed to have tuberculosis; (b) tuberculous meningitis in children presumed to have tuberculosis; (c) lymph node tuberculosis in children presumed to have tuberculosis; and (d) rifampicin resistance in children presumed to have tuberculosis - For tuberculosis detection, index tests were used as the initial test, replacing standard practice (i.e. smear microscopy or culture) - For detection of rifampicin resistance, index tests replaced culture-based drug susceptibility testing as the initial test Secondary objectives • To compare the accuracy of Xpert MTB/RIF and Xpert Ultra for each of the four target conditions • To investigate potential sources of heterogeneity in accuracy estimates - For tuberculosis detection, we considered age, disease severity, smear-test status, HIV status, clinical setting, specimen type, high tuberculosis burden, and high tuberculosis/HIV burden - For detection of rifampicin resistance, we considered multi-drug-resistant tuberculosis burden • To compare multiple Xpert MTB/RIF or Xpert Ultra results (repeated testing) with the initial Xpert MTB/RIF or Xpert Ultra result SEARCH METHODS: We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, the Cumulative Index to Nursing and Allied Health Literature (CINAHL), Scopus, the WHO International Clinical Trials Registry Platform, ClinicalTrials.gov, and the International Standard Randomized Controlled Trials Number (ISRCTN) Registry up to 29 April 2019, without language restrictions. SELECTION CRITERIA: Randomized trials, cross-sectional trials, and cohort studies evaluating Xpert MTB/RIF or Xpert Ultra in HIV-positive and HIV-negative children younger than 15 years. Reference standards comprised culture or a composite reference standard for tuberculosis and drug susceptibility testing or MTBDRplus (molecular assay for detection of Mycobacterium tuberculosis and drug resistance) for rifampicin resistance. We included studies evaluating sputum, gastric aspirate, stool, nasopharyngeal or bronchial lavage specimens (pulmonary tuberculosis), cerebrospinal fluid (tuberculous meningitis), fine needle aspirates, or surgical biopsy tissue (lymph node tuberculosis). DATA COLLECTION AND ANALYSIS: Two review authors independently extracted data and assessed study quality using the Quality Assessment of Studies of Diagnostic Accuracy - Revised (QUADAS-2). For each target condition, we used the bivariate model to estimate pooled sensitivity and specificity with 95% confidence intervals (CIs). We stratified all analyses by type of reference standard. We assessed certainty of evidence using the GRADE approach. MAIN RESULTS: For pulmonary tuberculosis, 299 data sets (68,544 participants) were available for analysis; for tuberculous meningitis, 10 data sets (423 participants) were available; for lymph node tuberculosis, 10 data sets (318 participants) were available; and for rifampicin resistance, 14 data sets (326 participants) were available. Thirty-nine studies (80%) took place in countries with high tuberculosis burden. Risk of bias was low except for the reference standard domain, for which risk of bias was unclear because many studies collected only one specimen for culture. Detection of pulmonary tuberculosis For sputum specimens, Xpert MTB/RIF pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 64.6% (55.3% to 72.9%) (23 studies, 493 participants; moderate-certainty evidence) and 99.0% (98.1% to 99.5%) (23 studies, 6119 participants; moderate-certainty evidence). For other specimen types (nasopharyngeal aspirate, 4 studies; gastric aspirate, 14 studies; stool, 11 studies), Xpert MTB/RIF pooled sensitivity ranged between 45.7% and 73.0%, and pooled specificity ranged between 98.1% and 99.6%. For sputum specimens, Xpert Ultra pooled sensitivity (95% CI) and specificity (95% CI) verified by culture were 72.8% (64.7% to 79.6%) (3 studies, 136 participants; low-certainty evidence) and 97.5% (95.8% to 98.5%) (3 studies, 551 participants; high-certainty evidence). For nasopharyngeal specimens, Xpert Ultra sensitivity (95% CI) and specificity (95% CI) were 45.7% (28.9% to 63.3%) and 97.5% (93.7% to 99.3%) (1 study, 195 participants). For all specimen types, Xpert MTB/RIF and Xpert Ultra sensitivity were lower against a composite reference standard than against culture. Detection of tuberculous meningitis For cerebrospinal fluid, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 54.0% (95% CI 27.8% to 78.2%) (6 studies, 28 participants; very low-certainty evidence) and 93.8% (95% CI 84.5% to 97.6%) (6 studies, 213 participants; low-certainty evidence). Detection of lymph node tuberculosis For lymph node aspirates or biopsies, Xpert MTB/RIF pooled sensitivity and specificity, verified by culture, were 90.4% (95% CI 55.7% to 98.6%) (6 studies, 68 participants; very low-certainty evidence) and 89.8% (95% CI 71.5% to 96.8%) (6 studies, 142 participants; low-certainty evidence). Detection of rifampicin resistance Xpert MTB/RIF pooled sensitivity and specificity were 90.0% (67.6% to 97.5%) (6 studies, 20 participants; low-certainty evidence) and 98.3% (87.7% to 99.8%) (6 studies, 203 participants; moderate-certainty evidence). AUTHORS' CONCLUSIONS: We found Xpert MTB/RIF sensitivity to vary by specimen type, with gastric aspirate specimens having the highest sensitivity followed by sputum and stool, and nasopharyngeal specimens the lowest; specificity in all specimens was > 98%. Compared with Xpert MTB/RIF, Xpert Ultra sensitivity in sputum was higher and specificity slightly lower. Xpert MTB/RIF was accurate for detection of rifampicin resistance. Xpert MTB/RIF was sensitive for diagnosing lymph node tuberculosis. For children with presumed tuberculous meningitis, treatment decisions should be based on the entirety of clinical information and treatment should not be withheld based solely on an Xpert MTB/RIF result. The small numbers of studies and participants, particularly for Xpert Ultra, limits our confidence in the precision of these estimates.


Assuntos
Tipagem Molecular/métodos , Tuberculose dos Linfonodos/diagnóstico , Tuberculose Meníngea/diagnóstico , Tuberculose Resistente a Múltiplos Medicamentos/diagnóstico , Tuberculose Pulmonar/diagnóstico , Adolescente , Antibióticos Antituberculose/uso terapêutico , Viés , Criança , Fezes/microbiologia , Conteúdo Gastrointestinal/microbiologia , Humanos , Tipagem Molecular/normas , Mycobacterium tuberculosis/efeitos dos fármacos , Mycobacterium tuberculosis/isolamento & purificação , Rifampina/uso terapêutico , Sensibilidade e Especificidade , Escarro/microbiologia , Tuberculose dos Linfonodos/tratamento farmacológico , Tuberculose dos Linfonodos/microbiologia , Tuberculose Meníngea/líquido cefalorraquidiano , Tuberculose Meníngea/tratamento farmacológico , Tuberculose Meníngea/microbiologia , Tuberculose Resistente a Múltiplos Medicamentos/tratamento farmacológico , Tuberculose Resistente a Múltiplos Medicamentos/microbiologia , Tuberculose Pulmonar/tratamento farmacológico , Tuberculose Pulmonar/microbiologia
7.
Viruses ; 12(8)2020 07 24.
Artigo em Inglês | MEDLINE | ID: mdl-32722343

RESUMO

The aim of this study is the characterization and genomic tracing by phylogenetic analyses of 59 new SARS-CoV-2 Italian isolates obtained from patients attending clinical centres in North and Central Italy until the end of April 2020. All but one of the newly-characterized genomes belonged to the lineage B.1, the most frequently identified in European countries, including Italy. Only a single sequence was found to belong to lineage B. A mean of 6 nucleotide substitutions per viral genome was observed, without significant differences between synonymous and non-synonymous mutations, indicating genetic drift as a major source for virus evolution. tMRCA estimation confirmed the probable origin of the epidemic between the end of January and the beginning of February with a rapid increase in the number of infections between the end of February and mid-March. Since early February, an effective reproduction number (Re) greater than 1 was estimated, which then increased reaching the peak of 2.3 in early March, confirming the circulation of the virus before the first COVID-19 cases were documented. Continuous use of state-of-the-art methods for molecular surveillance is warranted to trace virus circulation and evolution and inform effective prevention and containment of future SARS-CoV-2 outbreaks.


Assuntos
Betacoronavirus/classificação , Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , Teorema de Bayes , Betacoronavirus/isolamento & purificação , Monitoramento Epidemiológico , Genoma Viral , Humanos , Itália/epidemiologia , Funções Verossimilhança , Epidemiologia Molecular , Tipagem Molecular , Mutação , Filogenia , Fatores de Tempo , Sequenciamento Completo do Genoma
8.
PLoS One ; 15(7): e0232860, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32645001

RESUMO

Limited information is available that seed biopriming with plant growth-promoting Enterobacter spp. play a prominent role to enhance vegetative growth of plants. Contrary to Enterobacter cloacae, Enterobacter hormaechei is a less-studied counterpart despite its vast potential in plant growth-promotion mainly through the inorganic phosphorus (P) and potassium (K) solubilization abilities. To this end, 18 locally isolated bacterial pure cultures were screened and three strains showed high P- and K-solubilizing capabilities. Light microscopy, biochemical tests and 16S rRNA gene sequencing revealed that strains 15a1 and 40a were closely related to Enterobacter hormaechei while strain 38 was closely related to Enterobacter cloacae (Accession number: MN294583; MN294585; MN294584). All Enterobacter spp. shared common plant growth-promoting traits, namely nitrogen (N2) fixation, indole-3-acetic acid production and siderophore production. The strains 38 and 40a were able to produce gibberellic acid, while only strain 38 was able to secrete exopolysaccharide on agar. Under in vitro germination assay of okra (Abelmoschus esculentus) seeds, Enterobacter spp. significantly improved overall germination parameters and vigor index (19.6%) of seedlings. The efficacy of root colonization of Enterobacter spp. on the pre-treated seedling root tips was confirmed using Scanning Electron Microscopy (SEM). The pot experiment of bioprimed seeds of okra seedling showed significant improvement of the plant growth (> 28%) which corresponded to the increase of P and K uptakes (> 89%) as compared to the uninoculated control plants. The leaf surface area and the SPAD chlorophyll index of bioprimed plants were increased by up to 29% and 9% respectively. This report revealed that the under-explored species of P- and K-solubilizing Enterobacter hormaechei sp. with multiple plant beneficial traits presents a great potential sustainable approach for enhancement of soil fertility and P and K uptakes of plants.


Assuntos
Abelmoschus/crescimento & desenvolvimento , Enterobacter/fisiologia , Fósforo/metabolismo , Potássio/metabolismo , Sementes/microbiologia , Abelmoschus/classificação , Abelmoschus/metabolismo , Abelmoschus/microbiologia , Contenção de Riscos Biológicos , Enterobacter/isolamento & purificação , Germinação , Tipagem Molecular , Desenvolvimento Vegetal , RNA Ribossômico 16S , Plântula/crescimento & desenvolvimento , Sementes/crescimento & desenvolvimento
9.
Arch Virol ; 165(10): 2335-2340, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32719956

RESUMO

Sapoviruses are increasingly being recognized as pathogens associated with gastroenteritis in humans. Human sapoviruses are currently assigned to 18 genotypes (GI.1-7, GII.1-8, GIV.1, and GV.1-2) based on the sequence of the region encoding the major structural protein. In this study, we evaluated 11 polymerase chain reaction (PCR) assays using published and newly designed/modified primers and showed that four PCR assays with different primer combinations amplified all of the tested human sapovirus genotypes using either synthetic DNA or cDNA prepared from human sapovirus-positive fecal specimens. These assays can be used as improved broadly reactive screening tests or as tools for molecular characterization of human sapoviruses.


Assuntos
Infecções por Caliciviridae/virologia , Primers do DNA/química , Gastroenterite/virologia , Reação em Cadeia da Polimerase Via Transcriptase Reversa/métodos , Sapovirus/genética , Proteínas Estruturais Virais/genética , Sequência de Bases , Infecções por Caliciviridae/diagnóstico , Primers do DNA/genética , Fezes/virologia , Gastroenterite/diagnóstico , Expressão Gênica , Genótipo , Humanos , Tipagem Molecular/métodos , Filogenia , Sapovirus/classificação , Sapovirus/isolamento & purificação , Alinhamento de Sequência
10.
PLoS Negl Trop Dis ; 14(6): e0008311, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32497037

RESUMO

BACKGROUND: Trypanosoma cruzi has a high genetic and biological diversity and has been subdivided into seven genetic lineages, named TcI-TcVI and TcBat. DTUs TcI-TcII-TcV and TcVI are agents of ChD in different regions of Latin America. Due to population movements, the disease is an emergent global public health problem. Thus, the aim of this study was to quantify the parasitic load and identify the presence of T. cruzi DTUs in 101 Latin American immigrants with chronic ChD, residing in Barcelona, Spain. METHODOLOGY / PRINCIPAL FINDINGS: 5ml of peripheral blood were collected in guanidine/EDTA from each patient for DNA extraction, quantification of the parasitic load and genotyping. A great variation of the parasitic load of the patients was verified: from 0.001 to 22.2 T. cruzi DNA (fg) / Blood DNA (ng). In patients from Bolivia the parasitic load was 3.76±4.43 T. cruzi DNA (fg) / Blood DNA (ng) (mean ± SD), in patients of other countries was 0.95±1.38 T. cruzi DNA (fg) / Blood DNA (ng). No statistically significant difference was observed in the parasitic load between patients with the indeterminate and cardiac forms of ChD (p = 0,57). Parasite genotyping was performed by multilocus conventional PCR. In patients from Bolivia there was a nearly equal prevalence of DTUs TcV (27/77), TcII/TcV/TcVI (26/77), and TcII/TcVI (22/77). TcVI was detected in only 2 samples (2/77). A higher prevalence of TcII/TcVI (19/24) was verified in patients of other countries, with low prevalence of TcII/TcV/TcVI (4/24) and TcV (1/24). CONCLUSIONS/SIGNIFICANCE: In this study, low/medium parasitic load was found in all patients evaluated. Our data corroborate previous conclusions indicating that patients from the Bolivia, living in Spain, are predominantly infected by TcV, and TcVI DTUs. On the other hand, in Non-Bolivians patients TcII/TcVI predominated. Surprisingly, in our cohort of 101 patients no infection by TcI DTU was observed.


Assuntos
Doença de Chagas/etnologia , Doença de Chagas/parasitologia , DNA de Protozoário/genética , Emigrantes e Imigrantes , Trypanosoma cruzi/classificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Animais , Bolívia/etnologia , Feminino , Variação Genética , Genótipo , Humanos , Masculino , Pessoa de Meia-Idade , Tipagem Molecular , Carga Parasitária , Análise de Sequência de DNA , Espanha/epidemiologia , Trypanosoma cruzi/isolamento & purificação , Adulto Jovem
11.
BMC Infect Dis ; 20(1): 444, 2020 Jun 23.
Artigo em Inglês | MEDLINE | ID: mdl-32576149

RESUMO

BACKGROUND: The syphilis epidemic continues to cause substantial morbidity and mortality worldwide, particularly in low- and middle-income countries, despite several recent disease control initiatives. Though our understanding of the pathogenesis of this disease and the biology of the syphilis agent, Treponema pallidum subsp. pallidum has improved over the last two decades, further research is necessary to improve clinical diagnosis and disease management protocols. Additionally, such research efforts could contribute to the identification of possible targets for the development of an effective vaccine to stem syphilis spread. METHODS: This study will recruit two cohorts of participants with active syphilis infection, one with de novo infection, one with repeat infection. Whole blood specimens will be collected from each study participant at baseline, 4, 12, 24, 36, and 48 weeks, to track specific markers of their immunological response, as well as to compare humoral reactivity to Treponema pallidum antigens between the two groups. Additionally, we will use serum specimens to look for unique cytokine patterns in participants with early syphilis. Oral and blood samples, as well as samples from any syphilitic lesions present, will also be collected to sequence any Treponema pallidum DNA found. DISCUSSION: By furthering our understanding of syphilis pathogenesis and human host immune response to Treponema pallidum, we will provide important data that will help in development of new point-of-care tests that could better identify active infection, leading to improved syphilis diagnosis and management. Findings could also contribute to vaccine development efforts.


Assuntos
Vacinas Bacterianas/uso terapêutico , Sífilis/epidemiologia , Sífilis/prevenção & controle , Treponema pallidum/imunologia , Vacinação , Antígenos de Bactérias/imunologia , Sequência de Bases , Estudos de Coortes , Citocinas/análise , DNA Bacteriano/genética , Seguimentos , Humanos , Tipagem Molecular , Peru/epidemiologia , Sífilis/sangue , Sífilis/imunologia , Treponema pallidum/genética
12.
Indian J Med Res ; 151(5): 450-458, 2020 May.
Artigo em Inglês | MEDLINE | ID: mdl-32474553

RESUMO

Background & objectives: SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is evolving with the progression of the pandemic. This study was aimed to investigate the diversity and evolution of the coronavirus SARS-CoV-2 with progression of the pandemic over time and to identify similarities and differences of viral diversity and evolution across geographical regions (countries). Methods: Publicly available data on type definitions based on whole-genome sequences of the SARS-CoV-2 sampled during December and March 2020 from 3636 infected patients spread over 55 countries were collected. Phylodynamic analyses were performed and the temporal and spatial evolution of the virus was examined. Results: It was found that (i) temporal variation in frequencies of types of the coronavirus was significant; ancestral viruses of type O were replaced by evolved viruses belonging to type A2a; (ii) spatial variation was not significant; with the spread of SARS-CoV-2, the dominant virus was the A2a type virus in every geographical region; (iii) within a geographical region, there was significant micro-level variation in the frequencies of the different viral types, and (iv) the evolved coronavirus of type A2a swept rapidly across all continents. Interpretation & conclusions: SARS-CoV-2 belonging to the A2a type possesses a non-synomymous variant (D614G) that possibly eases the entry of the virus into the lung cells of the host. This may be the reason why the A2a type has an advantage to infect and survive and as a result has rapidly swept all geographical regions. Therefore, large-scale sequencing of coronavirus genomes and, as required, of host genomes should be undertaken in India to identify regional and ethnic variation in viral composition and its interaction with host genomes. Further, careful collection of clinical and immunological data of the host can provide deep learning in relation to infection and transmission of the types of coronavirus genomes.


Assuntos
Betacoronavirus/genética , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/virologia , Pandemias , Pneumonia Viral/epidemiologia , Pneumonia Viral/virologia , RNA Viral/análise , Betacoronavirus/patogenicidade , Evolução Molecular , Humanos , Índia/epidemiologia , Internacionalidade , Tipagem Molecular , Filogeografia , RNA Viral/genética , Análise Espaço-Temporal
13.
Aust Vet J ; 98(8): 405-410, 2020 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-32390155

RESUMO

OBJECTIVE: The aim of this study was to evaluate formalin-inactivated autovaccination to treat cutaneous papillomatosis and to perform molecular typing of the papillomavirus in four horses (two foals, one 3-year-old filly and a 5-year-old stallion). METHODS: Histopathological slides of lesions were prepared and stained with haematoxylin and eosin (H&E) to establish a diagnosis that was based on observation koilocytosis, which is a pathognomonic cytopathic change that is associated with papillomatosis, using light microscopy. Polymerase chain reaction (PCR) and DNA sequencing were performed using the EPV-R and EPV-F primer set. RESULTS: In histopathological examination, koilocyte formation and occasional intranuclear viral inclusions were detected in the papillomas. A 334-base pair (bp) fragment of the E2 and L2 genes from the EPV genome was amplified using the EPV-R and EPV-F primer set. This fragment contained 215 bp from the E2 gene and 56 bp from the L2 gene; these were found to be 98.78% to 98.97% identical to the known EcPV type-1 sequence (AF498323). CONCLUSION: Three horses with cutaneous papillomatosis were administered two doses of a formalin-inactivated preparation of papillomatous lesions at 7-day intervals. The papillomatous lesions were observed to decrease gradually 1 week after the last vaccination, and all warts had resolved within 2-3 weeks. One horse with cutaneous papillomatosis was left as an unvaccinated control, and no changes to the lesions were noted. To the best of our knowledge, this is the first report of EcPV type-1 infection, autovaccine preparation and molecular typing in Turkey.


Assuntos
Doenças dos Cavalos , Papiloma/veterinária , Papillomaviridae/genética , Animais , DNA Viral , Feminino , Cavalos , Masculino , Tipagem Molecular/veterinária , Turquia
14.
Am J Trop Med Hyg ; 103(1): 175-182, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32394881

RESUMO

Chronic hepatitis C virus (HCV) infection can lead to liver cirrhosis and hepatocellular carcinoma. To eliminate HCV infection in an endemic area, an epidemiological baseline of the current HCV infection in the population is required. We therefore aimed to evaluate the HCV burden in the Thai Province of Phetchabun, which has the highest HCV infection rate in the country. Toward this, a province-wide district-based representative sampling of 4,769 individuals ages 35-64 years previously shown to represent high-risk age-groups were tested for anti-HCV antibodies using the automated chemiluminescent microparticle assays. Active HCV infection and subsequent genotyping were determined from serologically reactive samples by amplification of the HCV core gene. We found that 6.9% (327/4,769) were anti-HCV positive, of which 75.8% (248/327) had detectable HCV RNA and 5.8% (19/327) were in the presence of hepatitis B virus coinfection. Nucleotide sequencing and phylogenetic analysis revealed that HCV genotype 6 was the most prevalent (41%, 101/248), followed by genotype 3 (31%, 78/248), and genotype 1 (28%, 69/248). Socioeconomic and demographic factors including male gender, education, and agricultural work were associated with HCV seropositivity. From these results, we defined the regional HCV genotypes and estimated the HCV burden necessary toward the implementation of pan-genotypic direct-acting antivirals, which may be appropriate and effective toward the diversity of genotypes identified in this study. Micro-elimination of HCV in Phetchabun may serve as a model for a more comprehensive coverage of HCV treatment in Thailand.


Assuntos
Doenças Endêmicas/estatística & dados numéricos , Hepacivirus/genética , Hepatite B/epidemiologia , Hepatite C Crônica/epidemiologia , RNA Viral/genética , Adulto , Anticorpos Antivirais/sangue , Doença Crônica , Coinfecção , Erradicação de Doenças/organização & administração , Monitoramento Epidemiológico , Feminino , Genótipo , Hepacivirus/classificação , Hepatite B/diagnóstico , Hepatite B/patologia , Hepatite B/virologia , Vírus da Hepatite B/classificação , Vírus da Hepatite B/genética , Hepatite C Crônica/diagnóstico , Hepatite C Crônica/patologia , Hepatite C Crônica/virologia , Humanos , Masculino , Pessoa de Meia-Idade , Tipagem Molecular , Filogenia , Prevalência , Tailândia/epidemiologia , Carga Viral/genética
15.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(3): 423-428, 2020 Mar 10.
Artigo em Chinês | MEDLINE | ID: mdl-32294847

RESUMO

Objective: To investigate the isolation rate, antimicrobial resistance phenotype, and molecular type characteristics of Klebsiella pneumoniae from infectious diarrhea outpatients in Tai'an. Methods: A total of 866 stool samples were collected from infectious diarrhea cases in sentinel hospitals in 6 counties of Tai'an from 2013 to 2017. The strains were isolated from stool samples of the cases and identified by biochemical test. Micro broth dilution method was used to detect the drug resistance of the strains. The molecular typing was conducted by using pulsed field gel electrophoresis (PFGE). Results: The detection rate of Klebsiella pneumoniae in the stool samples was 7.97% (69/866), with significant differences among the 6 counties (χ(2)=39.627, P=0.000). Sixty- eight out of the 69 strains were resistant to 15 antibiotics with resistance rate 98.55%(68/69). The resistance to ampicillin (AMP) was highest (84.06%) (58/69), followed by sulfamethoxazole (SOX) (72.46%)(50/69). There were 40 drug resistance profiles, and the predominant resistance profile was AMP-SOX detected (n=10). The multi-drug resistant (MDR) strains accounted for 33.33% (23/69). The 69 strains could be divided into 65 PFGE patterns, and no predominant PFGE pattern or cluster was observed. Conclusions: Klebsiella pneumoniae was detected in the stool samples of diarrhea- syndrome outpatients, indicating the risk for community-acquired infection; the strains were resistant to multiplex antibiotics, with wide drug-resistance profiles and high multi-drug resistance rates. The PFGE patterns were diverse, which showed no correlation with drug resistance profiles. Our study indicated that it necessary to strengthen the surveillance and detection of Klebsiella pneumoniae from diarrhea outpatients, which could facilitate the prevention of the emergence and spread of drug resistance strains and the protection of susceptible population.


Assuntos
Farmacorresistência Bacteriana , Disenteria/microbiologia , Infecções por Klebsiella/diagnóstico , Klebsiella pneumoniae , Pacientes Ambulatoriais/estatística & dados numéricos , Antibacterianos/farmacologia , China , Eletroforese em Gel de Campo Pulsado , Humanos , Klebsiella pneumoniae/classificação , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/isolamento & purificação , Tipagem Molecular
17.
New Microbiol ; 43(2): 82-88, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32310301

RESUMO

In order to investigate molecular typing and fatty acid methyl esters (FAMEs) typing of clinical Stenotrophomonas maltophilia (S.maltophilia) isolates based on Random Amplification Polymorphic DNA (RAPD) and Gas Chromatography-Mass Spectrometer (GC-MS) methods, we collected 35 drug-resistant S. maltophilia isolates from March to December 2017 in a comprehensive hospital. The VITEK 2 Compact System was used to determine bacterial antibiotic susceptibility. The analysis of molecular typing was performed by RAPD. GC-MS was used to obtain FAMEs profiles. In total, all 35 isolates were multidrug-resistant S.maltophilia. Their resistance rates to CAZ and LEV were 21.4% and 21.1%, and to SXT up to 13.5%. S. maltophilia isolates were typed to six main clones by RAPD methods and four main clones by FAMEs fingerprint, respectively. The concordance rate of these two methods was 69.0%. Clonal typing provides evidence that multidrug-resistant isolates are prevalent among wards in the hospital. FAMEs profiles may be an easy and sensitive method for bacteria classification. The effectiveness and feasibility of different typing methods should be comprehensively considered.


Assuntos
Ácidos Graxos , Tipagem Molecular , Stenotrophomonas maltophilia , Antibacterianos/farmacologia , Ácidos Graxos/análise , Cromatografia Gasosa-Espectrometria de Massas , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Testes de Sensibilidade Microbiana , Técnica de Amplificação ao Acaso de DNA Polimórfico , Stenotrophomonas maltophilia/química , Stenotrophomonas maltophilia/classificação , Stenotrophomonas maltophilia/efeitos dos fármacos
18.
PLoS Negl Trop Dis ; 14(3): e0008040, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32155148

RESUMO

Salmonella Typhi (S. Typhi) is the causative agent of typhoid fever; a systemic disease affecting ~20 million people per year globally. There are little data regarding the contemporary epidemiology of typhoid in Latin America. Consequently, we aimed to describe some recent epidemiological aspects of typhoid in Colombia using cases reported to the National Public Health Surveillance System (Sivigila) between 2012 and 2015. Over the four-year reporting period there were 836 culture confirmed cases of typhoid in Colombia, with the majority (676/836; 80.1%) of reported cases originated from only seven departments. We further characterized 402 S. Typhi isolates with available corresponding data recovered from various departments of Colombia through antimicrobial susceptibility testing and molecular subtyping. The majority (235/402; 58.5%) of these typhoid cases occurred in males and were most commonly reported in those aged between 10 and 29 years (218/402; 54.2%); there were three (0.74%) reported fatalities. The overwhelming preponderance (339/402; 84.3%) of S. Typhi were susceptible to all tested antimicrobials. The most common antimicrobial to which the organisms exhibited non-susceptibility was ampicillin (30/402;7.5%), followed by nalidixic acid (23/402, 5.7%). Molecular subtyping identified substantial genetic diversity, which was well distributed across the country. Despite the diffuse pattern of S. Typhi genotypes, we identified various geographical hotspots of disease associated with local dominant genotypes. Notably, we found limited overlap of Colombian genotypes with organisms reported in other Latin American countries. Our work highlights a substantial burden of typhoid in Colombia, characterized by sustained transmission in some regions and limited epidemics in other departments. The disease is widely distributed across the country and associated with multiple antimicrobial susceptible genotypes that appear to be restricted to Colombia. This study provides a current perspective for typhoid in Latin America and highlights the importance of pathogen-specific surveillance to add insight into the limited epidemiology of typhoid in this region.


Assuntos
Salmonella typhi/isolamento & purificação , Febre Tifoide/epidemiologia , Adolescente , Adulto , Distribuição por Idade , Idoso , Idoso de 80 Anos ou mais , Criança , Pré-Escolar , Colômbia/epidemiologia , Farmacorresistência Bacteriana , Monitoramento Epidemiológico , Feminino , Variação Genética , Genótipo , Humanos , Lactente , Masculino , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Tipagem Molecular , Estudos Retrospectivos , Salmonella typhi/classificação , Salmonella typhi/efeitos dos fármacos , Salmonella typhi/genética , Distribuição por Sexo , Adulto Jovem
19.
MMWR Morb Mortal Wkly Rep ; 69(12): 335-338, 2020 Mar 27.
Artigo em Inglês | MEDLINE | ID: mdl-32214081

RESUMO

Cryptosporidium is an enteric pathogen that is transmitted through animal-to-person or person-to-person contact or through ingestion of contaminated water or food. In the United States, Cryptosporidium affects an estimated 750,000 persons each year; however, only approximately 11,000 cases are reported nationally (1,2). Persons infected with Cryptosporidium typically develop symptoms within 2 to 10 days after exposure. Common symptoms include watery diarrhea, abdominal cramps, nausea, vomiting, or fever, which can last 1 to 2 weeks. Cryptosporidiosis is a nationally notifiable disease in the United States. Nebraska presents a unique setting for the evaluation of this pathogen because, compared with other states, Nebraska has a greater reliance on agriculture and a higher proportion of the population residing and working in rural communities. Cryptosporidium species and subtypes are generally indistinguishable using conventional diagnostic methods. Using molecular characterization, Nebraska evaluated the genetic diversity of Cryptosporidium and found a dichotomy in the distribution of cases of cryptosporidiosis caused by Cryptosporidium parvum and Cryptosporidium hominis among rural and urban settings. Characterizing clusters of C. hominis cases revealed that several child care facilities were affected by the same subtype, suggesting community-wide transmission and indicating a need for effective exclusion policies. Several cases of cryptosporidiosis caused by non-C. parvum or non-C. hominis species and genotypes indicated unique animal exposures that were previously unidentified. This study enhanced epidemiologic data by validating known Cryptosporidium sources, confirming outbreaks, and, through repeat interviews, providing additional information to inform cryptosporidiosis prevention and control efforts.


Assuntos
Criptosporidiose/epidemiologia , Criptosporidiose/transmissão , Cryptosporidium/classificação , Cryptosporidium/genética , Adolescente , Adulto , Idoso , Criança , Pré-Escolar , Feminino , Genótipo , Humanos , Lactente , Masculino , Pessoa de Meia-Idade , Tipagem Molecular , Nebraska/epidemiologia , Fatores de Risco , Adulto Jovem
20.
Parasitol Res ; 119(4): 1221-1236, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32179988

RESUMO

Members of the myxozoan genus Kudoa (Myxosporea: Multivalvulida: Kudoidae) are characterized as having four or more shell valves in a myxospore, with a corresponding number of polar capsules. Certain Kudoa spp. are critical pathogens in fish, causing postmortem myoliquefaction, unmarketable fish musculature due to unsightly macroscopic cysts, and reduced aquaculture production due to the outbreaks of neurological symptoms or cardiac diseases. Molecular genetic techniques have enabled the differentiation of Kudoa spp. with morphologically similar myxospores. In the present study, we employed integrated taxonomic approaches on five Kudoa spp. forming cysts between the trunk muscle myofibers (K. bora from Osteomugil perusii and K. lutjanus from Acanthopagrus latus), or cysts in the gallbladder wall (K. petala from Sillago sihama), and pseudocysts in the trunk muscle myofibers (K. uncinata from Nuchequula nuchalis and K. fujitai n. sp. from O. perusii). These four host fishes, which originated in the South China Sea, were purchased in the wet markets in Zhanjiang City, Guangdong Province, China, between August 2016 and April 2018. We have redescribed the four Kudoa spp. (K. bora, K. lutjanus, K. petala, and K. uncinata) on which little data are available after their original descriptions. Particularly, genetic characterization of K. bora and K. lutjanus, which are known to have myxospores morphologically similar to those of K. iwatai, was performed based on the nuclear ribosomal RNA gene and partial mitochondrial DNA genes such as cytochrome c oxidase subunit I and small and large ribosomal genes, demonstrating the validity and independence of these three kudoid species. We also provide description of a new species-K. fujitai n. sp.-in the present study. Application of integrated taxonomic approaches to known species characterized solely based on morphological criteria, as well as unknown species (e.g., K. fujitai n. sp. in the present study), contributes to better understanding of the biodiversity of Kudoa and multivalvulid myxosporeans.


Assuntos
Doenças dos Peixes/microbiologia , Myxozoa/classificação , Animais , Aquicultura , Biodiversidade , China , DNA Ribossômico , Tipagem Molecular , Myxozoa/isolamento & purificação , Filogenia , RNA Ribossômico 18S/genética , Análise de Sequência de DNA
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