Monitoring of airborne biological particles in outdoor atmosphere. Part 2: Metagenomics applied to urban environments

The air we breathe contains microscopic biological particles such as viruses, bacteria, fungi and pollen, some of them with relevant clinic importance. These organisms and/or their propagules have been traditionally studied by different disciplines and diverse methodologies like culture and microscopy. These techniques require time, expertise and also have some important biases. As a consequence, our knowledge on the total diversity and the relationships between the different biological entities present in the air is far from being complete. Currently, metagenomics and next-generation sequencing (NGS) may resolve this shortage of information and have been recently applied to metropolitan areas. Although the procedures and methods are not totally standardized yet, the first studies from urban air samples confirm the previous results obtained by culture and microscopy regarding abundance and variation of these biological particles. However, DNA-sequence analyses call into question some preceding ideas and also provide new interesting insights into diversity and their spatial distribution inside the cities. Here, we review the procedures, results and perspectives of the recent works that apply NGS to study the main biological particles present in the air of urban environments (AU)

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Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios

The first part of this review (‘Monitoring of airborne biological particles in outdoor atmosphere. Part 1: Importance, variability and ratios’) describes the current knowledge on the major biological particles present in the air regarding their global distribution, concentrations, ratios and influence of meteorological factors in an attempt to provide a framework for monitoring their biodiversity and variability in such a singular environment as the atmosphere. Viruses, bacteria, fungi, pollen and fragments thereof are the most abundant microscopic biological particles in the air outdoors. Some of them can cause allergy and severe diseases in humans, other animals and plants, with the subsequent economic impact. Despite the harsh conditions, they can be found from land and sea surfaces to beyond the troposphere and have been proposed to play a role also in weather conditions and climate change by acting as nucleation particles and inducing water vapour condensation. In regards to their global distribution, marine environments act mostly as a source for bacteria while continents additionally provide fungal and pollen elements. Within terrestrial environments, their abundances and diversity seem to be influenced by the land-use type (rural, urban, coastal) and their particularities. Temporal variability has been observed for all these organisms, mostly triggered by global changes in temperature, relative humidity, et cetera. Local fluctuations in meteorological factors may also result in pronounced changes in the airbiota. Although biological particles can be transported several hundreds of meters from the original source, and even intercontinentally, the time and final distance travelled are strongly influenced by factors such as wind speed and direction (AU)

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Evaluación de la contaminación microbiológica de la lechuga (lactuca sativa) en la cadena alimentaria, provincia de Quillacollo, Cochabamba, Bolivia 2015 / Evaluation of microbiological contamination of lettuce (Lactuca sativa) in the food chain, province of Quillacollo, Cochabamba, Bolivia 2015

Las enfermedades transmitidas por alimentos constituyen un problema de salud, diversos estudios demuestran la alta contaminación microbiológica de la lechuga en la cadena alimentaria. El objetivo de la presente investigación fue evaluar la contaminación microbio-lógica de la lechuga (Lactuca sativa) en la cadena alimentaria, en la provincia Quillacollo-Cochabamba-Bolivia. Muestras de lechugas fueron tomadas en los meses de abril y mayo, con el mismo de número de muestras, en tres puntos de la cadena alimentaria: parcelas de producción (localidad Combuyo), puestos de venta de lechuga y de comida de los Mercados 9 de diciembre y Central de Quillacollo. El procesamiento de las muestras fue realizado en los laboratorios de Microbiología de LABIMED, y Post Grado de Medicina Tropical de la Facultad de Medicina, UMSS. Los resultados demuestran la contaminación de las lechugas con bacterias Aerobias Mesófilas, colifor-mes totales y fecales en concentraciones superiores a los estándares permitidos en los tres puntos de la cadenas alimentaria evaluadas; identificándose Salmonella sp en una de las muestras de lechugas procesada de los puestos de venta de comida de los mercados. La contaminación parasitaria fue evidenciada en los puestos de venta solo en el mes de mayo en 83% (n=10) de las 12 muestras analizadas, detectándose quistes de Entamoeba coli y larvas de Strongyloides sp, contaminación relacionada con la utilización de abono de aves en el cultivo y la manipulación inadecuada de la lechuga en la cadena alimentaria. En conclusión podemos indicar que las lechugas presentan una importante contaminación microbiana en los tres puntos evaluados de la cadena alimentaria, por lo que constituye un riego para la salud pública.

Infectious diseases transmitted by food, are considered a public health issue, several studies shown the high microbiological contamination of the letucce in particular (Lactuca sativa). The aim of this study was to evaluate the contamination of letucce at Quillacollo Province of Cochabamba- Bolivia. The samples were taken between april and may, with the same number of samples at production plots (Combuyo location), and at selling places of vegetables and food (markets) such as "9 de diciembre” market and "Central Quillacollo” market. The samples were processed at LABIMED laboratories (microbiology, and Tropical Medicine Post grade of medicine Faculty of San Simón University). Results shows contamination of lettuce with Aerobic Mesophilic Bacterias, and total coliforms and fecal coliforms, in higher concentration than standard allowed, at any point of chain food that has been evaluate; Sallmonella sp was identify at selling points with 83% of the samples and only at the month of may (n=10 of 12 samples examined) also Entamoeba coli cysts and Strongyloides sp worms; the contamination was associate with bird fertilizer at crops and at inapropiate food management of the lettuce. Therefore we can conclude that lettuce's contamination is present at the three evaluated points of its chain, production selling points until consume, wich must be considered as a public health risk.

Molecular detection of hepatitis E virus in feces and slurry from swine farms, Rio Grande do Sul, Southern Brazil / Detecção molecular do vírus da hepatite E em fezes e chorume de propriedades suinícolas, Rio Grande do Sul, Sul do Brasil

Hepatitis E virus (HEV) is highly disseminated among swine herds worldwide. HEV is also a threat to public health, since particularly genotypes 3 and 4 may cause acute hepatitis in human beings. No previous studies were done on the occurrence of HEV in environmental samples in Rio Grande do Sul, Brazil. In the present study, reverse transcriptase-polymerase chain reaction (RT-PCR) was employed to detect the presence of HEV in swine feces and in effluents from slurry lagoons in farms located in the municipality of Teutônia, inside the area of swine husbandry in the state. Pooled fecal samples from the floor of pig barns from 9 wean-to-finish farms and liquid manure samples were collected from the slurry lagoons from 8 of these farms. From the pooled fecal samples, 8/9 were positive for the HEV ORF1 gene by RT-PCR; all the slurry lagoon samples were positive for HEV RNA (100%). The identity of the HEV ORF1 amplicons was confirmed by sequencing belonging to HEV genotype 3, which was previously shown to be circulating in South America.

O vírus da hepatite E (HEV) é altamente disseminado entre rebanhos suínos no mundo todo. O HEV é também uma ameaça à saúde pública, já que os genótipos 3 e 4 podem causar hepatite aguda em seres humanos. Não há estudos anteriores sobre a ocorrência de HEV em amostras ambientais no Rio Grande do Sul. No presente estudo, empregou-se transcrição reversa e reação em cadeia da polimerase (RT-PCR) para detectar a presença de HEV em fezes de suínos e efluentes de lagoas de chorume em fazendas localizadas no município de Teutônia, representativo da região de maior produção de suínos no estado. Pools de amostras fecais foram coletadas a partir do chão de galpões de suínos provenientes de 9 propriedades de terminação; outra amostra de esterco líquido foi coletada das lagoas de chorume de 8 dessas fazendas. A partir das amostras fecais reunidas, 8/9 foram positivas para o gene ORF1 de HEV por PCR convencional; todas as amostras de lagoas de chorume foram positivas para RNA de HEV (100%). A identificação dos produtos de amplificação de HEV ORF1 foi confirmada por sequenciamento pertencente ao HEV genótipo 3, o qual foi previamente detectado na América do Sul.

Antibiotic treatments in zootechnology and effects induced on the food chain of domestic species and, comparatively, the human specie / Tratamientos antibióticos en zootecnología y los efectos inducidos sobre la cadena alimenticia de las especies domésticas y comparativamente sobre la especie humana

Introduction: Antibiotics are largely employed in zootechnical feed to preserve human and animal species from zoonosis due pathogenic infective agents. Aim: Due to the increasing number of pathologies related to diet (e.g. food intolerances), we investigated the toxic effects induced by antibiotics residues, oxytetracyclines, present within the industrial food on both human and domestic animals’ health. Zootechnical products obtained from animal bones industrial transformation, and their related toxic effects have been pointed out. Methods: Comparative analysis of published papers has been conducted from 1910 up to 2014. Results: The comparative analysis revealed the presence of oxytetracycline residues and other antibiotics in food intended for human and animal consumption, which resulted in multisystemic toxic effects. Discussion: Either metabolism and possible measures to prevent exposure to oxytetracycline have also been examined, however a more detailed understanding of biochemical effects of such class of antibiotics is required (AU)

Introducción: los antibióticos se emplean ampliamente en la alimentación zootécnica para proteger a las especies humana y animal de las zoonosis por agentes infecciosos patogénicos. Objetivo: dado el creciente número de enfermedades relacionadas con la dieta (p. ej., intolerancias alimentarias), investigamos los efectos tóxicos inducidos por los residuos antibióticos, oxitetraciclinas, presentes en los alimentos industriales tanto sobre la salud humana como animal. Se destacan los productos zootécnicos obtenidos de la transformación industrial de los huesos animales y sus efectos tóxicos relacionados. Métodos: análisis comparativo de las publicaciones realizadas desde 1910 hasta 2014. Resultados: el análisis comparativo reveló la presencia de residuos de oxitetraciclina y otros antibióticos en alimentos pensados para el consumo humano y animal, lo que produjo efectos tóxicos multisistémicos. Discusión: el metabolismo y las posibles medidas para evitar la exposición a la oxitetraciclina también se han examinado, sin embargo, se precisa de un conocimiento más detallado de los efectos bioquímicos de tal clase de antibióticos (AU)

Bugs, hosts and ICU environment: Countering pan-resistance in nosocomial microbiota and treating bacterial infections in the critical care setting / Gérmenes, huéspedes y el entorno de la Unidad de Cuidados Intensivos: contrarrestando la panresistencia en la microbiota nosocomial para tratar las infecciones bacterianas en cuidados críticos

ICUs are areas where resistance problems are the largest, and these constitute a major problem for the intensivist's clinical practice. Main resistance phenotypes among nosocomial microbiota are (I) vancomycin-resistance/heteroresistance and tolerance in grampositives (MRSA, enterococci) and (II) efflux pumps/enzymatic resistance mechanisms (ESBLs, AmpC, metallo-betalactamases) in gramnegatives. These phenotypes are found at different rates in pathogens causing respiratory (nosocomial pneumonia/ventilator-associated pneumonia), bloodstream (primary bacteremia/catheter-associated bacteremia), urinary, intraabdominal and surgical wound infections and endocarditis in the ICU. New antibiotics are available to overcome non-susceptibility in grampositives; however, accumulation of resistance traits in gramnegatives has led to multidrug resistance, a worrisome problem nowadays. This article reviews microorganism/infection risk factors for multidrug resistance, suggesting adequate empirical treatments. Drugs, patient and environmental factors all play a role in the decision to prescribe/recommend antibiotic regimens in the specific ICU patient, implying that intensivists should be familiar with available drugs, environmental epidemiology and patient factors (AU)

UCIs son las áreas donde los problemas de resistencia son los más grandes, y éstos constituyen un problema importante para la práctica clínica de los intensivistas . Fenotipos de resistencia principales entre la microbiota nosocomial son ( I ) vancomycin-resistance/heteroresistance y tolerancia en grampositives ( MRSA, enterococos ) y ( II ) las bombas de flujo / mecanismos enzimáticos de resistencia ( BLEE , AmpC , metalo- betalactamasas ) en gramnegativos . Estos fenotipos se encuentran en diferentes tipos de patógenos causantes de las vías respiratorias (neumonía / pulmonía nosocomial asociada a ventilación mecánica), el torrente sanguíneo ( bacteremia primaria / bacteriemia asociada a catéter ) , urinario, infecciones de las heridas quirúrgicas intraabdominales y endocarditis y en la UCI. Nuevos antibióticos están disponibles para superar la no - susceptibilidad in grampositives, sin embargo, la acumulación de rasgos de resistencia en gramnegativos ha dado lugar a la resistencia a múltiples fármacos, un problema preocupante en la actualidad. Este artículo revisa los factores de riesgo microorganismo / infección de la resistencia a múltiples fármacos, lo que sugiere tratamientos empíricos adecuados. Las drogas, el paciente y los factores ambientales juegan un papel en la decisión de prescribir / recomendar regímenes de antibióticos en el paciente en la UCI específica, lo que implica que los intensivistas deben familiarizarse con los fármacos disponibles, epidemiología ambiental y los factores del paciente (AU)

Assays for the in vitro establishment of Swietenia macrophylla and Cedrela odorata / Ensayos para el establecimiento in vitro de Swietenia macrophyllay Cedrela odorata

Recalcitrance and contamination in Mahogany (Swietenia macrophylla King) and Spanish cedar (Cedrela odorata L.) stem tissues are the main causes of its ineffective in vitro propagation. The objectives of this research were: a) to evaluate sodium hypochlorite (NaOCl) and plant preservative mixture (PPM®) as surface disinfectants and/or added to the culture medium for the in vitro establishment of nodal explants taken from 10-year-old Mahogany and Spanish cedar plants, and b) to evaluate the in vitro response of such explants treated with N6-benzylaminopurine (BAP) (0, 2.2, 4.4, 8.8, 17.7 μM), silver nitrate (AgNO3) (0, 3 mg l-1), activated charcoal (0, 1 g l-1) and vented caps. All the experiments were arranged in a completely randomized design. The NaOCl at 15%, for 20 min, as a surface sterilization or PPM® at 2 ml l-1 into the culture medium, were the best treatments to reduce contamination for both species. For Mahogany explants, BAP at 17.7 μM resulted in higher percentages of bud breaks than Spanish cedar (64% and 25%, respectively). Leaves on elongated shoots dropped off by 20 days after starting the explants in culture and neither the activated charcoal nor the AgNO3 alone or combined prevented leaf abscission. The AgNO3 decreased contamination, but also increased leaf abscission. Bud breaks was two-fold higher for nodal explants established in vessels with vented caps than with normal caps. Mahogany nodal explants were easier to surface sterilize and more buds broke from BAP treated explants than Spanish cedar treated explants in the in vitro establishment.

La contaminación y la recalcitrancia de tejidos de tallo de Caoba (Swietenia macrophylla King) y Cedro español (Cedrela odorata L.) son las causas principales de su inefectiva micro-propagación. Los objetivos de la investigación fueron: a) evaluar el hipoclorito de sodio (NaClO) y una mezcal preservadora de plantas (PPM®) como desinfectantes superficiales y/o agregados al medio de cultivo para el establecimiento in vitro de explantes nodales de Caoba y Cedro español de 10 años de edad; b) evaluar la respuesta in vitro de tales explantes tratados con N6-benzylaminopurine (BAP) (0, 2.2, 4.4, 8.8, 17.7 μM), nitrato de plata (AgNO3) (0, 3 mg l-1), carbón activado (0, 1 g l-1) y tapas porosas. Los experimentos fueron establecidos bajo un diseño completamente al azar. La contaminación se redujo en ambas especies con NaOCl al 15% durante 20 min como desinfección superficial o con PPM® (2 ml l-1) agregado al medio de cultivo. El mayor porcentaje de brotación de explantes se obtuvo con BAP a 17.7 μM en caoba (64%) comparado con cedro (25%). Los brotes se defoliaron a los 20 días de cultivo y ni el carbón activado ni el AgNO3, solos o combinados evitaron la defoliación. El AgNO3 disminuyó la contaminación, pero incrementó la defoliación. La brotación fue dos veces mayor en los explantes nodales establecidos en recipientes con tapas porosas que cuando se utilizaron tapas normales. Los explantes nodales de Caoba respondieron mejor a la desinfección superficial y a los tratamientos de BAP comparados con los de Cedro español en el establecimiento in vitro.

Indicadores de contaminação biológica: uma análise das areias de praia e brinquedos de áreas recreativas da zona sul do Rio de Janeiro / Biological indicators of contamination: an analysis of the sand beach toys and recreational areas in the south zone of Rio de Janeiro

Areia e brinquedos de praias e praças da Zona Sul da cidade do Rio de Janeiro foram analisados, constatando-se a sua contaminação com material fecal humano e animal. O número de coliformes fecais esteve 2,3 a 240 vezes acima do permitido (até 800/100g) e o de fungos 2,5 a cinco vezes (2.000/100g). Também foram encontrados larvas e ovos de helmintos e cistos de protozoários de origem humana e animal. A mesma contaminação, embora em menor nível, foi detectada nos brinquedos. Cabe ao Poder Público o monitoramento e a manutenção da qualidade da areia das áreas de lazer do município, o que, efetivamente, não é feito. Esta opção de lazer para residentes e turistas é feita, baseada na balneabilidade atestada pelo monitoramento da água. Porém, o nível e os tipos de contaminantes biológicos encontrados nas areias mostram o risco potencial à saúde do usuário.

Samples of sand and toys of beaches and squares of the South Zone of Rio de Janeiro City were submitted to microbiological analysis. Both showed contamination with human and animal fecal material. The fecal coliforms were 2.3 to 240 times above the permitted standard (800 to 100g) and fungi were 2.5 to 5 higher (2,000 to 100g). Larvae and eggs of helminthes and cysts of protozoa of man and animal origin were also found. The same contamination, although at lower levels, was found in toys. The Government must monitor and maintain the quality of the sand of recreational areas of the city but it is not done. The choice of seashore leisure activities for residents and tourists is made solely based on attested by the bathing water monitoring. However, the level and types of biological contaminants found in the sands show the potential risk for the health of users.

Contaminación de las puntas de papel usando cuatro protocolos diferentes de manejo / Paper point contamination using four different management protocols

El tratamiento endodóntico debe garantizar la reducción o eliminación de los microorganismos que ocasionan patología pulpar. Las puntas de papel son útiles para secar el conducto antes de la obturación. Objetivo: identificar microorganismos presentes en las puntas de papel y determinar si se contaminan durante su manipulación con bacterias del ambiente o por contaminación cruzada, según cuatro protocolos diferentes de manejo. Materiales y métodos: se entregaron 6 cajas nuevas y selladas de puntas de papel Hygenic(R) a cuatro IPS para realiar el protocolo de manejo habitual. Se analizaron 26 puntas incubadas en caldo tripticasa soya, y siembra en agar tripticasa soya en presencia de turbidez, a 37º C de 24-28 horas. Las puntas se distribuyeron de la siguiente manera: control positivo: una punta de papel introducida en conducto con diagnóstico de necrosis pulpar. Control negativo: una punta de papel de caja sin destapar, manipulada en el laboratorio bajo condiciones estériles. Protocolos 1, 2, 3 y 4: seis para cada protocolo (24) se analizaron en el laboratorio. Resultados: según los diferentes protocolos propuestos para este trabajo, se encontró que en el protocolo 1 hubo contaminación en 2 cajas de puntas, se detectó presencia de S. aureus y Epidermidis. En protocolos 2, 3 y 4 no hubo presencia de microorganismos. Conclusiones: la contaminación que sufren las puntas de papel es mínima; no hubo diferencia significativa según los 4 protocolos de manejo usados en este trabajo.