Genetic and virulence-phenotype characterization of serotypes 2 and 9 of Streptococcus suis swine isolates

The aim of this study was to analyze the genetic characteristics and virulence phenotypes of Streptococcus suis, specifically, in clinical isolates of serotypes 2 and 9 (n = 195), obtained from diverse geographical areas across Spain. Pulsed-field gel electrophoresis (PFGE) typing identified 97 genetic profiles, 68% of which were represented by single isolates, indicative of a substantial genetic diversity among the S. suis isolates analyzed. Five PFGE profiles accounted for 33.3% of the isolates and were isolated from 38% of the herds in nine different provinces, indicative of the bacterium's widespread distribution in the Spanish swine population. Representative isolates of the most prevalent PFGE profiles of both serotypes were subjected to multilocus sequence typing (MLST) analysis. The results indicated that serotypes 2 and 9 have distinct genetic backgrounds. Serotype 2 isolates belong to the ST1 complex, a highly successful clone that has spread over most European countries. In accordance with isolates of this complex, most serotype 2 isolates also expressed the phenotype MRP(+)EF(+)SLY(+). Serotype 9 isolates belong to the ST61 complex, which is distantly related to the widespread European ST87 clone. Also, in contrast to most isolates of the European ST87 clone, which express the large variant MRP*, the majority of serotype 9 isolates (97.9%) did not express the protein.

Genetic diversity of Mycobacterium avium isolates recovered from clinical samples and from the environment: molecular characterization for diagnostic purposes

Isolation of Mycobacterium avium complex (MAC) organisms from clinical samples may occur in patients without clinical disease, making the interpretation of results difficult. The clinical relevance of MAC isolates from different types of clinical samples (n = 47) from 39 patients in different sections of a hospital was assessed by comparison with environmental isolates (n = 17) from the hospital. Various methods for identification and typing (commercial probes, phenotypic characteristics, PCR for detection of IS1245 and IS901, sequencing of the hsp65 gene, and pulsed-field gel electrophoresis) were evaluated. The same strain was found in all the environmental isolates, 21 out of 23 (91.3%) of the isolates cultured from urine samples, and 5 out of 19 (26.3%) isolates from respiratory specimens. This strain did not cause disease in the patients. Testing best characterized the strain as M. avium subsp. hominissuis, with the unusual feature that 81.4% of these isolates lacked the IS1245 element. Contamination of certain clinical samples with an environmental strain was the most likely event; therefore, characterization of the environmental mycobacteria present in health care facilities should be performed to discard false-positive isolations in nonsterile samples, mainly urine samples. Molecular techniques applied in this study demonstrated their usefulness for this purpose.

Detection and Grading of Prostate Cancer in Temporal Enhanced Ultrasound using Convolutional Neural Networks

Prostate cancer is the most common non-dermatological cancer amongst men in the developed world. The current definitive diagnosis is core needle biopsy guided by transrectal ultrasound. However, this method suffers from low sensitivity and specificity in detecting cancer. Recently, a new ultrasound based tissue typing approach has been proposed, known as temporal enhanced ultrasound (TeUS). In this approach, a set of temporal ultrasound frames is collected from a stationary tissue location without any intentional mechanical excitation. The main aim of this thesis is to implement a deep learning-based solution for prostate cancer detection and grading using TeUS data. In the proposed solution, convolutional neural networks are trained to extract high-level features from time domain TeUS data in temporally and spatially adjacent frames in nine in vivo prostatectomy cases. This approach avoids information loss due to feature extraction and also improves cancer detection rate. The output likelihoods of two TeUS arrangements are then combined to form our novel decision support system. This deep learning-based approach results in the area under the receiver operating characteristic curve (AUC) of 0.80 and 0.73 for prostate cancer detection and grading, respectively, in leave-one-patient-out cross-validation. Recently, multi-parametric magnetic resonance imaging (mp-MRI) has been utilized to improve detection rate of aggressive prostate cancer. In this thesis, for the first time, we present the fusion of mp-MRI and TeUS for characterization of prostate cancer to compensates the deficiencies of each image modalities and improve cancer detection rate. The results obtained using TeUS are fused with those attained using consolidated mp-MRI maps from multiple MR modalities and cancer delineations on those by multiple clinicians. The proposed fusion approach yields the AUC of 0.86 in prostate cancer detection. The outcomes of this thesis emphasize the viable potential of TeUS as a tissue typing method. Employing this ultrasound-based intervention, which is non-invasive and inexpensive, can be a valuable and practical addition to enhance the current prostate cancer detection.

From field to fermentation: characterisation and application of non-dairy cultures in dairy foods

This thesis investigates the phenotypic and genotypic diversity of non-dairy L. lactis strains and their application to dairy fermentations. A bank of non-dairy lactococci were isolated from grass, vegetables and the bovine rumen. Subsequent analysis of these L. lactis strains revealed seven strains to possess cremoris genotypes which did not correlate with their observed phenotypes. Multi-locus sequence typing (MLST) and average nucleotide identity (ANI) highlighted the genetic diversity of lactis and cremoris subspecies. The application of these non-dairy lactococci to cheese production was also assessed. In milk, non-dairy strains formed diverse volatile profiles and selected strains were used as adjuncts in a mini Gouda-type cheese system. Sensory analysis showed non-dairy strains to be strongly associated with the development of off-flavours and bitterness. However, microfluidisation appeared to reduce bitterness. A novel bacteriophage, ɸL47, was isolated using the grass isolate L. lactis ssp. cremoris DPC6860 as a host. The phage, a member of the Siphoviridae, possessed a long tail fiber, previously unseen in dairy lactococcal phages. Genome sequencing revealed ɸL47 to be the largest sequenced lactococcal phage to date and owing to the high % similarity with ɸ949, a second member of the 949 group. Finally, to identify and characterise specific genes which may be important in niche adaptation and for applications to dairy fermentations, comparative genome sequence analysis was performed on L. lactis from corn (DPC6853), the bovine rumen (DPC6853) and grass (DPC6860). This study highlights the contribution of niche specialisation to the intra-species diversity of L. lactis and the adaptation of this organism to different environments. In summary this thesis describes the genetic diversity of L. lactis strains from outside the dairy environment and their potential application in dairy fermentations.

Methicillin-susceptible Staphylococcus aureus endocarditis isolates are associated with clonal complex 30 genotype and a distinct repertoire of enterotoxins and adhesins.

BACKGROUND: Using multinational collections of methicillin-susceptible Staphylococcus aureus (MSSA) isolates from infective endocarditis (IE) and soft tissue infections (STIs), we sought to (1) validate the finding that S. aureus in clonal complex (CC) 30 is associated with hematogenous complications and (2) test the hypothesis that specific genetic characteristics in S. aureus are associated with infection severity. METHODS: IE and STI isolates from 2 cohorts were frequency matched by geographic origin. Isolates underwent spa typing to infer CC and multiplex polymerase chain reaction for presence of virulence genes. RESULTS: 114 isolate pairs were genotyped. IE isolates were more likely to be CC30 (19.5% vs 6.2%; P = .005) and to contain 3 adhesins (clfB, cna, map/eap; P < .0001 for all) and 5 enterotoxins (tst, sea, sed, see, and sei; P ≤ .005 for all). CC30 isolates were more likely to contain cna, tst, sea, see, seg, and chp (P < .05 for all). CONCLUSIONS: MSSA IE isolates were significantly more likely to be CC30 and to possess a distinct repertoire of virulence genes than MSSA STI isolates from the same region. The genetic basis of this association requires further study.

Keyword search for building service-based systems

With the fast growth of applications of service-oriented architecture (SOA) in software engineering, there has been a rapid increase in demand for building service-based systems (SBSs) by composing existing Web services. Finding appropriate component services to compose is a key step in the SBS engineering process. Existing approaches require that system engineers have detailed knowledge of SOA techniques which is often too demanding. To address this issue, we propose KS3 (Keyword Search for Service-based Systems), a novel approach that integrates and automates the system planning, service discovery and service selection operations for building SBSs based on keyword search. KS3 assists system engineers without detailed knowledge of SOA techniques in searching for component services to build SBSs by typing a few keywords that represent the tasks of the SBSs with quality constraints and optimisation goals for system quality, e.g., reliability, throughput and cost. KS3 offers a new paradigm for SBS engineering that can significantly save the time and effort during the system engineering process. We conducted large-scale experiments using a real-world Web service dataset to demonstrate the practicality, effectiveness and efficiency of KS3.

Celiac disease in children from Madeira island and its prevalence in first degree relatives

Context - It is well recognized that celiac disease is an immune-mediated systemic disorder highly prevalent among relatives of celiac patients. Objectives - The aim of this study is to determine the prevalence of celiac disease in a group of first degree relatives of celiac children, and to access the frequency of human leukocyte antigen HLA-DQ2 and DQ8 in celiac disease patients and their affected relatives. Methods - A survey was conducted of 39 children with celiac disease with follow-up in the Pediatric outpatient’s clinic of Dr. Nélio Mendonça Hospital, in Madeira Island, Portugal. Were invited 110 first degree relatives to undergo serological screen for celiac disease with IgA antibody to human recombinant tissue transglutaminase (IgA-TGG) quantification. In all seropositive relatives, small intestinal biopsy and HLA typing was recommended. Results - HLA- typing was performed in 38 celiac patients, 28/74% DQ2 positive, 1/2% DQ8 positive and 9/24% incomplete DQ2. Positive IgA-TGG was found in five out of the 95 relatives, and CD was diagnosed in three of them. Three relatives had the presence of HLA-DQ2, two were DQ2 incomplete (DQB1*02). Conclusion - The prevalence of celiac disease among first degree celiac patients´ relatives was 3.1%, 4.5 times higher than the general Portuguese population (0,7%) witch reinforces the need of extensive diagnostic screening in this specific group. HLA-DQ2 typing may be a tool in the diagnostic approach.

Evaluación del desempeño de pruebas diagnósticas de tuberculosis en pacientes VIH positivo en dos hospitales públicos de Bogotá

La tuberculosis TB es una de las principales causas de muerte en el mundo en individuos con infección por VIH. En Colombia esta coinfección soporta una carga importante en la población general convirtiéndose en un problema de salud pública. En estos pacientes las pruebas diagnósticas tienen sensibilidad inferior y la enfermedad evoluciona con mayor frecuencia hacia formas diseminadas y rápidamente progresivas y su diagnóstico oportuno representa un reto en Salud. El objetivo de este proyecto es evaluar el desempeño de las pruebas diagnósticas convencionales y moleculares, para la detección de TB latente y activa pacientes con VIH, en dos hospitales públicos de Bogotá. Para TB latente se evaluó la concordancia entre las pruebas QuantiFERON-TB (QTF) y Tuberculina (PPD), sugiriendo superioridad del QTF sobre la PPD. Se evaluaron tres pruebas diagnósticas por su sensibilidad y especificidad, baciloscopia (BK), GenoType®MTBDR plus (Genotype) y PCR IS6110 teniendo como estándar de oro el cultivo. Los resultados de sensibilidad (S) y especificidad (E) de cada prueba con una prevalencia del 19,4 % de TB pulmonar y extrapulmonar en los pacientes que participaron del estudio fue: BK S: 64% E: 99,1%; Genotype S: 77,8% E: 94,5%; PCRIS6110 S: 73% E: 95,5%, de la misma forma se determinaron los valores predictivos positivos y negativos (VPP y VPN) BK: 88,9% y 94,8%, Genotype S: 77,8% E: 94,5%; PCRIS6110 S: 90% y 95,7%. Se concluyó bajo análisis de curva ROC que las pruebas muestran un rendimiento diagnóstico similar por separado en el diagnóstico de TB en pacientes con VIH, aumentando su rendimiento diagnostico cuando se combinan

Características preferidas por hombres y mujeres que buscan pareja estable de su mismo sexo

Las preferencias en elección de pareja de hombres y mujeres interesados en establecer relaciones a largo plazo con personas de su mismo sexo biológico ha sido un tema de interés para el análisis evolucionista, ya que existe debate frente a los resultados de las investigaciones y los planteamientos de las teorías de inversión parental y estrategias sexuales. Con el objetivo de identificar qué características son preferidas por hombres y mujeres interesados en establecer una relación a largo plazo con personas de su mismo sexo biológico y contribuir a esta discusión, se llevó a cabo un estudio descriptivo en el que analizamos el contenido de 732 perfiles de hombres y mujeres (H=491; M=241) que buscaban una relación estable con parejas de su mismo sexo biológico. Las categorías analizadas fueron: edad, atractivo físico (apariencia, contextura, estatura y peso), estatus socioeconómico (situación laboral, nivel educativo y zona de residencia buscada), estado civil, número de hijos y hábitos saludables (fumar y beber). Los resultados encontrados muestran que los hombres presentan rangos amplios en las características deseadas en una pareja (edad=16.87; estatura=11.37; peso=15.23) y además buscan personas menores a la edad ofrecida (M=-4.17 años). En las mujeres se encontró que los rangos son más restringidos (edad=13.85; estatura=9.83; peso=12.77) y además prefieren parejas mayores (M=2.89 años). A nivel general, se evidencia que los resultados encontrados en la mayoría de las variables podrían indicar congruencia con los planteamientos de la teoría de inversión parental y estrategias sexuales; sin embargo, en otras variables los resultados no son claros.

Descripción del análisis microbológico realizado mediante maldi-tof en muestras de la fundación santa fe de Bogotá.

Introducción: La rápida detección e identificación bacteriana es fundamental para el manejo de los pacientes críticos que presentan una patología infecciosa, esto requiere de métodos rápidos para el inicio de un correcto tratamiento. En Colombia se usan pruebas microbiología convencional. No hay estudios de espectrofotometría de masas en análisis de muestras de pacientes críticos en Colombia. Objetivo general: Describir la experiencia del análisis microbiológico mediante la tecnología MALDI-TOF MS en muestras tomadas en la Fundación Santa Fe de Bogotá. Materiales y Métodos: Entre junio y julio de 2013, se analizaron 147 aislamientos bacterianos de muestras clínicas, las cuales fueron procesadas previamente por medio del sistema VITEK II. Los aislamientos correspondieron a 88 hemocultivos (60%), 28 urocultivos (19%), y otros cultivos 31 (21%). Resultados: Se obtuvieron 147 aislamientos con identificación adecuada a nivel de género y/o especie así: en el 88.4% (130 muestras) a nivel de género y especie, con una concordancia del 100% comparado con el sistema VITEK II. El porcentaje de identificación fue de 66% en el grupo de bacilos gram negativos no fermentadores, 96% en enterobacterias, 100% en gérmenes fastidiosos, 92% en cocos gram positivos, 100% bacilos gram negativos móviles y 100% en levaduras. No se encontró ninguna concordancia en bacilos gram positivos y gérmenes del genero Aggregatibacter. Conclusiones: El MALDI-TOF es una prueba rápida para la identificación microbiológica de género y especie que concuerda con los resultados obtenidos de manera convencional. Faltan estudios para hacer del MALDI-TOF MS la prueba oro en identificación de gérmenes.

LOOKING INTO CALIPSO CLIMATOLOGICAL PRODUCTS: EVALUATION AND SUGGESTIONS FROM EARLINET

CALIPSO (Cloud-Aerosol Lidar and Pathfinder Satellite Observations) Level 3 (CL3) data were compared against EARLINET (European Aerosol Research Lidar Network) monthly averages obtained by profiles during satellite overpasses. Data from EARLINET stations of Évora, Granada, Leipzig, Naples and Potenza, equipped with advanced multi-wavelength Raman lidars were used for this study. Owing to spatial and temporal differences, we reproduced the CL3 filtering rubric onto the CALIPSO Level 2 data. The CALIPSO monthly mean profiles following this approach are called CALIPSO Level 3*, CL3*. This offers the possibility to achieve direct comparable datasets. In respect to CL3 data, the agreement typically improved, in particular above the areas directly affected by the anthropogenic activities within the planetary boundary layer. However in most of the cases a subtle CALIPSO underestimation was observed with an average bias of 0.03 km-1. We investigated the backscatter coefficient applying the same screening criteria, where the mean relative difference in respect to the extinction comparison improved from 15.2% to 11.4%. Lastly, the typing capabilities of CALIPSO were assessed outlining the importance of the correct aerosol type (and associated lidar ratio value) assessment to the CALIPSO aerosol properties retrieval.