Dissertation (PhD)--University of Stellenbosch, 2004 / ENGLISH ABSTRACT: Newcastle disease (NO) and mycoplasma infections in ostriches have considerable economic implications for the South African ostrich industry in that NO is a limiting factor in the export of ostrich products to the European Union and mycoplasma infections cause stock losses, reduced production, reduced hatchability and downgrading of carcasses. In the first section of this dissertation, the role of passively acquired and mucosal immunity in protection of ostrich chicks against Newcastle disease virus (NOV) was investigated. Ostrich hen serum IgG and yolk IgY were isolated and characterized, and the transfer of maternal anti-NOV antibodies to the egg yolk was determined using an enzyme-linked immunosorbent assay (ELISA). Results indicated that anti-NOV antibodies were successfully transferred from the ostrich hen to the egg yolk. In addition, ostrich IgA was isolated, characterized and rabbit anti-ostrich IgA antibodies produced and used for measuring mucosal anti- NOV IgA antibodies produced in response to mucosal vaccination. Results indicated that the live La Sota vaccine stimulates IgA production and thus mucosal immunity in ostrich chicks. In the second section of this dissertation, ostrich mycoplasmas were isolated and identified using 16S rRNA gene sequencing. These sequences indicated that ostriches carry three unique mycoplasmas, which are phylogenetically quite divergent. The 16S rRNA gene sequences of the ostrich mycoplasmas were subsequently used for the development of specific primers for the detection and diagnosis of mycoplasma infections in ostriches by PCR. The last section of this dissertation focuses on avian malaria in African penguins and the management of this disease during rehabilitation. The Foundation for the Conservation of Coastal Birds (SANCCOB) is a seabird rescue and rehabilitation centre, which is largely dedicated to the rehabilitation of diseased, injured and oiled penguins. Significant mortalities due to avian malaria occur at this facility. The aim of this study was the development of an ELISA for the purpose of assessing the natural levels of anti-Plasmodium antibodies in African penguins on entry into the SANCCOB facility and during rehabilitation. Results indicated significant increases in anti- Plasmodium antibody levels after entry, which was not influenced by oiling. Infection with malaria and not parasite recrudescence was viewed to be the cause of this increase, indicating a possible role of the SANCCOB facility in exposing penguins to avian malaria. / AFRIKAANSE OPSOMMING: Newcastlesiekte (NS) en mikoplasmainfeksies in voltruise het geweldige ekonomiese implikasies vir die Suid-Afrikaanse volstruisbedryf. Die rede hiervoor is dat NS 'n beperkende faktor in die uitvoer van volstruisprodukte na die Europese Unie is, en mikoplasmainfeksies tot kudde verliese, verlaagde produksie en uitbroei asook lae gradering van karkasse lei. In die eerste gedeelte van hierdie proefskrif is die rol van passiewe- en mukosale-immuniteit in die beskerming van volstruiskuikens teen NS virus (NSV) ondersoek. Volstruishenserum IgG en eier IgY is geïsoleer en gekarakteriseer en die oordrag van maternale anti-NSV antiliggame na die eier ondersoek met behulp van 'n 'enzyme-linked immunosorbent assay' (ELISA). Resultate het getoon dat anti-NSV antiliggame suksesvol van die hen na die eier oorgedra is. Volstruis IgA is ook geïsoleer, gekarateriseer en konyn anti-volstruis IgA antiliggame geproduseer wat gebruik is vir die bepaling van mukosale anti-NSV IgA antiliggame in reaksie op mukosale immunisering. Resultate het getoon dat lewendige La Sota entstof IgA produksie stimuleer en dus tot mukosale-immuniteit in volstruiskuikens lei. In die tweede gedeelte van hierdie proefskrif is volstruismikoplasmas geïsoleer en geïdentifiseer met behulp van 16S rRNA geenopeenvolgingsbepalings. Hierdie volgordes het getoon dat drie unieke mikoplasmas in volstruise voorkom wat filogeneties verskillend blyk te wees. Die 16S rRNA geenopeenvolgings van die volstruismikoplasmas is gebruik vir die ontwikkeling van spesifieke inleiers vir die PKR identifisering en diagnose van mikoplasmainfeksies in volstruise. Die laaste gedeelte van hierdie proefskrif fokus op voëlmalaria in die Afrika pikkewyn en die bestuur van hierdie siekte gedurende rehabilitasie. Die 'South African Foundation for the Conservation of Coastal Birds' (SANCCOB) is 'n seevoëlreddingsen rehabilitasie-sentrum vir siek, beseerde en ge-oliede pikkewyne. Hierdie sentrum het egter aansienlike vrektes as gevolg van voëlmalaria. In hierdie studie is 'n ELISA ontwikkel vir die bepaling van natuurlike anti-Plasmodium antiliggaamvlakke van pikkewyne by aankoms en tydens rehabilitasie by SANCCOB. Resultate het 'n toename in anti-Plasmodium antiliggaamvlakke getoon na toelating wat nie beïnvloed is deur olie nie. Hierdie toename kan toegeskryf word aan nuwe malariainfeksies en nie 'n heruitbraak van bestaande infeksies nie wat daarop dui dat pikkewyne aan voëlmalaria blootgestel word by die SANCCOB-sentrum.

En Amérique du Nord, Mycoplasma bovis est le plus pathogène des mycoplasmes retrouvés chez les bovins. Les principales maladies qu’on lui associe (maladies respiratoires, mammites, arthrites septiques et otites moyennes et/ou internes) constituent un défi à l’industrie laitière à cause de la difficulté à les traiter et à les prévenir par une vaccination. L’objectif principal de ce projet était d’étudier l’excrétion nasale et la réponse sérologique à M. bovis chez les génisses de remplacement, entre la naissance et 7 mois d’âge, dans 4 troupeaux laitiers au Québec. Quatre-vingt-trois paires mère/génisse provenant de 4 cohortes de bovins laitiers étaient prélevées mensuellement (génisses : 0 à 7 mois ; mères : 0, 1 et 5 mois après vêlage). Écouvillons nasaux et échantillons de lait étaient analysés par culture bactériologique et par immunofluorescence indirecte. Les anticorps circulants étaient détectés par le test ELISA. À la naissance, la prévalence sérologique des génisses était supérieure à celle des mères (P = 0,01). La transmission de M. bovis aux génisses par le lait et par l’excrétion nasale des mères était faible. L’âge moyen (jour) d’une génisse à sa 1ère excrétion nasale et sa 1ère séroconversion à M. bovis était loin de la période néonatale: 77,5 ± 11,2 (n = 22) et 96,8 ± 7,4 (n = 36) respectivement. Conclusion, les vaches adultes n’ont constitué qu’une voie mineure de transmission de M. bovis aux génisses, la principale voie de transmission était fort probablement le contact direct ou indirect avec d’autres génisses excrétrices nasales de M. bovis. / In North America, Mycoplasma bovis is the most pathogenic mycoplasma found in cattle. The main diseases associated with it (respiratory disease, mastitis, septic arthritis and otitis median and/or internal) are a challenge to the dairy industry because of the difficulty to treat them and to prevent them by vaccination. The principal objective of this project was to study nasal shedding and serological response to M. bovis in replacement heifers, between birth and 7 months of age, in four dairy herds in Quebec. Eighty three pairs cow/heifer in 4 cohorts of dairy cattle were sampled monthly (heifers: 0 to 7 months; cows: 0, 1 and 5 months after calving). Nasal swabs and milk samples were analyzed by bacteriological culture and by indirect immunofluorescence. Circulating antibodies were detected by ELISA test. At birth, the serologic prevalence of heifers was significantly higher than the serologic prevalence of cows (P = 0,01). Transmission of M. bovis to heifers in milk and nasal shedding from cows was low. The average age (days) of a heifer for first nasal shedding and first seroconversion to M. bovis was far from the neonatal period: 77,5 ± 11,2 days (n = 22) and 96,8 ± 7,4 days (n = 36) respectively. Conclusion, cows were only a minor route of transmission of M. bovis to heifers, the main route of transmission was most likely the direct or indirect contact with other heifers shedding M. bovis in their upper respiratory tract.

O complexo respiratório bovino é um dos principais problemas encontrados em bovinos tanto confinados quanto àqueles criados a pasto, levando a importantes perdas econômicas devido aos altos índices de morbidade e mortalidade. O objetivo geral deste trabalho foi determinar a prevalência de M. bovis, M. díspar, M. mycoides subsp. mycoides SC, P. multocida, M. haemolytica, Parainfluenza Bovino tipo-3 (PIb- 3) e Influenza vírus D e a prevalência de anticorpos contra Vírus da Diarreia Viral Bovina (VDVB), Herpesvírus tipo -1 (BoHV1) e o Vírus Respiratório Sincicial Bovino (VRSB) em bezerros sadios e com broncopneumonia criados nos assentamentos de Caiuá, Presidente Epitácio e Mirante de Paranapanema - SP. Além disso, objetivase avaliar a associação destes micro-organismos com a presença da broncopneumonia e dos sinais e sintomas apresentados pelos animais durante a avaliação física. Estudou-se 141 bezerros, machos e fêmeas de até um ano de idade, os quais, após exame físico, foram classificados em sadios e com pneumonia. Foram coletadas amostras de lavado traqueobrônquico e sangue total para obtenção do soro. As amostras foram utilizadas para isolamento e identificação de M. bovis, M. díspar, M. mycoides subsp. mycoides SC, P. multocida e M. haemolytica, detecção molecular de Parainfluenza Bovino tipo-3 (PIb-3) e Influenza vírus D (IVD) e detecção de anticorpos contra Vírus da Diarreia Viral Bovina (VDVB), Herpesvírus tipo -1 (HVBo-1) e o Vírus Respiratório Sincicial Bovino (VRSB). Não houve isolamento de P. multocida e M. haemolytica. Dentre as bactérias aeróbias isoladas, observou-se maior frequência de isolamento de Bacillus sp., Staphylococcus intermedius e bactérias Gram-negativas não fermentadoras. M. díspar foi a única espécie de micoplasma identificada com os oligonucleotídeos iniciadores utilizados. Faz-se necessário a busca por outras espécies de micoplasmas que podem estar relacionadas aos casos de broncopneumonia em bovinos. Não houve detecção de Parainfluenza Bovino tipo 3 e Influenza vírus D nas amostras de lavado traqueobrônquico. Os três municípios estudados apresentaram anticorpos para os vírus estudados. Observou-se prevalência de BoHV-1, VDVB e VRSB de 31,7%, 24,6 e 38,8%, respectivamente. Não houve associação entre o status de saúde dos bezerros e os achados microbiológicos e sorológicos. Foi observada associação entre enterobactérias e a variável “desidratação leve” (p=0,033/ OR= 11,25, IC: 1,809-41,834. Observou-se associações entre Mollicutes e a variável “secreção nasal serosa” (p=0,03). Concluiu-se que a broncopneumonia é uma enfermidade multifatorial. Faz-se, necessário, portanto, a associação dos achados de exames físico, microbiológicos e características do ambiente e manejo / Bovine respiratory disease complex is one of the major problems observed in feedlot and grazing cattle, causing economic losses due to high morbidity and mortality rates. The aim of this study was to determine the prevalence of M. bovis, M. díspar, M. mycoides subsp. mycoides SC, P. multocida, M. haemolytica, Bovine Parainfluenza type-3 (bPI-3) and Influenza vírus D (IVD) and the prevalence of antibodies against Bovine Viral Diarrhea Vírus (BVDV), Bovine Herpesvírus type -1 (BoHV1) and Bovine Respiratory Syncytial Vírus (VRSB) in healthy and pneumonic calves raised in settlements located in Caiuá, Presidente Epitácio e Mirante de Paranapanema São Paulo State. Moreover, we aimed to evaluate the association between those microorganisms and antibodies and the presence of bronchopneumonia and the symptoms observed during the physical examination. We studied 141 males and females calves that were classified as healthy and pneumonic calves. We collected tracheobronchial lavage samples and total blood to obtain serum samples. Isolation and biochemical/ molecular identification were performed in order to detect M. bovis, M. díspar, M. mycoides subsp. mycoides SC, P. multocida, M. haemolytica, Bovine Parainfluenza type-3 and Influenzavírus D. Serological survey was performed to detect antibodies aginst Bovine Viral Diarrhea Vírus (BVDV), Bovine Herpesvírus type -1 (BoHV1) and Bovine Respiratory Syncytial Vírus (VRSB). There was not any isolation of P. multocida and M. haemolytica. Bacillus sp., Staphylococcus intermedius and Non-fermenter Gram-negative bacteria were higher prevalent compared to the other aerobic bacteria isolated. M. díspar was the only mycoplasma species identified by the primers used. It is necessary the identification of other mycoplasma species that could be related to the cases of bronchopneumonia in cattle. Bovine Parainfluenza type-3 and Influenza vírus D were not identified. Antibodies were detected in all municipalities. The prevalence of BoHV, BVDV e VRSB was 31.7%, 24.6 and 38.8%, respectively. The association between health status and microbial/ serological findings was not observed. Enterobacterias were associated to “mild dehydration” (p=0.033/OR=11.25; IC: 1.809-41.834). Associations between Mollicutes and “serous nasal discharge” (p=0.03) was also detected. In conclusion, S. intermedius was associated to “nasal air flow” (p=0.097). In conclusion bovine bronchopneumonia is multi-factorial disease. It is necessary, though, physical examination, microbiology and management and environment feature results

O Brasil é o 18ª maior produtor de carne ovina e, apesar de ser em grande parte informal, é uma cultura crescente no país. Dentre as enfermidades infecciosas que acomete a ovinocultura a broncopneumonia é uma das mais recorrentes, no entanto, não há muitos estudos sobre esta enfermidade em pequenos ruminantes no Brasil. Por isso, esta pesquisa teve como objetivo verificar a ocorrência de doenças respiratórias no estado de São Paulo e Rio de Janeiro causadas por bactérias e vírus. Para a realização desse projeto foi utilizado a técnica de lavado traqueobrônquico transtraqueal e coleta de sangue total para obtenção do soro em 99 ovinos. Essas amostras foram submetidas a teste de virusneutralização para identificação de anticorpos contra vírus da Parainfluenza Tipo 3 (PI-3), Herpesvírus Bovino Tipo 1 (BoHV- 1), Vírus Sincicial Respiratório Bovino (BRSV) e Vírus da Diarreia Viral Bovina (VDVB). Utilização do teste de imunodifusão em gel de agarose e Eradikt® para detectar a presença de anticorpos contra Lentivírus de Pequenos Ruminantes (LVPR). Isolamento e identificação bioquímica para M. haemolytica e Pasteurella multocida. Cultivo e isolamento, identificação bioquímica e PCR foram testes utilizados para identificação de micoplasmas (Mycoplasma bovis, M. agalactiae, M. mycoides subsp. capri). Das 99 amostras coletadas, 33 foram de ovinos doentes e 66 de ovinos sadios. Não houve identificação de M. haemolytica e P. multocida, nem presença de anticorpos contra BoHV-1 e VDVB. No entanto, observou-se a prevalência de 52,52%, 48,48% e 21,87% de PI-3, BRSV e LVPR respectivamente. Em relação as bactérias aeróbias, houve maior frequência de isolamento de Bacillus sp. e Gram-negativas não fermentadoras. Apesar de identificar bactérias da classe Mollicutes em colônias isoladas em 23,28% das amostras, houve apenas uma identificação com os oligonucleotídeos utilizados, o M. mycoides subsp. capri, primeiro isolamento em ovinos no estado de São Paulo e Rio de Janeiro. Houve diferença estatística significativa (p<0,05) entre animais com broncopneumonia e manifestações clínicas como taquipneia, hipertermia, secreção nasal, tosse, dispneia, crepitação fina e ronco e entre animais com broncopneumonia e não realizam de quarentena e não separam animais doentes. A broncopneumonia envolve vários fatores, incluindo o manejo, agente infeccioso e a imunidade do animal. Por isso, é necessário conhecer todos esses aspectos e associá-los para uma melhor prevenção e tratamento. / Brazil is the 18th largest producer of sheep meat and, despite being largely informal, is a growing crop in the country. Among the infectious diseases that affect sheep production, bronchopneumonia is one of the most recurrent, however, there are not many studies on this disease in small ruminants in Brazil. Therefore, this research aimed to verify the occurrence of respiratory diseases in the state of São Paulo and Rio de Janeiro caused by bacteria and viruses. For the accomplishment of this project was used tracheobronchial lavage technique transtracheal and collection of whole blood to obtain serum in 99 sheep. These samples were submitted to virus neutralization test to identify antibodies against Parainfluenza Type 3 (PI-3), Bovine Herpesvirus Type 1 (BoHV-1), Bovine Respiratory Syncytial Virus (BRSV) and Bovine Viral Diarrhea Virus (BVDV). Use of the Eradikit ® and agarose gel immunodiffusion test to detect the presence of antibodies against Small Ruminant Lentiviruses (LVPR). Isolation and biochemical identification for M. haemolytica and Pasteurella multocida. Cultivation and isolation, biochemical identification and PCR were used to identify mycoplasmas (Mycoplasma bovis, M. agalactiae, M. mycoides subsp. Capri). Of the 99 samples collected, 33 were from diseased sheep and 66 from healthy sheep. There was no identification of M. haemolytica and P. multocida, nor presence of antibodies against BoHV-1 and BVDV. However, the prevalence of 52.52%, 48.48% and 21.87% of PI-3, BRSV and LVPR, respectively, was observed. In relation to aerobic bacteria, there was a higher frequency of isolation of Bacillus sp. and Gram-negative non-fermenters. Despite identifying Mollicute class bacteria in isolated colonies in 23.28% of the samples, there was only one identification with the oligonucleotides used, M. mycoides subsp. capri, first isolation in sheep in the state of São Paulo and Rio de Janeiro. There was a significant statistical difference (p <0.05) between animals with bronchopneumonia and clinical manifestations such as tachypnea, hyperthermia, nasal secretion, cough, dyspnea, fine crackling and snoring, and between animals with bronchopneumonia and quarantine and separation of diseased animals. Bronchopneumonia involves several factors, including management, infectious agent and the immunity of the animal. Therefore, it is necessary to know all these aspects and to associate them for a better prevention and treatment.

Computational evolutionary analyses, particularly phylogenetics and ancestral reconstruction, have been extensively exploited under different algorithms and evolutionary models to better understand genome evolution from both small- and large-scale perspectives in order to assign genotypes based on assortment, resolve species relationships and gene annotation issues, further understand gene gain/loss within individual gene families, measure functional divergence among homologs, and infer ancestral character states. These evolutionary studies provide us with insights into biologically relevant issues including paleoenvironments inferred from resurrected proteins, developmental physiology associated with functional divergence of duplicated genes, viral epidemics and modes of transmission in attempt to better prepare, prevent and control diseases, evolution of lineage-specific pathogenicity, and attempts to create a synthetic ancient organism that would benefit the field of synthetic biology. Our work also provides us with greater insights into the accuracies and limitations of ancestral sequence reconstruction methods. In total, our work highlights the diverse questions that evolutionary studies attempt to address and the different biological levels that can be studied to answer these questions.

En Amérique du Nord, Mycoplasma bovis est le plus pathogène des mycoplasmes retrouvés chez les bovins. Les principales maladies qu’on lui associe (maladies respiratoires, mammites, arthrites septiques et otites moyennes et/ou internes) constituent un défi à l’industrie laitière à cause de la difficulté à les traiter et à les prévenir par une vaccination. L’objectif principal de ce projet était d’étudier l’excrétion nasale et la réponse sérologique à M. bovis chez les génisses de remplacement, entre la naissance et 7 mois d’âge, dans 4 troupeaux laitiers au Québec. Quatre-vingt-trois paires mère/génisse provenant de 4 cohortes de bovins laitiers étaient prélevées mensuellement (génisses : 0 à 7 mois ; mères : 0, 1 et 5 mois après vêlage). Écouvillons nasaux et échantillons de lait étaient analysés par culture bactériologique et par immunofluorescence indirecte. Les anticorps circulants étaient détectés par le test ELISA. À la naissance, la prévalence sérologique des génisses était supérieure à celle des mères (P = 0,01). La transmission de M. bovis aux génisses par le lait et par l’excrétion nasale des mères était faible. L’âge moyen (jour) d’une génisse à sa 1ère excrétion nasale et sa 1ère séroconversion à M. bovis était loin de la période néonatale: 77,5 ± 11,2 (n = 22) et 96,8 ± 7,4 (n = 36) respectivement. Conclusion, les vaches adultes n’ont constitué qu’une voie mineure de transmission de M. bovis aux génisses, la principale voie de transmission était fort probablement le contact direct ou indirect avec d’autres génisses excrétrices nasales de M. bovis. / In North America, Mycoplasma bovis is the most pathogenic mycoplasma found in cattle. The main diseases associated with it (respiratory disease, mastitis, septic arthritis and otitis median and/or internal) are a challenge to the dairy industry because of the difficulty to treat them and to prevent them by vaccination. The principal objective of this project was to study nasal shedding and serological response to M. bovis in replacement heifers, between birth and 7 months of age, in four dairy herds in Quebec. Eighty three pairs cow/heifer in 4 cohorts of dairy cattle were sampled monthly (heifers: 0 to 7 months; cows: 0, 1 and 5 months after calving). Nasal swabs and milk samples were analyzed by bacteriological culture and by indirect immunofluorescence. Circulating antibodies were detected by ELISA test. At birth, the serologic prevalence of heifers was significantly higher than the serologic prevalence of cows (P = 0,01). Transmission of M. bovis to heifers in milk and nasal shedding from cows was low. The average age (days) of a heifer for first nasal shedding and first seroconversion to M. bovis was far from the neonatal period: 77,5 ± 11,2 days (n = 22) and 96,8 ± 7,4 days (n = 36) respectively. Conclusion, cows were only a minor route of transmission of M. bovis to heifers, the main route of transmission was most likely the direct or indirect contact with other heifers shedding M. bovis in their upper respiratory tract.

Diss. (sammanfattning) Linköping : Linköpings universitet, 2005. / Härtill 5 uppsatser.

Thèse (M.Sc.) -- Université Laval, 1998. / Bibliogr.: f. 74-87. Publié aussi en version électronique.

As doenças respiratórias são muito comuns na produção intensiva de suínos, já em javalis são escassas informações sobre prevalência, etiologia e apresentação clínico-patológica destas enfermidades. No entanto, a presença de patógenos respiratórios comuns entre javalis selvagens e confinados e suínos domésticos já foi relatada. Este trabalho descreve as principais lesões macroscópicas e histológicas de pneumonias de javalis e os agentes comumente envolvidos. Foram examinados pulmões de javalis, ao abate, provenientes de criatórios comerciais e a principal lesão macroscópica foi consolidação crânio-ventral dos lobos craniais e médios e lesões crônicas cursando com hiperplasia linfóide na histologia. O principal agente bacteriano detectado foi o Mycoplasma hyopneumoniae (58,6%). Outros patógenos bacterianos detectados foram Actinobacillus pleuropneumoniae (48,8%), Haemophilus parasuis (49,6%), Mycoplasma hyorhinis (41,3%), Pasteurella multocida (9,1%) e Streptococcus suis (9,1%). Na segunda parte do trabalho, a pesquisa de patógenos virais foi direcionada para o Vírus da influenza suína (VIS) com objetivo de estudar o envolvimento em pneumonias de javalis de criatórios e a relação com agentes bacterianos encontrados. O vírus pandêmico A/H1N1/2009 foi detectado em 18,3% (11/60) e sua identidade foi confirmada por sequenciamento. A carga viral para H1N1 clássico variou de 4,58 a 6275 cópias/μL e para o H1N1 pandêmico, de 4,65 a 3863 cópias/μL. Nenhuma amostra apresentou título viral após a inoculação em ovos embrionados. As lesões histológicas principais foram broncopneumonia crônica difusa e pneumonia intersticial mononuclear leve, além de hiperplasia linfóide. As amostras positivas por RT-PCR para o VIS para o pH1N1 foram testadas por IHQ, sendo todas negativas para influenza A, mas todas eram positivas para M. hyopneumoniae. Quando testadas por bacteriologia, 18,2% das amostras foram positivas para P. multocida. O estudo mostrou que as pneumonias em javalis de criatório apresentaram lesões e patógenos associados similares aos encontrados em suínos domésticos ao abate. Este é o primeiro relato da infecção pelo vírus pH1N1 em javalis no Brasil. / Respiratory diseases are very common in swine intensive production, although in wild-boars the knowledge of the prevalence, etiology and clinic-pathological presentation of these diseases are very limited. However, the presence of common respiratory pathogens among wild-boar, captive wild-boar and domestic pigs has been reported. This paper describes the main macroscopic and histologic pneumonic lesions of captive wild-boars and pathogens commonly involved. Captive wild-boar lungs at slaughter were examined and the main macroscopic lesion observed was cranio-ventral consolidation of cranial and middle lobes and chronic lesions associated with lymphoid hyperplasia by histology. The main bacterial pathogen detected was Mycoplasma hyopneumoniae (58.6%). Other bacterial pathogens detected were Actinobacillus pleuropneumoniae (48.8%), Haemophilus parasuis (49.6%), Mycoplasma hyorhinis (41.3%), Pasteurella multocida (9.1%) and Streptococcus suis (9.1%). In the second part of this work, the survey of viral pathogens was directed to swine influenza virus (SIV) in order to study the involvement in captive wild-boar pneumonias and the relation with bacterial pathogens. The A/H1N1/2009 pandemic virus was detected in 18.3% (11/60) and its identity was confirmed by sequencing. The classical H1N1 viral load ranged from 4.58 to 6275 copies/uL and the pandemic H1N1, from 4.65 to 3863 copies/uL. No samples had viral titers after inoculation in embryonated eggs. The main histological lesions were chronic diffuse bronchopneumonia and interstitial mononuclear pneumonia as well as mild lymphoid hyperplasia. Samples positive to pH1N1 were assayed by IHC for SIV, all with negative results, and to M. hyopneumoniae, all were positive. When assayed by bacteriology, 18.2% of samples were positive to P. multocida. This study showed that pneumonia in captive wild-boar had similar lesions and associated pathogens were similar to those found in domestic pigs at slaughter. This is the first report of pH1N1 virus infection in captive wild-boars in Brazil.

Com o advento das tecnologias que propiciaram os seqüenciamentos e as análises de genomas completos em tempo relativamente curto, muitos dados sobre vias metabólicas de procariotos e eucariotos puderam ser gerados. Análises comparativas de vias metabólicas de diferentes genomas podem auxiliar no entendimento das relações organizacionais dentre e fora das espécies. Com base em tais perspectivas, este trabalho tem como finalidade implementar um sistema que permita comparar, através de diferentes critérios, vias metabólicas de bactérias. O sistema SAMPA (System for comparative Analysis of Metabolic PAthways) é composto por um banco de dados, com informações sobre vias metabólicas de diversos organismos, e um conjunto de 5 ferramentas utilizadas para comparar estas vias metabólicas e agrupar os organismos que possuam vias metabólicas relacionadas. Como estudo de caso para teste da ferramenta, foi utilizada a família Mycoplasmataceae. / The advent of genome sequencing technology and complete genome analysis has provided new data on prokaryote and eukaryote metabolic pathways. The comparative analysis of metabolic pathways from different organisms can help us understand inter and intra species organizational relationships. Having this in mind, this work focused on building a system that allows for comparing the bacterial metabolic pathways, according to a set of pre-established criteria. SAMPA (System for comparative Analysis of Metabolic PAthways) comprises a database containing information on metabolic pathways in many organisms, and a set of five tools that can be used to compare these metabolic pathways and to group organisms carrying metabolic pathways that are related. As a case study to validate the tool, we the Mycoplasmataceae family of organisms was used.