Aplicación de PCR a partir de cultivo en la identificación de subespecies del complejo Mycobacterium Tuberculosis / The use of culture-based PCR for the identification of subspecies of the mycobacterium tuberculosis complex

Los métodos diagnósticos clásicos de tuberculosis (TB) se basan en la utilización de baciloscopía y cultivo. La identificación del agente etiológico desde la positivización del cultivo requiere entre 10 y 15 días, mientras que el empleo de la reacción en cadena de la polimerasa (PCR) disminuye el tiempo a 24 h, lo que permite no solo identificar las subespecies del complejo Mycobacterium tuberculosis (CMTB) sino también diferenciarlas de otras especies ambientales clínicamente importantes (MOTT) facilitando el diagnóstico y tratamiento. El objetivo del presente trabajo fue determinar la utilidad de la PCR en la identificación temprana de las micobacterias pertenecientes al CMTB, a partir de cultivos positivos, de pacientes con sospecha de TB, atendidos en un hospital pediátrico de alta complejidad, durante un período de cuatro años. A cada muestra, se le realizó baciloscopía y cultivo en medio líquido. A los cultivos positivos, una inmunocromatografía lateral (TBIDR) y luego PCR. El 4,6% del total de muestras (510/11.162) pertenecientes a 198 pacientes presentó cultivos positivos. Cuatrocientos veintiseis (84%) correspondieron a muestras respiratorias. El rendimiento de la baciloscopía directa fue del 41% (194/470). Cuatrocientos treinta y ocho (86%) resultaron M. tuberculosis, 21 (4%) Mycobacterium bovis, 7 (1%), M. bovis-BCG y 44 (9%) MOTT. La utilización de medios de cultivos líquidos junto con el empleo de PCR favorecen una rápida orientación microbiológica y constituye una estrategia útil para optimizar el manejo clínico de estas infecciones, desde el punto de vista terapéutico y epidemiológico, especialmente en pediatría (AU)

Classical diagnostic methods for tuberculosis (TB) are based on the use of smear microscopy and culture. The identification of the etiological agent from positive culture requires 10 to 15 days, while the use of the polymerase chain reaction (PCR) reduces the time to 24 h, which allows not only to identify the subspecies of the Mycobacterium tuberculosis complex (MTC) but also to differentiate them from clinically important environmental mycobacteria other than tuberculosis (MOTT), facilitating diagnosis and treatment. The aim of this study was to determine the usefulness of PCR in the early identification of mycobacteria belonging to the MTC, from positive cultures of patients with suspected TB seen in a pediatric tertiary hospital over a 4-year period. For each sample, smear microscopy and culture in liquid medium was performed. Positive cultures were subjected to lateral immunochromatography (TBIDR) and then PCR. Of the total number of samples (510/11,162) belonging to 198 patients, 4.6% showed positive cultures; 426 (84%) were respiratory samples. The direct smear microscopy yield was 41% (194/470). Overall, 438 (86%) were found to be M. tuberculosis, 21 (4%) Mycobacterium bovis, 7 (1%), M. bovis-BCG, and 44 (9%) MOTT. The use of liquid culture media together with the use of PCR favors a rapid microbiological orientation and is a useful strategy to optimize the clinical management of these infections, from a therapeutic and epidemiological point of view, especially in children (AU)

Lyophilization of Molecular Biology Reactions: A Review.

Molecular biology is a widely used and widespread technique in research and as a laboratory diagnostic tool, aiming to investigate targets of interest from the obtainment, identification, and analysis of genetic material. In this context, methods, such as Polymerase Chain Reaction (PCR), Reverse Transcription Polymerase Chain Reaction (RT-PCR), real-time PCR, loopmediated isothermal amplification (LAMP), and loop-mediated isothermal amplification with reverse transcription (RT-LAMP), can be cited. Such methods use enzymes, buffers, and thermosensitive reagents, which require specific storage conditions. In an attempt to solve this problem, the lyophilization procedure (dehydration process by sublimation) can be applied, aiming to preserve and prolong the useful life of the reaction components in cases of temperature variation. In this review, we present a synthesis of the lyophilization process, describing the events of each step of the procedure and providing general information about the technique. Moreover, we selected lyophilization protocols found in the literature, paying attention to the conditions chosen by the authors for each step of the procedure, and structured the main data in tables, facilitating access to information for researchers who need material to produce new functional protocols.

Ocorrência de Babesia sp, Ehrlichia canis e Hepatozoon canis em cães domiciliados, em dois municípios do estado do Espírito Santo - Brasil / Occurrence of Babesia sp, Ehrlichia canis and Hepatozoon canis in domiciled dogs in two municipalities of the state of Espírito Santo - Brazil / Ocurrencia de Babesia sp, Ehrlichia canis y Hepatozoon canis em perros domiciliados em dos municipios del estado de Espírito Santo - Brasil

As doenças transmitidas por carrapatos são afecções de grande importância na clínica médica de pequenos animais, devido à alta casuística e ampla distribuição vetorial no território brasileiro. Os principais agentes responsáveis pelas infecções em cães são Babesia sp., Ehrlichia canis e Hepatozoon canis. Os animais infectados são assintomáticos ou apresentam sinais clínicos inespecíficos, sendo necessário a utilização de testes diagnósticos para definição do agente etiológico, e diagnóstico seguro. O objetivo do presente estudo foi determinar a ocorrência desses micro-organismos em cães naturalmente infectados, domiciliados nos municípios de Vila Velha e Anchieta, Espírito Santo, utilizando diferentes testes de detecção: Reação em cadeia polimerase (PCR), sorologia para detecção de anticorpos anti Ehrlichia canis e pesquisa de hematozoários em esfregaço sanguíneo. Foram analisadas 65 amostras de sangue obtidas por venopunção de veia cefálica de cães. No teste de PCR, 4,62% dos animais foram positivos para Babesia vogeli e 1,54% para Ehrlichia canis sendo os resultados para Hepatozoon canis negativos. No teste sorológico para E. canis 90,77% dos animais foram positivos para a presença de anticorpos, e na pesquisa em lâminas de esfregaço sanguíneo 3,02% apresentavam outros hemoparasitas. Os resultados indicam a dispersão desses hemoparasitas na população canina da região de estudo, entretanto com baixa ocorrência. O teste de PCR demonstrou-se como o mais sensível no qual Babesia vogeli foi o agente mais observado.(AU)

Tick-borne diseases are diseases of great importance in the medical practice of small animals, due to the high casuistry and wide vectorial distribution in the Brazilian territory. The main agents responsible for infections in dogs are Babesia sp., Ehrlichia canis and Hepatozoon canis. Infected animals are asymptomatic or present nonspecific clinical signs, requiring the use of diagnostic tests to define the etiologic agent, and safe diagnosis. The objective of the present study was to determine the occurrence of these microorganisms in naturally infected dogs domiciled in the municipalities of Vila Velha and Anchieta, Espírito Santo, using different detection tests: polymerase chain reaction (PCR), serology to detect antibodies against Ehrlichia canis and research of hematozoa in blood smears. Sixty-five blood samples obtained by venipuncture of the cephalic vein of dogs were analyzed. In the PCR test, 4.62% of the animals were positive for Babesia vogeli and 1.54% for Ehrlichia canis, and the results for Hepatozoon canis were negative. In the serological test for E. canis, 90.77% of the animals were positive for the presence of antibodies, and in the research in blood smear slides, 3.02% presented other hemoparasites. The results indicate the dispersion of these hemoparasites in the canine population of the study region, however with low occurrence. The PCR test proved to be the most sensitive, in which Babesia vogeli was the most observed agent.(AU)

Las enfermedades transmitidas por garrapatas son enfermedades de gran importancia en la práctica médica de los pequeños animales, debido a la alta casuística y amplia distribución vectorial en el territorio brasileño. Los principales agentes responsables de las infecciones en los perros son Babesia sp., Ehrlichia canis y Hepatozoon canis. Los animales infectados son asintomáticos o presentan signos clínicos inespecíficos, siendo necesario el uso de pruebas diagnósticas para la definición del agente etiológico, y el diagnóstico seguro. El objetivo del presente estudio fue determinar la ocurrencia de estos microorganismos en perros infectados naturalmente, domiciliados en los municipios de Vila Velha y Anchieta, Espírito Santo, utilizando diferentes pruebas de detección: reacción en cadena de la polimerasa (PCR), serología para detectar anticuerpos anti Ehrlichia canis e investigación de hematozoos en frotis de sangre. Se analizaron sesenta y cinco muestras de sangre obtenidas por venopunción de la vena cefálica de los perros. En la prueba PCR, el 4,62% de los animales fueron positivos para Babesia vogeli y el 1,54% para Ehrlichia canis, y los resultados para Hepatozoon canis fueron negativos. En la prueba serológica para E. canis, el 90,77% de los animales fueron positivos a la presencia de anticuerpos, y en la investigación en láminas de frotis de sangre el 3,02% presentaron otros hemoparásitos. Los resultados indican la dispersión de estos hemoparásitos en la población canina de la región de estudio, aunque con una baja presencia. La prueba PCR resultó ser la más sensible, en la que Babesia vogeli fue el agente más observado.(AU)

Evaluation of Analytical Sensitivity of Sdf I based PCR and Sandwich ELISA for Salmonella Enteritidis detection and On-Farm prevalence in Punjab, Pakistan

Salmonella Enteritidis (SE) is a dominant serotype among non-typhoidal Salmonella which renders poultry products unsafe for human consumption. Due to frequent reporting of egg associated outbreaks, broiler breeder flocks are understudied although farm environment present supporting conditions for the growth of SE. In this study, two rapid detection techniques for SE were compared in terms of analytical sensitivity and the extent of SE contamination in broiler breeder farm environment was determined. Analytical sensitivity as limit of detection (LOD) was evaluated quantitatively for serotype specific PCR based on amplification of Sdf I gene and a commercially available sandwich ELISA for antigen detection. In triplicate experiments, tenfold serial dilutions of SE were prepared and tested with each technique. Using pure cultures, analytical sensitivity of PCR and ELISA were found to be 18.6 CFU/ml and 2.77×105 CFU/ml respectively. PCR (LOD, log 1.2) was found to be more sensitive and rapid than ELISA (LOD, log 5.4). Environmental swab samples (n = 260) were collected from 22 hen houses representing 8 broiler breeder farms located in and around Lahore and Sheikhupura districts of Punjab province. From each hen house swab samples were collected from litter, nests, feeders, drinkers, fans, pads, ceiling, walls and walkways. Following selective enrichment, pooled swab samples were subjected to PCR. Results showed that 36.3 % (8/22) hen houses were detected positive for SE. These findings suggest improvement in farm biosecurity measures and advocate implementation of integrated Salmonellosis control programs in broiler breeder houses to minimize carcass contamination.(AU)

Effect of Leptin, Pituitary Transcription Factor and Luteinizing Hormone Receptor Genes Polymorphisms on Reproductive Traits and Milk Yield in Holstein Cattle

Abstract The aim of this study was to estimate allelic and genotypic frequencies of markers in the leptin (LEP), pituitary transcription factor (PIT-1) and luteinizing hormone receptor (LHR) genes and evaluate their effects on reproductive traits and milk yield of Holstein cattle. Data from 147 cows from department of Francisco Morazán, Honduras, were collected and PCR-Restriction Fragment Length Polymorphism (RFLP) assays were performed to characterize the PIT-1-HinfI, LEP- A59V and LHR-rs41256848 polymorphisms. To estimate the effect of genotypes on reproductive traits and milk yield fixed and mixed linear models were fitted. The frequencies of the genotypes CC, CT and TT of A59V, AA, AB and BB of HinfI, and CC, CG and GG of rs41256848 were 0.46, 0.33 and, 0.21; 0.09, 0.32 and 0.58; and 0.37, 0.61 and 0.02, respectively. The genotypes of LEP and LHR showed deviations from Hardy-Weinberg equilibrium. The A59V polymorphism was significantly associated with the calving to conception interval (CCI) (p=0.01), being the C allele favorable. The HinfI and rs41256848 polymorphism were significantly associated (p=0.08 and p=0.04) with age to first calving (AFC), being the A and G the alleles favorable associated, respectively. The results suggest that LEP, PIT and LHR polymorphisms can probably act as candidate to be used in marker-assisted selection for AFC and CCI traits.

Portable sequencing as a teaching tool in conservation and biodiversity research.

As biodiversity loss continues to accelerate, there is a critical need for education and biomonitoring across the globe. Portable technologies allow for in situ molecular biodiversity monitoring that has been historically out of reach for many researchers in habitat nations. In the realm of education, portable tools such as DNA sequencers facilitate in situ hands-on training in real-time sequencing and interpretation techniques. Here, we provide step-by-step protocols as a blueprint for a terrestrial conservation genetics field training program that uses low-cost, portable devices to conduct genomics-based training directly in biodiverse habitat countries.

Active human herpesvirus infections in adults with systemic lupus erythematosus and correlation with the SLEDAI score

Abstract Background: Human herpesviruses (HHVs) are responsible for a significant number of clinical manifestations in systemic lupus erythematous (SLE) patients. The aim of this study was to determine the frequency of active HHV infections in SLE patients and correlating them with disease activity. Methods: Serum samples were collected from 71 SLE patients and their DNAs were extracted and analyzed to detect HHV-DNA viruses using the nucleic acid amplification technique. Results: Fifteen out of the 71 (21.1%) patients tested positive for the HHV-DNA virus. Of them, 11/15 HHV-DNA-positive patients (73.3%) had SLE activity index (SLEDAI - Systemic Lupus Erythematosus Disease Activity Index) ≥8 (p = 0.0001). Active HCMV infection was the mostly frequently observed infection, occurring in 6/15 patients (40%). The frequencies of other active viral infections were 22% for HSV-1, 16.7% for HHV-7, and 5.5% for HSV-2. Viral coinfection (two or more viruses detected in the same sample) occurred in three patients (16.7%). Active HHV infections in SLE patients are more frequent in those with active SLE (≥8), who is at high risk of HHV reactivation and HCMV disease. Conclusion: Viral surveillance is important to identify active HHV infections that can cause clinical symptoms and other complication in SLE patients.

Design and validation of an immuno-PCR assay for IFN-α2b quantification in human plasma.

Aim: Nowadays, IFN-α is considered a promising therapeutic target for systemic lupus erythematosus. An immuno-PCR (iPCR) was developed to quantify low amounts of IFN-α in human plasma followed by a deep analysis of the methodologic robustness throughout quality by design approach. Results: An accurate, sensitive, selective and versatile iPCR was validated. The critical iPCR procedural steps were identified, applying a Plackett-Burman design. Also, this assay demonstrated an outstanding LOD of 0.3 pg/ml. A significant aspect relies on its high versatility to detect and quantify other cytokines in human plasma as the appropriate biotinylated antibody is employed. Conclusion: This reliable iPCR assay can be clinically used as an alternative method for quantitating and detecting low IFN-α2b concentrations in human plasma samples.

¿Existe evidencia sobre el uso de PCR para diagnosticar hantavirus a contactos cercanos? / Is there evidence on the use of PCR to diagnose hantavirus in close contacts?

INTRODUCCIÓN: El hantavirus es una enfermedad zoonótica transmitida por roedores, y que es causante de un síndrome cardiopulmonar de prognosis variable, y que en algunos casos puede ocasionar la muerte (1,2). Su transmisión ocurre generalmente desde roedores de áreas rurales, luego de la inhalación de orina y heces. Por otro lado, la transmisión humano-humano aún se encuentra en estudio por no encontrar evidencia suficiente (1). No se han determinado antivirales efectivos para el hantavirus, no obstante la detección temprana de los síntomas permitiría mejorar el pronóstico de la infección (3). Como no existe claridad en cuanto a la transmisión entre humanos, es importante poder notificar lo antes posible los casos, de manera de contar con la precaución necesaria. OBJETIVO DE ESTA SÍNTESIS: Informar la toma de decisiones respecto del uso de PCR para contactos de personas con hantavirus. Se presentan los principales hallazgos encontrados en la evidencia recopilada. RESUMEN DE HALLAZGOS: Esta síntesis busca aportar evidencia sobre el uso de PCR para el diagnóstico de hantavirus en contactos cercanos de alguien que ya presente el virus. Se incluyeron todo tipo de estudios que describieran o evaluaran protocolos de realización de PCR para el diagnóstico de hantavirus en contactos. Se excluyeron estudios que evaluaran la precisión de técnicas diagnósticas, o que consideraran eficacia de tratamiento, y estudios realizados en animales. Al realizar la búsqueda, los títulos y resúmenes fueron seleccionados por un único revisor. Como no se encontraron revisiones sistemáticas, se realizó una búsqueda de estudios primarios. se encontraron inicialmente 492 referencias. De éstas, se excluyeron 467 por título y resumen, evaluando finalmente 16 textos completos. De éstos, finalmente se seleccionó un único estudio primario, que abordaba parcialmente la pregunta formulada (4).

Catharanthus roseus (Apocynaceae) naturally infected with diverse phytoplasmas in Costa Rica / Catharanthus roseus (Apocynaceae) naturalmente infectada con diversos fitoplasmas en Costa Rica

Abstract Phytoplasmas (class Mollicutes) are causal agents of plant diseases with an economic impact on crops or threatening local biodiversity. A survey was conducted from 2012 to 2016 on infected Catharanthus roseus plants that exhibited symptoms reminiscent of phytoplasma infection throughout Costa Rica. A total of 73 plants were collected exhibiting symptoms such as virescence, phyllody, axillary proliferation, little leaf, leaf malformation, chlorosis, or yellowing. All samples were tested by nested PCR using phytoplasma universal and specific primer pairs. Phytoplasma infection was detected in 52 (71.2 %) of the plants collected. Phytoplasmas of six subgroups belonging to 16Sr groups I, III, IX, XIII and XV were identified based on sequencing and in silico RFLP analyses. 'Candidatus Phytoplasma asteris' (16SrI) was the predominant group among the positive samples (n = 30) showing variety of symptoms and wide distribution from sea level to ca. 1 400 m.a.s.l. in six of the seven Costa Rican provinces. Group 16SrIII was the second most abundant (14 samples); and the remaining three groups were seldom found in C. roseus (8 samples). Moreover, group 16SrXIII phytoplasma was detected for the first time in the country. To the best of our knowledge, this is the first report of natural infection of C. roseus with phytoplasma subgroups 16SrI-B, 16SrI-P, 16SrIII-F, 16SrIX-F, 16SrXIII-A, and 16SrXV-B in Costa Rica and Central America.

Resumen Los fitoplasmas (clase Mollicutes) son agentes causales de enfermedades de plantas que provocan pérdidas económicas o amenazan la biodiversidad local. Una recolecta de plantas de Catharanthus roseus que mostraban síntomas de posible infección con fitoplasmas se realizó en diferentes lugares de Costa Rica desde 2012 a 2016. Un total de 73 plantas fueron recolectadas con síntomas tales como viriscencia, filodia, brotación axilar múltiple, reducción foliar, deformación foliar, clorosis, y amarillamiento. Todas las muestras fueron evaluadas mediante PCR anidado usando los pares de imprimadores universales y específicos para fitoplasmas. Infección por fitoplasmas se detectó en 52 (71.2 %) de las muestras. Fitoplasmas de seis subgrupos dentro de los grupos 16Sr I, III, IX, XIII y XV fueron identificados basados en secuenciación del ADN y análisis de polimorfismos de restricción (RFLP) in silico. El grupo predominante encontrado en las muestras positivas (n = 30) fue el 16SrI ('CandidatusPhytoplasma asteris'), éste mostró variedad de síntomas y amplia distribución desde el nivel del mar hasta casi los 1 400 m.s.n.m. en seis de las siete provincias de Costa Rica. El grupo 16SrIII fue el segundo más abundante (14 muestras); y los restantes tres grupos se encontraron en pocas muestras de C. roseus (8 muestras). Además, fitoplasmas del grupo 16SrXIII se detectaron por primera vez en el país. De acuerdo a nuestro conocimiento, este es el primer informe de infección natural de C. roseus con fitoplasmas de los subgrupos 16SrI-B, 16SrI-P, 16SrIII-F, 16SrIX-F, 16SrXIII-A y 16SrXV-B en Costa Rica y Centroamérica.

Methodological aspects of Universal immuno-PCR on standard tubes.

One of the most used formats in inmuno-polymerase chain reaction (IPCR) is known as "Universal" IPCR (signal-generating complexes is based on conjugates of biotinylated DNA, biotinylated IgG and avidin). In the present study, we evaluated the utility of using mono- and bi-biotinylated DNA probes, pre-self-assembled DNA-neutravidin complex, blocking step and glutaraldehyde pretreatment of standard PCR tubes to improve the analytical performance of the hTSH-IPCR assay. The use of pre-self-assembled mono-biotinylated DNA-neutravidin complex enhances both the sensitivity and the reproducibility of the hTSH-IPCR assay, even without blocking step: hTSH-IPCR assay showed an improved limit of detection (LOD: 0.01 µIU/ml), calibration sensitivity (SEN: 2.4) and analytic sensitivity (γ: 9 µIU/ml-1) in comparison with both a self-made ELISA and a commercial one.

Functional status and severity of osteoarthritis in elderly is associated to the polymorphism of TNFA gene

Abstract Background: Osteoarthritis (OA) is a major musculoskeletal disease with high prevalence in the elderly. The study of genetic polymorphisms of inflammatory mediators involved in OA may contribute to the elucidation of the complex pathophysiology of this disease and identification of susceptibility individuals. Aim: This study aimed to evaluate the association between polymorphism at tumor necrosis factor alpha gene (SNP - 308 G/A TNFA) with presence, severity and functional status of osteoarthritis in elderly. Methods: This study was characterized as case-control and encompassed 257 physically independent elderly (Mean Age: 68.55 ± 5.2; Minimum age: 60 and Maximum age: 82) were recruited. After this selection, the groups were divided in: 92 elderly individuals with osteoarthritis (case group) and 165 without the disease (control group). Methods: The individuals were genotyped by the TaqMan real-time PCR system. The subjects were classified based on the degree of radiological impairment according to the criteria of Kellgren-Laurence and regarding functional impairment using the WOMAC and LEQUESNE questionnaires. Results: TNFA gene polymorphic individuals (subjects harboring allele A) are more affected by OA (χ2 = 8.7, p = 0.003), once they have major radiological lesion both in hip (Fisher-Freeman-Halton Test = 3.9, p = 0.04) and knee (Fisher- Freeman-Halton Test = 4.0, p = 0.04) as well as worse functional status assessed by the Lequesne questionnaire (Mann- Whitney, p = 0.04). At the multivariate analysis, after adjustment for age, gender, body mass index, the presence of rare allele for TNFA (allele A) increases the susceptibility to OA development [OR: 1.87 (95% CI: 1.1 —3.2)]. Conclusion: We conclude that the SNP - 308 G/A of TNFA gene may affect osteoarthritis susceptibility, severity and functional status of individuals with osteoarthritis.

Cloning and high-level expression of Thermus thermophilus RecA in E. coli: purification and novel use in HBV diagnostics

ABSTRACT We studied the role of Thermus thermophilus Recombinase A (RecA) in enhancing the PCR signals of DNA viruses such as Hepatitis B virus (HBV). The RecA gene of a thermophilic eubacterial strain, T. thermophilus, was cloned and hyperexpressed in Escherichia coli. The recombinant RecA protein was purified using a single heat treatment step without the use of any chromatography steps, and the purified protein (>95%) was found to be active. The purified RecA could enhance the polymerase chain reaction (PCR) signals of HBV and improve the detection limit of the HBV diagnosis by real time PCR. The yield of recombinant RecA was ∼35 mg/L, the highest yield reported for a recombinant RecA to date. RecA can be successfully employed to enhance detection sensitivity for the diagnosis of DNA viruses such as HBV, and this methodology could be particularly useful for clinical samples with HBV viral loads of less than 10 IU/mL, which is interesting and novel.

Genotyping based on thermal denaturation of amplification products identifies species of the Mycobacterium tuberculosis complex.

PURPOSE: To develop a fast and inexpensive genotyping assay to identify the Mycobacterium tuberculosis complex (MTC) species most prevalent in human tuberculosis (TB), based on the thermal denaturation profiles of PCR products from mycobacterial 16S rDNA and three MTC genomic regions of difference (RD). METHODOLOGY: Genotypes were determined by the presence and thermal denaturation profiles of the amplicons generated in the 'preliminary' PCR mixture (16S rDNA), followed by those of the simultaneous D1 (RD9+, RD1-) and D2 (RD4+, RD4-) PCR mixtures. The 16S rDNA profile identifies the genus Mycobacterium; the absence of any additional RD profile identifies Mycobacterium non-tuberculous (MNT) strains; additional RD4+ and RD9+ profiles without RD1- identify M. tuberculosis; an additional RD4+ profile per se identifies M. africanum; an additional RD4- profile per se identifies Mycobaterium bovis; additional RD1- and RD4- profiles identify M. bovis BCG. RESULTS: Genotypes of a panel with 44 mycobacterial strains coincided in 16 MB and five non-MTC strains; in the remaining 23 MTC strains, 17 MTB and five MA concordant genotypes and one discordant MB genotype were resolved. The genotypes of 13 human and bovine MTC isolates coincided in all four MB and eight of the nine MTB isolates. CONCLUSION: Sensitivity, specificity and positive and negative predictive values of the method are 100 % for the genus Mycobacterium, which resolves MB, MTB and MA genotypes. Species/genotype agreement is 97.7 % for the panel and 92.3 % for the MTC isolates. This method may be advantageously used to identify the most prevalent MTC species in humans.

FilmArray® en infecciones respiratorias agudas y sepsis / FilmArray® in acute respiratory infections and sepsis

CONTEXTO CLÍNICO: Las enfermedades infecciosas son la tercera causa de muerte en Argentina, con una tasa de mortalidad ajustada por edad de 77 fallecidos por 100.000 habitantes en 2013. Por su parte, las enfermedades respiratorias son la primera causa de consulta y hospitalización en Argentina, y una de las principales causas de muerte. Las infecciones respiratorias agudas (IRA) son aquellas con una evolución menor a 15 días; en su mayoría son cuadros virales autolimitados que no requieren estudio etiológico, y afectan predominantemente a menores de cinco años, mayores de 65 años e inmunocomprometidos. El diagnóstico microbiológico se utiliza en pacientes graves o con factores de riesgo y se basa principalmente en la detección de antígenos virales por inmunofluorescencia (IF) de secreciones nasofaríngeas. La sepsis se define como una disfunción orgánica con riesgo de muerte causada por una respuesta inadecuada del huésped ante una infección.4 Es un problema sanitario que afecta a millones de personas en todo el mundo cada año y una de cada cuatro personas muere a causa de ella. El diagnóstico se basa en hemocultivos cuyos resultados normalmente se obtienen luego de dos días. Sin embargo, la celeridad y precisión del tratamiento influyen en los resultados y el exceso de mortalidad asociado al tratamiento antibiótico inadecuado es del 10-40%. Se postula el uso del panel de PCR múltiple (FilmArray®) para el diagnóstico etiológico de enfermedades infecciosas respiratorias y sepsis. TECNOLOGÍA: FilmArray® es un sistema automatizado de identificación microbiológica rápida basado en la técnica de reacción en cadena de polimerasa (PCR, del inglés Polymerase Chain Reaction). Consiste en una plataforma en donde se coloca una muestra biológica (sangre, secreciones respiratorias, materia fecal o líquido cefalorraquídeo). La técnica no requiere entrenamiento significativo, un software guía el proceso y los resultados, que se obtienen en 60 minutos aproximadamente, se presentan en un formato fácil de leer. La misma plataforma se puede utilizar con diferentes paneles que se aplican a diferentes situaciones clínicas. Cada panel diagnostica una variedad de virus, bacterias, hongos y/o genes de resistencia antibiótica prevalentes. En la tabla 1 se detallan los organismos identificados por el panel respiratorio y de sangre. Otros dos paneles para la identificación de microrganismos asociados a cuadros de diarrea y meningitis/encefalitis se encuentran disponibles, sin embargo, no son focos de este documento. OBJETIVO: El objetivo del presente informe es evaluar la evidencia disponible acerca de la eficacia, seguridad y aspectos relacionados a las políticas de cobertura del uso de Panel de PCR múltiple (FilmArray®) para el diagnóstico de infecciones. MÉTODOS: Se realizó una búsqueda en las principales bases de datos bibliográficas, en buscadores genéricos de internet, y financiadores de salud. Se priorizó la inclusión de revisiones sistemáticas (RS), ensayos clínicos controlados aleatorizados (ECAs), evaluaciones de tecnologías sanitarias (ETS), evaluaciones económicas, guías de práctica clínica (GPC) y políticas de cobertura de diferentes sistemas de salud. RESULTADOS: Se incluyeron una RS, un ECA, tres ensayos clínicos prospectivos, tres series de casos (antes-después no controlado), seis GPC, una ETS, dos evaluaciones económicas y un informe de política de cobertura de FilmArray® en pacientes con infecciones respiratorias agudas o sepsis. Adicionalmente se identificó un ECAs en curso que evalúa el rendimiento diagnostico e impacto clínico de FilmArray® (NCT03391076) en pacientes con infecciones respiratorias bajas que requirieron internación. CONCLUSIONES: Evidencia de moderada calidad sugiere que el sistema FilmArray® para el diagnóstico etiológico de infecciones respiratorias agudas y sepsis tiene una elevada sensibilidad y especificidad para detectar los organismos y mecanismos de resistencia antibiótica para los cuales fue diseñado. Escasa evidencia de baja calidad sugiere que en pacientes con sospecha de sepsis y hemocultivos positivos su uso no se traduciría en beneficios clínicos como mortalidad o del sistema de salud. En pacientes con infecciones respiratorias evidencia de baja calidad muestra resultados contradictorios en cuanto al posible beneficio de disminuir el tiempo de estadía hospitalaria o la tasa de prescripción de antibióticos. Diferentes guías de práctica clínica y políticas de cobertura relevadas no mencionan de manera al panel de PCR múltiple (FilmArray®) entre los estudios diagnósticos de estas patologías. Sin embargo, sí consideran la utilización de PCR simple y específica para microorganismos en forma individual. No se encontraron estudios de costo-efectividad o de impacto presupuestario en Latinoamérica. La evaluación económica encontrada concluye que su utilización en niños evaluados en emergencias para diagnóstico de infección por el virus influenza no sería costo-efectiva.

Cloning and high-level expression of Thermus thermophilus RecA in E. coli: purification and novel use in HBV diagnostics.

We studied the role of Thermus thermophilus Recombinase A (RecA) in enhancing the PCR signals of DNA viruses such as Hepatitis B virus (HBV). The RecA gene of a thermophilic eubacterial strain, T. thermophilus, was cloned and hyperexpressed in Escherichia coli. The recombinant RecA protein was purified using a single heat treatment step without the use of any chromatography steps, and the purified protein (>95%) was found to be active. The purified RecA could enhance the polymerase chain reaction (PCR) signals of HBV and improve the detection limit of the HBV diagnosis by real time PCR. The yield of recombinant RecA was ∼35mg/L, the highest yield reported for a recombinant RecA to date. RecA can be successfully employed to enhance detection sensitivity for the diagnosis of DNA viruses such as HBV, and this methodology could be particularly useful for clinical samples with HBV viral loads of less than 10IU/mL, which is interesting and novel.