Parmi les 24 espèces de Pantoea décrites à nos jours, cinq ont été signalées jusqu'à 46 fois dans 21 pays comme phytopathogènes d'au moins 31 cultures. En effet, P. ananatis et P. agglomerans ont été signalés comme bactéries phytopathogènes pour au moins dix cultures économiquement importantes, y compris le riz. Récemment, le Centre du riz pour l'Afrique et ses partenaires ont soupçonné la présence d'une bactérie émergente qui provoque le flétrissement bactérienne du riz dans plusieurs pays africains, et l'agent causal a été confirmé comme appartenant au genre Pantoea. Les objectifs de notre projet de thèse étaient (i) d'améliorer la collection d'isolats d’AfricaRice existante par de nouvelles collections (ii) de développer des outils de diagnostic et de caractérisations pour une analyse fine de la diversité génétique, phénotypique et des études d’épidémio-suivaillance. Nos résultats ont montré que les bactéries capables de produire des symptômes de flétrissement bactérien du riz en Afrique forment un complexe d'espèces composé principalement de P. ananatis, P. stewartii et P. agglomerans. Différents types d'outils de diagnostic et de caractérisations ont ensuite été développés et validés. Les résultats de l'utilisation de ces outils ont permis de mettre en évidence la présence de ce complexe bactérien dans plusieurs pays Africains et de fournir des détails sur sa repartition géographique. Ainsi, au total, nous avons diagnostiqué un complexe d'espèces bactériennes, phytopathogènes du riz dans 11 pays africains (Bénin, Burkina Faso, Burundi, Ghana, Côte d'Ivoire, Mali, Niger, Nigeria, Sénégal, Tanzanie, Togo). En outre, l'analyse de trois génomes de P. ananatis Africain isolé du riz, et le développement, l'évaluation et l'application d'outils d'analyse VNTR à locus multiples (MLVA) ont permis de mieux comprendre les relations phylogénétiques et phylogénomiques existant entre les souches de P. ananatis isolées du riz et des souches d' autres sources (plantes, animaux et environnement). En effet, les résultats préliminaires ont montré que plusieurs souches de P. ananatis isolées du riz en Afrique, en Asie et en Europe étaient phylogénétiquement liées et formaient un groupe qui les différenciait de P. ananatis d'autres sources. En conclusion, les résultats de ce projet de thèse fournissent une base solide qui facilitera les futures études de Pantoea spp en Afrique. / Among the 24 species of Pantoea described so far, five have been reported up to 46 times in 21 countries as phytopathogens of at least 31 crops. Indeed, P. ananatis and P. agglomerans have been reported as phytopathogenic bacteria for at least ten economically important crops, including rice. Recently, Africa Rice Center and its partners have suspected the presence of an emerging bacterium that causes rice bacterial blight in several African countries, and the causal agent has been confirmed as belonging to the genus Pantoea. The objectives of our thesis project were (i) to improve the collection of existing AfricaRice isolates by new collections (ii) to develop diagnostic and characterization tools for fine analysis of genetic, phenotypic and epidemio-follow-up studies. Our results showed that bacteria capable of producing bacterial blight symptoms of rice in Africa form a species complex composed mainly of P. ananatis, P. stewartii and P. agglomerans. Different types of diagnostic tools and characterizations were then developed and validated. The results from the use of these tools helped to point out the presence of this bacterial complex in several African countries and to provide details on its geographical structure. Thus, in total, we diagnosed a bacterial species complex, phytopathogenic of rice in 11 African countries (Benin, Burkina Faso, Burundi, Ghana, Ivory Coast, Mali, Niger, Nigeria, Senegal, Tanzania, Togo). In addition, analyzes of three genomes of african P. ananatis and the development, evaluation, and application of Multiple Locus VNTR Analysis (MLVA) tools provided insights into the phylogenetic and phylogenomic relationships that exist between P. ananatis strains isolated from rice and strains from other sources (plants, animals and environment). Indeed, preliminary results showed that several strains of P. ananatis isolated from rice in Africa, Asia and Europe were phylogenetically linked and formed a group that differentiated them from P. ananatis from other sources. In conclusion, the results of this thesis project provide a solid foundation that will facilitate future studies of Pantoea spp in Africa.

Made available in DSpace on 2014-06-11T19:23:32Z (GMT). No. of bitstreams: 0 Previous issue date: 2011-12-02Bitstream added on 2014-06-13T19:09:24Z : No. of bitstreams: 1 andrade_phm_me_arafcf.pdf: 233794 bytes, checksum: 4fb09f68aeeb569be13ec267ab33fc6f (MD5) / Universidade Estadual Paulista (UNESP) / O objetivo do trabalho foi a análise bacteriológica e físico-química de amostras da água do Sistema de Pré-resfriamento de um abatedouro de aves e na análise bacteriológica de carcaças de frango antes, no interior e após o Sistema de Pré-resfriamento. As variáveis físico-químicas da água foram relacionadas com presença ou ausência de Salmonella spp. nas carcaças após sistema de pré-resfriamento. Em relação à contagem bacteriana, observamos que a saída do pré-chiller é o ponto de coleta onde há maior contaminação da água. No entanto, há uma queda significativa na contaminação da água na saída do chiller. Na análise por agrupamento hierárquico adotando a variável Salmonella spp. como classe, não foi possível verificar tendência de separação entre as amostras contaminadas e as não contaminadas, porém, pode-se perceber que com o aumento da velocidade de abate a separação entre as amostras passa a existir. Ao analisar as componentes principais, considerando todas as variáveis, observamos que existe uma relação entre a contaminação por Salmonella spp. e a vazão da renovação da água do pré-chiller. Assim, foi possível verificar que o controle dos parâmetros físico-químicos e microbiológicos da água do sistema de pré-resfriamento, bem como as diversas variáveis das condições de abate, são fundamentais para garantirem carcaças pré-resfriadas livres de Salmonella spp. Torna-se necessário propor estudos específicos de cada variável a fim de que as condições ideais de abate sejam estabelecidas e o processo seja autocontrolado / This study was based on microbiological and physicochemical analysis of water samples from the pre-cooling system of a poultry slaughterhouse and the bacteriological analysis of chicken carcasses before, during and after the pre-cooling system. The physicochemical variables of the water were related to the presence or absence of Salmonella spp. in the carcasses after the pre-cooling system. Regarding the amount of bacteria, it was observed that the output of the pre-chiller is the collecting point where the water is most contaminated. However, there is a significant decrease of contamination in the water leaving the chiller. In the hierarchical cluster analysis taking the variable Salmonella spp. as a class it was not possible to verify the trend of separation between the contaminated samples and the non-contaminated ones, although it was realized that with the increase in speed of slaughter the separation between samples exists. By analyzing the main components, considering all variables, it was observed that there is a relation between the contamination by Salmonella spp. and the flow rate of the water renewal in the pre-chiller. Therefore, it was verified that the control of physicochemical and microbiological parameters of the water in the pre-cooling system and the variables of slaughtering conditions are essential to guarantee pre-cooled carcasses free from Salmonella spp. This it becomes necessary to propose specific studies of each variable so that the ideal conditions for slaughter are established and the process can become self-controlled

Comparou-se a eficácia da baciloscopia in natura e pós concentração (Coloração Ziehl Neelsen) e cultura tradicional e automatizada MA de amostras de escarro ou saliva/muco para a detecção do Complexo M. tuberculosis (MTB) em Centro de Referencia Ambulatorial para Tuberculose na Cidade de São Paulo. A identificação do grupo MTB baseou-se no crescimento em meio com Ácido para nitrobenzóico, e visualização do fator corda. Do total de 374 amostras, 228 eram de pacientes sob diagnóstico inicial e 146 em tratamento. 83 amostras eram saliva/muco. Destas, sete foram positivas à baciloscopia, 03 (3,6%) no material concentrado e uma (1,2%) in natura (p=0.5 McNemar Test). Cinco amostras (6%) positivas na cultura pelo método tradicional e 07 (8,4%) p=0.5 pelo MA. As amostras de escarro eram 74 foram positivas na baciloscopia, sendo 34 (11,7%) in natura e 45 (15,5%) no material concentrado, p=0.001. No método tradicional 56 (19,2%) e 67 (23%) pelo MA p=0.001. Independente da característica da amostra a baciloscopia pós concentração e a cultura pelo MA foram mais sensíveis. / Effectiveness of bacilloscopy were compared in natura and pos-concentrated (Ziehl Neelsen staining), and tradicional and automated culture-AM of sputum or saliva/mucus samples for detection of M. tuberculosis complex (MTB) in Ambulatory Reference Center in the city of São Paulo. Identification of MTB group was based on growth in medium with para nitrobenzoic acid, and cord factor visualization. From the total 374 samples, 228 were from patients under initial diagnostic and 146 in treatment. 83 samples were saliva/mucus. Seven of these were bacilloscopy positive, 03 (3.6%) in concentrated material and one (1.2%) in natura (p=.500ª McNemar Test). Five samples (6%) positive for culture by traditional method and 07 (8.4%) p=0.5 for AM. For sputum 74 were bacilloscopy positive, being 34 (11.7%) in in natura and 45 in concentrated material, p=0.001. In traditional method, 56 (19.2%) and 67 (23%) for AM, p=0.001. Independently of sample characteristics, pos-concentrated bacilloscopy and culture by AM were more effectiveness.

A presente tese estudou o diagnóstico e tratamento da mastite bovina pela avaliação do uso de um teste prático de CCS, pela utilização de cultura bacteriológica a campo e pela definição de protocolos de tratamento. Para rápida determinação da CCS, o teste Somaticell® foi usado em amostras de leite tendo o resultado comparado à contagem eletrônica e avaliado por tipo de amostra e pessoa. O Somaticell determinou corretamente a CCS de amostras frescas de leite de quartos mamários. A correlação registrada entre o Somaticell e a CCS eletrônica foi 0,92 e o coeficiente de concordância 0,82. O teste mostrou adequada validade para determinar infecções intramamárias (sensibilidade 91,3%; especificidade 96,0%) e apresentou contagens mais elevadas em amostras contendo patógenos. Pequena variação foi verificada nos resultados do teste quando realizado em duplicata. Entretanto na análise geral dos dados, a variação observada não foi significativa nem afetou a quantidade de amostras com mastite subclínica. Amostras de leite conservadas a 4 ºC por até 5 horas não influenciaram os resultados do Somaticell, mas amostras congeladas ou adicionadas do conservante bronopol não devem ser usadas. Quanto ao diagnóstico da mastite clínica, as infecções causadas por bactérias Gram positivas foram em maioria isoladas de casos clínicos com alteração visual do leite e edema de úbere, de vacas reincidentes e com CCS mensal média maior de 200.000 céls/mL. Por outro lado, as mastites causadas por bactérias Gram negativas apresentaram em maioria casos clínicos com comprometimento sistêmico em vacas de alta produção. Enquanto isso, as amostras mastíticas com ausência de crescimento na cultura laboratorial apresentaram grau da mastite e perfil do animal variado. A cultura bacteriológica realizada na propriedade leiteira com o conjunto dos meios Sangue Base Azida, MacConkey e Vogel-Johnson, mostrou adequada recuperação dos patógenos causadores de mastite clínica. Do total de 203 cultivos realizados na fazenda e em laboratório 79,3% mostraram concordância. A taxa de concordância das culturas foi afetada pelo número de unidades formadoras de colônia presente na amostra de leite. A sensibilidade e especificidade registradas para a cultura a campo foram 83,0 e 76,5%, respectivamente, as quais foram positivamente influenciadas pelo isolamento de bactérias Gram positivas, e negativamente pelo isolamento de bactérias Gram negativas e resultados com ausência de crescimento. O cultivo feito na fazenda mostrou vantagens em usar amostras de leite frescas, porém a leitura precoce do crescimento bacteriano e a metodologia simples reduzem sua acurácia. Para o tratamento das mastites clínicas com base no resultado da cultura a campo, foi encontrada taxa geral de cura bacteriológica de 69,7%. A CCS da maioria dos tetos que apresentaram mastite se manteve elevada até 21 dias pós-detecção da doença. Mastites causadas por bactérias Gram negativas mostraram taxas de cura mais altas. Já as mastites causadas por Staphylococcus aureus tiveram as menores taxas de cura apesar da utilização de tratamento antibiótico estendido. As mastites de grau 1 e 2, com isolamento de bactérias Gram negativas e ausência de crescimento na cultura bacteriológica, não apresentaram diferença em cura sendo ou não tratadas com antibiótico intramamário. / The present thesis investigated the diagnosis and treatment of bovine mastitis by using a simple test for somatic cell count, on-farm bacteriological culture and guided treatment protocols. To rapidly determine SCC, Somaticell® test was used on milk samples having the results compared to electronic count and evaluated by sample type and reader. The Somaticell test correctly determined the SCC in fresh milk samples of mammary quarters. The correlation between Somaticell and electronic SCC was 0.92, being kappa coefficient equals to 0.82. This test presented good reliability to determine intramammary infections using a threshold of 205.000 cells/mL (sensitivity = 91.3% and specificity = 96.0%) and showed greater SCC in samples containing major mastitis pathogens. Minor intra-individual variation was detected when performing the test. Probably, the homogenization procedure of the test is the most likely explanation for the observed variation. However, the final analysis indicated that this variation was not significant and did not affect the amount of samples classified as having subclinical mastitis. Milk samples preserved at 4 ºC up to 5 hours did not change test results. Nevertheless, frozen or bronopol preserved samples were not suitable for this test. Clinical mastitis data indicated that infections caused by Gram positive bacteria were mainly seen on clinical cases with visual milk abnormalities and udder edema of clinical recurrent animals showing monthly average SCC greater than 200,000 cells/mL. In contrast, clinical mastitis caused by Gram negative bacteria was frequently associated with systemic signs in high producing cows. In addition, mastitic samples without bacterial growth in the laboratory did not present a defined pattern in relation to mastitis grade and animal characteristic. The on-farm bacteriological culture using Azide Blood Agar Base, MacConkey Agar and Vogel-Johnson Agar, showed adequate recovery of mastitis causing pathogens. In 79.3% of the cultures (n = 203) the on-farm results agreed with the standard laboratory culture. Interestingly, the concordance rate was affected by the number of colony forming units in the milk sample. The sensitivity and specificity of on-farm culture were 83.0 and 76.5%, respectively. These results were positively influenced by growth of Gram positive bacteria and negatively influenced by growth of Gram negative bacteria and samples with no growth. The use of fresh milk samples in on-farm culture seemed advantageous for bacterial recovery, although premature plate reading of bacterial growth and simplicity of this methodology might reduce its accuracy. Mastitis treatment guided by on-farm culture showed an overall bacteriological cure rate of 69.7%. In the majority of quarters, SCC remained elevated within 21 days after detection of clinical mastitis. Gram negative bacteria presented greater cure rates. On the contrary, Staphylococcus aureus mastitis displayed the lowest cure rate even by using extended antibiotic treatment. Intramammary antibiotic treatment did not show effect on cure rates of grade 1 and 2 clinical mastitis caused by Gram negative bacteria or with negative growth in the on-farm culture.

A leptospirose é uma zoonose de importância mundial causada por bactérias do gênero Leptospira. No Brasil, a maioria dos casos é causada por L. interrogans sorovar Copenhageni. O objetivo destre trabalho foi identificar adesinas de leptospira pela técnica de Phage display. Bibliotecas com fragmentos genômicos resultaram na idendificação de ligantes de leptospira com afinidade por tecidos de hamster. Uma varredura dessas bibliotecas contra heparan sulfato proteoglicano (HSPG) identificou como ligantes as proteínas LigA e LigB. Proteínas recombinantes foram produzidas e submetidas à ligação às células de mamíferos e aos componentes de matriz extracelular. LigB recombinante foi capaz de se ligar ao HSPG, à heparina e às células de mamíferos. HSPG e heparina foram capazes de reduzir significativamente a interação dessa proteína com as células. Estes resultados evidenciam o papel de proteínas da leptospira na sua interação com o hospedeiro e ilustram a possibilidade do uso da técnica de phage display para identificar possíveis adesinas. / Leptospirosis is a worldwide important zoonosis caused by bacteria of the genus Leptospira. In Brazil, most cases is caused by L. interrogans serovar Copenhageni. Our goal was to identify leptospiras adhesins by phage display technique. Libraries of genomic fragments resulted in the identification of ligands with affinity for leptospiras hamster tissues. Screening these libraries against heparan sulfate proteoglycan (HSPG) identified the proteins LigA and LigB. Recombinant proteins were produced and subjected to binding to mammalian cells and extracellular matrix components. LigB recombinant was able to bind to HSPG, heparin and mammalian cells. HSPG and heparin were able to significantly reduce the interaction of this protein with cells. These results highlight the role of leptospiras proteins in its interaction with the host and illustrate the possibility of the use of phage display technique to identify potential adhesins.

The objectives of this paper were (i) to perform a systematic review of the literature over the last 21 yr and (ii) to evaluate the efficacy of selective dry cow treatment (SDCT) vs. blanket dry cow treatment (BDCT) in dairy cows regarding the risk of intramammary infection (IMI) after calving, new IMI risk after calving, cure risk during the dry period, and a reduction in antibiotic use at drying-off by meta-analysis. The final number of included studies was n = 3 for IMI risk after calving and n = 5 for new IMI risk after calving, cure risk during the dry period, and antibiotic use. The relative risk (RR) levels for IMI, new IMI, and cure did not differ significantly between SDCT and BDCT. This meta-analysis provides evidence that SDCT seems to be an adequate alternative to BDCT regarding udder health with a simultaneous reduction in antibiotic use. Limitations might arise because of the small number of studies included.:1. Introduction 2. Material and Methods 2.1 Search Strategy 2.2 Study Selection 2.3 Data Extraction 2.4 Assessment of Bias Risk 2.5 Statistical Analysis 3. Results 3.1 Study Selection 3.2 Study Characteristics 3.3 Outcomes 3.4 Risk of Bias 3.5 Pairwise Meta-Analysis 3.6 Subgroup Meta-Analysis 4. Discussion 4.1 Risk of IMI after Calving 4.2 Risk of new IMI after Calving 4.3 Cure Risk during Dry Period 4.4 Antibiotic Use at Drying-Off 4.5 Strengths and Limitations / Ziele dieser Studie waren (i) ein systematisches Review über die Literatur der letzten 21 yr zu erstellen sowie (ii) die Effizienz von selektivem Trockenstellen (SDCT) im Vergleich zu konventionellem Trockenstellen (BDCT) bei Milchkühen anhand von Risiko an intramammären Infektionen (IMI) post partum (pp), Neuinfektionenrisiko pp, Heilungsrisiko während dem Trockenstehen und Reduktion des Antibiotikaeinsatzes zum Trockenstellen mittels einer Meta-Analyse zu untersuchen. Die finale Anzahl eingeschlossener Studien war n = 3 für das IMI-Risiko pp sowie n = 5 für Neuinfektionenrisiko pp, Heilungsrisiko während dem Trockenstehen und Antibiotikaeinsatz zum Trockenstellen. Die relativen Risiken für IMI pp, Neuinfektionen pp und Heilung während der Trockenstehperiode unterschieden sich dabei nicht signifikant zwischen SDCT und BDCT. Diese Meta-Analyse erbringt Evidenz, dass SDCT eine adäquate Alternative zu BDCT im Hinblick auf Eutergesundheit und Antibiotikareduktion ist. Limitationen entstehen durch die geringe Anzahl an eingeschlossenen Studien.:1. Introduction 2. Material and Methods 2.1 Search Strategy 2.2 Study Selection 2.3 Data Extraction 2.4 Assessment of Bias Risk 2.5 Statistical Analysis 3. Results 3.1 Study Selection 3.2 Study Characteristics 3.3 Outcomes 3.4 Risk of Bias 3.5 Pairwise Meta-Analysis 3.6 Subgroup Meta-Analysis 4. Discussion 4.1 Risk of IMI after Calving 4.2 Risk of new IMI after Calving 4.3 Cure Risk during Dry Period 4.4 Antibiotic Use at Drying-Off 4.5 Strengths and Limitations

A prospective study was performed to evaluate a biological medication in the treatment of digital dermatitis (DD) in dairy cattle. The study was divided into four parts; i) on farm evaluation of DD and treatment effects and comparison between the biological ointment and OTC-spray, ii) statistical evaluation, iii) histological examination using FISH and iv) microbiological examination and culture if bacteria found in biopsies from infected skin.

Huit cent trente et un troupeaux de vaches laitières répartis dans 5 états américains ont été enrôlés dans une étude de cohorte prospective. Un modèle d’équations d'estimation généralisées a été utilisé pour étudier l'association entre les signes cliniques et la détection de salmonelles dans les fèces des animaux soupçonnés de salmonellose clinique. La sensibilité et la spécificité de la culture bactériologique ont été estimées à l’aide d’un modèle de classes latentes. Dix-huit pour cent des 874 échantillons provenant de veaux et 29% des 1479 échantillons de vaches adultes étaient positifs pour Salmonella spp. Il n’a pas été possible d’établir une association claire entre les différents signes cliniques observés et la détection de salmonelles. Les 2 sérotypes les plus fréquemment isolés étaient Typhimurium et Newport. La probabilité de détecter des salmonelles était plus élevée chez les veaux où un autre agent entéropathogène était également détecté. La proportion d’échantillons positifs était plus élevée parmi les vaches ayant reçu des antibiotiques dans les jours précédant l’échantillonnage. La sensibilité de la culture a été estimée à 0,48 (intervalle de crédibilité à 95% [ICr95%]: 0,22-0,95) pour les veaux et 0,78 (ICr95%: 0,55-0,99) pour les vaches. La spécificité de la culture était de 0,94 (ICr95%: 0,87-1,00) pour les veaux et de 0,96 (ICr95%: 0,90-1,00) pour les vaches. Malgré une sensibilité imparfaite, la culture bactériologique demeure utile pour obtenir une meilleure estimation de la probabilité post-test de salmonellose clinique chez un bovin laitier, par rapport à la probabilité estimée suite au seul examen clinique. / Eight hundred and thirty-one dairy herds in 5 states in the northeast USA were enrolled in a prospective cohort study. A generalized estimating equations model including herd as a random effect was built to study the association between clinical signs and detection of Salmonella spp. in the faeces of animals suspected of clinical salmonellosis. The sensitivity and specificity of the bacteriological culture were estimated using a latent class model. Eighteen percent of the 874 samples from calves and 29% of the 1479 samples from adult cows were positive for Salmonella spp. It was not possible to establish a clear association between the various clinical signs and detection of Salmonella spp. in the faeces. The two most frequently isolated serotypes were Typhimurium and Newport. The probability of detecting salmonellas was higher for calves when another enteric pathogen was also detected. The proportion of positive samples was higher among cows that received antibiotics in the days preceding the sampling. The sensitivity of the bacteriological culture was estimated at 0.48 (95% credibility interval [95%CrI]: 0.22 to 0.95) for calves and 0.78 (95%CrI 0.55 to 0.99) for cows. The specificity of the culture was 0.94 (95%CrI: 0.87 to 1.00) for calves and 0.96 (95%CrI: 0.90 to 1.00) for cows. Despite imperfect sensitivity, bacterial culture remains useful to obtain a better estimate of the post-test probability of clinical salmonellosis in dairy cattle, compared to the estimated probability following the clinical examination alone.

L’essor de la discipline bactériologique est l’un des phénomènes les plus célébrés de l’historiographie médicale. Les approches qu’ont empruntées les historiens pour aborder le sujet depuis le tournant du XXe siècle se sont progressivement modifiées pour passer, le plus souvent, d’une interprétation endogène des développements de la science, où les concepts, les théories, les méthodes de la médecine sont perçus comme se développant isolément du contexte social dans lequel ils s’insèrent, à l’approche inverse, sociologique, où chacune des facettes de l’entreprise médico-scientifique est influencée par son milieu dans une interaction où les instances publiques, gouvernementales et professionnelles impliquées par les projets de médicalisation, formant une dynamique impassible, modifient le cours de chaque aspect de l’histoire médicale. Mais, en dehors des éléments professionnels, le développement de la pensée médico-scientifique est-il invariablement subjugué par cette dynamique sociale ? L’idéal de scientificité prôné par les médecins, formant un archétype dans lequel la rigueur du professionnel doit être isolée de ces facteurs extrinsèques n’est-il pas en mesure d’avoir conféré aux démarches médico-scientifiques une stabilité authentique vis-à-vis les fluctuations de l’environnement sociopolitique et professionnel dans lequel elles s’inscrivent ? Cette étude répond à ce questionnement par l’analyse exhaustive du discours défini par les périodiques médicaux du Québec entre 1840 et 1880. Elle s’articule sur deux développements inédits : l’un qui présente les assises méthodologiques de la vérification, c’est-à-dire la définition de l’archétype médical, son rôle dans la légitimation professionnelle, les critères de scientificité qu’il détermine de même qu’une typologie du discours qu’il permet d’inférer ; l’autre, ses résultats. L’étude montre que l’archétype décrit par le corps médical québécois, loin de n’être qu’un outil discursif par lequel la profession a pu être socialement reconnue au XIXe siècle, exerça une influence déterminante sur la formation de l’attitude professionnelle à l’égard des nouveautés étiologiques présentées par les pionniers de la bactériologie. En plus de dévoiler la trame exacte du développement de la pensée étiologique au Québec, la thèse souligne la complémentarité des approches internes et externes de l’historiographie médicale. Elle contribue ainsi à une représentation plus juste des processus à l’oeuvre dans le développement scientifique. / The rise of bacteriology is one of the most celebrated phenomenon in medical historiography. Historian’s approaches taken to address the issue since the turn of the twentieth century were gradually modified to pass, most often, from an endogenous interpretation of scientific development, where medical concepts, theories, and methods are seen as developing in isolation from the social context in which they occur, to the opposite, sociological approach, where every element of the medical-scientific enterprise is rather seen as being influenced by its context in an interaction by which the public, governmental and professional instances involved in medicalization, forming an impassive dynamic, change the course of every aspect of medical history. But beyond the professional elements, is the development of medical and scientific thought invariably subjugated to this social dynamic? Could not the ideal of scientificity advocated by doctors, forging an archetype in which professional rigor is meant to be isolated from these extrinsic factors, confer to the medical and scientific endeavor a genuine stability towards fluctuations in the socio-political and professional environment in which they evolve? Our study addresses these questions by the exhaustive analysis of the discourse defined by the Quebec medical journals between 1840 and 1880. It is based on two new developments, one that presents the methodological foundations of the audit - that is to say, the definition of the medical archetype, its role in professional recognition, the scientific criteria that it determines, and a typology of discourse that can be inferred from it - and the other, the results. The study shows that the archetype described by the Quebec medical profession, far from being solely a discursive tool by which the profession has been socially recognized in the nineteenth century, exerted a decisive influence on the formation of the professional attitude towards etiological novelties presented by the pioneers of bacteriology. Thus, in addition to revealing the exact framework of the development of causal thinking in Quebec, the thesis shows the complementarity of internal and external approaches to medical historiography. It contributes to a fairer representation of the processes at work in scientific development.

Huit cent trente et un troupeaux de vaches laitières répartis dans 5 états américains ont été enrôlés dans une étude de cohorte prospective. Un modèle d’équations d'estimation généralisées a été utilisé pour étudier l'association entre les signes cliniques et la détection de salmonelles dans les fèces des animaux soupçonnés de salmonellose clinique. La sensibilité et la spécificité de la culture bactériologique ont été estimées à l’aide d’un modèle de classes latentes. Dix-huit pour cent des 874 échantillons provenant de veaux et 29% des 1479 échantillons de vaches adultes étaient positifs pour Salmonella spp. Il n’a pas été possible d’établir une association claire entre les différents signes cliniques observés et la détection de salmonelles. Les 2 sérotypes les plus fréquemment isolés étaient Typhimurium et Newport. La probabilité de détecter des salmonelles était plus élevée chez les veaux où un autre agent entéropathogène était également détecté. La proportion d’échantillons positifs était plus élevée parmi les vaches ayant reçu des antibiotiques dans les jours précédant l’échantillonnage. La sensibilité de la culture a été estimée à 0,48 (intervalle de crédibilité à 95% [ICr95%]: 0,22-0,95) pour les veaux et 0,78 (ICr95%: 0,55-0,99) pour les vaches. La spécificité de la culture était de 0,94 (ICr95%: 0,87-1,00) pour les veaux et de 0,96 (ICr95%: 0,90-1,00) pour les vaches. Malgré une sensibilité imparfaite, la culture bactériologique demeure utile pour obtenir une meilleure estimation de la probabilité post-test de salmonellose clinique chez un bovin laitier, par rapport à la probabilité estimée suite au seul examen clinique. / Eight hundred and thirty-one dairy herds in 5 states in the northeast USA were enrolled in a prospective cohort study. A generalized estimating equations model including herd as a random effect was built to study the association between clinical signs and detection of Salmonella spp. in the faeces of animals suspected of clinical salmonellosis. The sensitivity and specificity of the bacteriological culture were estimated using a latent class model. Eighteen percent of the 874 samples from calves and 29% of the 1479 samples from adult cows were positive for Salmonella spp. It was not possible to establish a clear association between the various clinical signs and detection of Salmonella spp. in the faeces. The two most frequently isolated serotypes were Typhimurium and Newport. The probability of detecting salmonellas was higher for calves when another enteric pathogen was also detected. The proportion of positive samples was higher among cows that received antibiotics in the days preceding the sampling. The sensitivity of the bacteriological culture was estimated at 0.48 (95% credibility interval [95%CrI]: 0.22 to 0.95) for calves and 0.78 (95%CrI 0.55 to 0.99) for cows. The specificity of the culture was 0.94 (95%CrI: 0.87 to 1.00) for calves and 0.96 (95%CrI: 0.90 to 1.00) for cows. Despite imperfect sensitivity, bacterial culture remains useful to obtain a better estimate of the post-test probability of clinical salmonellosis in dairy cattle, compared to the estimated probability following the clinical examination alone.