High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

With the availability of new generation sequencing technologies, bacterial genome projects have undergone a major boost. Still, chromosome completion needs a costly and time-consuming gap closure, especially when containing highly repetitive elements. However, incomplete genome data may be sufficiently informative to derive the pursued information. For emerging pathogens, i.e. newly identified pathogens, lack of release of genome data during gap closure stage is clearly medically counterproductive. We thus investigated the feasibility of a dirty genome approach, i.e. the release of unfinished genome sequences to develop serological diagnostic tools. We showed that almost the whole genome sequence of the emerging pathogen Parachlamydia acanthamoebae was retrieved even with relatively short reads from Genome Sequencer 20 and Solexa. The bacterial proteome was analyzed to select immunogenic proteins, which were then expressed and used to elaborate the first steps of an ELISA. This work constitutes the proof of principle for a dirty genome approach, i.e. the use of unfinished genome sequences of pathogenic bacteria, coupled with proteomics to rapidly identify new immunogenic proteins useful to develop in the future specific diagnostic tests such as ELISA, immunohistochemistry and direct antigen detection. Although applied here to an emerging pathogen, this combined dirty genome sequencing/proteomic approach may be used for any pathogen for which better diagnostics are needed. These genome sequences may also be very useful to develop DNA based diagnostic tests. All these diagnostic tools will allow further evaluations of the pathogenic potential of this obligate intracellular bacterium.

Direct Sensitivity Test of the MB/BacT System

In order to evaluate the direct-method test of sensitivity to drugs used in the principal tuberculosis treatment regimes, in the Organon Teknika MB/BacT system, we tested 50 sputum samples positive to microscopy taken from patients with pulmonary tuberculosis and with clinical indications for an antibiogram, admitted sequentially for examination during the routine of the reference laboratory. The material was treated v/v with 23% trisodium phosphate solution, incubated for 24 h at 35°C, and neutralized v/v with 20% monosodium phosphate solution. The material was then centrifuged and the sediment inoculated into flasks containing Rifampin - 2 µg/ml, Isoniazid - 0.2 µg/ml, Pyrazinamide - 100 µg/ml, Ethambutol - 2.5 µg/ml, Ethionamide - 1.25 µg/ml, and Streptomycin - 2 µg/ml. The tests were evaluated using the indirect method in the BACTEC 460 TB (Becton Dickinson) system as the gold standard. The results showed that the Rifampin test performed best, i.e., 100% sensitivity at 95% Confidence Interval (82.2-100) and 100% specificity at 95% Confidence Interval (84.5-100), followed by Isoniazid and Pyrazinamide. In this experiment, 92% of the materials showed a final reading in 30 days; this period represents the time for primary isolation as well as the results of the sensitivity profile, and is within Centers for Disease Control and Prevention recommendations regarding time for performance of the antibiogram. The inoculated flasks showed no contamination during the experiment. The MB/BacT is shown to be a reliable, rapid, fully automated nonradiometric system for the tuberculosis antibiogram.

Testing for anaplastic lymphoma kinase rearrangement to target crizotinib therapy: oncology, pathology and health economic perspectives.

Crizotinib is a first-in-class oral anaplastic lymphoma kinase (ALK) inhibitor targeting ALK-rearranged non-small-cell lung cancer. The therapy was approved by the US FDA in August 2011 and received conditional marketing approval by the European Commission in October 2012 for advanced non-small-cell lung cancer. A break-apart FISH-based assay was jointly approved with crizotinib by the FDA. This assay and an immunohistochemistry assay that uses a D5F3 rabbit monoclonal primary antibody were also approved for marketing in Europe in October 2012. While ALK rearrangement has relatively low prevalence, a clinical benefit is exhibited in more than 85% of patients with median progression-free survival of 8-10 months. In this article, the authors summarize the therapy and alternative test strategies for identifying patients who are likely to respond to therapy, including key issues for effective and efficient testing. The key economic considerations regarding the joint companion diagnostic and therapy are also presented. Given the observed clinical benefit and relatively high cost of crizotinib therapy, companion diagnostics should be evaluated relative to response to therapy versus correlation alone whenever possible, and both high inter-rater reliability and external quality assessment programs are warranted.

Analyse de la prise en charge médicale et de l'impact économique des patients ayant présentés des coûts extrêmes dans un hôpital universitaire [Analysis of the medical management and the economic impact of patients who have represented extreme costs at a university hospital]

Les coûts de traitement de certains patients s'avèrent extrêmement élevés, et peuvent faire soupçonner une prise en charge médicale inadéquate. Comme I'évolution du remboursement des prestations hospitalières passe à des forfaits par pathologie, il est essentiel de vérifier ce point, d'essayer de déterminer si ce type de patients peut être identifié à leur admission, et de s'assurer que leur devenir soit acceptable. Pour les années 1995 et 1997. les coûts de traitement dépassant de 6 déviations standard le coût moyen de la catégorie diagnostique APDRG ont été identifiés, et les dossiers des 50 patients dont les coûts variables étaient les plus élevés ont été analysés. Le nombre total de patients dont I'hospitalisation a entraîné des coûts extrêmes a passé de 391 en 1995 à 328 patients en 1997 (-16%). En ce qui concerne les 50 patients ayant entraîné les prises en charge les plus chères de manière absolue, les longs séjours dans de multiples services sont fréquents, mais 90% des patients sont sortis de l'hôpital en vie, et près de la moitié directement à domicile. Ils présentaient une variabilité importante de diagnostics et d'interventions, mais pas d'évidence de prise en charge inadéquate. En conclusion, les patients qualifiés de cas extrêmes sur un plan économique, ne le sont pas sur un plan strictement médical, et leur devenir est bon. Face à la pression qu'exercera le passage à un mode de financement par pathologie, les hôpitaux doivent mettre au point un système de revue interne de I'adéquation des prestations fournies basées sur des caractéristiques cliniques, s'ils veulent garantir des soins de qualité. et identifier les éventuelles prestations sous-optimales qu'ils pourraient être amenés à délivrer. [Auteurs] Treatment costs for some patients are extremely high and might let think that medical care could have been inadequate. As hospital financing systems move towards reimbursement by diagnostic groups, it is essential to assess whether inadequate care is provided, to try to identify these patients upon admission, and make sure that their outcome is good. For the years 1995 and 1997, treatment costs exceeding by 6 standard deviations the average cost of their APDRG category were identified, and the charts of the 50 patients with the highest variable costs were analyzed. The total number of patients with such extreme costs diminished from 391 in 1995 to 328 in 1997 (-16%). For the 50 most expensive patients, long stays in several services were frequent, but 90% of these patients left the hospital alive, and about half directly to their home. They presented an important variation in diagnoses and operations, but no evidence for inadequate care. Thus, patients qualified as extreme from an economic perspective cannot be qualified as such from a medical perspective, and their outcome is good. To face the pressure linked with the change in financing system, hospitals must develop an internal review system for assessing the adequacy of care, based on clinical characteristics, if they want to guarantee good quality of care and identify potentially inadequate practice.

Report of the Consultation for a National Rare Disease Plan for Ireland

This report presents findings from the National Consultation on Rare Disease overseen by the Institute of Public Health in Ireland on behalf of the Department of Health to inform the development of Irelandâ?Ts first National Rare Disease Plan. In 2009, the Council of the European Union recommended that all member countries develop a national plan for rare diseases with the framework of their health and social systems by the end of 2013. The aim is to ensure that all patients with rare disease in Europe have access to high quality care, including diagnostics, treatments and rehabilitation.  Download the report here

Evaluation of indirect susceptibility testing of Mycobacterium tuberculosis to the first- and second-line, and alternative drugs by the newer MB/BacT system

In order to evaluate the Organon Teknika MB/BacT system used for testing indirect susceptibility to the alternative drugs ofloxacin (OFLO), amikacin (AMI), and rifabutin (RIF), and to the usual drugs of standard treatment regimes such as rifampin (RMP), isoniazid (INH), pyrazinamide (PZA), streptomycin (SM), ethambutol (EMB), and ethionamide (ETH), cultures of clinical specimens from 117 patients with pulmonary tuberculosis under multidrug-resistant investigation, admitted sequentially for examination from 2001 to 2002, were studied. Fifty of the Mycobacterium tuberculosis cultures were inoculated into the gold-standard BACTEC 460 TB (Becton Dickinson) for studying resistance to AMI, RIF, and OFLO, and the remaining 67 were inoculated into Lowenstein Jensen (LJ) medium (the gold standard currently used in Brazil) for studying resistance to RMP, INH, PZA, SM, EMB, and ETH. We observed 100% sensitivity for AMI (80.8-100), RIF (80.8-100), and OFLO (78.1-100); and 100% specificity for AMI (85.4-100), RIF (85.4-100), and OFLO (86.7-100) compared to the BACTEC system. Comparing the results obtained in LJ we observed 100% sensitivity for RMP (80-100), followed by INH - 95% (81.8-99.1), EMB - 94.7% (71.9-99.7), and 100% specificity for all drugs tested except for PZA - 98.3 (89.5-99.9) at 95% confidence interval. The results showed a high level of accuracy and demonstrated that the fully automated, non-radiometric MB/BacT system is indicated for routine use in susceptibility testing in public health laboratories.

www.fevertravel.ch : an online study prototype to evaluate the safety and feasibility of computerized guidelines for fever in returning travellers and migrants

Résumé Suite à la publication des recommandations de pratiques cliniques sur la prise en soins de patients fébriles au retour des tropiques, nous avons développé un site internet de consultation www.fevertravel.ch qui comprend un arbre décisionnel et des caractéristiques diagnostiques spécifiques fournissant une assistance diagnostique aux médecins de premier recours. Nous avons ensuite intégré une composante de recherche afin d'évaluer l'implémentation de ces recommandations de pratiques cliniques informatisées. De plus, le site est capable d'enregistrer : (1) le chemin parcouru par le médecin au travers de l'arbre décisionnel, (2) les tests diagnostics effectués, (3) les diagnostics initial et final ainsi que les devenirs des patients et (4) les raisons de non-adhérence lorsque les médecins divergent de l'attitude proposée. Nous croyons que la technologie internat est un moyen puissant pour atteindre des médecins provenant de différents horizons dans leur propre environnement et qu'il pourrait se montrer être un outil de recherche efficace pour disséminer les recommandations de pratiques cliniques et évaluer leur justesse-adéquation. Dans cet article, nous décrivons le design, le contenu, l'architecture et l'implémentation du système de ce prototype d'étude interactive qui vise à intégrer une recherche opérationnelle en médecine de premier recours.

Immunoblotting for the serodiagnosis of Helicobacter pylori infection in Brazilian patients with and without gastric carcinoma

We evaluated the performance of a commercial immunoblotting in the serodiagnosis of Helicobacter pylori infection in Brazilian patients. The presence of anti-H. pylori antibodies was also investigated in a group of 20 duodenal ulcer patients after successful treatment. One hundred and ninety one patients were studied. Among the 164 infected patients, 46 had gastric carcinoma. The duodenal ulcer patients were treated with antimicrobial drugs and the eradication of the microorganism was confirmed in all of them one month after the end of the treatment by the 13C-urea breath test. Sera were assayed for H. pylori antibodies using the Helicoblot 2.0 (Genelabs Diagnostics, Singapore). The sensitivity, specificity, positive, and negative predictive values of the test were 93.9%, 92.6%, 98.7%, and 71.4%, respectively. The sensitivity of the test was similar in patients with (93.5%) and without (95.7%) gastric carcinoma. Twenty-four months after the end of the treatment, the band of 116 kDa was still detected in one of the patients. In conclusion, the Helicoblot 2.0 is an accurate test to diagnose H. pylori infection and although it can not be employed to monitor the bacterium eradication, it may be useful for diagnosing past infection, especially in gastric carcinoma patients.

DIP-STR: Highly Sensitive Markers for the Analysis of Unbalanced Genomic Mixtures.

Samples containing highly unbalanced DNA mixtures from two individuals commonly occur both in forensic mixed stains and in peripheral blood DNA microchimerism induced by pregnancy or following organ transplant. Because of PCR amplification bias, the genetic identification of a DNA that contributes trace amounts to a mixed sample represents a tremendous challenge. This means that standard genetic markers, namely microsatellites, also referred as short tandem repeats (STR), and single-nucleotide polymorphism (SNP) have limited power in addressing common questions of forensic and medical genetics. To address this issue, we developed a molecular marker, named DIP-STR that relies on pairing deletion-insertion polymorphisms (DIP) with STR. This novel analytical approach allows for the unambiguous genotyping of a minor component in the presence of a major component, where DIP-STR genotypes of the minor were successfully procured at ratios up to 1:1,000. The compound nature of this marker generates a high level of polymorphism that is suitable for identity testing. Here, we demonstrate the power of the DIP-STR approach on an initial set of nine markers surveyed in a Swiss population. Finally, we discuss the limitations and potential applications of our new system including preliminary tests on clinical samples and estimates of their performance on simulated DNA mixtures.

Study of the antibody response against Mycobacterium tuberculosis antigens in Warao Amerindian children in Venezuela

This study was aimed at investigating alternate methods for serodiagnosis of tuberculosis (TB), which are needed because bacteriologic diagnosis of childhood TB is difficult. A selection of 80 serum and saliva samples were tested from Warao indigenous children under 15 years of age; 34 high TB suspects (28 positive and 6 negative for the tuberculin skin test, TST) and 46 healthy contact children (32 positive and 14 negative for the TST). Several enzyme-linked immunosorbent assay (ELISA) serological tests were developed to test for Mycobacterium tuberculosis-specific antibodies, including serum IgA, IgG, IgE, and secretory IgA (sIgA) in saliva against 3 specific antigens (PPD, HSP60, 38 kDa). Of these, 2 antigens, PPD and 38 kDa, showed significantly higher reactivity. The sensitivity and specificity of these tests for diagnosis remained limited, between 26.5% and 38.2%, and 77.4% and 97%, respectively. Of all the samples studied and combinations realized between all isotypes and antigens combined with 3 isotypes (anti-PPD IgG, IgE, and anti-38kDa sIgA) managed to detect the largest number of patients, showing an improved sensitivity level of 64.7%, although specificity levels dropped to 81.8%. These results were compared with the Omega diagnostics commercial kit results. The commercial kits showed significantly lower reactivity (sensitivity of 20% and 13.33% to Myco G and Complex Plus, respectively) and a specificity of 100%. This study shows that in indigenous populations of Venezuela, where invasive procedures cannot be used to select samples but evaluation with a chest X-ray for radiological studies is available, the combination of 3 specific isotypes may be a useful tool to increase diagnostic accuracy with pulmonary TB in this population, when used together with clinical and epidemiological criteria.

Interpretation of array comparative genome hybridization data: a major challenge.

The advent and application of high-resolution array-based comparative genome hybridization (array CGH) has led to the detection of large numbers of copy number variants (CNVs) in patients with developmental delay and/or multiple congenital anomalies as well as in healthy individuals. The notion that CNVs are also abundantly present in the normal population challenges the interpretation of the clinical significance of detected CNVs in patients. In this review we will illustrate a general clinical workflow based on our own experience that can be used in routine diagnostics for the interpretation of CNVs.

Alzheimer's Disease Biomarkers, 2009

This report gives a comprehensive and up-to-date review of Alzheimer's disease biomarkers. Recent years have seen significant advances in this field. Whilst considerable effort has focused on A�_ and tau related markers, a substantial number of other molecules have been identified, that may offer new opportunities.This Report : Identifies 60 candidate Alzheimer's (AD) biomarkers and their associated studies. Of these, 49 are single species or single parameters, 7 are combinations or panels and 4 involve the measurement of two species or parameters or their ratios. These include proteins (n=34), genes (n=11), image-based parameters (n=7), small molecules (n=3), proteins + genes (n=2) and others (n=3). Of these, 30 (50%) relate to species identified in CSF and 19 (32%) were found in the blood. These candidate may be classified on the basis of their diagnostic utility, namely those which i) may allow AD to be detected when the disease has developed (48 of 75†= 64%), ii) may allow early detection of AD (18 of 75† = 24%) and iii) may allow AD to be predicted before the disease has begun to develop (9 of 75†= 12%). † Note: Of these, 11 were linked to two or more of these capabilities (e.g. allowed both early-stage detection as well as diagnosis after the disease has developed).Biomarkers: AD biomarkers identified in this report show significant diversity, however of the 60 described, 18 (30%) are associated with amyloid beta (A�_) and 9 (15%) relate to Tau. The remainder of the biomarkers (just over half) fall into a number of different groups. Of these, some are associated with other hypotheses on the pathogenesis of AD however the vast majority are individually unique and not obviously linked with other markers. Analysis and discussion presented in this report includes summaries of the studies and clinical trials that have lead to the identification of these markers. Where it has been calculated, diagnostic sensitivity, specificity and the capacity of these markers to differentiate patients with suspected AD from healthy controls and individuals believed to be suffering from other neurodegenerative conditions, have been indicated. These findings are discussed in relation to existing hypotheses on the pathogenesis of the AD and the current drug development pipeline. Many uncertainties remain in relation to the pathogenesis of AD, in diagnosing and treating the disease and many of the studies carried out to identify disease markers are at an early stage and will require confirmation through larger and longer investigations. Nevertheless, significant advances in the identification of AD biomarkers have now been made. Moreover, whilst much of the research on AD biomarkers has focused on amyloid and tau related species, it is evident that a substantial number of other species may provide important opportunities.Purpose of Report: To provide a comprehensive review of important and recently discovered candidate biomarkers of AD, in particular those with potential to reliably detect the disease or with utility in clinical development, drug repurposing, in studies of the pathogenesis and in monitoring drug response and the course of the disease. Other key goals were to identify markers that support current pipeline developments, indicate new potential drug targets or which advance understanding of the pathogenesis of this disease.Drug Repurposing: Studies of the pathogenesis of AD have identified aberrant changes in a number of other disease areas including inflammation, diabetes, oxidative stress, lipid metabolism and others. These findings have prompted studies to evaluate some existing approved drugs to treat AD. This report identifies studies of 9 established drug classes currently being investigated for potential repurposing.Alzheimer’s Disease: In 2005, the global prevalence of dementia was estimated at 25 million, with more than 4 million new cases occurring each year. It is also calculated that the number of people affected will double every 20 years, to 80 million by 2040, if a cure is not found. More than 50% of dementia cases are due to AD. Today, approximately 5 million individuals in the US suffer from AD, representing one in eight people over the age of 65. Direct and indirect costs of AD and other forms of dementia in the US are around $150 billion annually. Worldwide, costs for dementia care are estimated at $315 billion annually. Despite significant research into this debilitating and ultimately fatal disease, advances in the development of diagnostic tests for AD and moreover, effective treatments, remain elusive.Background: Alzheimer's disease is the most common cause of dementia, yet its clinical diagnosis remains uncertain until an eventual post-mortem histopathology examination is carried out. Currently, therapy for patients with Alzheimer disease only treats the symptoms; however, it is anticipated that new disease-modifying drugs will soon become available. The urgency for new and effective treatments for AD is matched by the need for new tests to detect and diagnose the condition. Uncertainties in the diagnosis of AD mean that the disease is often undiagnosed and under treated. Moreover, it is clear that clinical confirmation of AD, using cognitive tests, can only be made after substantial neuronal cell loss has occurred; a process that may have taken place over many years. Poor response to current therapies may therefore, in part, reflect the fact that such treatments are generally commenced only after neuronal damage has occurred. The absence of tests to detect or diagnose presymptomatic AD also means that there is no standard that can be applied to validate experimental findings (e.g. in drug discovery) without performing lengthy studies, and eventual confirmation by autopsy.These limitations are focusing considerable effort on the identification of biomarkers that advance understanding of the pathogenesis of AD and how the disease can be diagnosed in its early stages and treated. It is hoped that developments in these areas will help physicians to detect AD and guide therapy before the first signs of neuronal damage appears. The last 5-10 years have seen substantial research into the pathogenesis of AD and this has lead to the identification of a substantial number of AD biomarkers, which offer important insights into this disease. This report brings together the latest advances in the identification of AD biomarkers and analyses the opportunities they offer in drug R&D and diagnostics.��

Première hospitalisation en psychiatrie à l'âge avancé

Résumé : Cette étude a concerné un groupe de patients séjournant pour la première fois en milieu psychiatrique à l'âge avancé. La moitié étaient âgés de quatre-vingt ans ou plus et deux tiers étaient des femmes. Deux tiers provenaient de leur domicile et un quart étaient sous protection légale. L'admission a été faite pour une dépression dans la moitié des cas, pour une démence dans un tiers des cas, pour une symptomatologie anxieuse dans un quart des cas. Les diagnostics psychiatriques à la sortie de l'hôpital étaient différents de ceux annoncés à l'admission. Le syndrome démentiel concernait la moitié des patients et la maladie d'Alzheimer prédominait chez la femme, alors que les démences vasculaires et celles associées à d'autres maladies étaient deux fois plus fréquentes chez l'homme. Les troubles de l'humeur ne concernaient qu'un cinquième des cas et les troubles de l'adaptation un sixième des cas. Presque une moitié des patients présentaient deux ou trois diagnostics psychiatriques concomitants. La co-morbidité somatique était dominée par les maladies cardio-vasculaires, notamment chez l'homme. Un tiers des femmes et autant d'hommes présentaient au moins quatre diagnostics somatiques concomitants. La durée moyenne d'hospitalisation de quatre-vingt-cinq jours a été prolongée ou raccourcie par certains facteurs: le placement en Etablissement Médico-Social prolonge de plus de deux mois l'hospitalisation. Les personnes mariées restent presque deux mois de moins à l'hopital. Le trouble de la personnalité et du comportement et le trouble dépressif récurrent prolongent de presque six mois, respectivement trois mois, la durée de l'hospitalisation. Plus de la moitié des- patients sont placés en Etablissement Médico-Social. Certains facteurs augmentent le risque de placement: la démence d'Alzheimer accroît le risque de quatre fois ; avec chaque année en plus, le risque d'être placé en institution augmente de 20% ; il en va de même pour les hospitalisations prolongées. Les patients qui rentrent à domicile (moins de la moitié, surtout des femmes) ont besoin d'aide : suivi médico-infirmier, aide .aux tâches ménagères. Le suivi ambulatoire a été assuré par l'hôpital de jour avant tout, la Consultation ambulatoire en collaboration avec les centres médico-sociaux jouant un rôle important. Les ré-hospitalisations à l'Hôpital de Psychiatrie de l'Age Avancé dans l'année suivant la sortie ont concerné un quart de femmes et un septième d'hommes, avec une durée de séjour plus courte que celle lors de la première hospitalisation.

Hepatitis E Virus Seroprevalence among Blood Donors in Southwest Switzerland.

Aim: The aim of this study was to determine the seroprevalence of Hepatitis E virus (HEV) among blood donors in southwest Switzerland.Background: HEV is recognized as a food-borne disease in industrialized countries, transmitted mainly through pork meat. Cases of transmission through blood transfusion have also been reported. Recent studies have revealed seroprevalence rates of 13.5%, 16.6% and 20.6% among blood donors in England, France and Denmark, respectively.Methods: We analyzed 550 consecutive blood donor samples collected in the region of Lausanne, canton of Vaud, Switzerland, for the presence of anti-HEV IgG, using the MP Diagnostics HEV ELISA kit. For each donor, we documented age, sex and alanine aminotransferase (ALT) value.Results: The study panel was composed of 332 men (60.4%) and 218 women (39.6%). Overall, anti-HEV IgG was found in 27 of 550 samples (4.9%). The seroprevalence was 5.4% (18/332) in men and 4.1% (9/218) in women. The presence of anti-HEV IgG was not correlated with age, gender or ALT values. However, we observed a peak in seroprevalence of 5.3% in individuals aged 51 to 70 years old.Conclusions: Compared with other European countries, HEV seroprevalence among blood donors in southwest Switzerland is low. The low seroprevalence may be explained by the sensitivity of commercial tests used and/or the strict regulation of animal and meat imports. Data regarding HEV prevalence in Swiss livestock are lacking and merit exploration.

Report of the Consultation for a National Rare Disease Plan for Ireland

This IPH report (2013) (prepared for the ROI Department of Health) presents findings from the National Consultation on Rare Disease overseen by the Institute of Public Health in Ireland on behalf of the Department of Health to inform the development of Ireland’s first National Rare Disease Plan. In 2009, the Council of the European Union recommended that all member countries develop a national plan for rare diseases with the framework of their health and social systems by the end of 2013. The aim is to ensure that all patients with rare disease in Europe have access to high quality care, including diagnostics, treatments and rehabilitation.