Infectious diseases in the genomic era

Indexación: Web of Science; Scielo.La nueva generación de secuenciadores (NGS) ha llegado para cambiar el modo de realizar investigación. Particularmente en Infectología, estas tecnologías modernas la han dirigido a una próxima era, denominada la "era de la genómica". En países desarrollados, las NGS se están utilizando en un gran número de aplicaciones, las que incluyen diagnóstico clínico, epidemiología y microbiología. En la actualidad, secuenciar el genoma de un microorganismo completo, ya sea bacteriano o viral, cuesta aproximadamente $100 dólares, precio bastante asequible en comparación a los precios de las tecnologías más antiguas. En esta revisión se describen algunas publicaciones recientes que han utilizado la secuenciación de genomas completos para, (i) rastrear brotes de enfermedades transmitidas por alimentos, (ii) la preparación de base de datos de genomas para los Gobiernos (iii) investigación de enfermedades nosocomiales, y (iv) en diagnóstico clínico. La era de la genómica está aquí, y llegó para quedarse, por lo cual se debe enfocar todos los esfuerzos en aprender a utilizar la gran cantidad de "datos masivos" generados por estas tecnologías, para reducir el impacto de las enfermedades infecciosas y así, mejorar la salud de personas y animales.Next generation sequencing (NGS) technologies have arrived, changing research and infectious disease research into a new era, the "genomic era". Currently, the developed world is introducing NGS in a number of applications, including clinical diagnostics, epidemiology, and microbiology. In developing countries NGS is being progressively introduced. Technologies currently available allow to sequence the whole genome of bacterial and viral strains for an approximate cost of$100 USD, which is highly cost savings compared to old-technologies for genome sequencing. Here we review recent publication of whole genome sequencing used for, (i) tracking of foodborne outbreaks, with emphasis in Salmonella and Listeria monocytogenes, (ii) building genomic databases for Governments, (iii) investigating nosocomial infections, and (iv) clinical diagnosis. The genomic era is here to stay and researchers should use these "massive databases" generated by this technology to decrease infectious diseases and thus improve health of humans and animals.http://ref.scielo.org/dwxt9

Classical field theory. Advanced mathematical formulation

In contrast with QFT, classical field theory can be formulated in strict mathematical terms of fibre bundles, graded manifolds and jet manifolds. Second Noether theorems provide BRST extension of this classical field theory by means of ghosts and antifields for the purpose of its quantization.Comment: 30 p

Oral History Interview: Charles Switt

This interview is one of series conducted concerning the Oral History of Appalachia. The subject of this interview is Camp Washington Carver in Clifftop, WV. Mr. Switt discusses: his personal history; his family; Boy Scouts; segregation and integration at the camp; his experiences at the camp; and other topics.https://mds.marshall.edu/oral_history/1489/thumbnail.jp

Background Geometry in Gauge Gravitation Theory

Dirac fermion fields are responsible for spontaneous symmetry breaking in gauge gravitation theory because the spin structure associated with a tetrad field is not preserved under general covariant transformations. Two solutions of this problem can be suggested. (i) There exists the universal spin structure $S\to X$ such that any spin structure $S^h\to X$ associated with a tetrad field $h$ is a subbundle of the bundle $S\to X$. In this model, gravitational fields correspond to different tetrad (or metric) fields. (ii) A background tetrad field $h$ and the associated spin structure $S^h$ are fixed, while gravitational fields are identified with additional tensor fields q^\la{}_\m describing deviations \wt h^\la_a=q^\la{}_\m h^\m_a of $h$. One can think of \wt h as being effective tetrad fields. We show that there exist gauge transformations which keep the background tetrad field $h$ and act on the effective fields by the general covariant transformation law. We come to Logunov's Relativistic Theory of Gravity generalized to dynamic connections and fermion fields.Comment: 12 pages, LaTeX, no figure

Microevolution during the emergence of a monophasic Salmonella Typhimurium epidemic in the United Kingdom

Microevolutionary events associated with the emergence and clonal expansion of new 27 epidemic clones of bacterial pathogens hold the key to understanding the drivers of 28 epidemiological success. We describe a comparative whole genome sequence and 29 phylogenomic analysis of monophasic Salmonella Typhimurium isolates from the UK 30 and Italy from 2005-2012. Monophasic isolates from this time formed a single clade 31 distinct from recent monophasic epidemic clones described previously from North 32 America and Spain. The current UK monophasic epidemic clones encode a novel 33 genomic island encoding resistance to heavy metals (SGI-3), and composite transposon 34 encoding antibiotic resistance genes not present in other Typhimurium isolates, that 35 may have contributed to the epidemiological success. We also report a remarkable 36 degree of genotypic variation that accumulated during clonal expansion of a UK 37 epidemic including multiple independent acquisitions of a novel prophage carrying the 38 sopE gene and multiple deletion events affecting the phase II flagellin locus

A type III effector protease NleC from enteropathogenic Escherichia coli targets NF-κB for degradation.

Published versio

Animal contact as a source of human non-typhoidal salmonellosis

Non-typhoidal Salmonella represents an important human and animal pathogen world-wide. Most human salmonellosis cases are foodborne, but each year infections are also acquired through direct or indirect animal contact in homes, veterinary clinics, zoological gardens, farm environments or other public, professional or private settings. Clinically affected animals may exhibit a higher prevalence of shedding than apparently healthy animals, but both can shed Salmonella over long periods of time. In addition, environmental contamination and indirect transmission through contaminated food and water may complicate control efforts. The public health risk varies by animal species, age group, husbandry practice and health status, and certain human subpopulations are at a heightened risk of infection due to biological or behavioral risk factors. Some serotypes such as Salmonella Dublin are adapted to individual host species, while others, for instance Salmonella Typhimurium, readily infect a broad range of host species, but the potential implications for human health are currently unclear. Basic hygiene practices and the implementation of scientifically based management strategies can efficiently mitigate the risks associated with animal contacts. However, the general public is frequently unaware of the specific disease risks involved, and high-risk behaviors are common. Here we describe the epidemiology and serotype distribution of Salmonella in a variety of host species. In addition, we review our current understanding of the public health risks associated with different types of contacts between humans and animals in public, professional or private settings, and, where appropriate, discuss potential risk mitigation strategies

The invasome of Salmonella Dublin as revealed by whole genome sequencing

Background Salmonella enterica serovar Dublin is a zoonotic infection that can be transmitted from cattle to humans through consumption of contaminated milk and milk products. Outbreaks of human infections by S. Dublin have been reported in several countries including high-income countries. A high proportion of S. Dublin cases in humans are associated with invasive disease and systemic illness. The genetic basis of virulence in S. Dublin is not well characterized. Methods Whole genome sequencing was applied to a set of clinical invasive and non-invasive S. Dublin isolates from different countries in order to characterize the putative genetic determinants involved in the virulence and invasiveness of S. Dublin in humans. Results We identified several virulence factors that form the bacterial invasome and may contribute to increasing bacterial virulence and pathogenicity including mainly Gifsy-2 prophage, two different type 6 secretion systems (T6SSs) harbored by Salmonella pathogenicity islands; SPI-6 and SPI-19 respectively and virulence genes; ggt and PagN. Although Vi antigen and the virulence plasmid have been reported previously to contribute to the virulence of S. Dublin we did not detect them in all invasive isolates indicating that they are not the main virulence determinants in S. Dublin. Conclusion Several virulence factors within the genome of S. Dublin might contribute to the ability of S. Dublin to invade humans’ blood but there were no genomic markers that differentiate invasive from non-invasive isolates suggesting that host immune response play a crucial role in the clinical outcome of S. Dublin infection

Salmonella and tomatoes

Outbreak information linking fresh tomato fruit to illnesses is reviewed in this chapter. While tomato fruit appear to support substantial proliferation of certain serovars of Salmonella enterica, detection of this pathogen in tomato plants prior to harvest is rare, and reports of Salmonella existence in tomato fruit still attached to field-grown plants are virtually non-existent. The bacterium is sensitive to UV and can be outcompeted by the native phytomicrobiota, which may explain its absence in field-grown crops. However, the persistence of certain serovars in fields and ponds of certain production areas is noted. Together with evidence of bacteria becoming internalized in tomato fruit during crop development likely through natural apertures, the presence of S. enterica in and around production fields suggests that an unusual weather event could lead to Salmonella contamination of fruit prior to harvest. The bacterium appears physiologically adaptive toward proliferation in tomato fruit. Once inside tomatoes, Salmonella is capable of sensing the availability of nutrients and physiological state of the fruit and differentially regulates specific genes. However, because Salmonella is an efficient nutrient scavenger, removal of multiple metabolic and regulatory genes was required to reduce its fitness within the fruit. Plants do not appear to recognize human enterics as pathogens, and their defenses treat them as endophytes