Plasmodium vivax lineages: geographical distribution, tandem repeat polymorphism, and phylogenetic relationship

Background: Multi-drug resistance and severe/ complicated cases are the emerging phenotypes of vivax malaria, which may deteriorate current anti-malarial control measures. The emergence of these phenotypes could be associated with either of the two Plasmodium vivax lineages. The two lineages had been categorized as Old World and New World, based on geographical sub-division and genetic and phenotypical markers. This study revisited the lineage hypothesis of P. vivax by typing the distribution of lineages among global isolates and evaluated their genetic relatedness using a panel of new mini-satellite markers. Methods: 18S SSU rRNA S-type gene was amplified from 420 Plasmodium vivax field isolates collected from different geographical regions of India, Thailand and Colombia as well as four strains each of P. vivax originating from Nicaragua, Panama, Thailand (Pak Chang), and Vietnam (ONG). A mini-satellite marker panel was then developed to understand the population genetic parameters and tested on a sample subset of both lineages. Results: 18S SSU rRNA S-type gene typing revealed the distribution of both lineages (Old World and New World) in all geographical regions. However, distribution of Plasmodium vivax lineages was highly variable in every geographical region. The lack of geographical sub-division between lineages suggests that both lineages are globally distributed. Ten mini-satellites were scanned from the P. vivax genome sequence; these tandem repeats were located in eight of the chromosomes. Mini-satellites revealed substantial allelic diversity (7-21, AE = 14.6 +/- 2.0) and heterozygosity (He = 0.697-0.924, AE = 0.857 +/- 0.033) per locus. Mini-satellite comparison between the two lineages revealed high but similar pattern of genetic diversity, allele frequency, and high degree of allele sharing. A Neighbour-Joining phylogenetic tree derived from genetic distance data obtained from ten mini-satellites also placed both lineages together in every cluster. Conclusions: The global lineage distribution, lack of genetic distance, similar pattern of genetic diversity, and allele sharing strongly suggested that both lineages are a single species and thus new emerging phenotypes associated with vivax malaria could not be clearly classified as belonging to a particular lineage on basis of their geographical origin.

Comportamiento epidemiológico de la sepsis nosocomial en la Unidad de Recién Nacidos de la Fundación Cardioinfantil

Objetivo. Se realizó un estudio retrospectivo que describe las características demográficas, la etiología, los factores asociados, la mortalidad, la sensibilidad y la resistencia de los microorganismos a los antibióticos usados en sepsis nosocomial. Diseño del estudio. Se realizó la recolección de datos desde el 2004 hasta el primer trimestre del 2006. Se definió infección nosocomial probada como la infección diagnosticada después de 72 horas de hospitalización y que recibe manejo antibiótico mayor a 3 días. Resultados. Se revisaron 60 historias clínicas, en las cuales los gérmenes Gram negativos fueron los principales causantes de sepsis nosocomial, tanto intra como extrainstitucional; de ellos la k. pneumoniae fue el germen más frecuentemente encontrado. Conclusiones. Los gérmenes Gram negativos son los microorganismos predominantemente causantes de sepsis nosocomial en la Unidad de Recién Nacidos (URN) de la Fundación Cardioinfantil (FCI).

Evaluación muticéntrica de la actividad antimicrobiana in vitro de tigeciclina en aislados obtenidos de pacientes hospitalizados en Colombia

El aumento en la resistencia bacteriana es un problema global que afecta también a nuestro país y que puede llevar a fracasos terapéuticos, peores desenlaces clínicos, uso de terapia combinada, mayor riesgo de interacciones medicamentosas y de reacciones adversas asi como a aumento de los costos del tratamiento. Tigeciclina, un nuevo antibiótico de la clase de las glicilciclinas ha mostrado una promisoria actividad antibacteriana in vitro contra bacterias comunes incluyendo multiresistentes que cada vez son más prevalentes en nuestro país especialmente a nivel hospitalario. Este estudio fue desarrollado para determinar la actividad de tigeciclina en nuestro medio y conocer su potencial utilidad.

Mediastinitis post revascularización miocárdica: impacto del cambio de profilaxis antibiótica en la fundación Cardioinfantil 2012 - 2013

INTRODUCCIÓN. La mediastinitis posterior a cirugía de revascularización miocárdica es una infección infrecuente, pero potencialmente fatal. En la Fundación Cardioinfantil se ha observado una tendencia al incremento de la misma en los últimos años, obligando a un cambio en las medidas de profilaxis antimicrobiana, pasando de cefalosporinas a vancomicina – gentamicina, sin embargo no se conoce aún el impacto de estas medidas. OBJETIVO: Determinar si el cambio de la profilaxis antibiótica en pacientes sometidos a revascularización miocárdica influye en una disminución de la incidencia de mediastinitis durante los años 2012 – 2013. METODOLOGÍA: Estudio de cohortes retrospectivo, evaluando la incidencia de mediastinitis post revascularización miocárdica, en pacientes expuestos a 2 diferentes tipos de profilaxis antimicrobiana (cefalosporinas vs vancomicina-gentamicina). Se describieron los patrones de susceptibilidad y resistencia de los patógenos encontrados en mediastinitis y la mortalidad de esta patología. RESULTADOS: Los patógenos más frecuentemente aislados en la mediastinitis fueron Staphylococcus aureus y Klebsiella pneumoniae, en la mayoría monomicrobiano. Se encontraron patógenos con perfiles de resistencia como betalactamasas de espectro extendido en Gram negativos y resistencia a la meticilina en cocos Gram positivos. El RR de mediastinitis del grupo expuesto a vancomicina-gentamicina respecto al grupo de cefalosporinas fue de 0,9 con IC 95% 0,28 – 3,28. CONCLUSIÓN: la epidemiologia microbiana de la mediastinitis no difiere de la reportada en otras series. La profilaxis antimicrobiana con vancomicina - gentamicina en pacientes sometidos a revascularización miocárdica, no redujo la incidencia de mediastinitis. Se propone regresar a la terapia de profilaxis con cefalosporinas.

Perfil microbiológico, prevalencia de resistencia antibiótica y patrones de susceptibilidad en infección urinaria en una población pediátrica

Introducción: El incremento de la resistencia antibiótica se considera un problema de salud pública con consecuencias clínicas y económicas, por lo tanto se determinará la prevalencia de resistencia antibiótica en Infección del Tracto Urinario (ITU, el perfil microbiológico y los patrones de susceptibilidad en una población pediátrica atendida en la Fundación Cardioinfantil. Materiales y métodos: Estudio observacional de corte transversal, retrospectivo, entre 1 mes a 18 años de edad, con diagnóstico de ITU comunitaria atendidos entre Enero de 2011 y Diciembre de 2013. Se excluyeron pacientes con dispositivos en la vía urinaria, instrumentación quirúrgica previa, trayectos fistulosos entre la vía urinaria y sistema digestivo, ITU luego de 48 horas de hospitalización y recaída clínica en tratamiento. Se estableció la prevalencia de ITU resistente y se realizó un análisis descriptivo de la información. Resultados: Se evaluaron 385 registros clínicos, con una mediana de 1.08 años (RIQ 0.8 – 4.08), el 73.5% eran niñas. La fiebre predominó (76.5%), seguido de emesis (32.0%), disuria (23.7%) y dolor abdominal (23.1%). El uropatógeno más frecuente fue E.coli (75%), seguido de Proteus mirabilis (8.5%) y Klebsiella spp. (8.3%). La Ampicilina, el Trimetropim sulfametoxazol, la Ampicilina sulbactam y el ácido nalidixico tuvieron mayor tasa de resistencia. La prevalencia de BLEE fue 5.2% y AmpC 3.9%. La prevalencia de resistencia antimicrobiana fue de 11.9%. Conclusiones: La E.coli es el uropatogeno más frecuentemente aislado en ITU, con resistencia a la ampicilina en 60.2%, cefalosporinas de primera generación en 15.5%, trimetropin sulfametoxazol en 43.9%, cefepime 4.8%. La prevalencia de resistencia antimicrobiana fue de 11.9%.

Tipificación y perfiles de resistencia antibiótica en unidades neonatales de Bogotá durante los años 2008-2012

La sepsis neonatal ha sido un problema en las unidades de cuidado intensivo al rededor del mundo. Su incidencia aumenta diez veces cuando el recién nacido es de muy bajo peso. El aislamiento de gérmenes resistentes en los cultivos tomados a los recién nacidos ha permitido identificar el comportamiento de los antibióticos de uso común. El presente estudio analítico de corte transversal realizado durante los años 2008 al 2012 en diez unidades de cuidados intensivos neonatales de la ciudad de Bogotá analizó la base de datos de los laboratorios de microbiología, obteniendo un total de 22.153 muestras de las cuales 7.132 ( 32.9%) fueron elegibles. Utilizando el software Whonet 5.6 y tomando solo el primer aislamiento por año y por paciente se realizaron análisis descriptivos y de resistencia bacteriana. Los resultados obtenidos fueron similares a los reportados en la literatura donde los gérmenes gran positivos son los más comúnmente aislados con un 53.2%, seguidos en importancia por los gérmenes gran negativos. Klebsiella pneumoniae y Escherichia coli en conjunto aportan 27.22%, presentando un aumento en el porcentaje de BLEE (Betalactamasa de Espectro Extendido) y aparición de carbapenemasas durante los años de estudio. El Acinetobacter baumannii ha duplicado la resistencia a ampicilina sulbactam llegando al 66.7%. Las candidas fueron aisladas en un porcentaje muy bajo sin documentarse resistencias. El Estafilococo aureus no presenta resistencias que sugiera la aparición de nuevos clones.

A genomewide survey of developmentally relevant genes in Ciona intestinalis - III. Genes for Fox, ETS, nuclear receptors and NF kappa B

A survey against the draft genome sequence and the cDNA/EST database of Ciona intestinalis identified a number of genes encoding transcription factors regulating a variety of processes including development. In the present study, we describe almost complete sets of genes for Fox, ETS-domain transcription factors, nuclear receptors, and NFkappaB as well as other factors regulating NFkappaB activity, with their phylogenetic nature. Vertebrate Fox transcription factors are currently delineated into 17 subfamilies: FoxA to FoxQ. The present survey yielded 29 genes of this family in the Ciona genome, 24 of which were Ciona orthologues of known Fox genes. In addition, we found 15 ETS aenes, 17 nuclear receptor genes, and several NFkappaB signaling pathway genes in the Ciona genome. The number of Ciona genes in each family is much smaller than that of vertebrates, which represents a simplified feature of the ascidian genome. For example, humans have two NFkappaB genes, three Rel genes, and five NFAT genes, while Ciona has one gene for each family. The Ciona genome also contains smaller numbers of genes for the NFkappaB regulatory system, i.e. after the split of ascidians/vertebrates, vertebrates evolved a more complex NFkappaB system. The present results therefore provide molecular information for the investigation of complex developmental processes, and an insight into chordate evolution.

Physiological changes in Campylobacter jejuni on entry into stationary phase

Campylobacter jejuni NCTC 11168 does not exhibit the general increase in cellular stress resistance on entry into stationary phase that is seen in most other bacteria. This is consistent with the lack of global stationary phase regulatory elements in this organism. deduced from an analysis of its genome sequence. We now show that C. jejuni NCTC 11168 does undergo certain changes in stationary phase, of a pattern not previously described. As cells entered stationary phase there was a change in membrane fatty acid composition, principally a decrease in the proportion of unsaturated fatty acids and an increase in the content of cyclopropane and short-chain fatty acids. These changes in membrane composition were accompanied by an increase in the resilience of the cell membrane towards loss of integrity caused by pressure and an increase in cellular pressure resistance. By contrast. there were no major changes in resistance to acid or heat treatment. A similar pattern of changes in stress resistance on entry, into stationary phase was seen in C. jejuni NCTC 11351, the type strain. These changes appear to represent a restricted Physiological response to the conditions existing in stationary phase cultures, in an organism having limited capacity for genetic regulation and adaptation to environment. © 2004 Elsevier B.V. All rights reserved.

Type III secretion homologs are present in Brucella melitensis, B-ovis, and B-suis biovars 1, 2, and 3

Protein sequences from characterized type III secretion (TTS) systems were used as probes in silico to identify several TTS gene homologs in the genome sequence of Brucella suis biovar 1 strain 1330. Four of the genes, named flhB, fliP, fliR, and fliF on the basis of greatest homologies to known flagellar apparatus proteins, were targeted in PCR and hybridization assays to determine their distribution among other Brucella nomen species and biovars. The results indicated that flhB, fliP, fliR and fliF are present in Brucella melitensis, Brucella ovis, and Brucella suis biovars 1, 2 and 3. Similar homologos have been reported previously in Brucella abortus. Using RT-PCR assays, we were unable to detect any expression of these genes. It is not yet known whether the genes are the cryptic remnants of a flagellar system or are actively involved in a process contributing to pathogenicity or previously undetected motility, but they are distributed widely in Brucella and merit further study to determine their role.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast-and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Identification of potential drug targets in Salmonella Typhimurium using metabolic modelling and experimental validation

almonella enterica serovar Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of Salmonella Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in energy demand, while growing in glucose minimal medium. By grouping reactions with similar flux responses, a sub-network of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions, that when removed from the genome-scale model interfered with energy and biomass generation. 11 such sets were found to be essential for the production of biomass precursors. Experimental investigation of 7 of these showed that knock-outs of the associated genes resulted in attenuated growth for 4 pairs of reactions, while 3 single reactions were shown to be essential for growth.

The pgip family in soybean and three other legume species: evidence for a birth-and-death model of evolution

Background Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene copies whose evolutionary origin has been poorly investigated. Here we report the complete characterization of the full complement of the pgip family in soybean (Glycine max [L.] Merr.) and the characterization of the genomic region surrounding the pgip family in four legume species. Results BAC clone and genome sequence analyses showed that the soybean genome contains two pgip loci. Each locus is composed of three clustered genes that are induced following infection with the fungal pathogen Sclerotinia sclerotiorum (Lib.) de Bary, and remnant sequences of pgip genes. The analyzed homeologous soybean genomic regions (about 126 Kb) that include the pgip loci are strongly conserved and this conservation extends also to the genomes of the legume species Phaseolus vulgaris L., Medicago truncatula Gaertn. and Cicer arietinum L., each containing a single pgip locus. Maximum likelihood-based gene trees suggest that the genes within the pgip clusters have independently undergone tandem duplication in each species. Conclusions The paleopolyploid soybean genome contains two pgip loci comprised in large and highly conserved duplicated regions, which are also conserved in bean, M. truncatula and C. arietinum. The genomic features of these legume pgip families suggest that the forces driving the evolution of pgip genes follow the birth-and-death model, similar to that proposed for the evolution of resistance (R) genes of NBS-LRR-type.

Temperature and oxygen dependent metabolite utilization by Salmonella enterica Serovars Derby and Mbandaka

Salmonella enterica is a zoonotic pathogen of clinical and veterinary significance, with over 2500 serovars. In previous work we compared two serovars displaying host associations inferred from isolation statistics. Here, to validate genome sequence data and to expand on the role of environmental metabolite constitution in host range determination we use a phenotypic microarray approach to assess the ability of these serovars to metabolise ~500 substrates at 25°C with oxygen (aerobic conditions) to represent the ex vivo environment and at 37°C with and without oxygen (aerobic/anaerobic conditions) to represent the in vivo environment. A total of 26 substrates elicited a significant difference in the rate of metabolism of which only one, D-galactonic acid-g-lactone, could be explained by the presence (S. Mbandaka) or the absence (S. Derby) of metabolic genes. We find that S. Mbandaka respires more efficiently at ambient temperatures and under aerobic conditions on 18 substrates including: glucosominic acid, saccharic acid, trehalose, fumaric acid, maltotriose, N-acetyl-D-glucosamine, N-acetyl-beta-D-mannosamine, fucose, L-serine and dihydroxy-acetone; whereas S. Derby is more metabolically competent anaerobically at 37°C for dipeptides, glutamine-glutamine, alanine-lysine, asparagine-glutamine and nitrogen sources glycine and nitrite. We conclude that the specific phenotype cannot be reliably predicted from the presence of metabolic genes directly relating to the metabolic pathways under study.

Leukotrienes Target F-actin/Cofilin-1 to Enhance Alveolar Macrophage Anti-fungal Activity

Candida albicans is the most common opportunistic fungal pathogen and causes local and systemic disease in immunocompromised patients. Alveolar macrophages (AMs) are pivotal for the clearance of C. albicans from the lung. Activated AMs secrete 5-lipoxygenase-derived leukotrienes (LTs), which in turn enhance phagocytosis and microbicidal activity against a diverse array of pathogens. Our aim was to investigate the role of LTB(4) and LTD(4) in AM antimicrobial functions against C. albicans and the signaling pathways involved. Pharmacologic and genetic inhibition of LT biosynthesis as well as receptor antagonism reduced phagocytosis of C. albicans when compared with untreated or WT controls. Conversely, exogenous LTs of both classes augmented base-line C. albicans phagocytosis by AMs. Although LTB(4) enhanced mainly mannose receptor-dependent fungal ingestion, LTD(4) enhanced mainly dectin-1 receptor-mediated phagocytosis. LT enhancement of yeast ingestion was dependent on protein kinase C-delta (PKC delta) and PI3K but not PKC alpha and MAPK activation. Both LTs reduced activation of cofilin-1, whereas they enhanced total cellular F-actin; however, LTB(4) accomplished this through the activation of LIM kinases (LIMKs) 1 and 2, whereas LTD(4) did so exclusively via LIMK-2. Finally, both exogenous LTB(4) and LTD(4) enhanced AM fungicidal activity in an NADPH oxidase-dependent manner. Our data identify LTB(4) and LTD(4) as key mediators of innate immunity against C. albicans, which act by both distinct and conserved signaling mechanisms to enhance multiple antimicrobial functions of AMs.

Leukotrienes Produced in Allergic Lung Inflammation Activate Alveolar Macrophages

It has been well-documented that leukotrienes (LTs) are released in allergic lung inflammation and that they participate in the physiopathology of asthma. A role for LTs in innate immunity has recently emerged: Cys-LTs were shown to enhance Fc gamma R-mediated phagocytosis by alveolar macrophages (AMs). Thus, using a rat model of asthma, we evaluated Fc gamma R-mediated phagocytosis and killing of Klebsiella pneumoniae by AMs. The effect of treatment with a cys-LT antagonist (montelukast) on macrophage function was also investigated. Male Wistar rats were immunized twice with OVA/alumen intraperitoneally and challenged with OVA aerosol. After 24 h, the animals were killed, and the AMs were obtained by bronchoalveolar lavage. Macrophages were cultured with IgG-opsonized red blood cells (50: 1) or IgG-opsonized K. pneumoniae (30: 1), and phagocytosis or killing was evaluated. Leukotriene C(4) and nitric oxide were quantified by the EIA and Griess methods, respectively. The results showed that AMs from sensitized and challenged rats presented a markedly increased phagocytic capacity via Fc gamma R (10X compared to controls) and enhanced killing of K. pneumoniae (4X higher than controls). The increased phagocytosis was inhibited 15X and killing 3X by treatment of the rats with montelukast, as compared to the non-treated group. cys-LT addition increased phagocytosis in control AMs but had no effect on macrophages from allergic lungs. Montelukast reduced nitric oxide (39%) and LTC(4) (73%). These results suggest that LTs produced during allergic lung inflammation potentiate the capacity of AMs to phagocytose and kill K. pneumonia via Fc gamma R. Copyright (C) 2010 S. Karger AG, Basel