Antimicrobial Resistance Determinants in Genomes and Plasmids from Acinetobacter baumannii Clinical Isolates

Acinetobacter baumannii is a Gram-negative coccoid rod species, clinically relevant as a human pathogen, included in the ESKAPE group. Carbapenem-resistant A. baumannii (CRAB) areconsidered by the Worl Health Organization (WHO) as a critical priority pathogen for the research and development of new antibiotics. Some of the most relevant features of this pathogen are its intrinsic multidrug resistance and its ability to acquire rapid and effective new resistant determinants against last-resort clinical antibiotics, mostly from other ESKAPE species. The presence of plasmids and mobile genetic elements in their genomes contributes to the acquisition of new antimicrobial resistance determinants. However, although A. baumannii has arisen as an important human pathogen, information about these elements is still not well understood. Current genomic analysis availability has increased our ability to understand the microevolution of bacterial pathogens, including point mutations, genetic dissemination, genomic stability, and pan- and core-genome compositions. In this work, we deeply studied the genomes of four clinical strains from our hospital, and the reference strain ATCC®19606TM, which have shown a remarkable ability to survive and maintain their effective capacity when subjected to long-term stress conditions. With that, our aim was presenting a detailed analysis of their genomes, including antibiotic resistance determinants and plasmid composition.This research was funded by ‘Plan Nacional de I+D+i and Instituto de Salud Carlos III (Fondo de Investigaciones Sanitarias PI16/01103 to J.R.-V.), Subdirección General de Redes y Centros de Investigación Cooperativa, Spanish Ministry of Economy and Competitiveness, Spanish Network for Research in Infectious Diseases (REIPI RD12/0015) and (REIPI RD16/0016) co-financed by the European Development Regional Fund “A way to achieve Europe” ERDF and Ministerio de Ciencia e Innovación, Acciones de dinamización «Redes de Investigación» RED2018-102469-T

Aplicación a un receptor GPS de correcciones diferenciales recibidas mediante redes móviles (DGPS-IP)

El principal objetivo del presente proyecto ha consistido en el desarrollo de una aplicación que permite el estudio pormenorizado de los sistemas DGPS sobre IP. La aplicación proporciona los medios para conectarse a diversos receptores, recibiendo datos de estos equipos, habilitando su configuración y proporcionándole las correcciones diferenciales que habilitan el funcionamiento de los receptores diferenciales. En concreto este proyecto se ha centrado en los modelos de receptores Placer y Lassen de la casa Trimble, implementándose el protocolo TSIP para realizar las labores de configuración y toma de datos. El envío de las correcciones diferenciales al receptor se realizó mediante el protocolo RTCM, obtenendose dichas correcciones de servidores conectados por TCP/IP mediante la implementación de la parte cliente del protocolo NTRIP. La aplicación desarrollada proporciona un marco en el que desarrollar pruebas con diversos receptores GPS, permitiendo un funcionamiento interactivo con el que realizar una toma de contacto con los diversos escenarios o un uso automatizado que permite la toma de datos en escenarios más complejos. Estas características hacen de ella una competente herramienta auxiliar que se puede utilizar como entrenador de prácticas. Para la comprobación del funcionamiento de la aplicación se desarrollaron una serie de pruebas con las que caracterizar el comportamiento de los sistemas DGPS cuando reciben las correcciones mediante redes de datos inalámbricas. Dichas pruebas han consistido en la caracterización del error cuando se utilizan correcciones diferenciales correspondientes a estaciones situadas a distintas distancias, cuanticando la mejora de prestaciones respecto a la utilización del GPS sin correcciones, y el estudio del comportamiento de dichos sistemas frente a distintos retardos en la llegada de las correcciones

Especies de garrapatas duras en un área urbana protegida de la Ciudad Autónoma de Buenos Aires = Hard Tick Species in a Protected Urban Area of Buenos Aires City

INTRODUCCIÓN: Las garrapatas (Acari, Ixodida) son artrópodos vectores de gran diversidad de patógenos virales, bacterianos y protozoarios, muchos de los cuales son zoonóticos y emergentes. En Argentina se encuentran numerosas especies de garrapatas duras (familia Ixodidae) que también parasitan al hombre. Las áreas urbanas protegidas son ecosistemas naturales que están dentro de grandes urbes o limitan con ellas. En la Reserva Ecológica Costanera Sur (RECS) de la Ciudad Autónoma de Buenos Aires (CABA) circulan especies silvestres que no tienen presencia en otras áreas de la ciudad, con potenciales hospedadores y vectores. OBJETIVOS: Determinar las especies de garrapatas presentes en la RECS (CABA). MÉTODOS: Se realizó un estudio cuantitativo descriptivo transversal mediante muestreos para colectar garrapatas de vegetación y de hospedadores como perros y distintas especies de roedores. RESULTADOS: En total se recolectaron 1090 garrapatas de la vegetación (454 de la especie Amblyomma aureolatum, 635 Ixodes auritulus y 1 Amblyomma triste) y 67 de los perros (64 A. aureolatum, 2 Rhipicephalus sanguineus sensu lato y 1 A. triste). No se detectaron garrapatas en 200 roedores revisados. CONCLUSIONES: Las especies de garrapatas detectadas en este estudio tienen importancia en salud pública, tanto porque parasitan a humanos (A. aureolatum, A. triste y R. sanguineus s. l.) como porque participan en el ciclo y transmisión de distintos patógenos zoonóticos en distintas regiones del mundo, incluso Argentina.INTRODUCTION: Ticks (Acari, Ixodida) are arthropod vectors of great diversity of viral, bacterial and protozoan pathogens, many of which are zoonotic and emerging. In Argentina, there are numerous hard tick species (Ixodidae family) which also parasitize humans. Protected urban areas are natural ecosystems located within or near large urban centers. The Costanera Sur Ecological Reserve (RECS) of Buenos Aires city shows a circulation of wild species that have no presence in other areas of the city. There are potential hosts and vectors. OBJECTIVES: A quantitative cross sectional study was carried to detect the species of ticks present in the RECS of Buenos Aires city. METHODS: A quantitative cross - sectional study was carried out by sampling to collect ticks from vegetation and hosts (rodents and dogs). RESULTS: In total, 1090 ticks were collected from the vegetation (454 of the species Amblyomma aureolatum, 635 Ixodes auritulus and 1 Amblyomma triste) and 67 from dogs (64 A. aureolatum, 2 Rhipicephalus sanguineus sensu lato and 1 A. triste). No ticks were detected in 200 examined rodents. CONCLUSIONS: Ticks species detected in this study are important for public health, because they are parasites of humans (A. aureolatum, A. triste and R. sanguineus s. l.) and participate in the cycle and transmission of different zoonotic pathogens in different regions of the world, including Argentina.EEA RafaelaFil: Cicuttin, Gabriel L. Buenos Aires (Argentina). Ministerio de Salud. Instituto de Zoonosis Luis Pasteur; ArgentinaFil: de Salvo, María Nazarena. Buenos Aires (Argentina). Ministerio de Salud. Instituto de Zoonosis Luis Pasteur; ArgentinaFil: Nava, Santiago. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Rafaela; Argentina

Conjugation inhibitors effectively prevent plasmid transmission in natural environments

Plasmid conjugation is a major route for the spread of antibiotic resistance genes. Inhibiting conjugation has been proposed as a feasible strategy to stop or delay the propagation of antibiotic resistance genes. Several compounds have been shown to be conjugation inhibitors in vitro, specifically targeting the plasmid horizontal transfer machinery. However, the in vivo efficiency and the applicability of these compounds to clinical and environmental settings remained untested. Here we show that the synthetic fatty acid 2-hexadecynoic acid (2-HDA), when used as a fish food supplement, lowers the conjugation frequency of model plasmids up to 10-fold in controlled water microcosms. When added to the food for mice, 2-HDA diminished the conjugation efficiency 50-fold in controlled plasmid transfer assays carried out in the mouse gut. These results demonstrate the in vivo efficiency of conjugation inhibitors, paving the way for their potential application in clinical and environmental settings. IMPORTANCE The spread of antibiotic resistance is considered one of the major threats for global health in the immediate future. A key reason for the speed at which antibiotic resistance spread is the ability of bacteria to share genes with each other. Antibiotic resistance genes harbored in plasmids can be easily transferred to commensal and pathogenic bacteria through a process known as bacterial conjugation. Blocking conjugation is thus a potentially useful strategy to curtail the propagation of antibiotic resistance. Conjugation inhibitors (COINS) are a series of compounds that block conjugation in vitro. Here we show that COINS efficiently block plasmid transmission in two controlled natural environments, water microcosms and the mouse gut. These observations indicate that COIN therapy can be used to prevent the spread of antibiotic resistance.Acknowledgments: The work performed by the de la Cruz research group was supported by the European Union Seventh Framework Program (FP7-HEALTH-2011-single-stage) “Evolution and Transfer of Antibiotic Resistance” (EvoTAR), grant agreement number 282004. The work performed by C.P.-G. and M.G. was supported by Ph.D. fellowships funded by the University of Cantabria. The work performed by the B.G.-Z. laboratory was supported by The EFFORT project (www.effort-against-amr.eu) FP7-KBBE-2013-7, grant agreement 613754

Whole-genome sequence of Acinetobacter pittii HUMV-6483 isolated from human urine

Acinetobacter pittii strain HUMV-6483 was obtained from urine from an adult patient. We report here its complete genome assembly using PacBio singlemolecule real-time sequencing, which resulted in a chromosome with 4.07 Mb and a circular contig of 112 kb. About 3,953 protein-coding genes are predicted from this assembly

COPLA, a taxonomic classifier of plasmids

Background: Plasmids are mobile genetic elements, key in the dissemination of antibiotic resistance, virulence determinants and other adaptive traits in bacteria. Obtaining a robust method for plasmid classification is necessary to better understand the genetics and epidemiology of many pathogens. Until now, plasmid classification systems focused on specific traits, which limited their precision and universality. The definition of plasmid taxonomic units (PTUs), based on average nucleotide identity metrics, allows the generation of a universal plasmid classification scheme, applicable to all bacterial taxa. Here we present COPLA, a software able to assign plasmids to known and novel PTUs, based on their genomic sequence. Results: We implemented an automated pipeline able to assign a given plasmid DNA sequence to its cognate PTU, and assessed its performance using a sample of 1000 unclassified plasmids. Overall, 41% of the samples could be assigned to a previously defined PTU, a number that reached 63% in well-known taxa such as the Enterobacterales order. The remaining plasmids represent novel PTUs, indicating that a large fraction of plasmid backbones is still uncharacterized. Conclusions: COPLA is a bioinformatic tool for universal, species-independent, plasmid classification. Offered both as an automatable pipeline and an open web service, COPLA will help bacterial geneticists and clinical microbiologists to quickly classify plasmids.This work was supported by the Spanish Ministry of Science and Innovation [PID2020-117923GB-I00 to FdlC]; the Spanish Ministry of Economy, Industry and Competitiveness [DI-17-09164 to SR-S]; and USA Centers for Disease Control and Prevention [200-2019-06679 to FdlC]. The funders had no role in the design of the study, nor in the collection, analysis, and interpretation of data, nor in writing the manuscript included in this submission

Effects of Cannabis on Cell Viability and the Sleep-Wake Cycle in an Animal Model

Juan Laluz: Estudiante de Medicina, Ciclo de Metodología Científi ca II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Analía Ríos: Estudiante de Medicina, Ciclo de Metodología Científica II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Santiago Salvo: Estudiante de Medicina, Ciclo de Metodología Científica II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Agustín Scasso: Estudiante de Medicina, Ciclo de Metodología Científica II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Antonella Techera: Estudiante de Medicina, Ciclo de Metodología Científica II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Gimena Vargas: Estudiante de Medicina, Ciclo de Metodología Científica II, Facultad de Medicina, Universidad de la República, Uruguay. La contribución en la realización del trabajo fue equivalente a la de los demás estudiantes.-- Burix Mechoso: Docente supervisor, Laboratorio de Radiobiología, Departamento de Biofísica de la Facultad de Medicina, Universidad de la República, Uruguay.-- Verónica Sosa: Docente supervisor, Laboratorio de Radiobiología, Departamento de Biofísica de la Facultad de Medicina, Universidad de la República, Uruguay.-- Alejandra Mondino: Docente supervisor, Laboratorio de Neurobiología del Sueño, Departamento de Fisiología de la Facultad de Medicina, Universidad de la República, Uruguay.-- Atilio Falconi: Docente supervisor, Laboratorio de Neurobiología del Sueño, Departamento de Fisiología de la Facultad de Medicina, Universidad de la República, Uruguay.-- Carlos García: Docente supervisor, Catedra de Farmacognosia y productos Naturales , Departamento de Química Orgánica de la Facultad de Química, Universidad de la República, Uruguay.-- Nélson Bracesco: Docente supervisor, Laboratorio de Radiobiología, Departamento de Biofísica de la Facultad de Medicina, Universidad de la República, Uruguay. Contacto: Burix Mechoso. Correo electrónico: [email protected] investigación básica en nuestro país en relación a los efectos biológicos del cannabis es relativa mente reciente. Si bien la ley 14.294 de 1974 ya habilitaba a realizar investigación con cannabis, no fue hasta la aprobación de la ley 19.172 en el año 2013 de Regulación y Control del cannabis que se logró un marco regulatorio amplio que realmente impulsa la concreción de programas de investigación en diferentes áreas del conocimiento. En el presente trabajo se propone la aproximación al trabajo que realiza el Núcleo Interdisciplinario de Estudios sobre Cannabis (NIEC). Se presentan ensayos realiza dos sobre la viabilidad celular tras la exposición a extractos de cannabis en el Laboratorio de Radio biología y los resultados obtenidos por integrantes del laboratorio de Neurobiología del Sueño de la Facultad de Medicina en relación a los efectos sobre el ciclo sueño-vigilia de la administración aguda de cannabis vaporizado en un modelo animal. Los resultados obtenidos de los ensayos de viabilidad celular muestran una disminución de la sobrevida con concentraciones bajas de cannabinoides (1,0 µM), mientras cuando las líneas celulares fueron expuestas concentraciones más elevadas (10 µM y 100 µM), no se observó disminución de la fracción sobreviviente en ninguna de las líneas estudiadas. Este trabajo y los resultados obtenidos pretenden ser un insumo para la posterior profundización en la investigación sobre el potencial medicinal del cannabis en especial para futuros ensayos clínicos o terapéuticos del cannabis o los extractos de la planta.The basic research in our country in relation to the biological eff ects of cannabis is relatively recent. Although the law 14,294 of 1974 already enabled to carry out research with cannabis, it was not until the approval of the law 19,172 in the year 2013 of regulation and control of cannabis that a broad re gulatory framework was achieved that really drives the realization of research programs in diff erent areas of knowledge. In the present work, the approach to the work carried out by the Interdisciplinary Nucleus of Cannabis Studies (NIEC by its initials in Spanish) is proposed. The tests carried out on cell viability after exposure to cannabis extracts in the Radiobiology Laboratory are presented and also the results obtained by members of the Sleep Neurobiology Laboratory of the Faculty of Medicine in relation to the eff ects on the sleep-wake cycle of the acute administration of vaporized cannabis in an animal model. The results obtained from the cell viability tests show a decrease in survival with low concentrations of cannabinoids (1.0 μM), while when the cell lines were exposed to higher con centrations (10 μM and 100 μM), no decrease in the surviving fraction was observed in none of the lines studied. This work and the results obtained are intended to be an input for further research on the medicinal potential of cannabis, especially for future clinical or therapeutic trials of cannabis or plant extracts

XIPE: the X-ray Imaging Polarimetry Explorer

X-ray polarimetry, sometimes alone, and sometimes coupled to spectral and temporal variability measurements and to imaging, allows a wealth of physical phenomena in astrophysics to be studied. X-ray polarimetry investigates the acceleration process, for example, including those typical of magnetic reconnection in solar flares, but also emission in the strong magnetic fields of neutron stars and white dwarfs. It detects scattering in asymmetric structures such as accretion disks and columns, and in the so-called molecular torus and ionization cones. In addition, it allows fundamental physics in regimes of gravity and of magnetic field intensity not accessible to experiments on the Earth to be probed. Finally, models that describe fundamental interactions (e.g. quantum gravity and the extension of the Standard Model) can be tested. We describe in this paper the X-ray Imaging Polarimetry Explorer (XIPE), proposed in June 2012 to the first ESA call for a small mission with a launch in 2017 but not selected. XIPE is composed of two out of the three existing JET-X telescopes with two Gas Pixel Detectors (GPD) filled with a He-DME mixture at their focus and two additional GPDs filled with pressurized Ar-DME facing the sun. The Minimum Detectable Polarization is 14 % at 1 mCrab in 10E5 s (2-10 keV) and 0.6 % for an X10 class flare. The Half Energy Width, measured at PANTER X-ray test facility (MPE, Germany) with JET-X optics is 24 arcsec. XIPE takes advantage of a low-earth equatorial orbit with Malindi as down-link station and of a Mission Operation Center (MOC) at INPE (Brazil).Comment: 49 pages, 14 figures, 6 tables. Paper published in Experimental Astronomy http://link.springer.com/journal/1068

Detection of SARS-CoV-2 RNA by PCR in a series of corpses sent for autopsy

A partir de la aparición del SARS-CoV-2 en el mundo se desató la pandemia de COVID-19 que afectó a 185 países aparecieron numerosas publicaciones científicas presentando datos epidemiológicos, clínicos, estadísticos y microbiológicos. La elevada mortalidad ha implicado la necesidad de contar con datos cada vez más precisos en relación al virus y a su comportamiento en el medio y, por otro lado, enfrentó a los equipos de salud con un grave problema en relación al manejo seguro de cadáveres y a los riesgos de transmisión viral que ello implica. El objetivo del presente estudio ha sido detectar la presencia de ARN del SARS-CoV-2 en cadáveres remitidos a la Morgue Judicial que no estuvieran comprendidos en la definición de caso sospechoso propuesta por el Ministerio de Salud de la República Argentina. De un total de 153 cadáveres ingresados entre el 16 y el 24 de abril del 2020 en la Morgue Judicial se realizaron hisopados nasofaríngeos y orofaríngeos en 50 cadáveres elegidos basándose en criterios de inclusión previamente establecidos para efectuar una detección de ARN viral mediante técnica RT PCR. De todos éstos, a 2 de los cadáveres (4%) se les detectó ARN viral, los mismos no estaban clasificados como casos sospechosos de COVID-19. En el caso de 28 cadáveres remitidos como casos sospechosos de COVID-19, en el mismo período, se observó una prevalencia similar, 3,6%.Following the emergence of SARS-CoV-2 in the world, the COVID-19 pandemic broke out, affecting 185 countries. There have been numerous scientific publications presenting epidemiological, clinical, statistical, and microbiological data. The high mortality has implied the need for increasingly accurate data regarding the virus and its behaviour in the environment and, on the other hand, faced health teams with a serious problem in relation to the safe handling of corpses and the risks of transmission that this implies. The objective of this study was to detect the presence of SARS-CoV-2 RNA in corpses sent to the National Judicial Morgue that were not included in the definition of a suspected case submitted by the Argentine Ministry of Health. Nasopharyngeal and oropharyngeal swabs were taken from 101 cadavers chosen randomly and based on inclusion criteria for detection of viral RNA using the RT-PCR technique. Of the cadavers included in the study, 16.8%, not classified as suspected cases of COVID-19, were tested for the presence of viral RNA in the samples collected.Fil: D'Addario, Adriana Claudia. Morgue Judicial de la Nación; ArgentinaFil: Bustos, Cristina A.. Morgue Judicial de la Nación; ArgentinaFil: Cohen, Roberto V.. Morgue Judicial de la Nación; ArgentinaFil: Rullan Corna, Alejandro Félix. Morgue Judicial de la Nación; ArgentinaFil: Gómez, Patricia Elizabeth. Morgue Judicial de la Nación; ArgentinaFil: Torrisi, Rubén H.. Morgue Judicial de la Nación; ArgentinaFil: Di Salvo, Héctor. Morgue Judicial de la Nación; ArgentinaFil: Herbstein, Jorge A.. Morgue Judicial de la Nación; ArgentinaFil: Remes Lenicov, Federico. Universidad de Buenos Aires; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones Biomédicas en Retrovirus y Sida. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones Biomédicas en Retrovirus y Sida; ArgentinaFil: Maffia Bizzozero, Santiago. Morgue Judicial de la Nación; Argentin

XIPE: the X-ray imaging polarimetry explorer

Abstract X-ray polarimetry, sometimes alone, and sometimes coupled to spectral and temporal variability measurements and to imaging, allows a wealth of physical phenomena in astrophysics to be studied. X-ray polarimetry investigates the acceleration process, for example, including those typical of magnetic reconnection in solar flares, but also emission in the strong magnetic fields of neutron stars and white dwarfs. It detects scattering in asymmetric structures such as accretion disks and columns, and in the so-called molecular torus and ionization cones. In addition, it allows fundamental physics in regimes of gravity and of magnetic field intensity not accessible to experiments on the Earth to be probed. Finally, models that describe fundamental interactions (e.g. quantum gravity and the extension of the Standard Model) can be tested. We describe in this paper the X-ray Imaging Polarimetry Explorer (XIPE), proposed in June 2012 to the first ESA call for a small mission with a launch in 2017. The proposal was, unfortunately, not selected. To be compliant with this schedule, we designed the payload mostly with existing items. The XIPE proposal takes advantage of the completed phase A of POLARIX for an ASI small mission program that was cancelled, but is different in many aspects: the detectors, the presence of a solar flare polarimeter and photometer and the use of a light platform derived by a mass production for a cluster of satellites. XIPE is composed of two out of the three existing JET-X telescopes with two Gas Pixel Detectors (GPD) filled with a He-DME mixture at their focus. Two additional GPDs filled with a 3-bar Ar-DME mixture always face the Sun to detect polarization from solar flares. The Minimum Detectable Polarization of a 1 mCrab source reaches 14 % in the 2-10 keV band in 105 s for pointed observations, and 0.6 % for an X10 class solar flare in the 15-35 keV energy band. The imaging capability is 24 arcsec Half Energy Width (HEW) in a Field of View of 14.7 arcmin × 14.7 arcmin. The spectral resolution is 20 % at 6 keV and the time resolution is 8 mus. The imaging capabilities of the JET-X optics and of the GPD have been demonstrated by a recent calibration campaign at PANTER X-ray test facility of the Max-Planck-Institut für extraterrestrische Physik (MPE, Germany). XIPE takes advantage of a low-earth equatorial orbit with Malindi as down-link station and of a Mission Operation Center (MOC) at INPE (Brazil). The data policy is organized with a Core Program that comprises three months of Science Verification Phase and 25 % of net observing time in the following 2 years. A competitive Guest Observer program covers the remaining 75 % of the net observing time