Rapid bacterial genome sequencing: methods and applications in clinical microbiology.

The recent advances in sequencing technologies have given all microbiology laboratories access to whole genome sequencing. Providing that tools for the automated analysis of sequence data and databases for associated meta-data are developed, whole genome sequencing will become a routine tool for large clinical microbiology laboratories. Indeed, the continuing reduction in sequencing costs and the shortening of the 'time to result' makes it an attractive strategy in both research and diagnostics. Here, we review how high-throughput sequencing is revolutionizing clinical microbiology and the promise that it still holds. We discuss major applications, which include: (i) identification of target DNA sequences and antigens to rapidly develop diagnostic tools; (ii) precise strain identification for epidemiological typing and pathogen monitoring during outbreaks; and (iii) investigation of strain properties, such as the presence of antibiotic resistance or virulence factors. In addition, recent developments in comparative metagenomics and single-cell sequencing offer the prospect of a better understanding of complex microbial communities at the global and individual levels, providing a new perspective for understanding host-pathogen interactions. Being a high-resolution tool, high-throughput sequencing will increasingly influence diagnostics, epidemiology, risk management, and patient care.

Rapid detection of bacterial resistance to antibiotics using AFM cantilevers as nanomechanical sensors.

The widespread misuse of drugs has increased the number of multiresistant bacteria, and this means that tools that can rapidly detect and characterize bacterial response to antibiotics are much needed in the management of infections. Various techniques, such as the resazurin-reduction assays, the mycobacterial growth indicator tube or polymerase chain reaction-based methods, have been used to investigate bacterial metabolism and its response to drugs. However, many are relatively expensive or unable to distinguish between living and dead bacteria. Here we show that the fluctuations of highly sensitive atomic force microscope cantilevers can be used to detect low concentrations of bacteria, characterize their metabolism and quantitatively screen (within minutes) their response to antibiotics. We applied this methodology to Escherichia coli and Staphylococcus aureus, showing that live bacteria produced larger cantilever fluctuations than bacteria exposed to antibiotics. Our preliminary experiments suggest that the fluctuation is associated with bacterial metabolism.

Personal experience with diagnostic and therapeutic aspects of human Leishmania (Viannia) braziliensis in Três Braços

Diagnostic and therapeutic aspects of human infection with Leishmania (Viannia) braziliensis found in the littoral forest of the state of Bahia are reviewed. There is pressing need for alternative cheap oral drug therapy.

La depuradora de Begues: reactor biològic o aiguamolls construïts?. Estudi comparatiu dels vectors: paràmetres de l'H2O, fangs produïts, costos capitals i d'explotació, personal

L’objectiu del present estudi és comparar els vectors de paràmetres de l’aigua, producció de fangs, costos i personal entre 2 tipus d’instal·lacions EDAR al municipi de Begues; una ja existent amb tractament secundari i terciari mitjançant un reactor biològic i una potencial amb tractament secundari i terciari mitjançant aiguamolls construïts. La finalitat del projecte és determinar, gràcies a l’estudi dels principals vectors ambientals de la infraestructura i a altres estudiats per na Susana Forero Sánchez, quina de les 2 tipologies d’instal·lació s’ajusta més al territori i a les necessitats de tractament de les aigües del mateix. Els resultats de la investigació indiquen que tant els costos d’explotació com la producció de fangs i el personal donen avantatge als aiguamolls construïts, però els costos capitals i el tractament de nutrients són favorables per a la depuradora actual. Amb el projecte de Susana Forero Sánchez, les conclusions que es poden establir en referència a la decisió d’instal·lar una depuradora o una altra segons els vectors estudiats indiquen que l’EDAR sense aiguamolls té més probabilitat de ser escollida com la més adient per les necessitats del territori d’estudi.

Exercise induces rapid interstitial lung water accumulation in patients with chronic mountain sickness.

BACKGROUND: Chronic mountain sickness (CMS) is a major public health problem in mountainous regions of the world. In its more advanced stages, exercise intolerance is often found, but the underlying mechanism is not known. Recent evidence indicates that exercise-induced pulmonary hypertension is markedly exaggerated in CMS. We speculated that this problem may cause pulmonary fluid accumulation and aggravate hypoxemia during exercise. METHODS: We assessed extravascular lung water (chest ultrasonography), pulmonary artery pressure, and left ventricular function in 15 patients with CMS and 20 control subjects at rest and during exercise at 3,600 m. RESULTS: Exercise at high altitude rapidly induced pulmonary interstitial fluid accumulation in all patients but one (14 of 15) with CMS and further aggravated the preexisting hypoxemia. In contrast, in healthy high-altitude dwellers exercise did not induce fluid accumulation in the majority of subjects (16 of 20) (P = .002 vs CMS) and did not alter arterial oxygenation. Exercise-induced pulmonary interstitial fluid accumulation and hypoxemia in patients with CMS was accompanied by a more than two times larger increase of pulmonary artery pressure than in control subjects (P < .001), but no evidence of left ventricular dysfunction. Oxygen inhalation markedly attenuated the exercise-induced pulmonary hypertension (P < .01) and interstitial fluid accumulation (P < .05) in patients with CMS but had no detectable effects in control subjects. CONCLUSIONS: To our knowledge, these findings provide the first direct evidence that exercise induces rapid interstitial lung fluid accumulation and hypoxemia in patients with CMS that appear to be related to exaggerated pulmonary hypertension. We suggest that this problem contributes to exercise intolerance in patients with CMS. TRIAL REGISTRY: ClinicalTrials.gov; No.: NCT01182792; URL: www.clinicaltrials.gov.

The rapid urinary drug toxicology screen in the emergency room: a useful tool ?

Intoxications are a frequent problem in the ER. In the vast majorityof cases, supportive treatment is sufficient. Severe intoxications withunknown agents are considered an indication for a urinary drug screen,and are recommended by several toxicology centers. However, theirusefulness for patient management remains uncertain.Study objectives: Evaluation of the impact of a urinary drug screen(Biosite Triage TOX Drug Screen) testing 11 substances(acetaminophen, amphetamines, methamphetamines, barbiturates,benzodiazepines, cocaïne, methadone, opioids, phencyclidine,cannabis, tricyclic antidepressants) on initial adult patient managementin the emergency department of a university hospital with ~35.000annual admissions.Methods: Observational retrospective analysis of all tests performedbetween 09/2009 and 09/2010. A test utility was defined as useful if itresulted in the administration of a specific antidote (Flumazenil/Naloxone), the use of a quantitative confirmatory toxicologic test, or achange in patient's disposition.Results: 57 tests were performed. Patient age was 32 ± 11 (SD) years;58% were men; 30% were also intoxicated with alcohol. Two patientsdied (3.5%): the first one of a diphenhydramin overdose, the other of ahypertensive intracerebral hemorrhage believed to be caused cocaineabuse but a negative urine test. Test indications were: 54% firstpsychotic episode; 25% acute respiratory failure; 18% coma; 12%seizure; 11% opioids toxidrome; 7% sympathicomimetic toxidrome; 5%hypotension; 4% ventricular arrhythmia (VT, VF, torsades de pointes)or long QT. 75% of tests were positives for >=1 substance (mean 1.7 ±0.9). 47% of results were unexpected by history. 18% of resultsinfluenced patient management: 7% had a negative test that confirmedthe diagnosis of endogenous psychosis in a first psychotic episode, andallowed transfer to psychiatry; 5% received flumazenil/naloxone;2% had an acetaminophen blood level after a positive screen; finally,4% had an unexpected methadone abuse that required prolongationof hospital stay.Conclusions: A rapid urinary toxicologic screen was seldom used inour emergency department, and its impact on patient managementwas marginal: only one in 6 tests influenced treatment decisions.

Aplicación de soporte para personal docente en dispositivo móvil: iPhone

Actualment és difícil no veure a gent de totes les edats amb algun tipus de Gadget electrònic. En forma de telèfons mòvils, GPS, agendes electròniques, reproductors de música, tablets o qualsevol altre dispositiu, el món digital ens aborda, la informació i les dades es digitalitzen i arriben fins a les nostres butxaques per ser accessibles en qualsevol moment. Es fa indispensable familiaritzar-se amb aquestes eines i per això s’introdueixen en els centres educatius de tot el món. En aquest projecte es combinen tots aquests fets per desenvolupar un herbari digital sobre un dispositiu mòbil, amb finalitat educativa i ús privat.

Naltrexone-assisted rapid methadone discontinuation : a pilot study

Rapport de Synthèse : Un sevrage lent comme méthode élective pour l'interruption de la méthadone est coûteux en termes de temps, le plus souvent associé à un taux élevé d'abandon. Bien que les méthodes ultrarapides de désintoxication des opiacés aient gagné en popularité récemment, elles sont chères et posent les problèmes spécifiques liés aux patients traités par la méthadone. Méthodologie: ont été inclus dans l'étude dix patients en traitement de substitution avec de la méthadone. La dernière dose de méthadone a été administrée le matin même du jour de l'admission, en préalable à l'hospitalisation. Les médicaments suivants ont été administrés le jour suivant l'admission: ondansetron 36mg, ranitidine 40mg, loperamide 8m., clonazepam 4m., promazine 1OOmg, metoclopramide 70mg, naltrexone 5Omg. L'échelle objective de sevrage des opiacés (Objective Opiate Withdrawal Scale) a été appliquée au deuxième, troisième et quatrième jour d'hospitalisation, deux fois par jour, à 8h00 et 18h00. Un suivi a été réalisé sous la forme d'entretiens téléphoniques pendant une semaine, respectivement six mois après la date de sortie de l'hôpital, faisant suite à la désintoxication. Un autre entretient téléphonique a été réalisé dans les six mois suivant le "post-sevrage", avec pour objectif d'investiguer la continuité du traitément, une éventuelle rechute dans l'abus de drogues et une possible réintroduction de la méthadone. Résultats: nous avons pu déterminer quatre groupes de symptômes, sur la base d'une observation de trois jours d'évolution: 1) Les signes typiques du syndrome de sevrage de retrait des opiacés, symptôme de froid et chaud, pilo-érection, anxiété caractérisée par une intensité initiale élevée et une disparition relativement continue. 2) Hyperactivité neurovégétative caractérisée par une intensité initiale élevée et une rapide disparition. 3) Phénomènes neurovégétatifs dont l'intensité s'est maintenue durant toute la période d'observation. 4) Contractions musculaires, insomnies et anorexie, manque d'appétit, réapparaissant chez certains patients au 2ème et au début du 3ème jour. Conclusions: une procédure courte de désintoxication utilisant une dose unique de naltrexone s'avère être une méthode alternative valable pour un sevrage de la méthadone. Cette méthode semble accélérer et écourter la symptomatologie associée au sevrage. Le cours des symptômes peut être interprété comme biphasique. Une première phase de retrait est éminemment caractérisée par tous les symptômes typiques eux-mêmes et probablement induits par la naltrexone. La seconde phase, pour un plus petit nombre de patients, peut être interprétée comme en corrélation avec une concentration de méthadone en diminution significative ultérieurement.

Rapid, combinatorial analysis of membrane compartments in intact plants with a multicolor marker set.

Plant membrane compartments and trafficking pathways are highly complex, and are often distinct from those of animals and fungi. Progress has been made in defining trafficking in plants using transient expression systems. However, many processes require a precise understanding of plant membrane trafficking in a developmental context, and in diverse, specialized cell types. These include defense responses to pathogens, regulation of transporter accumulation in plant nutrition or polar auxin transport in development. In all of these cases a central role is played by the endosomal membrane system, which, however, is the most divergent and ill-defined aspect of plant cell compartmentation. We have designed a new vector series, and have generated a large number of stably transformed plants expressing membrane protein fusions to spectrally distinct, fluorescent tags. We selected lines with distinct subcellular localization patterns, and stable, non-toxic expression. We demonstrate the power of this multicolor 'Wave' marker set for rapid, combinatorial analysis of plant cell membrane compartments, both in live-imaging and immunoelectron microscopy. Among other findings, our systematic co-localization analysis revealed that a class of plant Rab1-homologs has a much more extended localization than was previously assumed, and also localizes to trans-Golgi/endosomal compartments. Constructs that can be transformed into any genetic background or species, as well as seeds from transgenic Arabidopsis plants, will be freely available, and will promote rapid progress in diverse areas of plant cell biology.