Use of Targeted Exome Sequencing for Molecular Diagnosis of Skeletal Disorders

Genetic disorders of the skeleton comprise a large group of more than 450 clinically distinct and genetically heterogeneous diseases associated with mutations in more than 300 genes. Achieving a definitive diagnosis is complicated due to the genetic heterogeneity of these disorders, their individual rarity and their diverse radiographic presentations. We used targeted exome sequencing and designed a 1.4Mb panel for simultaneous testing of more than 4,800 exons in 309 genes involved in skeletal disorders. DNA from 69 individuals from 66 families with a known or suspected clinical diagnosis of a skeletal disorder was analyzed. Of 36 cases with a specific clinical hypothesis with a known genetic basis, mutations were identified for eight cases (22%). Of 20 cases with a suspected skeletal disorder but without a specific diagnosis, four causative mutations were identified. Also included were 11 cases with a specific skeletal disorder but for which there was at the time no known associated gene. For these cases, one mutation was identified in a known skeletal disease genes, and re-evaluation of the clinical phenotype in this case changed the diagnoses from osteodysplasia syndrome to Apert syndrome. These results suggest that the NGS panel provides a fast, accurate and cost-effective molecular diagnostic tool for identifying mutations in a highly genetically heterogeneous set of disorders such as genetic skeletal disorders. The data also stress the importance of a thorough clinical evaluation before DNA sequencing. The strategy should be applicable to other groups of disorders in which the molecular basis is largely known.

[Determination of hyperregeneratory esophagopathy in dogs with clinical signs attributable to esophageal disease]

OBJECTIVE

It was hypothesized that typical characteristics of hyperregeneratory esophagopathy (HRE) in humans such as basal cell hyperplasia and elongation of stromal papillae are also histologically detectable in canine esophageal epithelium, and that these changes are associated with clinical signs and endoscopic findings suggesting gastroesophageal reflux (GER).

MATERIAL AND METHODS

Sixty-five adult dogs with clinical signs attributable to esophageal disease underwent esophagoscopy and biopsy. Clinical signs suggesting GER (regurgitation, ptyalism, painful discomfort) were prospectively evaluated through a questionnaire. Endoscopic mucosal alterations suggesting GER such as minimal endoscopic changes and obvious mucosal defects were assessed via video endoscopy. Biopsy specimens obtained from the esophageal squamous epithelium were evaluated histologically. The squamous epithelium's substructures of esophageal biopsies were quantitatively assessed through microscopic morphometry.

RESULTS

Esophageal squamous epithelium was considered normal in 48 dogs, and HRE was detected histologically in 17 dogs; both pathognomonic changes (basal cell hyperplasia, elongation of stromal papillae) were consistently present. Morphometrically assessed stromal papillary length and basal cell layer thickness was significantly (each, p < 0.0001) higher in the 17 dogs with HRE than in the 48 dogs without HRE, respectively. Overall, clinical signs suggesting GER were significantly (p = 0.02) more frequently encountered and regurgitation was significantly (p = 0.009) more common in the 17 dogs with HRE than in the 48 dogs without HRE. Similarly, endoscopic changes were significantly (p = 0.002) more frequently observed and minimal endoscopic changes suggesting GER were significantly (p = 0.004) more common in 17 dogs with HRE than in the 48 dogs without HRE.

CONCLUSION AND CLINICAL RELEVANCE

Typical characteristics of hyperregeneratory esophagopathy in humans are also histologically detectable in canine esophageal epithelium. Histological changes are associated with clinical signs and endoscopic findings suggesting GER.

Unpredictable susceptibility of emerging clinical moulds to tri-azoles: review of the literature and upcoming challenges for mould identification

Tri-azoles represent the front-line drugs for the treatment of mould diseases; nevertheless, some emerging moulds, such as Fusarium spp., Scedosporium spp., Mucorales and others, may be less susceptible or resistant to these antifungals. A review of the literature was conducted on the susceptibility of rare moulds to the tri-azoles itraconazole, posaconazole and voriconazole. Particular attention was paid to isolates identified by molecular analyses. The range of susceptibility values described for the three tri-azoles was frequently large (from 0.06 to >16), and a high variability was found within each species; isolates were rarely reported as entirely susceptible to all tri-azoles. In addition, the susceptibility of 76 emerging moulds from our collection (including Hypocreales, Dothideomycetes, Scedosporium spp., Mucorales and rare Aspergillus spp.) to itraconazole and voriconazole was determined by the Clinical and Laboratory Standards Institute (CLSI) M38-A2 and European Committee for Antimicrobial Susceptibility Testing (EUCAST) methods. Susceptibility discrepancies (of two dilutions) were found comparing CLSI and EUCAST for Dothideomycetes; the values for the remaining moulds were similar. More practical, faster and inexpensive susceptibility tools are welcome for testing emerging moulds, as these tests still represent a critical tool to support clinicians on the selection of proper antifungal treatment. The susceptibility of emerging moulds to tri-azoles cannot be predicted exclusively following mould identification, as the isolates' susceptibilities showed highly variable values. Some emerging moulds still remain very difficult to identity, even following standard molecular analyses which result in complex fungal collections. This fact limits the definition of epidemiological cut-offs and clinical breakpoints that are still imperative for emerging moulds.

Multilocus sequence typing of Campylobacter jejuni and Campylobacter coli strains isolated from environmental waters in the Mediterranean area

Campylobacter jejuni and Campylobacter coli are important animal-related waterborne pathogens that are distributed worldwide. To further understand Campylobacter populations in water from the Mediterranean area, the genetic diversity of environmental strains was analyzed using multilocus sequence typing (MLST). MLST was also used to determine the potential geographical differences between these bacterial strains and other campylobacters isolated worldwide. The typing study was conducted using 58 strains isolated from the Llobregat river and other water sources, such as urban sewage, animal wastewater and clinical samples. Thirty-nine different sequence types were obtained; eight of these sequences were described for the first time in this study, suggesting the presence of local strains. The identified C. jejuni strains were the most diverse population, whereas the identified C. coli strains showed a high clonal structure, which clustered most of the sequence types into a few clonal complexes. The strains were not exclusively related to specific water sources. However, comparing the identified strains with an international database showed that most of the Mediterranean strains that were exclusively isolated from environmental waters have previously been isolated from similar sources, particularly those obtained from river water. Additional studies, including those in different geographical areas using a wide range of Campylobacter sources, are required to improve the global knowledge concerning Campylobacter dissemination in the environment.

Diversidad morfológica y molecular de los Unionidae (Mollusca, Bivalvia) de Portugal

Las náyades de la familia Unionidae tienen gran plasticidad fenotípica, lo que se refleja en la forma de su concha. Esta variabilidad morfológica ha sido causa de gran confusión en la taxonomía y sistemática del grupo. Se han estudiado, genética y morfológicamente, numerosas poblaciones de náyades provenientes de nueve cuencas hidrográficas portuguesas. Para ello se han analizando dos fragmentos de genes mitocondriales (ARNr 16S y Citocromo Oxidasa I) así como diferentes variables morfológicas de la concha. Se han realizado además análisis filogenéticos para conocer la sistemática de la familia e inferir una hipótesis evolutiva de su distribución en el oeste de la península Ibérica. Los datos genéticos y morfológicos sugieren la existencia de cinco especies: Anodonta anatina, Anodonta cygnea, Potomida littoralis, Unio tumidiformis y Unio delphinus. La diferenciación de estas especies, con la excepción de A. cygnea, ha ocurrido durante el aislamiento de la península Ibérica y posterior formación de las actuales cuencas hidrográficas en el Terciario. Se discute la posibilidad de que la presencia de A. cygnea se deba a una introducción reciente. Los datos morfométricos analizados pueden ser útiles para separar las especies del género Unio, pero son también dependientes de las condiciones ambientales. La elevada variabilidad morfológica dentro de cada especie está relacionada con su plasticidad fenotípica, pero tiene a su vez un importante papel en el proceso evolutivo.

Effect of environmental parameters on the inactivation of the waterborne pathogen Campylobacter in a Mediterranean river

Campylobacter is a major waterborne pathogen that can be found in rivers of the Mediterranean area. Characteristics of these rivers change throughout the seasons due to variations in environmental parameters. As these variations may affect water survival of Campylobacter, we analyzed it in the Llobregat River using three approaches whose complexity increase progressively: (i) river water microcosms in the laboratory subjected to varying temperatures; (ii) in situ experiments carried out in the river, in which bacteria were exposed to varying levels of environmental parameters; and (iii) monitoring of thermotolerant Campylobacter in the river over two years. Campylobacter was quantified using the most probable number (MPN) method. The results showed that an increase in water temperature accelerates Campylobacter inactivation, measured as the loss of culturability. In situ experiments revealed that inactivation rates were also affected by sunlight, but not by pH, oxygen concentration or water conductivity. These observations are supported by the seasonality detected in Llobregat River. Campylobacter inactivation was fastest in spring and summer, when temperature and solar radiation were at their highest. The results highlight the importance of considering the inactivation rates in natural conditions to improve the monitoring of this pathogen and thus evaluate properly the health risk associated to water.

Fetal death in cows experimentally infected with Neospora caninum at 110 days of gestation

Neospora caninum is a major cause of abortion in cattle, but the reasons why some animals abort and not others remain unclear. Most of the N. caninum experimental primary infections in cattle late in gestation, after 120 days of pregnancy, result in birth of full-term congenitally infected fetuses. In the present study, the distribution of parasites and pathogenesis of infection in both dams and fetuses after inoculation with 10(7) culture derived tachyzoites of N. caninum NC-Illinois cattle strain at 110 days of gestation were analyzed at 3 weeks, 6 weeks and 9 weeks after infection (WAI) in eight Angus heifers. One dam from the group euthanized at 6 WAI had a dead fetus at necropsy. Extensive lesions were observed in the placenta and tachyzoites were detected in both the placenta and the fetus. The fetus was seropositive and had high IFN-gamma g production in fetal fluids. Another fetus, still alive when euthanized at 3 WAI, had severe lesions and high IFN-gamma production and a similar fate could have been expected if the experimental period would have been longer. Lesions in the placenta of the remaining six dams that had live fetuses at necropsy were mild. In those dams, the fetal and maternal placentas had not separated and contained focal areas of placentitis at the materno-fetal junction. Transplacental infection took place on all fetuses based on detection of parasitic DNA in fetal tissues. The present study shows that experimental N. caninum infection of naïve dams after 110 days of pregnancy can lead to fetal death. The results suggest that the severity of placental lesions and the strong IFN-gamma response in some fetuses, possibly as part of the immune response trying to control the high parasitemia, might, in fact, be the cause of their death.

Simple and highly discriminatory microsatellite-based multiplex PCR for Aspergillus fumigatus strain typing

The answers to important questions concerning Aspergillus fumigatus pathogenicity, transmissions routes and efficacy of treatments require highly discriminating and reproducible genotyping methods. The present study was aimed at improving microsatellite methodology for A. fumigatus typing by reducing the task of strain identification to a single multiplex reaction and by selecting highly accurate short tandem repeat polymorphisms. A set of eight primer pairs was used for the genotype determination of 116 clinical isolates of A. fumigatus obtained from three healthcare centres. A new, automated and highly discriminatory typing method is described for A. fumigatus strains. The optimized multiplex PCR was successfully performed with all tested clinical strains and showed a discriminatory power of 0.9997 among presumably unrelated isolates. The comparison of groups of strains from different health centres showed that 99.6% of the genotypic variation was present within groups. Strains with the same genotype were isolated from the same patient, sometimes recovered more than 1 year later. A few cases of patients at the same clinic unit carrying strains of identical genotype strongly suggested colonization by A. fumigatus during their hospitalization. Specific measures must therefore be taken in order to prevent and restrict such incidents.

Learning sensor-based navigation of a real mobile robot in unknown worlds

In this paper, we address the problem of navigating an autonomous mobile robot in an unknown indoor environment. The parti-game multiresolution learning approach is applied for simultaneous and cooperative construction of a world model, and learning to navigate through an obstacle-free path from a starting position to a known goal region. The paper introduces a new approach, based on the application of the fuzzy ART neural architecture, for on-line map building from actual sensor data. This method is then integrated, as a complement, on the parti-game world model, allowing the system to make a more efficient use of collected sensor information. Then, a predictive on-line trajectory filtering method, is introduced in the learning approach. Instead of having a mechanical device moving to search the world, the idea is to have the system analyzing trajectories in a predictive mode, by taking advantage of the improved world model. The real robot will only move to try trajectories that have been predicted to be successful, allowing lower exploration costs. This results in an overall improved new method for goal-oriented navigation. It is assumed that the robot knows its own current world location-a simple dead-reckoning method is used for localization in our experiments. It is also assumed that the robot is able to perform sensor-based obstacle detection (not avoidance) and straight-line motions. Results of experiments with a real Nomad 200 mobile robot are presented, demonstrating the effectiveness of the discussed methods.

Attitudes of general dental practitioners in Europe to the microbial risk associated with dental unit water systems

Dental Unit Water Systems (DUWS) are used in dental practices to provide water for cooling of dental equipment and irrigation of the oral cavity. However, they have been demonstrated to be contaminated with micro-organisms. There are currently no European Union (EU) Commission guidelines for the microbial quality of water discharged by DUWS. This study was part of an EU research programme to investigate the microbial contamination of DUWS in general dental practice (GDP) in the UK, Denmark, Germany, The Netherlands, Ireland, Greece and Spain.

OBJECTIVE

To undertake a questionnaire survey on the type of DUWS in use and determine the attitude of GDPs to the risk of microbial infection from DUWS.

MATERIALS AND METHODS

The questionnaire was written and translated into the language of each country before being posted to each participating dentist. Dentists were asked to complete the questionnaire survey and return it by post.

RESULTS AND CONCLUSIONS

The major findings were that the majority of dentists did not clean, disinfect or determine the microbial load of their DUWS, and that dentists would welcome regular monitoring and advice on maintaining their DUWS; the introduction of guidelines; and recommendations on controlling the microbial load of DUWS.

Comparison of the efficacies of disinfectants to control microbial contamination in dental unit water systems in general dental practices across the European Union

Water delivered by dental unit water systems (DUWS) in general dental practices can harbor high numbers of bacteria, including opportunistic pathogens. Biofilms on tubing within DUWS provide a reservoir for microorganisms and should be controlled. This study compared disinfection products for their ability to meet the American Dental Association's guideline of <200 CFU x ml(-1) for DUWS water. Alpron, BioBlue, Dentosept, Oxygenal, Sanosil, Sterilex Ultra, and Ster4Spray were tested in DUWS (n = 134) in Denmark, Germany, Greece, Ireland, The Netherlands, Spain, and the United Kingdom. Weekly water samples were tested for total viable counts (TVCs) on yeast extract agar, and, where possible, the effects of products on established biofilm (TVCs) were measured. A 4- to 5-week baseline measurement period was followed by 6 to 8 weeks of disinfection (intermittent or continuous product application). DUWS water TVCs before disinfection ranged from 0 to 5.41 log CFU x ml(-1). Disinfectants achieved reductions in the median water TVC ranging from 0.69 (Ster4Spray) to 3.11 (Dentosept) log CFU x ml(-1), although occasional high values (up to 4.88 log CFU x ml(-1)) occurred with all products. Before treatment, 64% of all baseline samples exceeded American Dental Association guidelines, compared to only 17% following commencement of treatment; where tested, biofilm TVCs were reduced to below detectable levels. The antimicrobial efficacies of products varied (e.g., 91% of water samples from DUWS treated with Dentosept or Oxygenal met American Dental Association guidelines, compared to 60% of those treated with Ster4Spray). Overall, the continuously applied products performed better than those applied intermittently. The most effective products were Dentosept and Oxygenal, although Dentosept gave the most consistent and sustained antimicrobial effect over time.

Detection of Helicobacter pylori DNA in human faeces and water with different levels of faecal pollution in the north-east of Spain

AIMS

To assess the role of water in the faecal transmission of Helicobacter pylori by detecting the DNA of this pathogen in human faecal samples and environmental water samples with a range of faecal pollution from the north-east of Spain.

METHODS AND RESULTS

Semi-nested PCR was used to detect H. pylori in stools and water, both matrices with a complex biota. DNA was detected using highly specific primers of an ureA gene fragment. In addition, antigens were used to detect the bacteria in stools. Helicobacter pylori was detected in 33% of 36 human faecal samples and in 66% of wastewater samples, and 11% of river samples, but in none of the spring waters samples. Faecal pollution of the aquatic environment was tested analysing the presence of microbial indicators.

CONCLUSIONS

We report the presence of H. pylori DNA in stools and in aquatic environments with different levels of faecal pollution, from the north-east of Spain. In this study a higher number of positive results were obtained in the more faecally polluted waters.

SIGNIFICANCE AND IMPACT OF THE STUDY

These data indicate that water may be a vector of H. pylori in its faecal-oral route.

Microbiological evaluation of dental unit water systems in general dental practice in Europe

A range of opportunistic pathogens have been associated with dental unit water systems (DUWS), particularly in the biofilms that can line the tubing. This study therefore aimed to assess the microbiology of DUWS and biofilms in general dental practices across seven European countries, including the United Kingdom (UK), Ireland (IRL), Greece (GR), Spain (ES), Germany (D), Denmark (DK) and the Netherlands (NL). Water supplied by 51% of 237 dental unit water lines exceeded current American Dental Association recommendations of < or = 200 colony-forming units (CFU) ml(-1). Microbiological loading of the source waters was between 0 (Denmark, the Netherlands and Spain) and 4.67 (IRL) log CFU ml(-1); water line samples from the DUWS ranged from 1.52 (ES) to 2.79 (GR) log CFU ml(-1); and biofilm counts ranged from 1.49 (GR) to 3.22 (DK) log CFU.cm(-2). Opportunistic pathogens such as legionellae (DK and ES), including Legionella pneumophila SG1 (DK and GR), and Mycobacterium spp. (DK, NL, GR, D and ES) were recovered occasionally. Presumptive oral streptococci (ES and NL), oral anaerobes (GR), Candida spp. (UK, NL and ES) and blood (GR and IRL) were detected at relatively low frequencies, but their presence indicated a failure of the 3-in-1 antiretraction valve, leading to back siphonage of oral fluids into the water and biofilm phase. These findings confirm that a substantial proportion of DUWS have high levels of microbial contamination, irrespective of country, type of equipment and source water. The study emphasizes the need for effective mechanisms to reduce the microbial burden within DUWS, and highlights the risk of occupational exposure and cross-infection in general dental practice.