Detección molecular de patógenos en deposiciones en niños consultantes por diarrea aguda en Servicios de Urgencia / Molecular detection of pathogens in stool samples of children consulting for acute diarrhea in emergency services

INTRODUCCIÓN: La diarrea aguda continúa siendo una de las principales causas de morbilidad en niños; sin embargo, el diagnóstico etiológico presenta limitaciones dada la baja sensibilidad de los métodos tradicionales. OBJETIVO: Describir los microorganismos identificados en niños que acudieron al Servicio de Urgencia (SU) de un hospital universitario en Santiago, Chile, por diarrea aguda y a los que se le solicitó panel molecular gastrointestinal. MÉTODOS: Se revisaron fichas clínicas y resultados de panel gastrointestinal realizados entre junio de 2017 y marzo de 2020. RESULTADOS: Se incluyeron 198 pacientes, edad promedio de 54,5 meses y 60,6% (120/198) de sexo masculino. La positividad del panel fue de 78,8% (156/198) con 35,3% (55/156) de las muestras polimicrobianas. Se identificaron 229 microorganismos, de los cuales 72,9% (167/229) corresponden a bacterias, 25,8% (59/229) a virus y 1,3% (3/229) a parásitos. Destacaron Campylobacter spp. y Escherichia coli enteropatógena (ECEP) como las bacterias más frecuentemente identificadas. Los pacientes con detección de Campylobacter spp. presentaron con mayor frecuencia fiebre (p = 0,00). ECEP se aisló principalmente (82,5%) en muestras polimicrobianas. DISCUSIÓN: Los resultados enfatizan el potencial que poseen los estudios moleculares para mejorar el diagnóstico etiológico de la diarrea, pero a la vez llevan a cuestionar el rol patogénico de algunos microorganismos identificados.

BACKGROUND: Acute diarrhea continues to be one of the main causes of morbidity in children, however the etiologica diagnosis presents limitations given the low sensitivity of traditional methods. AIM: To describe the microorganisms identified in children who attended the emergency department (ED) in Santiago, Chile, due to acute diarrhea and to whom a gastrointestinal panel was requested as part of their study. MATERIAL AND METHODS: Clinical records and results of the gastrointestinal panel carried out between June 2017 and March 2020 were reviewed. RESULTS: 198 patients were included, the average age was 54.5 months and 60.6% (120/198) were males. Positivity was 78.8% (156/198) with 35.3% (55/156) of the samples being polymicrobial. 229 microorganisms were identified, of which 72.9% (167/229) corresponded to bacteria, 25.8% (59/229) to viruses, and 1.3% (3/229) to parasites. Campylobacter spp. and enteropathogenic Escherichia coli (EPEC) were the most frequently identified bacteria. Patients with detection of Campylobacter spp. presented a higher frequency of fever (p = 0.00). EPEC was isolated in 82.5% of the cases in polymicrobial samples. DISCUSSION: The results emphasize the potential of molecular studies to improve the etiological diagnosis of diarrhea and at the same time lead to question the pathogenic role of some microorganisms.

Utilidad del lavado broncoalveolar para la detección microbiológica, y factores asociados, en receptores de trasplante de precursores hematopoyéticos: estudio de cohorte retrospectivo / Usefulness of bronchoalveolar lavage for microbiological detection and asssociated factors in hematopoietic stem cell transplant receivers: a retrospective cohort study

INTRODUCCIÓN: Las opacidades pulmonares en receptores de trasplante de precursores hematopoyéticos (TPH) representan un desafío diagnóstico y son una causa de morbimortalidad. Existen grandes discrepancias con respecto a la sensibilidad diagnóstica del lavado broncoalveolar (LBA), sus complicaciones, y los factores asociados a la identificación microbiológica. OBJETIVO: Conocer la utilidad del estudio microbiológico del LBA en el diagnóstico, modificación de la conducta médica y estimar las complicaciones y mortalidad asociada al procedimiento, en receptores de TPH con opacidades pulmonares. PACIENTES Y MÉTODOS: Estudio de cohorte, retrospectivo, en adultos receptores de TPH a los que se les realizó una broncoscopía con LBA por presentar opacidades pulmonares, en el Hospital Italiano de Buenos Aires entre el 01/01/2011 y el 31/12/2020. RESULTADOS: De los 189 procedimientos analizados, en 79 se logró un hallazgo microbiológico (41,8%) y 122 permitieron modificar la conducta médica (64,6%). En 11 casos se observaron complicaciones graves dentro de las 12 horas (5,8%) de efectuado el LBA. La mortalidad intrahospitalaria fue de 16,8% (N = 21/125). El valor de neutrófilos en sangre previo al LBA (p = 0,037) y la presencia de nódulos pulmonares como lesión tomográfica predominante (p = 0,029) se asociaron independientemente al hallazgo microbiològico global. CONCLUSIONES: Nuestra investigación apoya la realización del LBA como herramienta diagnóstica en pacientes que reciben un TPH y presentan opacidades pulmonares.

BACKGROUND: Lung opacities are a cause of morbimortality in bone marrow transplant patients, and represent a diagnostic challenge. There are large discrepancies regarding the diagnostic sensitivity of bronchoalveolar lavage (BAL), its complications, and the factors associated with microbiological detection. AIM: To know the usefulness of the microbiological study of BAL in the diagnosis, in the modification in medical behavior and to estimate the complications and associated mortality of this diagnostic procedure in patients transplanted with hematopoietic progenitor cells with pulmonary opacities. METHODS: Retrospective cohort study in bone marrow transplant adult patients who underwent bronchoscopy with BAL due to lung opacities at Hospital Italiano de Buenos Aires between 01/01/2011 and 12/31/2020. RESULTS: Of the 189 BAL analyzed, 79 presented a microbiological detection (41.8%) and 122 allowed to modify the medical behavior (64.6%). Severe complications were observed within 12 hours after the procedure in11 cases (5.8%). In-hospital mortality was 16,8% (N = 21/125). The value of blood neutrophils prior to bronchoalveolar lavage (p = 0.037) and the presence of pulmonary nodules as the predominant tomographic lesion (p = 0.029) were independently associated with global microbiological detection. CONCLUSION: Our research supports the performance of BAL as a diagnostic tool in bone marrow transplant patients with lung opacities.

Experiencia de dos años con el uso de panel de RPC múltiple de meningitis-encefalitis en pacientes pediátricos en un hospital de tercer nivel en Argentina / Two-year experience with the multiple PCR panel meningitis-encephalitis panel in children in a third level hospital in Argentina

INTRODUCCIÓN: La meningitis bacteriana aguda (MBA) y la encefalitis son infecciones graves y el retraso en el tratamiento determina mayor morbimortalidad. En 2015 la FDA. aprobó un panel de RPC múltiple, BioFire® Filmarray® meningitis-encefalitis (FA-ME), que desde el 2019 se encuentra disponible en nuestro hospital. OBJETIVOS: Estimar número de determinaciones positivas mediante FA-ME, evaluar concordancia con cultivo convencional (CC) y describir si FA-ME permitió realizar cambios en el tratamiento. MATERIAL Y MÉTODOS: Estudio retrospectivo, descriptivo, realizado durante 2019-2021 en el Hospital de Niños Pedro Elizalde. Se revisaron reportes de niños con meningitis, encefalitis y meningoencefalitis y líquido-cefalorraquídeo patológico a quienes se les realizó FA-ME. RESULTADOS: Se incluyó a 32 niños, edad promedio: 48 meses. Fueron positivas 13 determinaciones de FA-ME: siete bacterias y seis virus. En dos MBA obtuvo desarrollo mediante CC. Con FA-ME se ajustó el tratamiento en dos MBA y se acortó el tratamiento intravenoso (IV). DISCUSIÓN: Nuestro trabajo permitió conocer la etiología de cinco MBA con cultivo negativo, de las cuales dos habían recibido antimicrobianos, administrar quimioprofilaxis a contactos epidemiológicos, acortar el tratamiento IV y suministrar menos dosis de aciclovir; en concordancia con la literatura médica. CONCLUSIONES: FA-ME permitió identificar la etiología en cinco MBA que no desarrollaron en CC, ajustar tratamientos empíricos inadecuados y acortar duración del tratamiento parenteral.

BACKGROUND: Bacterial meningitis and encephalitis are life-threatening infections, a delay in its treatment is associated with high mortality. In 2015, FDA approved the Multiplex PCR FilmArray™ meningitis/encephalitis syndromic panel (FA-MEP), and it is available in our hospital since 2019. AIM: To estimate the number of positive FA-MEP, to evaluate the correlation to conventional culture (CC) results and to describe if the FA-MEP technology allowed changes in the treatment. METHODS: Retrospective analysis of children with meningitis, encephalitis and meningoencephalitis and pathological cerebrospinal fluid analysis between 2019-2021, who were subject to FA-MEP testing at the Pedro Elizalde Children's Hospital. RESULTS: 32 children, mean age: 48 months. 11 patients had positive FA-ME tests: 7 bacterial, 6 viral. 2 patients correlated with CC. Based on the FAMEP results, treatment was adjusted in 2 bacterial meningitis and the duration of intravenous treatment was shortened. DISCUSSION: Our study allowed to establish the etiology of 5 culture negative bacterial meningitis, (2 had prior antibiotics), administer chemoprophylaxis to close contacts, and to administer fewer doses of acyclovir. CONCLUSIONS: The FA-MEP allowed us to identify 5 bacterial meningitis that tested negative by CC and early adjustment of inappropriate empirical antibiotics and to shorten the duration of parenteral treatments.

Características radiográficas de la neumonía adquirida en la comunidad en el adulto inmunocompetente hospitalizado según el agente causal / Radiographic characteristics of community-acquired pneumonia in the immunocompetent adult hospitalized according to the etiologic agent

Resumen En la práctica clínica, la radiografía de tórax permite confirmar el diagnóstico y la extensión de la neumonía adquirida en la comunidad (NAC). Objetivos: Examinar las características radiográficas de la NAC según el agente causal y el grado de concordancia interobservador (CI) en la descripción de los hallazgos radiográficos. Métodos: Se evaluaron las radiografías de tórax de 300 pacientes adultos inmunocompetentes hospitalizados por NAC, tres residentes de radiología consignaron el patrón de los infiltrados pulmonares, su localización anatómica y extensión, la presencia de derrame pleural y otros hallazgos radiográficos. Se realizaron cultivos de esputo, hemocultivos, pruebas serológicas y técnicas de biología molecular de hisopado nasofaríngeo para identificar los principales patógenos respiratorios. Resultados: Las manifestaciones clínicas y los hallazgos de la radiografía de tórax fueron similares en las neumonías causadas por diferentes patógenos respiratorios: bacterias clásicas, virus respiratorios y microorganismos atípicos. En las neumonías bacterianas predominó el patrón de relleno alveolar de distribución lobar, en las neumonías vírales y atípicas predominó el patrón intersticial o mixto alvéolo-intersticial con opacidades en vidrio esmerilado. La CI fue satisfactoria (kappa > 0,6) para determinar el patrón principal de los infiltrados pulmonares, su localización anatómica y la presencia de derrame pleural, su localización y extensión. La CI fue moderada (kappa 0,4-0,6) para definir la extensión de la neumonía y detectar signos radiológicos asociados a congestión pulmonar. Conclusión: Los hallazgos de la radiografía de tórax no permitieron identificar con precisión el agente causal de la neumonía, siendo útil en la caracterización de los infiltrados pulmonares y para detectar complicaciones como el derrame paraneumónico.

In a clinical setting the chest radiograph is the reference standard in establishing the diagnosis of community-acquired pneumonia (CAP). Objectives: This study aimed to assess interobserver reliability (IR) of radiographic findings and the relationship to different respiratory pathogens in CAP. Methods: Chest radiographs of 300 immunocompetent adult patients hospitalized with pneumonia, obtained from a database, were reviewed by three residents of radiology without specific clinical information. Main pattern of pulmonary infiltrates, topographic localization, extent of pneumonia, presence of pleural fluid, thickened bronchial walls, lymphadenopathy and air bronchogram were scored. Sputum and blood cultures, serological tests and nasopharyngeal swab for respiratory virus detection by molecular diagnostic techniques were performed to identify the causative pathogen. Results: Clinical manifestations and chest X-ray findings were similar in pneumonias caused by different respiratory pathogens: classic bacteria, respiratory viruses and atypical microorganisms. The alveolar pattern of lobar distribution predominated in bacterial pneumonia; meanwhile, interstitial or mixed alveolar-interstitial pattern with ground glass opacities predominated in viral and atypical pneumonias. IR was fair to good (kappa > 0.6) for determining the main pattern of infiltrates, anatomical location and the presence of pleural effusion, their anatomical location and extension. IR was moderate (kappa 0.4-0.6) for determining the extent of pneumonia and signs of congestive heart failure. Conclusion: Simple features such as main pattern description, anatomical location, identifying the involved lobes and pleural fluid recognition showed fair to excellent interobserver reliability. Chest radiographs was of limited value in predicting the causative pathogen but were of beneficial use to characterize pulmonary infiltrates and to detect complications such as parapneumonic effusion.

FilmArray Meningitis/Encephalitis (ME) panel in the diagnosis of bacterial meningitis

ABSTRACT The precise diagnosis of bacterial meningitis is essential. Cytological and biochemical examination of cerebrospinal fluid (CSF) are not specific. Conventional methods for bacterial meningitis lack sensitivity or take too long for a final result. Therefore, other methods for rapid and accurate diagnosis of central nervous system infections are required. FilmArray meningitis/encephalitis (ME) panel is a PCR multiplex for simultaneous and rapid identification of 14 pathogens, including 6 bacteria, 7 viruses, and Cryptococcus. We evaluated 436 CSF samples submitted to FilmArray ME Panel. Among them, 25 cases were positive for bacteria, being Streptococcus pneumonia the most frequent (48 %). Among positive cases for bacteria, 60 % were positive only with FilmArray. All the bacterial meningitis cases in which the only positive test was FilmArray had CSF findings suggestive of bacterial meningitis, including neutrophilic pleocytosis, increased CSF protein and lactate, and decreased CSF glucose. These findings suggest that FilmArray may increase the diagnostic sensitivity for bacterial meningitis.

Estudo epidemiológico das queratites infeciosas internadas num centro hospitalar terciário - revisão de 5 anos / Epidemiological study of infeccious keratitis in inpatients of a terciary hospital center - revision of 5 years

Resumo Objetivo: A queratite infeciosa é uma doença de incidência relativamente elevada e é responsável por um número importante de internamentos. Neste estudo pretende-se estudar diversas características epidemiológicas e clínicas associadas às queratites infeciosas de alto risco num hospital terciário em Portugal. Métodos: Realizou-se um estudo retrospetivo, onde foram incluídos todos os doentes internados por abcesso da córnea no Centro Hospitalar Universitário do Porto (CHUP), entre Abril de 2013 a Março de 2018. Caracterizou-se a população em relação aos fatores de risco, apresentação clínica, tempo de internamento, resultados de culturas, resistência antibiótica in vitro, tratamento efetuado e resultado funcional. Resultados: O estudo incluiu 105 doentes. Os principais fatores de risco foram antecedentes de cirurgia de córnea, uso de lentes de contacto e história recente de trauma ocular. 74,3% dos doentes tiveram cultura positiva com 87,9% a corresponderem a cultura bacteriana pura, sendo a Pseudomonas aeruginosa e o Streptococcus pneumoniae os agentes etiológicos mais frequentes. 27,9% das culturas positivas eram resistentes a 3 ou mais classes de antibióticos. Todos os doentes iniciaram tratamento com colírios fortificados. 29,5% dos doentes necessitaram de realizar transplante de córnea. Ao final de 6 meses de seguimento, apenas 20,9% apresentavam AV>20/40. Conclusão: Na maioria dos casos, a etiologia foi bacteriana. Observou-se um número considerável de bactérias multirresistentes. Apesar do tratamento ter permitido uma melhoria da visão na maioria dos casos, um número considerável de doentes ficou com sequelas visuais importantes.

Abstract Objective: Infectious keratitis is a pathology with a high incidence and is responsible for a large number of prolonged stay hospital admissions. The purpose was to analyze the epidemiological and clinical data associated with high risk microbial keratitis at a central hospital in Portugal. Methods: A retrospective study of all inpatients presenting with corneal abscess in Centro Hospitalar Universitário do Porto, from April 2013 to March 2018 was performed. Target population was characterized by risk factors, clinical features, length of stay, culture results, in vitro antibiotic resistance, treatment and outcome. Results: This study included 105 patients. The main risk factors were previous corneal surgery, contact lenses wear and recent history of ocular trauma. 74.3% of patients had a positive culture, 87.9% of these corresponding to a pure bacterial culture, with Pseudomonas aeruginosa and Streptococcus pneumoniae being the most common pathogens. 27.9% of positive cultures were resistant to 3 or more classes of antibiotics. All patients began treatment with fortified drops. 29.5% of patients required a corneal transplant. After 6 months of follow-up, only 20.9% presented a VA>20/40. Conclusion: Most cases were caused by bacteria. A considerable number of multi-resistant bacteria was identified. Despite most cases having improved after treatment, a large number of patients had a significant visual acuity sequelae.

Inmunofluorescencia indirecta versus reacción de polimerasa en cadena para el diagnóstico de virus respiratorios en niños ingresados en un hospital de la Región Metropolitana / Indirect immunofluorescence technique versus polymerase chain reaction for the diagnosis of respiratory viruses in children admitted to a hospital in the Metropolitan Region

Resumen Introducción: La temprana detección viral en infecciones respiratorias agudas (IRA) es esencial para establecer una terapia apropiada y prevenir el contagio intrahospitalario. Objetivo: Comparar la eficacia de la técnica de inmunofluorescencia indirecta (IFI) con la reacción de polimerasa en cadena (RPC) para identificar virus respiratorios en niños hospitalizados por IRA. Métodos: Se incluyeron 47 aspirados nasofaríngeos de niños ≤ 2 años con IRA. La IFI incluyó virus respiratorio sincicial (VRS), adenovirus, influenza A y B y parainfluenza. La RPC incluyó, además, la detección de metapneumovirus, enterovirus/rinovirus, bocavirus y coronavirus. Se estimó sensibilidad, especificidad, valor predictor positivo y negativo (VPP/VPN) y correlación kappa para VRS mediante IFI en comparación a la RPC. Resultados: La IFI detectó únicamente VRS (29; 61,7%). La RPC detectó diversos virus, entre ellos VRS en 26 casos (55,3%), seguido por bocavirus (29,8%), enterovirus/ rinovirus (21,3%), adenovirus (14,9%) y parainfluenza (4,3%) entre otros, con 35,5% de co-infección. La IFI presentó sensibilidad: 85,7%, especificidad: 73,6%, VPP: 82,7%, VPN: 77,7% y kappa: 0,5990 (IC 95%; 0,36360,8346) para VRS. Conclusión: La IFI presenta buena sensibilidad, pero moderada especificidad para VRS. Sin embargo, falla en la detección de otros virus respiratorios. La introducción de RPC permitiría mejorar el diagnóstico etiológico de las IRA de origen viral.

Background: Early viral detection in acute respiratory infections (ARI) is essential to establish appropriate therapy and prevent nosocomial transmission. Objective: To compare the efficacy of indirect immunofluorescence technique (IIF) with the polymerase chain reaction (PCR) to identify respiratory viruses in children hospitalized for ARI. Methods: 47 nasopharyngeal aspirates of children ≤ 2 years with ARI were included. IFI included respiratory syncytial virus (RSV), adenovirus, influenza A and B and parainfluenza. PCR also included the detection of metapneumovirus, enterovirus/rhinovirus, bocavirus and coronavirus. Sensitivity, specificity, positive and negative predictive value (VPP/NPV) and kappa correlation for RSV were estimated by IIF compared to PCR. Results: The IIF detected only RSV (29; 61.7%). PCR detected several viruses, including RSV in 26 cases (55.3%), followed by bocavirus (29.8%), rhinovirus/enterovirus (21.3%), adenovirus (14.9%) and parainfluenza (4,3%) among others, with 35.5% of coinfection. The IIF presented sensitivity: 85.7%, specificity: 73.6%, PPV: 82.7%, NPV: 77.7% and kappa: 0.5990 (95% CI, 0.3636-0.8346) for RSV. Conclusion: The IIF presents good sensitivity, but moderate specificity for RSV. However, IIF fails to detect other respiratory viruses. The introduction of PCR would improve the etiological diagnosis of ARI of viral origin.

Viral detection profile in children with severe acute respiratory infection

ABSTRACT Objectives: The role of viral co-detection in children with severe acute respiratory infection is not clear. We described the viral detection profile and its association with clinical characteristics in children admitted to the Pediatric Intensive Care Unit (PICU) during the 2009 influenza A(H1N1) pandemic. Method: Longitudinal observational retrospective study, with patients aged 0-18 years, admitted to 11 PICUs in Rio de Janeiro, with suspected H1N1 infection, from June to November, 2009. The results of respiratory samples which were sent to the Laboratory of Fiocruz/RJ and clinical data extracted from specific forms were analyzed. Results: Of 71 samples, 38% tested positive for H1N1 virus. Of the 63 samples tested for other viruses, 58 were positive: influenza H1N1 (43.1% of positive samples), rhinovirus/enterovirus (41.4%), respiratory syncytial vírus (12.1%), human metapneumovirus (12.1%), adenovirus (6.9%), and bocavirus (3.5%). Viral codetection occured in 22.4% of the cases. H1N1-positive patients were of a higher median age, had higher frequency of fever, cough and tachypnea, and decreased leukometry when compared to H1N1-negative patients. There was no difference in relation to severity outcomes (number of organic dysfunctions, use of mechanical ventilation or amines, hospital/PICU length of stay or death). Comparing the groups with mono-detection and co-dection of any virus, no difference was found regarding the association with any clinical variable. Conclusions: Other viruses can be implicated in SARI in children. The role of viral codetection has not yet been completely elucidated.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L )

Abstract Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p = 1.24e-12), Candidatus koribacter versatilis (p = 2.66e-10)] and fungi [(Fusarium oxysporum (p = 0.013), Talaromyces stipitatus (p = 0.219) and Pestalotiopsis fici (p = 0.443)] in terms of abundance in population and bacterial chemotaxis (p = 0.012), iron metabolism (p = 2.97e-5) with the reduction in abundance for pathogenicity islands (p = 7.30e-3), phages and prophages (p = 7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p = 2.34e-4), and degradation of heterocyclic aromatic compounds (p = 3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper.

Evaluation of skimmed milk flocculation method for virus recovery from tomatoes

Abstract This study aimed to evaluate the elution-concentration methodology based on skimmed milk flocculation from three varieties of tomatoes (Solanum lycopersicum L. [globe], Solanum lycopersicum var. cerasiforme [cherry] and hybrid cocktail [grape tomato]) for further monitoring of field samples. Spiking experiments were performed to determine the success rate and efficiency recovery of human norovirus (NoV) genogroup II, norovirus murine-1 (MNV-1) used as sample process control virus and human adenovirus (HAdV). Mean values of 18.8%, 2.8% and 44.0% were observed for NoV GII, MNV-1 and HAdV, respectively with differences according to the types of tomatoes, with lower efficiency for cherry tomatoes. Analysis of 90 samples, obtained at commercial establishments in the metropolitan region of Rio de Janeiro State, revealed 4.5% positivity for HAdV. Bacterial analysis was also performed with no detection of Salmonella spp., L. monocytogenes and fecal coliforms. Data demonstrated that the skimmed milk flocculation method is suitable for recovering HAdV from tomatoes and highlights the need for considering investigation in order to improve food safety.

Survey of pathogens in threatened wild red-tailed Amazon parrot (Amazona brasiliensis) nestlings in Rasa Island, Brazil

ABSTRACT The red-tailed Amazon parrot (Amazona brasiliensis) is a threatened species of psittacine bird that inhabit coastal regions of Brazil. In view of the threat of this species, the aim of this study was to perform a health evaluation in wild nestlings in Rasa Island, determining the prevalence of enterobacteria and infectious agents according to type of nest. Blood samples were collected from 64 birds and evaluated for antibodies of Chlamydia psittaci by commercial dot-blot ELISA. Cloacal and oropharyngeal swabs samples were collected from 23 birds from artificial wooden nests, 15 birds from PVC nests and 2 birds from natural nests for microbiological analysis. Swab samples were collected from 58 parrots for C. psittaci detection by PCR and from 50 nestlings for Avian Influenza, Newcastle Disease and West Nile viruses' detection analysis by real-time RT-PCR. Ten bacterial genera and 17 species were identified, and the most prevalent were Escherichia coli and Klebsiella oxytoca. There was no influence of the type of nest in the nestlings' microbiota. All samples tested by ELISA and PCR were negative. There is currently insufficient information available about the health of A. brasiliensis and data of this study provide a reference point for future evaluations and aid in conservation plans.

Prevalence of honey bee (Apis mellifera) viruses in temperate and subtropical regions from Argentina / Prevalencia de virus en abejas melíferas (Apis mellifera) en ambientes templados y subtropicales de Argentina

In Argentina, bee virus studies are still incipient, and there are no studies regarding the climatic effect. The aim of this study was to assess and compare the presence of honeybee viruses in different climatic regions from Argentina. A total of 385 colonies distributed in five Argentinean eco-regions were examined to evaluate the percentage of infestation with Varroa destructor and the presence of seven virus species (Deformed wing virus, DWV; Acute bee paralysis virus, ABPV; Chronic bee paralysis virus, CBPV; Black queen cell virus, BQCV; Kashmer bee virus, KBV; Israeli acute bee paralysis virus, IAPV; and Sacbrood bee virus, SBV) after honey yield. Two viruses, KBV and IAPV, were not detected. The other five viruses were found in different prevalences: DWV (35%), ABPV (21.5%), BQCV (8.0%), CBPV (2.2%), and SBV (1.1%). We found double and triple viral associations in approximately 25% of the sampled colonies. The mean V. destructor infestation in the colonies prior to the acaricide treatment was 7.12% ± 8.7%. The knowledge of the prevalence of these viruses in the region and their relation with the mite and other possible influencing factors is important for preventing colony losses. Further studies are necessary to identify the risk factors associated with virus presence and its relationship with other pathogens such as V. destructor.

En Argentina, los estudios sobre prevalencia de virus en abejas continúan siendo incipientes y no existen reportes acerca de cómo inciden sobre dicha prevalencia las variables climáticas. El objetivo de este estudio fue evaluar y comparar la presencia de virus en abejas melíferas en diferentes regiones agroecológicas de Argentina. A tal fin se evaluaron 385 colmenas distribuidas en 5 regiones agroecológicas de las provincias de Chaco y Santa Fe; en ellas se analizó el porcentaje de infestación con Varroa destructor (ácaro patógeno de abejas) y la presencia de 7 especies de virus (DWV, virus de las alas deformadas; ABPV, virus de la parálisis aguda de la abeja; CBPV, virus de la parálisis crónica de la abeja; BQCV, virus de celda negra de la reina; KBV, virus de la abeja de Cachemira; IAPV, virus israelí de la parálisis aguda y SBV, virus de la cría ensacada). luego de la cosecha de miel. Dos virus (KBV y IAPV) no fueron detectados. Las otras 5 especies de virus se encontraron con prevalencias variables: DWV (35%), ABPV (21,5%), BQCV (8%), CBPV (2,2%) y SBV (1,1%). Fue posible identificar la presencia de 3 y hasta 3 virus simultáneamente en el 25% de las colmenas evaluadas. El promedio de infestación por V. destructor en las colmenas luego de la cosecha de miel y antes del tratamiento con acaricidas fue de 7,12% (±8,7). Conocer la prevalencia de virus en las diferentes regiones agroecológicas y su relación con la presencia del ácaro V. destructor e identificar otros posibles factores que podrían influir en su presencia es relevante para definir estrategias que reduzcan la mortandad de colmenas. Es necesario realizar estudios adicionales para identificar los factores de riesgo asociados a la presencia de virus en las colmenas y su relación con otros patógenos, como V. destructor.

Diagnóstico de patógenos respiratorios mediante PCR en tiempo real: una realidad en el Hospital Roberto del Río / Diagnosis of respiratory pathogens using real-time PCR: a reality at the Roberto del Río Hospital

La técnica de la reacción de polimerasa en cadena (PCR) en tiempo real o PCR está disponible en el Hospital Roberto del Río desde el 2015. Esta técnica rápida y muy sensible, mejora los tiempos de respuesta y facilita la toma de decisiones clínicas. Sin embargo, es importante conocer los distintos aspectos del método para hacer una correcta interpretación clínica de un resultado de PCR.

Real time polymerase chain reaction (PCR) is a rapid and sensitive technique. It improves answer time for clinical decisions. It is important to know it well for a better clinical understanding.

Aislamientos virales en niños y adultos con infecciones respiratorias agudas / Viral isolations in children and adults with acute respiratory infections

Introducción: las infecciones respiratorias agudas constituyen un grupo de enfermedades que varían desde un catarro común hasta procesos broncopulmonares graves. Entre los agentes causales figuran los virus, los cuales se diseminan por las secreciones respiratorias. Objetivos: mostrar la positividad de aislamientos virales en niños y adultos, vivos o fallecidos, con infecciones respiratorias agudas. Métodos: se efectuó un estudio descriptivo y observacional de 364 pacientes de la provincia de Camagüey, ingresados con el diagnóstico de infecciones respiratorias agudas, desde enero de 2011 hasta diciembre de 2012. A cada enfermo se le llenó una encuesta epidemiológica y se le tomó muestra de exudado nasofaríngeo o biopsia del tejido pulmonar en el caso de los fallecidos. Estas se inocularon en medio de transporte y fueron remitidas a centros especializados para realizar el diagnóstico virológico. Resultados: del total de pacientes con positividad viral, 221 eran niños (30,3 %) y 143 adultos (36,3 %). Entre los virus predominantes figuraron: rinovirus, sincitial respiratorio de tipo A e influenza A (H1N1) pdm09. Conclusiones: más de la cuarta parte de los pacientes tuvieron virus respiratorios. La población infantil fue la más dañada, la de mayor letalidad y coinfecciones de rinovirus con otros virus respiratorios.

Introduction: the acute respiratory infections constitute a group of diseases which vary from a common cold to serious bronchopulmonary processes. Among the causal agents there are the viruses, which are disseminated by the respiratory secretions. Objectives: to show the positivity of viral isolations in children and adults, alive or dead, with acute respiratory infections. Methods: a descriptive and observational study of 364 patients in Camagüey province admitted with the diagnosis of acute respiratory infections was carried out from January, 2011 to December, 2012. An epidemiological survey was filled and samples of nasopharyngeal exudates were taken from each sick person, or lung tissue biopsy were obtained in cases of deads. These were inoculated in transport media and they were referred to specialized centers to carry out the virological diagnosis. Results: of the total of patients with viral positivity, 221 were children (30.3%) and 143 adults (36.3%). Among the predominant viruses there were: rhinovirus, respiratory syncytial type A and influenza A (H1N1) pdm09. Conclusions: more than the fourth part of patients had respiratory virus and the child population was the most affected, with higher lethality and rhinovirus coinfections with other respiratory viruses.

Diagnóstico laboratorial da dengue: situação atual e perspectivas / Dengue laboratory diagnosis: actual situation and perspectives

0 diagnóstico da infecção pelo vírus da dengue é baseado, em grande parte dos casos, apenas no exame clínico do paciente, já que somente alguns poucos grandes centros possuem laboratórios clinicos que disponibilizam testes diagnósticos para confirmar sintomas clinicos de infecção. Atualmente, o diagnóstico laboratorial da dengue pode ser feito por diferentes tipos de testes. Entre eles estao os métodos de pesquisa sorológica, de isolamento viral, de detecção de antigenos virais e do genoma viral. 0 desenvolvimento continuado de testes diagnósticos baratos, sensíveis, especificos e de fácil execucção, que sejam capazes de proporcionar diagnóstico precoce da infecção pelos virus da dengue, é ainda uma necessidade. Existem também outros obstáculos que nao são especificamente relacionados ao desenvolvimento tecnológico dos métodos diagnósticos. Por exemplo, a infra-estrutura dos laboratórios, o treinamento do pessoal técnico e a capacidade de pesquisa ainda são limitados em muitas partes do Brasil e do mundo, onde a dengue é endêmica. Laboratórios clinicos, principalmente os que atendem às regiões de maior incidência da dengue, devem se interar de todos os métodos diagnósticos disponíveis para a rotina atualmente e definir qual se adapta melhor às suas condições de trabalho e população atendida, com o intuito de salvarvidas.

The diagnosis of the infection caused by the dengue virus relies in most cases on the clinical examination of the patient, since only a few major centers have clinical laboratories providing diagnostic tests to confirm the clinical symptons of infection. Currently, routine laboratory diagnosis can be done by different kinds of testing. Among them the methods ofserological research, virus isolation, detection of viral antigens and of viral genome are included. The continued development of diagnostic tests that are cheap, sensitive, specific, easy to perform, and that are capable of giving early diagnosis of the dengue virus infection is still a need. There are also other obstacles not specifically related to the technological development ofdiagnostic methods. For instance, the laboratories' infrastructure, the workers training and the research capacity are still limited in many parts of Brazil and the world, where dengue is endemic. Clinical laboratories, specially those situated in regions with high incidence of dengue, should be aware of all the diagnostic methods available four routine nowadays, and choose the best one that fulfills their working conditions and populations served, in order to save lives.

Etiology of respiratory viral infections using rapid virus isolation methods at a tertiary care center in Riyadh, Saudi Arabia

Mixed cell line cultures were used for the first time in Saudi Arabia to accelerate virus isolation. This method was used for detection of respiratory viral infections in order to provide timely information to the physician for effective patient management. In this retrospective study we describe etiology and 'time to detection' of respiratory viral infections between November 2006 and October 2007 at King Abdulaziz Medical City [KAMC], a 1,000 bed tertiary care facility in Riyadh. Rapid testing algorithms allowed all Respiratory Syncytial Virus [RSV] isolates to be detected in one day, influenza isolates to be detected in two days, Parainfluenza isolates within 3 days, adenovirus in 2-5 days. Ninety two percent of RSV infections occurred in children one year and under. RSV infections were found to occur between November and February with a peak in January, Influenza and adenovirus outbreaks were found to occur in November and December. Parainfluenza occurred in two waves firstly in November and December followed by another peak in April. Rapid diagnosis of viral diseases can now be performed by most laboratories to determine which viruses are circulating in their communities and provide information on disease trends to aid control and prevention

Bio-aerosols in indoor environment: composition, health effects and analysis.

Bio-aerosols are airborne particles that are living (bacteria, viruses and fungi) or originate from living organisms. Their presence in air is the result of dispersal from a site of colonization or growth. The health effects of bio-aerosols including infectious diseases, acute toxic effects, allergies and cancer coupled with the threat of bioterrorism and SARS have led to increased awareness on the importance of bio-aerosols. The evaluation of bio-aerosols includes use of variety of methods for sampling depending on the concentration of microorganisms expected. There have been problems in developing standard sampling methods, in proving a causal relationship and in establishing threshold limit values for exposures due to the complexity of composition of bio-aerosols, variations in human response to their exposure and difficulties in recovering microorganisms. Currently bio-aerosol monitoring in hospitals is carried out for epidemiological investigation of nosocomial infectious diseases, research into airborne microorganism spread and control, monitoring biohazardous procedures and use as a quality control measure. In India there is little awareness regarding the quality of indoor air, mould contamination in indoor environments, potential source for transmission of nosocomial infections in health care facilities. There is an urgent need to undertake study of indoor air, to generate baseline data and explore the link to nosocomial infections. This article is a review on composition, sources, modes of transmission, health effects and sampling methods used for evaluation of bio-aerosols, and also suggests control measures to reduce the loads of bio-aerosols.

Total quality management in clinical virology laboratories.

The diagnostic laboratories in India are progressively promoting higher standards and are moving towards accreditation and international acceptance. Hence, the concept of "Quality" will need to be understood and implemented. Total quality management (TQM) in a laboratory is an integrated program involving all laboratory staff and management. TQM is a framework to operate and it is aiming for integration, consistency, increase in efficiency and a continuous drive for improvement. A well structured clinical virology service will include serology setup, cell culture facility and capacity for molecular diagnosis. The quality of results from the laboratory is significantly influenced by many pre-analytical and post-analytical factors which needed attention. The end goal of the TQM should be to provide the best care possible for the patient.

Etiología de la neumonía adquirida en la comunidad en adultos hospitalizados en Santiago, Chile: implicancias para las guías clínicas / Etiology of community acquired pneumonia requiring hospitalization in Chile: implications for the guidelines

Background: There are a few studies examining the etiology of community acquired pneumonia (CAP) in Chile. Aim: To evaluate the etiology of CAP in hospitalized adults. Method: We prospectively studied 130 patients (mean age +/- SD: 68 +/- 18 y.o.; overall hospital mortality: 6.2 percent), over a 16 month period. Microbiological evaluation included blood and sputum cultures for bacteria; serology for C. pneumoniae, C. psittaci and M. pneumoniae; urine antigen for L. pneumophila; and nasopharyngeal swab for respiratory viruses. Results: Etiology was identified from 64 (49 percent) patients (two or more pathogens in 6). The most frequent microorganisms were S. pneumoniae (34 percent), Parainfluenza types 1 to 3 (22 percent), Influenza A or B (14 percent ), C. pneumoniae (6 percent), M. pneumoniae (6 percent), H. influenzae (5 percent) and S. marcescens (5 percent). Twenty-five of 27 (93 percent) respiratory viruses were identified in autumn or winter. Pneumococcal pneumonia patients (19) compared to those infected with respiratory virus (23) were younger (59 +/- 18 versus 72 +/- 17 y.o.; p = 0.021) and had less comorbidities (47 versus 87 percent; p = 0.0001). No patients with bacteremia (13 of 121: 11 percent) died. Conclusions: S. pneumoniae remains the most important pathogen to cover by initial antibiotic therapy; the second most frequent etiological agents were respiratory viruses followed by "atypical pathogens". Recommendations for the management of patients infected with these two last categories of agents should be included in future national guidelines.

Fundamento: Hay escasos estudios que examinen la etiología de la neumonía adquirida en la comunidad (NAC) en población adulta chilena. Objetivo: Identificar la etiología de la NAC en adultos inmunocompetentes hospitalizados. Método: Estudiamos, prospectiva y consecutivamente durante 16 meses, a 130 pacientes (edad promedio +/ - DS: 68 +/ - 18 años; letalidad en el hospital: 6,2 por ciento). La evaluación microbiológica incluyó cultivo de expectoración y hemocultivos para bacterias; Financiamiento: Fondo de Investigación de la Sociedad Chilena de Enfermedades Respiratorias (2002) y fondo de la Dirección de Investigación de la Pontificia Universidad Católica de Chile (DIPUC 2003/10E). Serología para C. pneumoniae, C. psittaci, M. pneumoniae; antígeno urinario para L. pneumophila e hisopado nasofaríngeo para virus respiratorios. Resultados: Se identificó la etiología en 64 (49 por ciento) pacientes (dos o más patógenos en 6). Los principales microorganismos fueron: S. pneumoniae (34 por ciento), virus Parainfluenza 1 a 3 (22 por ciento), virus Influenza A o B (14 por ciento), C. pneumoniae (6 por ciento), M. pneumoniae (6 por ciento), H. influenzae (5 por ciento) y S. marcescens (5 por ciento). El 93 por ciento (25/27) de los virus respiratorios se identificaron en otoño-invierno. Los pacientes con neumonía neumocócica (19) comparados con aquéllos infectados por virus respiratorios (23) eran más jóvenes (59 + /- 18 versus 72 +/ - 17 años; p = 0,021) y tenían menos comorbilidades (47 por ciento versus 87 por ciento; p = 0,0001). Ninguno de los 13 (11 por ciento) pacientes con bacteremia falleció en el hospital. Conclusiones: S. pneumoniae sigue siendo el principal patógeno a cubrir por el tratamiento antibiótico empírico; los virus respiratorios y los agentes atípicos fueron los que siguieron en frecuencia. Las futuras guías clínicas nacionales deberían incluir recomendaciones para el manejo de los pacientes infectados por estos dos últimos grupos de...