ABSTRACT
Objective@#To evaluate multidrug resistant loop-mediated isothermal amplification (MDR-LAMP) assay for the early diagnosis of multidrug-resistant tuberculosis and to compare the mutation patterns associated with the @*Methods@#MDR-LAMP assay was evaluated using 100 @*Results@#The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of MDR-LAMP were 85.5%, 93.6%, 96.7%, and 74.4% for the detection of resistance to isoniazid and rifampicin, respectively, and 80.5%, 92.3%, 98.6%, and 41.4% for the detection of @*Conclusion@#MDR-LAMP is a rapid and accessible assay for the laboratory identification of rifampicin and isoniazid resistance of
Subject(s)
Antitubercular Agents , Bacterial Proteins/genetics , Catalase/genetics , DNA, Bacterial/analysis , DNA-Directed RNA Polymerases/genetics , Drug Resistance, Multiple, Bacterial/genetics , Isoniazid , Molecular Diagnostic Techniques/methods , Mutation , Mycobacterium tuberculosis/isolation & purification , Nucleic Acid Amplification Techniques/methods , Oxidoreductases/genetics , Phenotype , Rifampin , Whole Genome SequencingABSTRACT
Resumen Azospirillum brasilense Az39 es utilizada por empresas productoras de inoculantespara la formulación de bioinsumos en América del Sur desde hace más de 30 a˜nos. Esta cepapuede promover el crecimiento, desarrollo, así como la capacidad de tolerar diferentes tiposde estrés en las plantas inoculadas, lo que determina un aumento de la productividad de culti-vos de interés agronómico. En la actualidad, no existen protocolos en Argentina que permitanconfirmar la identidad de Az39 en productos comerciales a nivel de laboratorios de control decalidad de inoculantes. Por ello, el objetivo de este trabajo fue desarrollar una metodología enbase molecular que permita la identificación certera de A. brasilense Az39. Con la secuenciacompleta del genoma y mediante herramientas bioinformáticas, se pudieron reconocer frag-mentos de ADN presentes únicamente en el genoma de Az39. Se dise˜naron cebadores dirigidosa amplificar por PCR dichas secuencias. Como resultado se observaron los productos específicosúnicamente en la presencia de la cepa de interés. La reacción pudo detectar un título mínimode 105UFC/ml (4,5 ng/l ADN) o de 102UFC/ml (0,88 ng/l ADN) o una concentración mínimade 0,098 ng/l ADN, dependiendo del método de extracción utilizado. Los cebadores fueronevaluados en el análisis de productos comerciales obtenidos del mercado nacional, arrojandoresultados positivos, tanto en muestras directas como así también en pruebas confirmatoriasa partir de colonias aisladas de tales productos. La metodología desarrollada en este trabajo,permite la detección certera de A. brasilense Az39 en cultivos puros o mezclas complejas demicroorganismos.
Abstract Azospirillum brasilense Az39 has been used since more than 30 years by several companies in South America for biofertilizers production. This strain may promote plants growth and development, as well as the ability of inoculated plants to tolerate environmental stresses, which determines an increase in the productivity under field conditions. At present, there are no protocols in Argentina to confirm the identity of Az39 in commercial products; however, such biofertilizers are formulated almost exclusively with this strain. Therefore, the objective of this paper was to develop a molecular methodology that allows the accurate identification of A. brasilense Az39. Using the complete genome sequence and several bioinformatics tools, fragments of DNA present only in the Az39 genome were recognized. A set of PCR primers to amplify these sequences were designed, and the specific products were observed only in the strain of our interest. The sensitivity of the methodology was evaluated, where the strain could be detected up to a titer of 105 CFU/ml (4.5 ng/pl ADN) or 102 CFU/ml (0.88 ng/pl DNA) or in a minimal concentration of 0.098 ng/pl DNA, depending on the DNA extraction methodology used. Primers were tested against direct samples of commercial inoculants and cultures, in both cases there were specifics products, both in direct samples and in confirmatory tests from isolated colonies from those products. The procedure presented in this paper allows the accurate identification of A. brasilense Az39 in pure cultures, mixtures of microorganisms, and commercial biofertilizers.
Subject(s)
Azospirillum brasilense/isolation & purification , Azospirillum brasilense/genetics , Argentina , DNA, Bacterial/analysis , Bacteriological Techniques/methods , Nucleic Acid Amplification TechniquesABSTRACT
BACKGROUND Bacillus anthracis is the aetiologic agent of anthrax, a re-emerging, septicaemic, haemorrhagic and lethal disease that affects humans, domestic ruminants and wildlife. Plasmids pXO1 and pXO2 are attributes that confer pathogenicity to B. anthracis strains. This bacterium was used as biological weapon in the World Wars and in the biological attack in the United States of America at 2001. B. anthracis is classified as a Tier 1 bioterrorism agent by the Centers for Diseases Control and Prevention. Anthrax is recognised as a re-emerging disease. Several studies concerning the dynamics of B. anthracis cycle in soil revealed that nonpathogenic B. anthracis strains due to lack of pXO2 plasmid are commonly found in some types of soil. OBJECTIVES This study aimed isolation and identification of B. anthracis spores in soil samples of the state of Rio de Janeiro, Brazil. METHODS Phenotypic and genotypic approaches were used to identify isolates including MALDI-TOF/MS, motility test, susceptibility to gamma phage and penicillin, survey for pag and cap genes as surrogates of pXO1 and pXO2 plasmids, respectively, and sequencing of 16SrRNA-encoding gene. Physicochemical analysis of the soil samples were carried out to describe soil characteristics. FINDINGS We observed the presence of one B. anthracis pXO1+ and pXO2- isolated from clay loam soil; one B. anthracis-like strain pXO1+ and pXO2-isolated from loamy sand; and 10 Bacillus spp. strains sensitive to phage-gamma that need better characterisation to define which their species were recovered from loamy sand. MAIN CONCLUSIONS This work showed promising results and it was the first study to report results from an active surveillance for B. anthracis in Brazil.
Subject(s)
Humans , Plasmids/analysis , Soil Microbiology , Spores, Bacterial , Bacillus anthracis/isolation & purification , DNA, Bacterial/genetics , Polymerase Chain Reaction/methods , Virulence Factors/genetics , Plasmids/genetics , Soil , Bacillus anthracis/genetics , Bacillus anthracis/pathogenicity , Bacterial Toxins , Virulence , Brazil , DNA, Bacterial/analysis , Sequence Analysis, DNA , Antigens, BacterialABSTRACT
Abstract 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.
Resumo A ocorrência de doenças transmitidas por Amblyomma ovale em 61 cães monitorados por três anos através de coletas de carrapatos, sangue, entrevistas, telemetria e armadilhas fotográficas foi avaliada em três áreas do Parque Estadual da Serra do Mar - SP. Amostras de sangue foram utilizadas para investigação de Rangelia vitalii através de PCR TaqMan em tempo real e Rickettsia parkeri através da RIFI. Carrapatos coletados foram submetidos à PCR convencional para investigação de R. parkeri . Estes dados foram comparados considerando os resultados do monitoramento e entrevistas. Cães de companhia apresentaram risco de infecção pela R. parkeri cepa Mata Atlântica 5,4 vezes maior que os não considerados como de companhia (p = 0,009). Cães que tiveram pelo menos um A. ovale coletado apresentaram risco de infecção por R. parkeri cepa Mata Atlântica 10 vezes maior do que aqueles que não tiveram (p = 0,009). Um cão positivo para R. vitalii através de PCR TaqMan em tempo real foi parasitado por A. ovale durante o monitoramento. Amostras positivas para o gene ompaA possuíam 100% de identidade do clone As106 de R. parkeri cepa de Mata Atlântica. Assim, é urgente o controle de cães na Mata Atlântica para redução dos riscos de zoonoses.
Subject(s)
Animals , Dogs , Rickettsia/isolation & purification , Rickettsia Infections/veterinary , Ixodidae/microbiology , Dog Diseases/epidemiology , Rickettsia/classification , Rickettsia/genetics , Rickettsia Infections/diagnosis , Rickettsia Infections/epidemiology , Telemetry , Brazil/epidemiology , DNA, Bacterial/analysis , Polymerase Chain Reaction , Sequence Analysis, DNA , Fluorescent Antibody Technique, Indirect , Dog Diseases/diagnosis , Dog Diseases/microbiology , RainforestABSTRACT
ABSTRACT BACKGROUND: Colorectal cancer is one of the most commonly diagnosed cancers around the world. One of the factors involved in the development of colorectal cancer is the changes in the normal flora of the intestine. OBJECTIVE: In this study, the mean copy number of Enterococcus faecalis in people with polyps and people with colorectal cancer has been evaluated in comparison with healthy controls. METHODS: In this study, 25 patients with colorectal cancer and 28 patients with intestinal polyps were selected and stool specimens were taken. In addition, 24 healthy individuals were selected as control group. Extraction of bacterial DNA from the stool sample were performed. The molecular methods of PCR for confirmation of standard strain and absolute Real Time PCR (qRT-PCR) method were used to evaluate the number of Enterococcus faecalis in the studied groups. RESULTS: The results of this study indicate that the mean copy number of Enterococcus faecalis in patients with colorectal cancer was 11.2x109 per gram of stool, and in patients with polyps was 9.4x108 per gram of stool. In healthy people, this number was 9x108 per gram of stool. There was a significant difference between the implicit copy numbers in the three groups. (P<0.05). CONCLUSION: Enterococcus faecalis in faecal flora of people with colorectal cancer was significantly higher than those with polyps and healthy people. This could potentially signify the ability of this bacterium to induce colorectal cancer. More studies are needed to prove this theory.
RESUMO CONTEXTO: O câncer colorretal é um dos cânceres mais comumente diagnosticados em todo o mundo. Um dos fatores envolvidos no desenvolvimento do câncer colorretal é a mudança na flora normal do intestino. OBJETIVO: O número médio de cópias de Enterococcus faecalis em pessoas com pólipos e pessoas com câncer colorretal foram avaliados em comparação com controles saudáveis. MÉTODOS: Neste estudo, 25 pacientes com câncer colorretal e 28 pacientes com pólipos intestinais foram selecionados e amostras de fezes foram adquiridas. Além disso, 24 indivíduos saudáveis foram selecionados como grupo controle. A extração do DNA bacteriano da amostra coletada foi executada. Os métodos moleculares de PCR para confirmação da cepa padrão e o método absoluto de PCR em tempo real (qRT-PCR) foram utilizados para avaliar o número de Enterococcus faecalis nos grupos estudados. RESULTADOS: Os resultados deste estudo indicam que o número médio de cópias de Enterococcus faecalis em pacientes com câncer colorretal foi de 11,2x109 por grama de fezes, e em pacientes com pólipos foi de 9,4x108 por grama de fezes. Em pessoas saudáveis, este número foi de 9x108 por grama de fezes. Houve diferença significativa entre os números de cópia implícita nos três grupos. (P<0,05). CONCLUSÃO: Enterococcus faecalis na flora fecal de pessoas com câncer colorretal foi significativamente maior do que aqueles com pólipos e pessoas saudáveis. Isto poderia potencialmente significar a capacidade desta bactéria para induzir o câncer colorretal. Mais estudos são necessários para provar esta teoria.
Subject(s)
Humans , Male , Female , Aged , Colorectal Neoplasms/microbiology , Colonic Polyps/microbiology , Enterococcus faecalis/isolation & purification , Feces/microbiology , DNA, Bacterial/analysis , Case-Control Studies , Enterococcus faecalis/genetics , Real-Time Polymerase Chain Reaction , Middle AgedABSTRACT
Abstract The aim of this study is to detect the presence of tick-borne agents of genera Rickettsia, Borrelia, Babesia, Ehrlichia and Anaplasma in ticks collected from native wild birds in the state of Rio de Janeiro. Birds were captured and observed carefully to find the ectoparasites. DNA detection of hemoparasites was performed by means of the polymerase chain reaction (PCR). The sequences obtained were analyzed and their homologies were compared to the available isolates in the GenBank platform database. A total of 33 birds were captured from 20 different species, of which 14 were parasitized by Amblyomma longirostre (n = 22). There was absence of DNA from agents of the genera Babesia, Anaplasma and Ehrlichia in the evaluated samples. The phylogenetic analysis indicated that one sample had 100% identity with Rickettsia bellii (KJ534309), the other two samples showed 100% identity with Rickettsia sp. Aranha strain and strain AL (EU274654 and AY360216). The positive sample for R. bellii was also demonstrated to be positive for Borrelia sp., which presented a similarity of 91% with Borrelia turcica (KF422815). This is the first description of Borrelia sp. in ticks of the genus Amblyomma in South America.
Resumo Este trabalho teve como objetivo detectar evidências moleculares da presença de agentes dos gêneros Rickettsia, Borrelia, Babesia, Anaplasma e Ehrlichia transmitidos por carrapatos coletados de aves silvestres no estado do Rio de Janeiro. Aves foram capturadas e observadas cuidadosamente a procura de ectoparasitos. A detecção de DNA de hemoparasitos foi realizada por meio da reação em cadeia da polimerase (PCR). As sequências obtidas foram analisadas e sua homologia comparada aos isolados disponíveis na base de dados da plataforma GenBank. Foram capturadas 33 aves, de 20 espécies diferentes das quais 14 estavam parasitadas por Amblyomma longirostre (n = 22). Houve ausência de DNA de agentes dos gêneros Babesia, Anaplasma e Ehrlichia nas amostras avaliadas. A análise filogenética indicou que uma amostra apresentou 100% de identidade com Rickettsia bellii (KJ534309), as outras duas amostras apresentaram 100% de identidade com Rickettsia sp. cepa Aranha e Cepa AL (EU274654 e AY360216.). A amostra positiva para R. bellii também apresentou positividade para Borrelia sp. que apresentou similaridade de 91% com Borrelia turcica (KF422815). Esta é a primeira descrição de Borrelia sp. em carrapatos do gênero Amblyomma na América do Sul.
Subject(s)
Animals , Babesia/isolation & purification , Ticks/microbiology , Birds/parasitology , DNA, Bacterial/analysis , Gram-Negative Bacteria/isolation & purification , Animals, Wild/parasitology , Phylogeny , Rickettsia/genetics , Babesia/classification , Borrelia/genetics , Brazil , Polymerase Chain Reaction , Ehrlichia/genetics , Parks, Recreational , Anaplasma/geneticsABSTRACT
Abstract This study aimed to determine the prevalence, factors associated, laboratory findings (with and without coinfection by retroviruses) among naturally infected cats by hemoplasmas in northeastern Brazil. For convenience, 200 domesticated and healthy cats were selected. Blood samples were taken to perform complete blood counts, serum biochemical, immunochromatography tests and nPCR for FIV and FeLV, and PCR for hemoplasma recognition. An interview was conducted to determine the factors associated with hemoplasmas. A total of 71/200 (35.5%) cats were positive for at least one hemoplasma species. Isolated infections were observed in 12,5% for 'Candidatus Mycoplasma haemominutum', 12% for Mycoplasma haemofelis and 3% for 'Candidatus Mycoplasma turicensis'. Regarding copositivity, 2% of the animals were positive for M. haemofelis and 'Candidatus Mycoplasma haemominutum', 1.5% for M. haemofelis and 'Candidatus Mycoplasma turicensis', and 4.5% for ' Candidatus Mycoplasma haemominutum' and 'Candidatus Mycoplasma turicensis'. No clinical and laboratory changes were observed in the animals that were concomitantly positive for retroviruses and hemoplasmas. Periurban region cats were more likely to be infected by M. haemofelis, while contact with other cats and infection by ' Candidatus Mycoplasma turicensis' were associated with 'Candidatus Mycoplasma haemominutum'. This study indicates that infection by hemoplasmas is a common find in cats from northeastern Brazil.
Resumo Objetivou-se com este estudo determinar a prevalência, fatores associados, achados laboratoriais (com e sem coinfecção com retrovírus) em gatos naturalmente infectados por hemoplasmas no Nordeste do Brasil. Selecionou-se, por conveniência, 200 gatos domiciliados, hígidos, sendo colhidas amostras de sangue para realização do hemograma, bioquímica sérica, imunocromatografia e nested-PCR para FIV e FeLV, e PCR para identificação dos hemoplasmas. Uma entrevista foi realizada para determinação dos fatores associados aos hemoplasmas. A frequência de positividade foi de 35,5% (71/200). Infecções isoladas foram observadas em 12,5% dos animais para 'Candidatus Mycoplasma haemominutum', 12% para Mycoplasma haemofelis e 3% para 'Candidatus Mycoplasma turicensis'. Quanto a co-positividades, 2% dos animais foram positivos para M. haemofelis e 'Candidatus Mycoplasma haemominutum', 1,5% foram positivos para M. haemofelis e 'Candidatus Mycoplasma turicensis', e 4,5% foram positivos para 'Candidatus Mycoplasma haemominutum' e 'Candidatus Mycoplasma turicensis'. Não foram observadas alterações clínicas ou laboratoriais nos animais positivos para retrovírus e hemoplasmas, concomitantemente. A região periurbana foi identificada como fator de risco associado a M. haemofelis. Enquanto o contato com outros gatos e a infecção por 'Candidatus Mycoplasma turicensis' foi associado à 'Candidatus Mycoplasma haemominutum'. Este estudo indica que a presença dos agentes da micoplasmose hemotrópica felina é comum no Nordeste brasileiro.
Subject(s)
Animals , Male , Female , Cats , DNA, Bacterial/analysis , Cat Diseases/microbiology , Mycoplasma Infections/veterinary , Brazil/epidemiology , Cat Diseases/diagnosis , Cat Diseases/epidemiology , Polymerase Chain Reaction/veterinary , Prevalence , Chromatography, Affinity , Mycoplasma Infections/diagnosis , Mycoplasma Infections/epidemiologyABSTRACT
ABSTRACT BACKGROUND: Colorectal cancer is one of the major causes of death worldwide. Many studies have been done on the biology of its formation as well as its treatment in recent years. One of the factors involved in the formation or treatment of this malignancy can be attributed to the microbial flora in the intestine. OBJECTIVE: This study investigate the potential preventive effect of Lactobacillus acidophilus and Lactobacillus plantarum in patients with polyps or colorectal cancer (CRC). METHODS: A total of 77 samples were selected in the form of three groups including individuals suffering from CRC, polyps and healthy subjects. Genomic DNA of fecal specimens and standard strains were extracted and amplified employing primers targeting of the 16S rRNA gene for initial detection. Absolute Real Time PCR quantification was used to determine the copy of the bacterial expression per gram of feces. RESULTS: No significant difference were observed between age and gender in the mentioned groups (P=0.06). The average copy number of Lactobacillus acidophilus shows Significant difference between the healthy group and those with polyps (P<0.0001), the healthy group and those with colorectal cancer (P<0.0001), as well as those with polyps and the colorectal cancer patients (P<0.0001). CONCLUSION: These results may indicate that taking Lactobacillus acidophilus in people with a family history of CRC and people with polyps may be a way of preventing, treating or reducing the severity of CRC.
RESUMO CONTEXTO: O câncer colorretal é uma das principais causas de morte em todo o mundo. Muitos estudos têm sido feitos sobre a biologia de sua formação, bem como o seu tratamento nos últimos anos. Um dos fatores envolvidos na formação ou no tratamento desta malignidade pode ser atribuído à flora microbiana no intestino. OBJETIVO: Este estudo investigou o potencial efeito preventivo de Lactobacillus acidophilus e Lactobacillus plantarum em pacientes com pólipos ou câncer colorretal (CCR). MÉTODOS: Um total de 77 amostras foram selecionadas e três grupos foram formados, a saber, indivíduos portadores de CCR, pólipos e indivíduos saudáveis. O DNA genomico de espécimes fecais e de amostras padrão foi extraído e amplificado empregando primers que focalizaram o gene do rRNA 16S para a deteção inicial. A quantificação do PCR em tempo real absoluto foi utilizada para determinar a cópia da expressão bacteriana por grama de fezes. RESULTADOS: Não foram observadas diferenças significativas entre idade e sexo nos grupos citados (P=0,06). O número médio de cópias de Lactobacillus acidophilus mostra diferença significativa entre o grupo saudável e aqueles com pólipos (P<0,0001), o grupo saudável e aqueles com câncer colorretal (P<0,0001), bem como aqueles com pólipos e câncer colorretal pacientes (P<0,0001). CONCLUSÃO: Estes resultados podem indicar que a ingestão de Lactobacillus acidophilus em pessoas com antecedentes familiares de CCR e pessoas com pólipos pode ser uma forma de prevenir, tratar ou reduzir a gravidade da CCR.
Subject(s)
Humans , Male , Female , Aged , Colorectal Neoplasms/microbiology , Colonic Polyps/microbiology , Lactobacillus plantarum/isolation & purification , Feces/microbiology , Lactobacillus acidophilus/isolation & purification , DNA, Bacterial/analysis , Colorectal Neoplasms/prevention & control , Colonic Polyps/prevention & control , Polymerase Chain Reaction , Lactobacillus plantarum/genetics , Lactobacillus acidophilus/genetics , Middle AgedABSTRACT
RESUMEN Con el objetivo de caracterizar molecularmente aislamientos rickettsiales procedentes de humanos con síndrome febril agudo inespecífico se realizó un estudio descriptivo transversal, con aislamientos propagados en cultivos celulares Vero ATCC y líneas alternativas, verificando viabilidad mediante Inmunofluoresencia Indirecta (IFI). Previa extracción del ADN, se amplificó el gen gltA mediante PCR convencional, y se analizó su secuencia. Doce aislamientos fueron amplificados, cinco con suficiente ADN para secuenciarlos, evidenciando compatibilidad con R. asembonensis en cuatro, y estrecha identidad con Coxiella burnetti en uno. Al menos tres de siete líneas celulares alternativas mostraron rendimiento significativo en sub cultivos. Se identificó R. asembonensis en cuatro aislamientos de humanos con síndrome febril agudo inespecífico, procedentes de las regiones de Ayacucho, Cajamarca y Madre de Dios en Perú, y Coxiella burnetti en uno procedente de la región Loreto.
ABSTRACT With the objective of molecularly characterizing rickettsial isolates from humans with non-specific acute febrile syndrome, a cross-sectional descriptive study was conducted, with isolates propagated in Vero ATCC cellular cultures and alternative lines, verifying the viability by means of Indirect Immunofluorescence. Prior to DNA extraction, the gltA gene was amplified by means of conventional PCR, and its sequence was analyzed. Twelve isolates were amplified, five with sufficient DNA so as to sequence them, exhibiting compatibility with R. asembonensis in four, and a close identity with Coxiella burnetti in one. At least three of seven alternative cellular lines showed significant yield in sub-cultures. R. asembonensis was identified in four isolates of humans with non-specific acute febrile syndrome, coming from the regions of Ayacucho, Cajamarca, and Madre de Dios in Peru, and Coxiella burnetti in one coming from the Loreto region.
Subject(s)
Humans , Rickettsia/isolation & purification , Rickettsia/genetics , Rickettsia Infections/microbiology , DNA, Bacterial/analysis , Fever/microbiology , Peru , Syndrome , Acute Disease , Cross-Sectional StudiesABSTRACT
RESUMEN Objetivos. Analizar curvas de melting para el diagnóstico de tuberculosis multidrogorresistente a partir de muestras de esputo. Materiales y métodos. Se colectaron muestras de esputo (n = 250) de pacientes con sospecha clínica de tuberculosis pulmonar según resultado de baciloscopia y cultivados en medio sólido Lowenstein Jensen. Según el método de referencia se trabajó con 124 muestras sensibles a rifampicina e isoniacida, 24 resistentes a rifampicina, 33 resistentes a isoniacida y 69 multidrogorresistentes. Se evaluó por PCR en tiempo real y luego por las curvas de melting, se utilizó el gen rpoB como biomarcador de resistencia a rifampicina, y el gen katG y región promotora inhA como biomarcadores de resistencia a isoniacida. La cepa H37Rv fue considerada como control sensible a drogas. Se compararon los resultados del método de referencia y los resultados del análisis de curvas de melting para evaluar los parámetros de sensibilidad, especificidad, valor predictivo positivo y valor predictivo negativo. Resultados. La resistencia a rifampicina mostró una sensibilidad de 90,3 %, especificidad de 90,4 %, valor predictivo positivo de 84,8 % y valor predictivo negativo de 94,0 %. La resistencia a isoniacida mostró una sensibilidad de 90,2 %, especificidad de 93,9 %, valor predictivo positivo de 91,1 % y valor predictivo negativo de 93,3 %. La detección de tuberculosis multidrogorresistente mostró valores de 89,9 %, 90,6 %, 78,5 % y 95,9 % para sensibilidad, especificidad, valor predictivo positivo y valor predictivo negativo, respectivamente. Conclusiones. El análisis de curvas de melting mostró ser seguro y confiable para ser utilizado en el diagnóstico rápido de tuberculosis multidrogorresistente en muestras de esputo.
ABSTRACT Objectives. To analyze melting curves for the diagnosis of multidrug-resistant tuberculosis from sputum samples. Materials and Methods. Sputum samples (n = 250) were collected from patients with clinical suspicion of pulmonary tuberculosis as a result of bacilloscopy and cultured in solid medium Lowenstein Jensen. According to the reference method, 124 samples sensitive to rifampicin and isoniazid, 24 resistant to rifampicin, 33 resistant to isoniazid, and 69 multidrug-resistant were used. It was evaluated by real-time PCR and then by melting curves, the rpoB gene was used as a biomarker of rifampicin resistance, and the katG gene and inhA promoter region were used as biomarkers of isoniazid resistance. The H37Rv strain was considered a drug-sensitive control. The results of the reference method and the results of the melting curve analysis were compared to evaluate the parameters of sensitivity, specificity, positive predictive value and negative predictive value. Results. Rifampicin resistance showed a sensitivity of 90.3%, specificity of 90.4%, positive predictive value of 84.8% and negative predictive value of 94.0%. Isoniazid resistance showed a sensitivity of 90.2%, specificity of 93.9%, positive predictive value of 91.1% and negative predictive value of 93.3%. The detection of multidrug-resistant tuberculosis showed values of 89.9%, 90.6%, 78.5% and 95.9% for sensitivity, specificity, positive predictive value and negative predictive value, respectively. Conclusions. The melting curve analysis showed to be safe and reliable to be used in the rapid diagnosis of multidrug-resistant tuberculosis in sputum samples.
Subject(s)
Humans , Sputum/microbiology , Tuberculosis, Multidrug-Resistant/diagnosis , Tuberculosis, Multidrug-Resistant/microbiology , DNA, Bacterial/analysis , Molecular Diagnostic Techniques , Mycobacterium tuberculosis/genetics , Nucleic Acid DenaturationSubject(s)
Humans , Animals , Dogs , Rickettsia rickettsii/isolation & purification , Tick-Borne Diseases/transmission , Anaplasma phagocytophilum/isolation & purification , Rhipicephalus sanguineus/microbiology , Anaplasmosis/transmission , Tick Infestations/parasitology , Tick Infestations/veterinary , DNA, Bacterial/analysis , Polymerase Chain Reaction , Anaplasma phagocytophilum/genetics , Dog Diseases/parasitology , Anaplasmosis/microbiology , Anaplasmosis/epidemiology , Mexico/epidemiologyABSTRACT
Abstract INTRODUCTION: This study evaluated the performance of the IS6110-TaqMan® assay in different types of biological samples and tissues for laboratory diagnosis of extrapulmonary tuberculosis. METHODS: 143 biological samples and tissues from patients with suspected extrapulmonary tuberculosis from the health services of Recife/Pernambuco/Brazil were evaluated with the IS6110-TaqMan® assay. RESULTS: The sensitivities of the IS6110-TaqMan® assay calculated for blood, urine, both blood and urine samples, tissue biopsies, extrapulmonary body fluid samples, and all samples from patients calculated together were 55.9%, 33.3%, 68.8%, 43.8%, 29.6%, and 73.7%, respectively, and the specificities were 80%, 100%, 78.6%, 100%, 100%, and 84.2%, respectively. CONCLUSIONS The accuracy of qPCR was high in various clinical sample types. The analysis of more than one type of clinical sample collected from the same patient with extrapulmonary tuberculosis enhances the diagnostic power of the IS6110-TaqMan® assay when compared with the use of only one clinical sample.
Subject(s)
Humans , Tuberculosis/diagnosis , DNA, Bacterial/analysis , Mycobacterium tuberculosis/genetics , DNA, Bacterial/isolation & purification , DNA, Bacterial/genetics , Double-Blind Method , Prospective Studies , Reproducibility of Results , Sensitivity and Specificity , Real-Time Polymerase Chain Reaction , Mycobacterium tuberculosis/isolation & purificationABSTRACT
ABSTRACT: Molecular techniques that provide valuable information about the epidemiology of oral strains. The purpose of this study was to determine the genetic relatedness of 83 Enterococcus faecalis strains isolated from treated root canals. These strains were obtained from patients who were treated for persistent endodontic infections. E. faecalis isolates were molecular typed by Pulsed Field Gel Electrophoresis using Smal. Ten clonal groups and 13 pulse types with 38.7 % similarity for the less related strains were identified. Genetic heterogeneity among strains from different patients and a high level of genetic homogeneity among intrapatient strains were observed. Therefore, restriction endonuclease fingerprinting of genomic DNA from E. faecalis strains confirmed the polyclonality of the isolates obtained from the root canals of patients diagnosed with persistent endodontic infections, compared with other reports. These results provide additional data for a better understanding of the epidemiological aspects of root canal infections by E. faecalis.
RESUMEN: Las técnicas moleculares proporcionan información valiosa sobre la epidemiología de aislados orales. El propósito de este estudio fue determinar la relación genética de 83 cepas de Enterococcus faecalis aisladas de conductos radiculares tratados. Estas cepas se obtuvieron de pacientes que fueron tratados por infecciones endodónticas persistentes. Los aislados de E. faecalis se tipificaron molecularmente por electroforesis en gel de campo pulsado usando Smal. Se identificaron diez grupos clonales y 13 pulsotipos con un 38,7 % de similitud para las cepas menos relacionadas. Se observó heterogeneidad genética entre las cepas de diferentes pacientes y un alto nivel de homogeneidad genética entre las cepas intrapacientes. Por lo tanto, la toma de huellas dactilares a traves de restricción de ADN genómico de cepas de E. faecalis confirmó la policlonalidad de los aislados obtenidos de los conductos radiculares de pacientes diagnosticados con infecciones endodónticas persistentes, en comparación con otros informes. Estos resultados proporcionan datos adicionales para una mejor comprensión de los aspectos epidemiológicos de las infecciones del conducto radicular por E. faecalis.
Subject(s)
Humans , Periapical Periodontitis/microbiology , Enterococcus faecalis/isolation & purification , Tooth Apex/microbiology , DNA, Bacterial/analysis , Bacterial Typing Techniques , Gram-Positive Bacterial Infections/microbiology , Electrophoresis, Gel, Pulsed-Field , Dental Pulp Cavity/microbiologyABSTRACT
OBJECTIVE@#To assess whether the same biological conclusion, diagnostic or curative effects regarding microbial composition of irritable bowel syndrome (IBS) patients could be reached through different bioinformatics pipelines, we used two common bioinformatics pipelines (Uparse V2.0 and Mothur V1.39.5)to analyze the same fecal microbial 16S rRNA high-throughput sequencing data.@*METHODS@#The two pipelines were used to analyze the diversity and richness of fecal microbial 16S rRNA high-throughput sequencing data of 27 samples, including 9 healthy controls (HC group), 9 diarrhea IBS patients before (IBS group) and after Rifaximin treatment (IBS-treatment, IBSt group). Analyses such as microbial diversity, principal co-ordinates analysis (PCoA), nonmetric multidimensional scaling (NMDS) and linear discriminant analysis effect size (LEfSe) were used to find out the microbial differences among HC group vs. IBS group and IBS group vs. IBSt group.@*RESULTS@#(1) Microbial composition comparison of the 27 samples in the two pipelines showed significant variations at both family and genera levels while no significant variations at phylum level; (2) There was no significant difference in the comparison of HC vs. IBS or IBS vs. IBSt (Uparse: HC vs. IBS, F=0.98, P=0.445; IBS vs. IBSt, F=0.47,P=0.926; Mothur: HC vs.IBS, F=0.82, P=0.646; IBS vs. IBSt, F=0.37, P=0.961). The Shannon index was significantly decreased in IBSt; (3) Both workshops distinguished the significantly enriched genera between HC and IBS groups. For example, Nitrosomonas and Paraprevotella increased while Pseudoalteromonadaceae and Anaerotruncus decreased in HC group through Uparse pipeline, nevertheless Roseburia 62 increased while Butyricicoccus and Moraxellaceae decreased in HC group through Mothur pipeline.Only Uparse pipeline could pick out significant genera between IBS and IBSt, such as Pseudobutyricibrio, Clostridiaceae 1 and Clostridiumsensustricto 1.@*CONCLUSION@#There were taxonomic and phylogenetic diversity differences between the two pipelines, Mothur can get more taxonomic details because the count number of each taxonomic level is higher. Both pipelines could distinguish the significantly enriched genera between HC and IBS groups, but Uparse was more capable to identity the difference between IBS and IBSt groups. To increase the reproducibility and reliability and to retain the consistency among similar studies, it is very important to consider the impact on different pipelines.
Subject(s)
Humans , Case-Control Studies , Computational Biology , DNA, Bacterial/analysis , Diarrhea , Feces , Gastrointestinal Microbiome/genetics , Irritable Bowel Syndrome/microbiology , Phylogeny , RNA, Ribosomal, 16S , Reproducibility of Results , Rifamycins , RifaximinABSTRACT
Introdução: os métodos moleculares de diagnóstico apresentam como uma das principais vantagens a detecção de microrganismos por meio do DNA bacteriano, levando a uma caracterização microbiana mais acurada. Objetivo: o presente estudo visou investigar a diversidade bacteriana presente nas infecções endodônticas primárias e secundárias/persistentes, comparando o perfil das comunidades microbianas existentes antes e após a terapia endodôntica. Métodos: as amostras microbiológicas foram coletadas antes (T1) e após terapia endodôntica (T2), utilizando cone de papel estéril/apirogênico em dentes com infecções endodônticas primárias (n = 10) e secundárias / persistentes (n = 10). A presença e os níveis de 40 espécies bacterianas nas infecções endodônticas foram investigados por meio da técnica de Checkerboard DNA-DNA Hybridization. Resultados: nas infecções endodônticas primárias em T1, as espécies encontradas em maiores níveis foram P. micra, F. nucleatum sp. nucleatum, S. constellatus, P. gingivalis, G. morbillorum, P. endodontalis, T. denticola, P. acnes, S. gordonii, S. mitis, V. parvula e C. rectus. Em T2, as bactérias mais encontradas foram P. micra, S. oralis e P. acnes. Nas infecções endodônticas secundárias em T1, as espécies mais frequentemente encontradas foram P. acnes, P. micra, S. constellatus, G. morbillorum, C. rectus, A. naeslundii, S. mitis e S. oralis. Em T2, as espécies mais encontradas foram Enterococcus faecalis e Propionibacterium acnes. Conclusão: o presente estudo confirmou comunidades microbianas distintas em infecções endodônticas primárias e secundárias. Além disso, os procedimentos clínicos endodônticos mostraram-se eficazes na redução significativa da prevalência, dos níveis de detecção e na diversidade bacteriana.
Subject(s)
Humans , Bacterial Infections/therapy , DNA, Bacterial/analysis , Endodontics , Root Canal Therapy/instrumentationABSTRACT
RESUMEN Objetivos. Determinar circulación de rickettsias durante los años 2010 al 2011 en localidades fronterizas de cuatroregiones del Perú, y sus características clínicas epidemiológicas y moleculares. Materiales y métodos. Estudio transversal realizado en Tumbes, Tacna, Madre de Dios y Loreto. Se obtuvo datos clínicos epidemiológicos y muestras de sangre total para cultivo y para ensayo de inmunofluorescencia indirecta (IFI). Fue utilizado ADN extraído de cultivos de leucocitos y de ectoparásitos, aquellos genes específicos para rickettsias que amplificaron exitosamente fueron secuenciados y analizados. Resultados. El 33,8% de los encuestados portaba anticuerpos a rickettsias; en Loreto 21,7%, en Madre de Dios 33,0%, en Tacna 48,2% y en Tumbes 33,3%, encontrándose seropositividad en más del 40% de aislamientos confirmados por IFI. Las pruebas moleculares evidenciaron la presencia de Rickettsia felis en Ctenocephalides felis de perros y gatos de Tacna y una especie recientemente reportada para Latinoamérica: Candidatus Rickettsia asemboensis en pulgas Ctenocephalides felis de gatos y perros de Loreto y Madre de Dios. De la población estudiada, el 81,4% informó antecedentes de contacto con ectoparásitos, el 22,6% eran asintomáticos y el 27,8% habitaban viviendas sin agua ni desagüe, con piso de tierra. Conclusiones. Evidencias serológicas y moleculares confirman la circulación de rickettsias en las localidades fronterizas estudiadas, con predisponentes epidemiológicos, demostrándose presencia de dos especies: Rickettsia felis y Candidatus Rickettsia asemboensis, las que representarían una amenaza potencial para la salud de los pobladores.
ABSTRACT Objectives. To determine the circulation of Rickettsia in the years 2010 and 2011 in border locations in four regions ofPeru and their clinical epidemiological and molecular characteristics. Materials and Methods. A cross-sectional study was carried out in Tumbes, Tacna, Madre de Dios, and Loreto. Whole blood samples were obtained from participants for culture and indirect immunofluorescence (IIF) testing. The DNA taken from leukocytes and ectoparasite cultures was used, and those genes detected for Rickettsia that were successfully amplified were sequenced and analyzed. Results. A total of 33.8% of those surveyed carried Rickettsia antibodies (21.7% in Loreto, 33.0% in Madre de Dios, 48.2% in Tacna, and 33.3% in Tumbes). Seropositivity was confirmed with IIF in over 40% of isolates. Molecular tests showed the presence of Rickettsia felis in Ctenocephalides felis of dogs and cats in Tacna and a recently reported species for Latin America, Candidatus Rickettsia asemboensis, in fleas of cats and dogs in Loreto, Madre de Dios, and Tacna. Of the population studied, 81.4% reported a history of contact with ectoparasites, 22.6% were asymptomatic, and 27.8% lived in earthen-floored homes without water or drainage. Conclusions. Serological and molecular evidence confirms the circulation of Rickettsia in the border locations studied, with predisposing epidemiological factors. Tests confirm the presence of two species, Rickettsia felis and Candidatus Rickettsia asemboensis, which represent a potential threat to the health of the inhabitants.
Subject(s)
Adolescent , Adult , Aged , Aged, 80 and over , Animals , Cats , Child , Child, Preschool , Dogs , Female , Humans , Infant , Male , Middle Aged , Young Adult , Rickettsia Infections/microbiology , Rickettsia Infections/epidemiology , Peru/epidemiology , Arthropods/microbiology , Rickettsia/isolation & purification , Rickettsia/genetics , Time Factors , DNA, Bacterial/analysis , Cross-Sectional StudiesABSTRACT
Resumen: Objetivo: Estudiar la calidad microbiológica del pulpo rojo dado su importante impacto económico y social en la región sur-sureste de México. Material y métodos: Se tomaron muestras en diversas zonas de captura de la especie y se analizaron con pruebas bioquímicas descritas en las normas oficiales mexicanas. Se identificaron cepas pertenecientes al género Vibrio, Salmonella, coliformes fecales y E. coli O157:H7. Con el empleo del Sistema BAx, se logró la identificación de microorganismos a través de su ADN bacteriano. Los resultados obtenidos en los métodos bioquímicos y moleculares fueron contrastados. Resultados: El método estadístico de Bland-Altman indicó que ambas técnicas pueden usarse indistintamente. La prueba de McNemar demostró que ambos métodos cuentan con la misma eficacia para la identificación de patógenos (valor X2=0.5 ρ=0.4795). Conclusión: La calidad microbiológica del pulpo en la región sur-sureste de México es deficiente debido a la presencia de flora bacteriana patógena que podría representar un riesgo epidemiológico. Los índices establecidos por las normas sugieren la necesidad de aplicar técnicas de identificación eficaces y rápidas como el Sistema BAx. Este método alternativo de análisis puede coadyuvar a la implementación de estrategias efectivas que permitan cumplir con especificaciones mínimas sanitarias durante el procesamiento de los productos pesqueros, y así elevar los sistemas de control para disminuir los riesgos de brotes epidemiológicos en la región.
Abstract: Objective: In this work we studied the microbiological quality of the red octopus given its important economic and social impact on the region South-Southeast of Mexico. Materials and methods: Samples were taken in different areas of capture of the species and analyzed with biochemical tests described in the Mexican official standards, identifying strains belonging to the genus Vibrio, Salmonella and faecal coliforms, and E. coli O157: H7. We used the BAx System for the identification of microorganisms through their bacterial DNA. The results obtained in biochemical and molecular methods were confirmed. Results: Bland-Altman statistical method pointed out that both techniques can be used interchangeably. McNemar test showed that both methods have the same efficacy for the identification of pathogens (value X2=0.5 ρ=0.4795). Conclusion: The microbiological quality of the octopus in the South-Southeast region of Mexico is deficient due to the presence of pathogenic intestinal flora that might represent an epidemiological risk. The indexes established by the regulations suggest the need to apply effective and rapid identification technologies, such as the BAx System.This alternative method of analysis can contribute to the implementation of effective strategies that allow compliance with the minimal sanitary specifications during the processing of fishing products, thus strengthening the control systems to decrease the risks of epidemiological outbreaks in the region.
Subject(s)
Animals , Octopodiformes/microbiology , Salmonella/isolation & purification , Staphylococcus aureus/isolation & purification , Vibrio/isolation & purification , DNA, Bacterial/analysis , Polymerase Chain Reaction , Bacterial Typing Techniques/methods , Enterobacteriaceae/isolation & purification , Food Microbiology , MexicoABSTRACT
Abstract Objective The diagnosis of extrapulmonary tuberculosis is still a challenge because of its pauci-bacillary nature. The aim of the study was to evaluate the role of a multiplex PCR assay in the diagnosis of extrapulmonary tuberculosis and to compare the efficiency of two targets, IS6110 and MPB64 to detect Mycobacterium tuberculosis. Methods 150 extrapulmonary samples (61 pus/aspirate, 46 tissue, 32 body fluids, and 11 urine) from clinically suspected cases of tuberculosis were included in the study. All the samples were subjected to direct fluorescent microscopy, TB culture (BacT/ALERT 3D, biomerieux, Durham, North Carolina, USA) and a Multiplexed Tandem PCR targeting two mycobacterial DNA sequences, IS6110 and MPB64. Master-Mix reagents and primers were prepared by AusDiagnostics Pvt. Ltd (Alexandria, New South Wales, Australia). The performance of the assay was assessed using a composite gold standard, which included clinical characteristics, microbiology smear as well as culture, histopathology, cytology, radiology, and response to antitubercular therapy. Results 20.3%, 23.6%, and 45.3% of specimens were positive by smear, culture, and PCR, respectively. The sensitivity and specificity of the multiplex PCR was 91.9% and 88.4%, respectively, using the composite gold standard. Positive and negative predictive values of the PCR were estimated as 85.1% and 93.8%, respectively. Higher positivity was observed with target IS6110 (44.6%) as compared to target MPB64 (18.9%). The sensitivities of IS6110 and MPB64 individual targets were 90.3% and 64.5%, respectively, and specificities were 88.4% and 97.7%, respectively. Conclusion PCR can play an important role in rapid and accurate diagnosis of extrapulmonary tuberculosis. IS6110 alone is an effective target in our part of the country.