Your browser doesn't support javascript.
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 22.914
Filtrar
1.
Artículo en Inglés | MEDLINE | ID: mdl-32520211

RESUMEN

Simple, low-cost and effective diagnostic tests for tuberculosis (TB) are needed especially in TB-high burden settings. The present study evaluated the performance of an in-house loop-mediated isothermal amplification (LAMP) for diagnosing TB by comparing it to Xpert MTB/RIF, microscopy and culture. In Thailand, a total of 204 excess sputum samples volume after the processing of cultures were used for Mycobacterium tuberculosis (MTB) detection by Xpert MTB/RIF and LAMP. Based on culture results as the gold standard, the overall sensitivity of LAMP and Xpert MTB/RIF were 82.1% (126/153; 95% confidential interval [CI]: 75.4-88.98%) and 86.9 % (133/153; 95% CI: 80.5-90.8%) respectively, and the specificity of both tests was 100% (51/51; 95% CI: 93.0-100.0%). In comparison with Xpert MTB/RIF, the sensitivity and specificity of LAMP were 94.7% (126/133; 95% CI: 89.5-97.9%), and 100.0% (73/73; 95% CI: 94.9-100.0%), respectively. The average threshold cycle (Ct) of Xpert MTB/RIF detection for positive and negative LAMP results was statistically different, of 18.4 and 27.0, respectively (p < 0.05). In comparison with the acid-fast staining technique, and analyzing LAMP and Xpert MTB/RIF in smear-negative/culture-positive specimens, there was an increase of the detection rate by 47.7% (21/44) and 54.6% (24/44). The diagnostic sensitivity and specificity of LAMP appeared to be comparable to those of Xpert MTB/RIF. We claim that this LAMP has potential to provide a sensitive diagnostic test for the rapid TB diagnosis. It allowed a fast detection of MTB before the cultures and it could be used in resource-limited laboratory settings.


Asunto(s)
Mycobacterium tuberculosis/aislamiento & purificación , Esputo/microbiología , Tuberculosis/diagnóstico , ADN Bacteriano/análisis , ADN Bacteriano/genética , Pruebas Diagnósticas de Rutina , Humanos , Técnicas de Diagnóstico Molecular/métodos , Mycobacterium tuberculosis/genética , Reacción en Cadena de la Polimerasa , Sensibilidad y Especificidad , Tailandia
2.
An Acad Bras Cienc ; 92 Suppl 1: e20180557, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32348408

RESUMEN

In Brazil and in other countries of the world, studies have been conducted to identify Listeria monocytogenes in cattle meat that is preferably consumed undercooked and, when marketed without meeting strict phytosanitary requirements, may cause outbreaks of listeriosis. In the such, foodborne outbreaks, the methods used for the detection of the pathogen and the efficiency associated with them are crucial for the proper assessment. In this study, we used the techniques biochemical and molecular for identification of the L. monocytogenes isolated from 30 samples of the fresh beef, marketed in ten butchers' shop of the free-fair from a municipality from the Bahia, Brazil. The results obtained from biochemical tests (catalase, motility, ß-hemolysis and carbohydrate fermentation), as well as PCR analysis for the hly gene (hemolysin production is an important factor in the pathogenesis of listeriosis) revealed that 50% of butchers shops presented bovine meat contaminated with bacteria of the Listeria sp. and confirmed that 54.16% of the analyzed meat samples were positive for L. monocytogenes. This study highlights the importance of microbiological surveillance in free-fair to minimize the exposure of consumers to this foodborne pathogen.


Asunto(s)
ADN Bacteriano/análisis , Proteínas Hemolisinas/genética , Listeria monocytogenes/aislamiento & purificación , Productos de la Carne/microbiología , Animales , Brasil , Bovinos , Microbiología de Alimentos , Proteínas Hemolisinas/análisis , Listeria monocytogenes/genética
3.
Rev Bras Parasitol Vet ; 29(1): e022419, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32236336

RESUMEN

This study aimed to evaluate the occurrence of diseases transmitted by Amblyomma ovale in 61 dogs monitored for three years through collections of ticks and blood, interviews, telemetry and camera traps in three areas of Serra do Mar State Park, Brazil. Blood samples were used to investigate infection by Rangelia vitalii by real-time TaqMan PCR and Rickettsia parkeri by IIFA. The collected ticks were submitted to conventional PCR to investigate the presence of R. parkeri . These data were compared with the monitoring results and interviews with the owners. Dogs considered as companion presented a risk of infection by R. parkeri strain Mata Atlantica 5.4 times higher than those not considered as companion (p = 0.009). Dogs that had at least one A. ovale collected during the campaigns had a 10 times higher risk of infection by R. parkeri strain Mata Atlantica than those who did not (p = 0.009). One dog positive for R. vitalii by real-time TaqMan PCR was parasitized by A. ovale frequently during monitoring. Sequenced ompaA - positive DNA samples had 100% identity of R. parkeri strain Mata Atlantica clone As106. From the findings, it is urgent to control domestic dogs around rainforests to reduce zoonoses transmission.


Asunto(s)
Enfermedades de los Perros/epidemiología , Ixodidae/microbiología , Infecciones por Rickettsia/veterinaria , Rickettsia/aislamiento & purificación , Animales , Brasil/epidemiología , ADN Bacteriano/análisis , Enfermedades de los Perros/diagnóstico , Enfermedades de los Perros/microbiología , Perros , Técnica del Anticuerpo Fluorescente Indirecta , Reacción en Cadena de la Polimerasa , Bosque Lluvioso , Rickettsia/clasificación , Rickettsia/genética , Infecciones por Rickettsia/diagnóstico , Infecciones por Rickettsia/epidemiología , Análisis de Secuencia de ADN , Telemetría
4.
PLoS Negl Trop Dis ; 14(3): e0008127, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32203502

RESUMEN

Understanding the prevalence of M. leprae infection in armadillos is important because of evidence from Brazil and other countries of an association between contact with armadillos and the development of Hansen's Disease (leprosy). Our aim was to characterize studies which have investigated natural M. leprae infection in wild armadillos in Brazil, and to quantify and explore variability in the reported prevalence of infection. We conducted a systematic review (PROSPERO CRD42019155277) of publications in MEDLINE, EMBASE, Global Health, Scopus, LILACS, Biblioteca Digital Brasileira de Teses e Dissertações, Catálogo de Teses e Dissertações de CAPES, and Biblioteca Virtual em Saúde up to 10/2019 using Mesh and text search terms (in English, Portuguese, Spanish, and French). The 10 included studies represented a total sample of 302 armadillos comprising 207 (69%) Dasypus novemcinctus, 67 (22%) Euphractus sexcinctus, 16 (5%) Priodontes maximus, 10 (3%) Cabassous unicinctus, and 2 (1%) Cabassous tatouay from 7 different states. Methods used included histopathology (4 studies), PGL-1 and LID-1 antigen detection (4 studies) and examination for clinical signs of disease (4 studies). Eight studies used PCR of which 7 targeted the RLEP repetitive element and 3 tested for inhibitory substances. M. leprae prevalence by PCR ranged from 0% (in 3 studies) to 100% in one study, with a summary estimate of 9.4% (95% CI 0.4% to 73.1%) and a predictive interval of 0-100%. The average prevalence is equivalent to 1 in 10 armadillos in Brazil being infected with M. leprae, but wide variation in sample estimates means that the prevalence in any similar study would be entirely unpredictable. We propose instead that future studies aim to investigate transmission and persistence of M. leprae within and between armadillo populations, meanwhile adopting the precautionary principle to protect human health and an endangered species in Brazil.


Asunto(s)
Armadillos/microbiología , Lepra/epidemiología , Lepra/veterinaria , Mycobacterium leprae/aislamiento & purificación , Animales , Animales Salvajes/microbiología , Brasil/epidemiología , ADN Bacteriano/análisis , Bases de Datos Factuales , Mapeo Geográfico , Mycobacterium leprae/genética , Reacción en Cadena de la Polimerasa , Prevalencia , Secuencias Repetitivas de Ácidos Nucleicos , Zoonosis/epidemiología , Zoonosis/microbiología
5.
Invest Ophthalmol Vis Sci ; 61(2): 47, 2020 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-32106294

RESUMEN

Purpose: Microbial ecosystems interact with the human body and affect human health. The microbial community on the ocular surface remains an underexplored territory despite its importance as the first line of defense barrier that protects the eye and ultimately sight. We investigated how age and sex affected human ocular surface microbiome, and in the present study wanted to understand how geographic difference shaped the microbiome in the ocular surface. Methods: We collected conjunctival specimens of 172 eyes from 86 healthy volunteers living in three Chinese cities, namely, Guangzhou, Wenzhou, and Beijing. Using the direct metagenomic shotgun sequencing approach, we characterized how geographic difference affected the human ocular microbiome. Results: We surveyed the taxonomic composition and metabolic function of the microbiota on human ocular surface. We showed that the ocular surface microbiota was composed of bacteria, viruses, and fungi. A geographical difference in both composition and function of the conjunctival microbiome suggests that the environment people lived in shapes their conjunctival microbiome, especially the dominate species. Conclusions: Our study provides a reference catalog of the healthy conjunctival metagenome and raises a concern for environmental influences on the ocular surface microbiome.


Asunto(s)
Conjuntiva/microbiología , Microbiota , Factores de Edad , China , ADN Bacteriano/análisis , ADN de Hongos/análisis , ADN Viral/análisis , Femenino , Humanos , Masculino , Metagenoma , Factores Sexuales
6.
PLoS One ; 15(2): e0228459, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32027671

RESUMEN

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a significant pathogen causing healthcare-associated infections. Matrix-assisted laser desorption/ionisation mass spectrometry time-of-flight mass spectrometry (MALDI-TOF MS) is used by clinical microbiology laboratories to address the need for rapid, cost-effective and accurate identification of microorganisms. We evaluated application of machine learning methods for differentiation of drug resistant bacteria from susceptible ones directly using the profile spectra of whole cells MALDI-TOF MS in 46 CRKP and 49 CSKP isolates. METHODS: We developed a two-step strategy for data preprocessing consisting of peak matching and a feature selection step before supervised machine learning analysis. Subsequently, five machine learning algorithms were used for classification. RESULTS: Random forest (RF) outperformed other four algorithms. Using RF algorithm, we correctly identified 93% of the CRKP and 100% of the CSKP isolates with an overall classification accuracy rate of 97% when 80 peaks were selected as input features. CONCLUSIONS: We conclude that CRKPs can be differentiated from CSKPs through RF analysis. We used direct colony method, and only one spectrum for an isolate for analysis, without modification of current protocol. This allows the technique to be easily incorporated into clinical practice in the future.


Asunto(s)
Algoritmos , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Infecciones por Klebsiella/diagnóstico , Klebsiella pneumoniae/aislamiento & purificación , Espectrometría de Masa por Láser de Matriz Asistida de Ionización Desorción/métodos , Aprendizaje Automático Supervisado , Antibacterianos/uso terapéutico , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Carbapenémicos/uso terapéutico , Infección Hospitalaria/diagnóstico , Infección Hospitalaria/tratamiento farmacológico , Infección Hospitalaria/microbiología , ADN Bacteriano/análisis , ADN Bacteriano/aislamiento & purificación , Humanos , Infecciones por Klebsiella/tratamiento farmacológico , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/genética , Pruebas de Sensibilidad Microbiana , Valor Predictivo de las Pruebas , Técnica del ADN Polimorfo Amplificado Aleatorio
8.
PLoS One ; 15(2): e0229172, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32092104

RESUMEN

Phosphorus (P) fertilizers are crucial to achieve peak productivity in agricultural systems. However, the fate of P fertilizers via microorganism incorporation and the exchange processes between soil pools is not well understood. 18Oxygen-labelled phosphate (18O- Pi) can be tracked as it cycles through soil systems. Our study describes biological and geochemical P dynamics using a tandem mass spectrometry (MS/MS) method for the absolute quantification of 18O- Pi. Soil microcosms underwent three treatments: (i) 18O- Pi, (ii) unlabelled phosphate (16O- Pi) or (iii) Milli-Q control, dissolved in a bio-stimulatory solution. During a 6-week series the microcosms were sampled to measure P by Hedley sequential fractionation and DNA extraction samples digested to 3'-deoxynucleoside 5'-monophosphates (dNMP). A MS/MS attached to a HPLC analyzed each P-species through collision-induced dissociation. The resin-extractable and bicarbonate 18O- Pi and 16O- Pi fractions displayed similar precipitation and adsorption-desorption trends. Biotic activity measured in the NaOH and dNMP fractions rapidly delabelled 18O- Pi; however, the MS/MS measured some 18O that remained between the P backbone and deoxyribose sugars. After 6 weeks, the 18O- Pi had not reached the HCl soil pool, highlighting the long-term nature of P movement. Our methodology improves on previous isotopic tracking methods as endogenous P does not dilute the system, unlike 32P techniques, and measured total P is not a ratio, dissimilar from natural abundance techniques. Measuring 18O- Pi using MS/MS provides information to enhance land sustainability and stewardship practices regardless of soil type by understanding both the inorganic movement of P fertilizers and the dynamic P pool in microbial DNA.


Asunto(s)
Agricultura/métodos , Isótopos de Oxígeno/análisis , Fosfatos/análisis , Espectrometría de Masas en Tándem/métodos , Fraccionamiento Químico , ADN Bacteriano/análisis , Fertilizantes/análisis , Suelo/química
9.
PLoS One ; 15(2): e0229485, 2020.
Artículo en Inglés | MEDLINE | ID: mdl-32109938

RESUMEN

Periodontal disease, the most prevalent infectious disease in the world, is caused by biofilms formed in periodontal pockets. No specific bacterial species that can cause periodontitis alone has been found in any study to date. Several periodontopathic bacteria are associated with the progress of periodontal disease. Consequently, it is hypothesized that dysbiosis of subgingival microbiota may be a cause of periodontal disease. This study aimed to investigate the relationship between the subgingival microbiota and the clinical status of periodontal pockets in a quantitative and clinically applicable way with the newly developed Oral Care Chip. The Oral Care Chip is a DNA microarray tool with improved quantitative performance, that can be used in combination with competitive PCR to quantitatively detect 17 species of subgingival bacteria. Cluster analysis based on the similarity of each bacterial quantity was performed on 204 subgingival plaque samples collected from periodontitis patients and healthy volunteers. A significant difference in the number of total bacteria, Treponema denticola, Campylobacter rectus, Fusobacterium nucleatum, and Streptococcus intermedia bacteria in any combination of the three clusters indicated that these bacteria gradually increased in number from the stage before the pocket depth deepened. Conversely, Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia, and Streptococcus constellatus, which had significant differences only in limited clusters, were thought to increase in number as the pocket depth deepened, after periodontal pocket formation. Furthermore, in clusters where healthy or mild periodontal disease sites were classified, there was no statistically significant difference in pocket depth, but the number of bacteria gradually increased from the stage before the pocket depth increased. This means that quantitative changes in these bacteria can be a predictor of the progress of periodontal tissue destruction, and this novel microbiological test using the Oral Care Chip could be effective at detecting dysbiosis.


Asunto(s)
Bacterias/aislamiento & purificación , ADN Bacteriano/análisis , Microbiota , Análisis de Secuencia por Matrices de Oligonucleótidos/métodos , Enfermedades Periodontales/microbiología , Bolsa Periodontal/microbiología , Adulto , Campylobacter rectus/aislamiento & purificación , Femenino , Fusobacterium nucleatum/aislamiento & purificación , Humanos , Masculino , Persona de Mediana Edad , Enfermedades Periodontales/diagnóstico , Índice Periodontal , Porphyromonas gingivalis/aislamiento & purificación , Prevotella intermedia/aislamiento & purificación , Streptococcus constellatus/aislamiento & purificación , Tannerella forsythia/aislamiento & purificación , Treponema denticola/aislamiento & purificación , Adulto Joven
10.
BMC Infect Dis ; 20(1): 43, 2020 Jan 14.
Artículo en Inglés | MEDLINE | ID: mdl-31937256

RESUMEN

BACKGROUND: In recent decades, there has been a marked increase in the number of reported cases of pertussis around the world, and pertussis continues to be a frequently occurring disease despite an effective childhood vaccination. This study aims to determine the role of household contacts of children diagnosed with pertussis in Casablanca Morocco. METHODS: From November 2015 to October 2017, children suspected of whooping cough that consulted Ibn Rochd University hospital at Casablanca with their household contacts were enrolled in the study. Nasopharyngeal (NP) samples of the suspected children were analyzed by culture and RT-PCR. For the household contacts, NP and blood samples were collected and analyzed by RT-PCR and specific detection of pertussis toxin antibodies by ELISA, respectively. RESULTS: During the study period, the survey was carried out on 128 infants hospitalized for pertussis suspicion and their families (N = 140). B. pertussis DNA was specifically detected in 73 (57%) samples, coexistence of B. pertussis and B. parapertussis DNA in 3 (2.3%) samples, coexistence of B. pertussis and B. holmesii DNA in 10 (7.81%) and only one (0.78%) sample was IS 481 RT-PCR positive without the possibility of determining the Bordetella species with the diagnostic tools used. Confirmations of Pertussis infection in household contacts by culture, RT- PCR and serology were 10, 46 and 39%, respectively. B. pertussis DNA was confirmed in the infants as well in their mothers in 38% of the cases. Co detection of B. pertussis and B. parapertussis DNA in 2% and co-detection of B. pertussis and B. holmesii DNA in 4%. B. holmesii DNA alone was detected in 5 NP samples of index cases and their mothers. CONCLUSIONS: The results of this study confirm that B. pertussis is still circulating in children and adults, and were likely a source of pertussis contamination in infants still not vaccinated. The use of RT-PCR specific for B. pertussis in the diagnosis of adults is less sensitive and should be associated with serologic tests to improve diagnosis of pertussis and contributes to preventing transmission of the disease in infants.


Asunto(s)
Bordetella pertussis/genética , Madres , Tos Ferina/diagnóstico , Tos Ferina/epidemiología , Adolescente , Adulto , Niño , Preescolar , Estudios Transversales , ADN Bacteriano/análisis , Pruebas Diagnósticas de Rutina , Ensayo de Inmunoadsorción Enzimática , Femenino , Humanos , Lactante , Recién Nacido , Masculino , Marruecos/epidemiología , Nasofaringe/microbiología , Toxina del Pertussis/inmunología , Prevalencia , Reacción en Cadena en Tiempo Real de la Polimerasa , Pruebas Serológicas
11.
BMC Infect Dis ; 20(1): 47, 2020 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-31941460

RESUMEN

BACKGROUND: Ureaplasma urealyticum is a fastidious bacteria which lacks a cell wall. Extragenital infections are rare in immunocompetent adults. There are few literature reports of perinephric abscess. We present a case of non-resolving multifocal "culture-negative" abscesses in a hypogammaglobulinemic adult female due to U. urealyticum. CASE PRESENTATION: 66-year-old female with a one-week history of fever, malaise and new right hip and leg pain. Past medical history was notable for chronic pancytopenia secondary to in remission B cell follicular lymphoma, ESRD on intermittent hemodialysis with bilateral nephrostomy tubes and Crohn's. CT abdomen/pelvis revealed a small left perinephric hematoma and proximal right femur fluid collection. Persistent right thigh pain led to additional ultrasound with anterior thigh collection and CT revealed an irregular rim-enhancing fluid collection in the left posterior pararenal space. Antimicrobial therapy included ertapenem and vancomycin followed by meropenem, trimethoprim-sulfamethoxazole, daptomycin and metronidazole in setting of persistent culture-negative results and clinical deterioration. Following detection of U. urealyticum by 16S rDNA PCR in both left pararenal and right trochanteric bursa abscesses doxycycline was started. Despite this, the patient died four days later. CONCLUSIONS: Disseminated infection by U. urealyticum has been documented in immunocompromised adult patients with few reports of perinephric abscess. We propose that ascending genitourinary route led to perinephric abscess. The multiple disseminated fluid collections make it highly suspicious for hematogenous spread given the lack of radiographic enhancement to suggest contiguous spread. Diagnosis and treatment of U. urealyticum-disseminated infection is extremely challenging as culture is laborious and not routinely performed. Furthermore, the lack of cell wall renders beta-lactams and vancomycin ineffective and therefore requirement for "atypical" coverage. Early diagnosis and treatment are key to prevent further complications and death.


Asunto(s)
Huésped Inmunocomprometido , Infecciones por Ureaplasma/diagnóstico , Ureaplasma urealyticum/genética , Absceso/tratamiento farmacológico , Absceso/microbiología , Anciano , Antibacterianos/uso terapéutico , ADN Bacteriano/análisis , ADN Ribosómico/análisis , Susceptibilidad a Enfermedades/inmunología , Doxiciclina/uso terapéutico , Resultado Fatal , Femenino , Humanos , Reacción en Cadena de la Polimerasa , Infecciones por Ureaplasma/tratamiento farmacológico , Infecciones por Ureaplasma/microbiología
12.
PLoS Comput Biol ; 16(1): e1007511, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31929521

RESUMEN

Antimicrobial resistance (AMR) is an increasing threat to public health. Current methods of determining AMR rely on inefficient phenotypic approaches, and there remains incomplete understanding of AMR mechanisms for many pathogen-antimicrobial combinations. Given the rapid, ongoing increase in availability of high-density genomic data for a diverse array of bacteria, development of algorithms that could utilize genomic information to predict phenotype could both be useful clinically and assist with discovery of heretofore unrecognized AMR pathways. To facilitate understanding of the connections between DNA variation and phenotypic AMR, we developed a new bioinformatics tool, variant mapping and prediction of antibiotic resistance (VAMPr), to (1) derive gene ortholog-based sequence features for protein variants; (2) interrogate these explainable gene-level variants for their known or novel associations with AMR; and (3) build accurate models to predict AMR based on whole genome sequencing data. We curated the publicly available sequencing data for 3,393 bacterial isolates from 9 species that contained AMR phenotypes for 29 antibiotics. We detected 14,615 variant genotypes and built 93 association and prediction models. The association models confirmed known genetic antibiotic resistance mechanisms, such as blaKPC and carbapenem resistance consistent with the accurate nature of our approach. The prediction models achieved high accuracies (mean accuracy of 91.1% for all antibiotic-pathogen combinations) internally through nested cross validation and were also validated using external clinical datasets. The VAMPr variant detection method, association and prediction models will be valuable tools for AMR research for basic scientists with potential for clinical applicability.


Asunto(s)
Antibacterianos/farmacología , Bacterias , Farmacorresistencia Microbiana/genética , Aprendizaje Automático , Secuenciación Completa del Genoma/métodos , Algoritmos , Bacterias/efectos de los fármacos , Bacterias/genética , Mapeo Cromosómico , ADN Bacteriano/análisis , ADN Bacteriano/genética , Genoma Bacteriano/genética , Modelos Estadísticos , Programas Informáticos
13.
Arch Oral Biol ; 110: 104606, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31739075

RESUMEN

OBJECTIVE: Although the prevalence and functions associated with members of Bacteria are well known in dental caries, the role of Archaea in cariogenic biofilms has not been studied yet. DESIGN: To detect the presence of Archaea in dental caries, a triplicate of carious dentine samples and duplicate of supragingival biofilms were collected, total microbial DNA was extracted and the composition of the microbiota was investigated. Total DNA was submitted to 16S rRNA gene amplification using universal prokaryotic primers; amplicons were sequenced by high-throughput DNA sequencing. As a second strategy to detect Archaea, a representative sample of caries was chosen and other PCR reactions were performed using specific primers targeting the archaeal 16S rRNA gene; amplicons were cloned and sequenced. Annotation of sequences was performed using SILVA database and the relative abundance of genus level OTUs was calculated. RESULTS: The high-throughput sequencing method detected archaeal sequences in all samples (identified as group I.1c of the phylum Thaumarchaeota), although in a very low abundance (≤0.03 % of the total sequences). For the second strategy, 14 archaeal clones were detected, with an OTU affiliated to Methanocella clade, and another one affiliated to group I.1b of the phylum Thaumarchaeota. CONCLUSIONS: Archaeal sequences were detected in dental caries and biofilms from surfaces without caries lesions. DNA sequences of Thaumarchaeota were also identified, showing that overall archaeal diversity in the human oral cavity could be currently underestimated and not restricted to methanogens.


Asunto(s)
Archaea , Biopelículas , ADN Bacteriano , Caries Dental , Archaea/genética , Archaea/aislamiento & purificación , Bacterias , ADN Bacteriano/análisis , Caries Dental/microbiología , Humanos , Filogenia , ARN Ribosómico 16S , Análisis de Secuencia de ADN
14.
Anal Bioanal Chem ; 412(1): 93-101, 2020 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-31797016

RESUMEN

The aim of this study was to develop an effective and specific visual method to rapidly detect and identify Vibrio parahaemolyticus (V. parahaemolyticus) based on the polymerase spiral reaction (PSR). The method utilized only two pairs of primers designed specifically to target the conserved tlh gene sequence of V. parahaemolyticus. Nucleic acid amplification can be achieved under isothermal conditions using DNA polymerase. The reaction could be accomplished in < 40 min with high specificity and sensitivity. The limits of detection of V. parahaemolyticus in purified genomic DNA and pure culture were 300 fg/µL and 2.4 CFU/mL per reaction, respectively, which were 100-fold more sensitive than with conventional PCR. The model food samples showed consistent specificity and sensitivity to the pure bacterial culture. With these encouraging results, it is expected that the novel, effortless and reliable isothermal nucleic acid testing assay developed in this study has potential to be applied to screening for V. parahaemolyticus in seafood samples.


Asunto(s)
Técnicas de Amplificación de Ácido Nucleico/métodos , Vibrio parahaemolyticus/aislamiento & purificación , Cartilla de ADN , ADN Bacteriano/análisis , Genes Bacterianos , Límite de Detección , Vibrio parahaemolyticus/genética
15.
Ann Lab Med ; 40(2): 169-173, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31650734

RESUMEN

The GENEDIA MTB/NTM Detection Kit (GENEDIA MTB/NTM; Green Cross Medical Science Corp., Chungbuk, Korea) is a multiplex real-time PCR assay used for differential identification of Mycobacterium tuberculosis complex (MTBC) and nontuberculous mycobacteria (NTM). While the importance of differential identification of MTB/NTM is recognized, there is limited data on the performance of GENEDIA MTB/NTM assay to date. A total of 687 consecutive sputum specimens were cultured and analyzed with the GENEDIA MTB/NTM and GENEDIA MTB assays. Nineteen specimens (2.8%) were MTBC-positive, and 69 (10.0%) were NTM-positive based on mycobacterial culture. All specimens showed concordant results for MTBC using both assays, with a kappa value of 1.00, overall sensitivity of 63.2% (12/19), and specificity of 100% (668/668). The overall NTM sensitivity and specificity were 23.2% (16/69) and 99.7% (616/618) for GENEDIA MTB/NTM. The association between NTM-positivity using GENEDIA MTB/NTM and the diagnosis of NTM pulmonary disease was not statistically significant. In conclusion, the two real-time PCR assays showed similar diagnostic performance for MTBC detection. However, the sensitivity for NTM detection was lower than that for MTBC detection.


Asunto(s)
Infecciones por Mycobacterium no Tuberculosas/diagnóstico , Mycobacterium tuberculosis/genética , Micobacterias no Tuberculosas/genética , Esputo/microbiología , Tuberculosis/diagnóstico , ADN Bacteriano/análisis , Humanos , Reacción en Cadena de la Polimerasa Multiplex , Infecciones por Mycobacterium no Tuberculosas/microbiología , Mycobacterium tuberculosis/aislamiento & purificación , Micobacterias no Tuberculosas/aislamiento & purificación , Juego de Reactivos para Diagnóstico , Sensibilidad y Especificidad , Tuberculosis/microbiología
16.
J Dairy Sci ; 103(2): 1238-1249, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31864732

RESUMEN

Cheese is a fermented dairy product that is popular for its unique flavor and nutritional value. Recent studies have shown that microorganisms in cheese play an important role in the fermentation process and determine the quality of the cheese. We collected 12 cheese samples from different regions and studied the composition of their bacterial communities using PacBio small-molecule real-time sequencing (Pacific Biosciences, Menlo Park, CA). Our data revealed 144 bacterial genera (including Lactobacillus, Streptococcus, Lactococcus, and Staphylococcus) and 217 bacterial species (including Lactococcus lactis, Streptococcus thermophilus, Staphylococcus equorum, and Streptococcus uberis). We investigated the flavor quality of the cheese samples using an electronic nose system and we found differences in flavor-quality indices among samples from different regions. We found a clustering tendency based on flavor quality using principal component analysis. We found correlations between lactic acid bacteria and the flavor quality of the cheese samples. Biodegradation and metabolism of xenobiotics, and lipid-metabolism-related pathways, were predicted to contribute to differences in cheese flavor using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). This preliminary study explored the bacterial communities in cheeses collected from different regions and their potential genome functions from the perspective of flavor quality.


Asunto(s)
Bacterias/aislamiento & purificación , Queso/microbiología , Variación Genética , Bacterias/clasificación , Bacterias/genética , Queso/análisis , ADN Bacteriano/análisis , Microbiología de Alimentos , Lactobacillales/genética , Lactobacillales/aislamiento & purificación , Lactobacillus/genética , Lactobacillus/aislamiento & purificación , Lactococcus lactis/genética , Lactococcus lactis/aislamiento & purificación , Filogenia , Análisis de Secuencia de ADN , Streptococcus/genética , Streptococcus/aislamiento & purificación , Streptococcus thermophilus/genética , Streptococcus thermophilus/aislamiento & purificación
17.
Enzyme Microb Technol ; 133: 109466, 2020 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-31874682

RESUMEN

Acinetobacter baumannii is a non-motile, gram-negative member of the gamma proteobacteria. A specific and sensitive approach was established for the detection of Acintobacter baumannii via DNA based bio-assay. In this study, gold nano-star was synthesized and used for bio-conjugation with pDNA toward the detection of target sequences. Synthesized probe (5' TTG TGA ACT ATT TAC GTC AGC ATG C3') of Acinetobacter baumannii was found with excellent sensitivity. After the hybridization of pDNA with cDNA, target DNA (5' GCA TGC TGA CGT AAA TAG TTC ACA A 3') was easily measured. According to ultra-sensitivity of the engineered optical DNA-based bio-assay, it is potentially applied in the bacterial detection of the environmental and clinical specimens. Here, the selection of engineered biosensor in the presence of two mismatch sequences was investigated. The results indicated an acceptable choice for DNA-based assays. The low limit of quantification (LLOQ) of genosensor was obtained as 1 fM. The present study is a very important diagnostic examination to recognize Acinetobacter baumannii, which can be a best alternative to the traditional methods.


Asunto(s)
Acinetobacter baumannii/genética , Bioensayo/métodos , ADN Bacteriano/análisis , Oro/química , Nanopartículas del Metal/química , Técnicas Biosensibles/métodos , Límite de Detección , Sensibilidad y Especificidad
18.
Biosens Bioelectron ; 148: 111817, 2020 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-31678826

RESUMEN

The rapid and robust detection of infectious bacteria is vital in sepsis treatment because of their ability to reveal multi-drug resistance. This study presents culture-free and self-driving DNA nanosensors by combining diffusometry and oligonucleotide probes to rapidly detect a lethal superbug, methicillin-resistant Staphylococcus aureus (MRSA). The DNA nanosensors were synthesized with conjugated fluorescent nanobeads and designed oligonucleotide probes that can recognize the target sequences on MRSA's genomic DNA. The high selectivity and specificity of this binding ensure the accuracy of detection. A DNA fragment tagged with gold nanoparticles (AuNPs) was attached to the same MRSA single-stranded DNA (ssDNA) to form a sandwiched configuration. The protrusive AuNPs surrounding the nanobeads decreased the diffusivity of the complexed nanobeads by increasing the bead size. Accordingly, diffusivity was inversely proportional to the concentration of the target MRSA ssDNA. Each measurement required only 10 s. An optimal limit of detection of 10 pM was achieved. This study successfully developed DNA nanosensors based on diffusometry for the rapid and robust detection of target superbugs and unknown pathogenic microorganisms.


Asunto(s)
Técnicas Biosensibles/instrumentación , ADN Bacteriano/análisis , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , ADN Bacteriano/genética , Diseño de Equipo , Colorantes Fluorescentes/química , Oro/química , Humanos , Nanopartículas del Metal/química , Staphylococcus aureus Resistente a Meticilina/genética , Sondas de Oligonucleótidos/química , Sondas de Oligonucleótidos/genética , Infecciones Estafilocócicas/microbiología
19.
Nat Commun ; 10(1): 5521, 2019 12 04.
Artículo en Inglés | MEDLINE | ID: mdl-31797927

RESUMEN

The origin of most bacterial infections in the urinary tract is often presumed to be the gut. Herein, we investigate the relationship between the gut microbiota and future development of bacteriuria and urinary tract infection (UTI). We perform gut microbial profiling using 16S rRNA gene deep sequencing on 510 fecal specimens from 168 kidney transplant recipients and metagenomic sequencing on a subset of fecal specimens and urine supernatant specimens. We report that a 1% relative gut abundance of Escherichia is an independent risk factor for Escherichia bacteriuria and UTI and a 1% relative gut abundance of Enterococcus is an independent risk factor for Enterococcus bacteriuria. Strain analysis establishes a close strain level alignment between species found in the gut and in the urine in the same subjects. Our results support a gut microbiota-UTI axis, suggesting that modulating the gut microbiota may be a potential novel strategy to prevent UTIs.


Asunto(s)
Bacterias/genética , Infecciones Bacterianas/microbiología , ADN Bacteriano/genética , ARN Ribosómico 16S/genética , Infecciones Urinarias/microbiología , Bacterias/clasificación , Bacteriuria/etiología , Bacteriuria/microbiología , Bacteriuria/orina , ADN Bacteriano/análisis , Infecciones por Escherichia coli/etiología , Infecciones por Escherichia coli/microbiología , Heces/microbiología , Microbioma Gastrointestinal/genética , Humanos , Trasplante de Riñón/efectos adversos , Trasplante de Riñón/métodos , Factores de Riesgo , Infecciones Urinarias/etiología , Infecciones Urinarias/orina
20.
Mikrochim Acta ; 187(1): 1, 2019 12 03.
Artículo en Inglés | MEDLINE | ID: mdl-31797052

RESUMEN

Aminopropyltrimethoxysilane (APTMS)-functionalized zinc oxide (ZnO) nanorods and carboxylated graphene nanoflakes (c-GNF) were used in a composite that was electrophoretically deposited on an indium tin oxide (ITO) coated glass substrate. The modified ITO electrodes were characterized using various microscopic and spectroscopic techniques which confirm the deposition of the APTMS-ZnO/c-GNF composite. The electrodes have been used for the covalent immobilization of an Escherichia coli O157:H7 (E. coli)-specific DNA prob. Impedimetric studies revealed that the gene sensor displays linear response in a wide range of target DNA concentration (10-16 M to 10-6 M) with a detection limit of 0.1 fM. The studies on the cross-reactivity to other water-borne pathogens show that the bioelectrode is highly specific. Graphical abstractSchematic illustration for fabrication of nucleic acid biosensor for E. coli DNA detection using an ITO electrode modified with siloxane-functionalized zinc oxide (ZnO) nanorods and carboxylated graphene nanoflakes (c-GNFs).


Asunto(s)
Técnicas Biosensibles/métodos , ADN Bacteriano/análisis , Escherichia coli O157/genética , Grafito/química , Nanotubos/química , Compuestos de Estaño/química , Óxido de Zinc/química , Técnicas Biosensibles/instrumentación , Ácidos Carboxílicos/química , Impedancia Eléctrica , Electrodos , Electroforesis , Límite de Detección
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA