Thesis (M. Med. Sc.)--University of Hong Kong, 2007.

Diss. (sammanfattning) Umeå : Umeå universitet, 2006. / Härtill 3 uppsatser.

As the leading cause of bacterial gastroenteritis, Campylobacter represents a significant public health burden; however, our knowledge of its epidemiology in low- and middle-income countries remains limited. Recent studies have demonstrated the power of whole-genome sequencing (WGS) for public health microbiology. The primary aim of this thesis was to exploit WGS to improve our understanding of the epidemiology of Campylobacter from the Republic of South Africa, a middle-income country. In the first half of this thesis, in silico approaches were developed to evaluate diagnostic assays and methods of species identification. Large-scale analyses of publicly available WGS data identified a robust real-time PCR assay for the detection of Campylobacter jejuni and Campylobacter coli, the primary causes of human campylobacteriosis. Evaluation of in silico speciation methods demonstrated that the atpA gene and ribosomal multilocus sequence typing can be used to identify Campylobacter from WGS data. The second half of this thesis extended concepts developed in the first half to investigate the epidemiology of Campylobacter from animals and humans from South Africa. Isolates from a study of Campylobacter from free-range broiler carcasses belonged to the agriculture-associated ST-828 lineage, but were atypically homogenous and differed at only 46/1,513 (3%) loci, providing novel insights into clonal infections in chickens. Analyses of human disease isolates collected in Cape Town in 1991, 2011, and 2012 confirmed that the local epidemiology of Campylobacter is distinct from that of high-income countries: in addition to major agriculture-associated C. jejuni and C. coli lineages, a putative novel C. jejuni subsp. jejuni/C. jejuni subsp. doylei hybrid clade and genetically diverse C. jejuni subsp. doylei and C. upsaliensis isolates were identified. This work delivers further evidence of the utility of WGS for clinical microbiology, presents approaches that address general problems in Campylobacter diagnostics and public health microbiology, and provides insights into the epidemiology of this important group of pathogens in South Africa.

Os objetivos do presente estudo foram avaliar os perfis de sensibilidade a antimicrobianos de MRSA isolados de sangue, identificar o tipo de SCCmec e analisar o perfil de DNA desses isolados para verificar a existência de linhagens predominantes. Amostras de MRSA isoladas de sangue foram submetidas ao teste de triagem em ágar para detecção de resistência a oxacilina, teste de sensibilidade aos antimicrobianos, PCR multiplex para detecção dos genes mecA e coa e do tipo de SCCmec, tipagem molecular por PFGE. 89% das amostras de MRSA foi de origem hospitalar. Foi observado multirresistência em 69% dos isolados. 83% dos isolados apresentaram SCCmec tipo IIIA e um perfil PFGE predominante. Foram observadas amostras de MRSA sensíveis a diversas classes de antimicrobianos, portando SCCmec tipo IV, associadas a infecção de origem hospitalar e a tipagem molecular permitiu observar o predomínio de um clone, disseminado em todo o complexo HC / The aims of this study were to evaluate the susceptibility profile of MRSA strains isolated from blood, identify the SCCmec types and analyze the DNA profile in order to determine if there were predominant lineages. Consecutive MRSA blood isolates were submitted to oxacillin agar screening test, antimicrobial susceptibility test, multiplex PCR to detect mecA and coa genes, SCCmec typing and molecular typing by PFGE. 89% of the isolates were nosocomial-acquired. 69% of strains were observed to be multiresistant. 83% of the 223 isolates had SCCmec type IIIA and had a predominant DNA pattern by PFGE. Some strains nosocomial-acquired had SCCmec type IV, resistance only to beta-lactams and demonstrated PFGE pattern with one predominant clone

Os objetivos do presente estudo foram avaliar os perfis de sensibilidade a antimicrobianos de MRSA isolados de sangue, identificar o tipo de SCCmec e analisar o perfil de DNA desses isolados para verificar a existência de linhagens predominantes. Amostras de MRSA isoladas de sangue foram submetidas ao teste de triagem em ágar para detecção de resistência a oxacilina, teste de sensibilidade aos antimicrobianos, PCR multiplex para detecção dos genes mecA e coa e do tipo de SCCmec, tipagem molecular por PFGE. 89% das amostras de MRSA foi de origem hospitalar. Foi observado multirresistência em 69% dos isolados. 83% dos isolados apresentaram SCCmec tipo IIIA e um perfil PFGE predominante. Foram observadas amostras de MRSA sensíveis a diversas classes de antimicrobianos, portando SCCmec tipo IV, associadas a infecção de origem hospitalar e a tipagem molecular permitiu observar o predomínio de um clone, disseminado em todo o complexo HC / The aims of this study were to evaluate the susceptibility profile of MRSA strains isolated from blood, identify the SCCmec types and analyze the DNA profile in order to determine if there were predominant lineages. Consecutive MRSA blood isolates were submitted to oxacillin agar screening test, antimicrobial susceptibility test, multiplex PCR to detect mecA and coa genes, SCCmec typing and molecular typing by PFGE. 89% of the isolates were nosocomial-acquired. 69% of strains were observed to be multiresistant. 83% of the 223 isolates had SCCmec type IIIA and had a predominant DNA pattern by PFGE. Some strains nosocomial-acquired had SCCmec type IV, resistance only to beta-lactams and demonstrated PFGE pattern with one predominant clone

Title from PDF of title page. / Document formatted into pages; contains 86 pages. / Thesis (M.S.P.H.)--University of South Florida, 2003. / Includes bibliographical references. / Text (Electronic thesis) in PDF format. / ABSTRACT: The Enterovirus genus within the family Picornaviridae contains over 100 serotypes, of which sixty-four are known to be human pathogens. Infection with this group of RNA viruses produces a myriad of clinical conditions including poliomyelitis, meningitis, encephalitis, respiratory illnesses, and hand-foot-and-mouth disease. Outbreaks have been documented worldwide; significant morbidity and mortality exist to warrant laboratory surveillance. Traditionally, enteroviruses have been identified to the level of serotype by the serum neutralization assay. However, numerous problems are associated with this assay. The serum neutralization assay is labor intensive, results are often ambiguous, and reagents are becoming difficult to obtain. Recently, molecular-based typing protocols have been described that are cost effective and produce results that are more reliable. / ABSTRACT: The overall objective of this thesis was to implement a molecular-based typing protocol to replace the serum neutralization method currently used. Three specific aims were identified to reach this objective. First, a database cataloging all enteroviruses isolated at the Florida Department of Health - Tampa Branch Laboratory from 1981 through 2002 was created. Serotype prevalence, specimen submission rates, and temporal trends were analyzed to demonstrate the public health importance of enterovirus surveillance. Next, five oligonucleotide primer sets were compared with respect to sensitivity, specificity, and overall utility in molecular typing protocols developed to accurately determine enterovirus type. Finally, the most effective molecular assay was used to conduct two basic molecular epidemiological analyses of intratypic variation of Coxsackievirus B5 isolates, and of intratypic variation of successive Echovirus 9 passages. / ABSTRACT: The results from this study show that implementation of a molecular-based typing system for enteroviruses would be an improvement over current enterovirus serotyping methods. Results are obtained more rapidly and are more reliable. The implementation of such a system would improve the surveillance capabilities of the State of Florida Department of Health. / System requirements: World Wide Web browser and PDF reader. / Mode of access: World Wide Web.

[EN] Investments in data infrastructures, data management, data repositories, and Open Data sharing policies and recommendations are viewed as increasingly important for scientific knowledge production. One of the underlying assumptions justifying these investments is that the more available Open Data becomes, then the greater the possibilities for creating new knowledge that can advance both science and human wellbeing. Yet efforts and investments in Open Data and other ways of data sharing only have value if data are actually reused. Recent scholarly efforts have brought forth some of the challenges and facilitators related to the reuse of data, in order to inform current and future policies and investments. However, despite these efforts, we still do not know why and how some researchers are successful in reusing data, despite the challenges they face, and why some researchers abandon the process of reusing data when facing such challenges. This dissertation aims to fill this gap by focusing on a causal explanation of the data reuse process, which it understands as being nested in broader patterns of researchers' motivations, scientific goals and decision-making strategies. The dissertation is comprised of three main elements. First, it proposes a heuristic model of the scientific actor, the bounded individual horizon (BIH) model, which understands that, on the one hand, researchers' work and careers are structured by their motivation to produce scientific contributions and rewards systems that prioritizes certain types of contributions. On the other hand, researchers' struggles to achieve their objective of creating new findings that accrue recognition and rewards occur within a frame of limited information and resources, conditioned by multiple institutional, social, and other factors. Second, the study proposes a mechanistic causal theoretical explanation that enables us to understand the data reuse process and its effects (outcomes). The data-reuse mechanism as it is called, enables us to understand how the satisficing behavior that characterizes scientific decision-making applies to the specific conditions and processes of data reuse. Third, a set of ten empirical case studies of data reuse in health research were conducted and are reported in the dissertation. These cases are analyzed and interpreted using the complementary theoretical lenses of the bounded individual horizon and the data-reuse mechanism approaches. The main findings explain that there is an apparent association between the extent and types of efforts required to reuse data, researchers' contextualized motivations, and broader goal-setting and decision-making frames. Access to data is a necessary condition for the reuse of data, yet is not sufficient for the reuse to happen. Characteristics of available data, including the context of their production, the extent of the preparation and stewarding of these data and their potential value in relation to researchers' motivations to make new scientific claims or generate background knowledge are found to be essential elements for understanding why some data reuse processes persist and succeed, while others do not. The thesis concludes that efforts and investments designed to reap the benefits of data reuse should also be expanded to include training researchers in data reuse, including to efficiently recognize opportunities, navigate the challenges of the reuse process, and be aware of and acknowledge the limitations of the use of secondary data. Without such investments, the promises and expectations linked to emerging data infrastructures, data repositories, data management guidelines and open science practices are argued to be far less likely to reach their full potential. / [ES] Las inversiones en infraestructuras de datos, gestión de datos, repositorios de datos y políticas y recomendaciones de intercambio de Datos Abiertos (Open Data) se consideran cada vez más importantes para la producción del conocimiento científico. Una de las razones que justifica estas inversiones es que cuanto más Datos Abiertos haya, mayores serán las posibilidades de crear nuevo conocimiento que pueda hacer avanzar tanto la ciencia como el bienestar humano. Sin embargo, los esfuerzos y la inversión en Datos Abiertos y otras formas de compartirlos sólo tienen valor si se reutilizan realmente. Recientes trabajos académicos han puesto de manifiesto algunos de los retos y factores facilitadores relacionados con la reutilización de los datos, a fin de asesorar las políticas e inversiones actuales y futuras. Sin embargo, a pesar de esos esfuerzos, todavía desconocemos por qué y cómo algunos/as investigadores/as logran reutilizar los datos, a pesar de los retos a los que enfrentan, y por qué otros/as investigadores/as abandonan el proceso de reutilización de los datos. La presente tesis tiene por objeto llenar este vacío centrándose en una explicación causal del proceso de reutilización de los datos, que se entiende está inmersa en pautas de conducta más amplias que se relacionan con las motivaciones, los objetivos científicos y las estrategias de toma de decisiones de los/as investigadores/as. Este estudio consta de tres elementos principales. En primer lugar, propone un modelo heurístico del actor científico, el modelo del horizonte individual delimitado (BIH por su nombre en inglés, bounded individual horizon). En él se entiende que, por una parte, el trabajo y la carrera de los/as investigadores/as se estructuran en función de su motivación para producir contribuciones científicas y de los sistemas de recompensa que dan prioridad a determinados tipos de contribuciones. Por otra parte, los esfuerzos de los/as investigadores/as para lograr su objetivo de crear nuevos hallazgos que acumulen reconocimiento y recompensas se producen en un marco de información y recursos limitados, condicionados por múltiples factores institucionales, sociales y de otra índole. En segundo lugar, esta tesis propone una explicación teórica causal mecanicista que permite comprender el proceso de reutilización de los datos y sus efectos (resultados). El mecanismo de reutilización de datos (datareuse mechanism), como se denomina, nos permite comprender cómo la toma de decisiones científicas está caracterizada por una conducta que tiende a satisfacer esos objetivos en unas condiciones y procesos específicos de reutilización de datos. En tercer lugar, este estudio incluye los resultados del estudio empírico de diez estudios de casos de reutilización de datos en ciencias de la salud. Estos casos se han analizado e interpretado utilizando el modelo teórico del horizonte individual delimitado y los enfoques del mecanismo de reutilización de datos. Los resultados principales explican que existe una aparente asociación entre el alcance el alcance y tipo de esfuerzo requerido para reutilizar datos, las motivaciones contextualizadas de los/as investigadores/as y marcos más amplios de fijación de objetivos y toma de decisiones. El acceso a los datos es una condición necesaria para su reutilización, pero no es suficiente para que ésta se produzca. Para comprender por qué algunos procesos de reutilización de datos persisten y tienen éxito, mientras que otros no,son elementos esenciales: las características de los datos disponibles, incluido el contexto de su producción; el grado de preparación y administración de esos datos; y su potencial valor en relación con las motivaciones de los investigadores para hacer nuevas afirmaciones científicas o generar conocimientos de base. Este estudio concluye que los esfuerzos e inversiones destinados a aprovechar los beneficios de la reutilización de los datos también deberían ampliarse para incluir la capacitación de los/as investigadores/as en materia de reutilización de datos. En particular, debe insistirse en la capacidad para reconocer eficientemente las oportunidades, sortear los problemas del proceso de reutilización y ser conscientes y reconocer las limitaciones de la utilización de datos secundarios. Sin estas inversiones, las promesas y expectativas vinculadas a las emergentes infraestructuras de datos, los repositorios de datos, las directrices de gestión de datos y las prácticas científicas abiertas tienen muchas menos probabilidades de alcanzar su pleno potencial. / [CA] Les inversions en infraestructures de dades, gestió de dades, repositoris de dades i polítiques i recomanacions d'intercanvi de Dades Obertes (Open Data) es consideren cada vegada més importants per a la producció del coneixement científic. Un dels supòsits subjacents que justifiquen aquestes inversions és que com més disponibles siguen les Dades Obertes, majors seran les possibilitats de crear nou coneixement que pugui fer avançar tant la ciència com el benestar humà. No obstant això, els esforços i les inversions en les Dades Obertes i altres maneres de compartir dades només tenen valor si les dades es reutilitzen realment. Recents investigacions acadèmics han posat de manifest alguns dels reptes i dels factors facilitadors relacionats amb la reutilització de les dades, a fi d'informar les polítiques i inversions actuals i futures. No obstant això, encara desconeixem per què i com alguns/es investigador(e)s aconsegueixen reutilitzar les dades, malgrat els reptes als quals s’enfronten, i per què altres investigador(e)s abandonen el procés de reutilització de les dades quan s'enfronten a aquests reptes. La present tesi té com a objectiu omplir aquest buit centrant-se en una explicació causal del procés de reutilització de dades, que s'entén que està associada amb pautes més àmplies derivades de les motivacions, els objectius científics i les estratègies de presa de decisions d’els/les investigador(e)s. La tesi consta de tres elements principals. En primer lloc, proposa un model heurístic de l'actor científic, el model de l'horitzó individual delimitat (BIH pel nom anglès, bounded individual horizon), que entén que, d'una banda, el treball i la carrera d’els/les investigador(e)s s'estructuren en funció de la seua motivació per a produir contribucions científiques i dels sistemes de recompensa que prioritzen determinats tipus de contribucions. D'altra banda, els esforços d’els/les investigador(e)s per aconseguir el seu objectiu d’obtenir nous resultats que acumulin reconeixement i recompenses es produeixen en un marc d'informació i recursos limitats, condicionats per múltiples factors institucionals, socials i d'altra índole. En segon lloc, aquesta tesi proposa una explicació teòrica causal mecanicista que permet comprendre el procés de reutilització de les dades i els seus efectes (resultats). El mecanisme de reutilització de dades (data-reuse mechanism), com es denomina, ens permet comprendre com el comportament satisfactori que caracteritza la presa de decisions científiques s'aplica a les condicions i processos específics de reutilització de dades. En tercer lloc, aquesta tesi inclou l'estudi empíric d'un conjunt de deu estudis de casos de reutilització de dades en ciències de la salut, així com també els resultats d’aquest estudi.. Aquests casos s'han analitzat i interpretat utilitzant les lents teòriques complementàries de l'horitzó individual delimitat i els enfocaments del mecanisme de reutilització de dades. Les principals conclusions expliquen que existeix una aparent associació entre l'abast i els tipus d'esforços necessaris per a reutilitzar dades, les motivacions contextualitzades d’els/les investigador(e)s i els marcs més amplis de fixació d'objectius i presa de decisions. L'accés a les dades és una condició necessària per a la seua reutilització, però no és suficient perquè aquesta es produeixi. Es considera que les característiques de les dades disponibles, inclòs el context de la seua producció, el grau de preparació i administració d'aquestes dades i el seu potencial valor en relació amb les motivacions d’els/les investigador(e)s per a fer noves afirmacions científiques o generar coneixements de base, són elements essencials per a comprendre per què alguns processos de reutilització de dades persisteixen i tenen èxit, mentre que uns altres no. Aquest estudi conclou que els esforços i inversions destinats a aprofitar els beneficis de la reutilització de dades també haurien d'ampliar-se per a incloure la capacitació d’els/les investigador(e)s en matèria de reutilització de dades, en particular per a reconèixer eficientment les oportunitats, superar els problemes del procés de reutilització i ser conscients i reconèixer les limitacions de la reutilització de dades secundàries. Sense aquests esforços i inversions, les promeses i expectatives vinculades a les infraestructures, repositoris i directrius de gestió de dades i les pràctiques científiques obertes tenen moltes menys probabilitats d'aconseguir el seu ple potencial. / Aleixos Borrás, MI. (2020). A causal model to explain data reuse in science: a study in health disciplines [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/153164 / TESIS

Streptococcus agalactiae is a pathogen of multiple hosts. The bacterium, an aetiological agent of septicaemia and meningo-encephalitis in freshwater and saltwater fish species, is considered a major threat to the aquaculture industry, particularly for tilapia. Cattle and humans are however the main known reservoirs for S. agalactiae. In humans, the bacterium (commonly referred to as Group B Streptococcus or GBS) is a member of the commensal microflora of the intestinal and genito-urinary tracts, but it is also a major cause of neonatal invasive disease and an emerging pathogen in adults. In cattle, S. agalactiae is a well-recognized causative agent of mastitis. Numerous studies focusing on S. agalactiae from human and bovine origins have provided insight into the population structure of the bacterium, as well as the genome content and pathogenic mechanisms through identification of virulence determinants. Concerning S. agalactiae from aquatic origins, scientific information mainly focused on case reporting and/or experimental challenges, with a limited or absence of information in terms of pathogenesis, virulence determinants and genotypes of the strains involved. The objective of this study was to enhance our understanding of the molecular epidemiology, host-adaptation and pathogenicity of S. agalactiae in aquatic species, with particular emphasis on tilapia. Firstly, a collection of 33 piscine, amphibian and sea mammal isolates originating from several countries and continents was assembled, with the aim of exploring the population structure and potential host specificity of aquatic S. agalactiae. Isolates were characterised using pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and a standardised 3-set genotyping system comprising molecular serotypes, surface protein gene profiles and mobile genetic element profiles. Two major subpopulations were identified in fish. The first subpopulation consisted of non-haemolytic isolates that belonged to sequence type (ST) 260 or 261, which are STs that have been reported only from teleosts. These isolates exhibited a low level of genetic diversity by PFGE and clustered with other STs that have been reported only in fish. Another common feature was the absence of all surface protein genes or mobile genetic elements targeted as part of the 3-set genotyping and that are usually found in human or bovine isolates. The second subpopulation consisted of β-haemolytic isolates recovered from fish, frogs and sea mammals, and that exhibited medium to high genetic diversity by PFGE. STs identified among these isolates have previously been identified from strains associated with asymptomatic carriage and invasive disease in humans. The human pathogenic strain ST7 serotype Ia was detected in fish from Asia. Moreover, ST283 serotype III-4 and its novel single locus variant ST491 detected in fish from Southeast Asia shared a 3-set genotype identical to that of an emerging ST283 clone associated with invasive disease of adult humans in Asia. These observations suggested that some strains of aquatic S. agalactiae may present a zoonotic or anthroponotic hazard. STs found among the seal isolates (ST23) have also been reported from humans and numerous other host species, but never from teleosts. This work provided an excellent basis for exploration of the virulence of selected strains in experimental challenges. The virulence of two strains of S. agalactiae was experimentally investigated by intra-peritoneal infection of Nile tilapia (Oreochromis niloticus), using an isolate originally recovered from fish and belonging to ST260, and an isolate originating from a grey seal and belonging to ST23. The clinical signs, the in vivo distribution of viable bacteria and bacterial antigens, and the gross and histopathological lesions that developed during the time course of the infection were investigated. The ST260 strain was highly virulent, whereas no major clinical sign or mortalities occurred in the fish challenged with the ST23 strain. After injection, both strains however gained access to the bloodstream and viable bacteria were recovered from all organs under investigation. During the early stages of infection, bacteria were mostly found within the reticulo-endothelial system of the spleen and kidney. Thereafter, the ST260 demonstrated a particular tropism for the brain and the heart, but granulomatous inflammation and associated necrotic lesions were observed in all organs. ST23 was responsible for a mixed inflammatory response associated with the presence of bacteria in the choroid rete and in the pancreatic tissue only. After 7 days post-challenge and for both strain, the formation or containment of bacteria within granulomata or other encapsulated structures appeared to be a major component of the fish response. However, the load of viable bacteria remained high within organs of fish infected with ST260, suggesting that, unlike ST23, this strain is able to survive within macrophages and/or to evade the immune system of the fish. This work demonstrates that the lack of report of ST23 strains in fish is possibly not due to a lack of exposure but to a lack of virulence in this host. The two strains, which differ in prevalence and virulence in fish, provide an excellent basis to investigate genomic differences underlying the host-association of distinct S. agalactiae subpopulations. The genome of the ST260 strain used in challenge studies was sequenced. We therefore provided the first description for the genome sequence of a non-haemolytic S. agalactiae isolated from tilapia (strain STIR-CD-17) and that belongs by multi-locus sequence typing (MLST) to clonal complex (CC) 552, which corresponds to a presumptive fish-adapted subgroup of S. agalactiae. The genome was compared to 13 S. agalactiae genomes of human (n=7), bovine (n=2), fish (n=3) and unknown (n=1) origins. Phylogenetic analysis based on the core genome identified isolates of CC552 as the most diverged of all S. agalactiae studied. Conversely, genomes from β-haemolytic isolates of CC7 recovered from fish were found to cluster with human isolates of CC7, further supporting the possibility that some strains may represent a zoonotic or anthroponotic hazard. Comparative analysis of the accessory genome enabled the identification of a cluster of genes uniquely shared between CC7 and CC552, which encode proteins that may provide enhanced fitness in specific niches. Other genes identified were specific to STIR-CD-17 or to CC552 based on genomic comparisons; however the extension of this analysis through the PCR screening of a larger population of S. agalactiae suggested that some of these genes may occasionally be present in isolates belonging to CC7. Some of these genes, occurring in clusters, exhibited typical signatures of mobile genetic elements, suggesting their acquisition through horizontal gene transfer. It is not possible to date to determine whether these genes were acquired through intraspecies transfer or through interspecies transfer from the aquatic environment. Finally, general features of STIR-CD-17 highlighted a distinctive genome characterised by an absence of well conserved insertion sequences, an abundance of pseudogenes, a smaller genomic size than normally observed among human or bovine S. agalactiae, and an apparent loss of metabolic functions considered conserved within the bacterial species, indicating that the fish-adapted subgroup of isolates (CC552) has undergone niche restriction. Finally, genes encoding recognised virulence factors in human S. agalactiae were selected and their presence and structural conservation was evaluated within the genome of STIR-CD-17.