Anaerobiosis, a neglected factor in phage-bacteria interactions.

IMPORTANCE: Many parameters affect phage-bacteria interaction. Some of these parameters depend on the environment in which the bacteria are present. Anaerobiosis effect on phage infection in facultative anaerobic bacteria has not yet been studied. The absence of oxygen triggers metabolic changes in facultative bacteria and this affects phage infection and viral life cycle. Understanding how an anaerobic environment can alter the behavior of phages during infection is relevant for the phage therapy success.

Prediction of SARS-CoV-2 infection with a Symptoms-Based model to aid public health decision making in Latin America and other low and middle income settings.

Symptoms-based models for predicting SARS-CoV-2 infection may improve clinical decision-making and be an alternative to resource allocation in under-resourced settings. In this study we aimed to test a model based on symptoms to predict a positive test result for SARS-CoV-2 infection during the COVID-19 pandemic using logistic regression and a machine-learning approach, in Bogotá, Colombia. Participants from the CoVIDA project were included. A logistic regression using the model was chosen based on biological plausibility and the Akaike Information criterion. Also, we performed an analysis using machine learning with random forest, support vector machine, and extreme gradient boosting. The study included 58,577 participants with a positivity rate of 5.7%. The logistic regression showed that anosmia (aOR = 7.76, 95% CI [6.19, 9.73]), fever (aOR = 4.29, 95% CI [3.07, 6.02]), headache (aOR = 3.29, 95% CI [1.78, 6.07]), dry cough (aOR = 2.96, 95% CI [2.44, 3.58]), and fatigue (aOR = 1.93, 95% CI [1.57, 2.93]) were independently associated with SARS-CoV-2 infection. Our final model had an area under the curve of 0.73. The symptoms-based model correctly identified over 85% of participants. This model can be used to prioritize resource allocation related to COVID-19 diagnosis, to decide on early isolation, and contact-tracing strategies in individuals with a high probability of infection before receiving a confirmatory test result. This strategy has public health and clinical decision-making significance in low- and middle-income settings like Latin America.

SARS-CoV-2 Drive/Walk-Thru screening centers in Colombia: The CoVIDA Project / Centros de tamizaje masivo para SARS COV-2 en Colombia: Proyecto CoVIDA

Abstract Objective: The CoVIDA project is a public-private collaboration led by Universidad de los Andes that contributed to the SARS-CoV-2 epidemiological surveillance in Bogotá and nearby municipalities. We aimed to describe the development and performance of the Drive/Walk-through free RT- PCR for SARS-CoV-2 testing strategy implemented by CoVIDA. Material and method: We performed a descriptive analysis of the characteristics and performance of the CoVIDA Drive/Walk-through testing centers. The model and the process indicators to assess the model's performance were based on international experiences and scientific literature. Two screening centers were imple mented in shopping centers in the north and south of Bogotá. We reported the number of tests taken, the number of positive tests, and the number of participants that used the model by the type of occupations. Results: In total, 36,689 nasopharyngeal RT-PCR tests for SARS-CoV-2 were performed with a 5.75% cumulative positivity. Process indicators showed an excellent performance and an important contribution in reducing barriers to access to testing. Conclusions: the CoVIDA Drive/Walk-through testing centers supported the epidemiological surveillance in asymptomatic or mild-symptomatic population in Bo gotá. Low and middle-income countries can use this model as a cost-effective and innovative solution strategy to intensify testing and help mitigate the pandemic.

Resumen Objetivo: El proyecto CoVIDA es una colaboración público-privada liderada por la Universidad de los Andes que contribuyó a la vigilancia epidemiológica del SARS-CoV-2 en Bogotá y municipios cercanos. Nuestro objetivo fue describir el desarrollo y rendimiento de la estrategia de tamizaje gratuito con RT-PCR mediante un modelo Drive/Walk through para SARS-CoV-2 implementado por CoVIDA. Materiales y métodos: Realizamos un análisis descriptivo de las características y desempeño de los centros de tamizaje Drive/Walk through de CoVIDA. El modelo y los indicadores de proceso para evaluar el desempeño del modelo se basaron en experiencias internacionales y la literatura científica. Se implementaron dos cen tros de tamizaje en centros comerciales del norte y sur de Bogotá. Se reportó la cantidad de pruebas tomadas, pruebas positivas y de participantes que utilizaron el modelo de acuerdo con el tipo de ocupaciones. Resultados : En total, se realizaron 36,689 pruebas RT-PCR nasofaríngeas para SARS-CoV-2 con una positividad acumulada del 5,75%. Los indicadores de proceso mostraron un excelente desempeño y una contribución importante en la reducción de las barreras de acceso a las pruebas. Conclusiones: los centros de tamizaje con modelo Drive/Walk through de CoVIDA apoyaron la vigilancia epidemiológica en población asintomática o con síntomas leves en Bogotá. Los países de ingresos bajos y medianos pueden utilizar este modelo como una estrategia innovadora y rentable para aumentar la realización de las pruebas y ayudar a mitigar la pandemia.

The environmental occurrence of Pseudomonas aeruginosa.

Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.

Economic evaluation of the development of a phage therapy product for the control of Salmonella in poultry.

Poultry products are one of the major transmission media of Salmonella enteritidis to humans. A promising alternative to reduce the load of Salmonella in poultry are bacteriophages. Elsewhere, a mixture of six bacteriophages has been used successfully, but large-scale production would be necessary to supply potential poultry market and costs analyses have not been calculated yet. For this, a powerful tool to predict production costs is bioprocess modeling coupled with economic analyses. This work aims to model the scaled-up production of a six bacteriophages mixture based on a laboratory/pilot-scale production using Biosolve Process. For the model construction, a combination of experimental and reported data was applied, in which different production alternatives and the range of 1-100% of the Colombian poultry market (at broiler's farm and slaughterhouse) were analyzed. Results indicate that the best cost-effective process configuration/scale is to use one bioreactor (156 L) for the six bacteriophages, then a 0.45 µm filtration for removal of biomass, and a 0.22 µm filtration for sterility; this to supply the 35% of the market size for broiler farms (equivalent to 210 million chickens). This configuration gives a production cost per chicken of US$ 0.02. Additionally, a sensitivity analysis and a theoretical contrast for understanding the impact that titer and recovery have on production scale determined that titer affects the most the cost and requires optimization. The present works serves as a first, and required, approach for the development of phage therapy products that are alternatives to present-day pathogens control strategies.

Behavioral responses of Rhodnius prolixus to volatile organic compounds released in vitro by bacteria isolated from human facial skin.

BACKGROUND: Previous studies have demonstrated the role of volatile organic compounds (VOCs) produced by skin microbiota in the attraction of mosquitoes to humans. Recently, behavioral experiments confirmed the importance of VOCs released by skin microbiota in the attraction of Rhodnius prolixus (Hemiptera: Triatominae), a vector of Chagas disease. METHODS/FINDINGS: In this study, we screened for VOCs released in vitro by bacteria isolated from human facial skin that were able to elicit behavioral responses in R. prolixus. The VOCs released in vitro by eight bacterial species during two growth phases were tested with adult Rhodnius prolixus insects using a dual-choice "T"-shaped olfactometer. In addition, the VOCs released by the bacteria were analyzed with headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS). The VOCs produced by Staphylococcus capitis 11C, Staphylococcus warneri and Staphylococcus epidermidis 1 were attractive to R. prolixus, while the VOCs released by Citrobacter koseri 6P, Brevibacterium epidermidis and Micrococcus luteus 23 were non-attractive. CONCLUSIONS: The results shown here indicate that VOCs released by bacteria isolated from human facial skin have a potential for biotechnological uses as a strategy to prevent the vectorial transmission of Chagas disease mediated by Rhodnius prolixus.

Captivity Shapes the Gut Microbiota of Andean Bears: Insights into Health Surveillance.

The Andean bear is an endemic species of the tropical Andes who has an almost exclusively plant-based diet. Since herbivorous mammals do not carry enzymes for fiber degradation, the establishment of symbiosis with cellulolytic microorganisms in their gastrointestinal (GI) tract is necessary to help them fulfill their nutritional needs. Furthermore, as described for other mammals, a stable, diverse, and balanced gut microbial composition is an indicator of a healthy status of the host; under disturbances this balance can be lost, leading to potential diseases of the host. The goal of this study was to describe the gut microbiota of wild and captive Andean bears and determine how habitat status influences the composition and diversity of the gut symbiotic community. Fecal samples from wild (n = 28) and captive (n = 8) Andean bears were collected in "Reserva Pantano de Martos" and "Fundación Bioandina", Colombia. Composition and diversity analyses were performed using amplicons from the V4 region of the 16S rDNA gene sequenced using the Ion PGM platform. PICRUSt algorithm was applied to predict the gene content of the gut microbiome of wild and captive Andean bears. A total of 5,411 and 838 OTUs were identified for wild and captive bears, respectively. Captive bears contained a lower number of bacterial phyla (n = 7) compared to wild individuals (n = 9). Proteobacteria (59.03%) and Firmicutes (14.03%) were the phyla that contributed the most to differences between wild and captive bears (overall dissimilarity = 87.72%). At family level, Enterobacteriaceae drove the main differences between the two groups (13.7%). PICRUSt metagenomics predictions suggested a similar pattern of relative abundance of gene families associated with the metabolism of carbohydrates across samples in wild individuals, despite the taxonomic differences of their gut microbiota. Captivity alters the availability and diversity of food resources, which likely reduces microbiota richness and diversity compared to wild individuals. Further considerations should be taken into account for nutritional schemes improving ex-situ conservation and its potential as a surveillance tool of endangered populations of wild Andean bears.

Fagoterapia, alternativa para el control de las infecciones bacterianas. Perspectivas en Colombia / Phage-therapy, an alternative to control bacterial infections. Perspectives in Colombia / Fagoterapia, alternativa para o controle das infeccóes bacterianas. Perspectivas na Colombia

La capacidad de las bacterias para adquirir resistencia a agentes antimicrobianos ha reducido el número de antibióticos efectivos para combatir infecciones bacterianas. De otro lado, existen bacterias contaminantes de alimentos, que no pueden controlarse con antibióticos por tratarse de productos de consumo humano, lo que se traduce en pérdidas económicas y riesgos para la salud. Si a esto se suma la falta de desarrollo de nuevos antibióticos, es evidente que se requiere desarrollar otras estrategias para el tratamiento y control de las bacterias. Los bacteriófagos (fagos), virus que infectan bacterias, se proponen como uno de estos tratamientos alternativos en una estrategia conocida como fagoterapia. Diversos estudios han evaluado y demostrado su efectividad contra bacterias patógenas y ya existen empresas privadas que desarrollan productos basados en cocteles de fagos para controlar algunas infecciones bacterianas. En Colombia no existen antecedentes del uso de fagos pero estos representan una gran oportunidad para el aprovechamiento de la diversidad de la microbiota nativa. En este artículo presentamos las perspectivas de uso de la fagoterapia en Colombia como tratamiento de infecciones bacterianas.

Bacteria easily acquire resistance to antimicrobial agents and this reduces the number of effective antibiotics available to treat bacterial infections. Food contamination by bacteria also generates important economic losses and health risks. Products for human consumption must be free of antibiotics used in clinical treatments, and the control of bacteria with antimicrobials is strictly regulated; however, there is a lack of development of new antibiotics. As a result, the development of new antimicrobial strategies is vital. Viruses that infect bacteria called bacteriophages (phages) have been proposed as an alternative treatment in an approach known as phage-therapy. Several studies have evaluated and demonstrated their effectiveness against pathogenic bacteria; currently, there are private companies dedicated to the development of new products based on phage cocktails, to control some bacterial infections. In Colombia, there is no previous information about the use of phages, but phage-therapy represents a great opportunity to use the diversity of the native microbiota. In this review, we present the perspectives for phage-therapy in Colombia as a treatment against bacterial infections.

A capacidade das bactérias para adquirir resistencia a agentes antimicrobianos tem levado a que o número de antibióticos efetivos para combater infectes bacterianas em humanos seja cada vez menor. Nos alimentos se reportam bactérias causantes de contaminares que representam grandes perdas económicas e riscos para a saúde; estas bactérias nao podem ser tratadas com antibióticos por tratar-se de produtos para consumo humano. Tendo em conta a situado, e a falta de novos antibióticos, precisa-se do desenvolvimento de novas estratégias para o tratamento e controle das bactérias. Os bacteriófagos (fagos), vírus que infectam bactérias, propoem-se como um destes tratamentos alternativos, numa estratégia conhecida como fagoterapia. Diversos estudos tem demostrada a efetividade contra bactérias patógenas e já existem empresas privadas desenvolvendo produtos baseados em coqueteis de fagos, para controlar algumas infectes bacterianas. Na Colombia nao existe antecedente do uso de fagos, mas este apresenta uma grande oportunidade para o aproveitamento da diversidade da microbiota nativa. Nesta revisao apresentamos as perspectivas para a fagoterapia na Colombia como tratamento alternativo contra infectes bacterianas.

Quorum quenching analysis in Pseudomonas aeruginosa and Escherichia coli: network topology and inhibition mechanism effect on the optimized inhibitor dose.

The discovery of quorum sensing as a mechanism for regulating specific phenotypes in bacteria based on population density has conveyed attention to find molecules capable of interfering quorum sensing networks (QSN) in a process coined quorum quenching. Here, we examined the dynamics of Escherichia coli AI-2 and Pseudomonas aeruginosa QSN exposed to signal degraders or competitors for binding transcriptional regulators. Stability analysis was performed for E. coli and P. aeruginosa finding no multistability in E. coli. However, our model allowed to discern that quenchers influence P. aeruginosa QSN multistability by reducing the interval of the amount of molecules of the extracellular signal that originate several steady states. We proposed a simulated annealing algorithm to optimize the quencher dose based on stochastic kinetics. E. coli QSN requires around 640 while P. aeruginosa QSN needs 253 quencher molecules per microorganism. This dose was found to be negatively influenced by the quencher-signal affinity.

Comparison of virulence between clinical and environmental Pseudomonas aeruginosa isolates / Comparación de la virulencia entre aislados clínicos y ambientales de Pseudomonas aeruginosa

New strains of Pseudomonas aeruginosa were isolated from clinical and environmental settings in order to characterize the virulence properties of this opportunistic pathogen. P. aeruginosa was frequently recovered from oil-contaminated samples but not from non-oil-contaminated soils. The virulence of five environmental and five clinical strains of P. aeruginosa was tested using two different models, Drosophila melanogaster and Lactuca sativa var. capitata L. There was no difference in the virulence between the two groups of isolates in either of the models. Since environmental P. aeruginosa strains are used for bioaugmentation in bioremediation programs, the results presented here should be taken into account in the future design of degradative consortia and/or in establishing containment measures (AU)

Para caracterizar la virulencia del patógeno oportunista Pseudomonas aeruginosa, se aislaron nuevas cepas a partir de muestras clínicas y ambientales. P. aeruginosa se recuperó con una elevada frecuencia a partir de muestras contaminadas con petróleo, mientras que la frecuencia de recuperación a partir de muestras no contaminadas fue muy baja. La virulencia de cinco cepas ambientales y cinco cepas clínicas de P. aeruginosa se evaluó usando dos modelos diferentes, Drosophila melanogaster y Lactucasativa var. capitata L. No se encontraron diferencias en la virulencia de los dos grupos de aislados con ninguno de los modelos. Dado que en procesos de biorremediación y bioaumento se usan cepas ambientales de P. aeruginosa, estos resultados deberían tenerse en cuenta en el futuro diseño de consorcios degradadores y para establecer las medidas de seguridad necesarias para su utilización (AU)

Comparison of virulence between clinical and environmental Pseudomonas aeruginosa isolates.

New strains of Pseudomonas aeruginosa were isolated from clinical and environmental settings in order to characterize the virulence properties of this opportunistic pathogen. P. aeruginosa was frequently recovered from oil-contaminated samples but not from non-oil-contaminated soils. The virulence of five environmental and five clinical strains of P. aeruginosa was tested using two different models, Drosophila melanogaster and Lactuca sativa var. capitata L. There was no difference in the virulence between the two groups of isolates in either of the models. Since environmental P. aeruginosa strains are used for bioaugmentation in bioremediation programs, the results presented here should be taken into account in the future design of degradative consortia and/or in establishing containment measures.