As exigências das condições higiênico-sanitárias na produção de animais de interesse zootécnico vêm aumentando progressivamente dada à necessidade de aliar-se produtividade a produtos de alta qualidade para atender a mercados consumidores cada vez mais exigentes. Nesse sentido, a utilização de antimicrobianos, tanto na profilaxia como na terapêutica, permanece como estratégia de controle para vários microrganismos patogênicos, de importância não apenas para a produção animal como também para a saúde humana, ainda que restrições ao uso indiscriminado desses produtos têm se intensificado. Não obstante, o uso excessivo desses produtos está associado à seleção de microrganismos resistentes nas áreas de produção. Por outro lado, investigações sobre circulação de cepas resistentes em rebanhos animais, até então restritas a populações humanas, ainda permanecem limitadas no Brasil. Bactérias do gênero Enterococcus, integrantes usuais da microbiota gastrointestinal animal e humana, são indicadoras ambientais de contaminação fecal e tem-se tornado objeto de preocupação em saúde pública e veterinária dada a ocorrência de cepas resistentes à vancomicina (VRE). O presente trabalho teve como objetivo isolar, quantificar e caracterizar VRE presentes em amostras fecais de ovinos oriundos de pequenas propriedades das regiões centro-leste e nordeste do estado de São Paulo. Para tanto, 132 amostras fecais foram coletadas diretamente do reto dos animais ou do piso das instalações. As amostras foram semeadas em ágar m-Enterococcus e subcultivadas em Ágar Bile Esculina acrescido de 6 µg/mL de vancomicina (ABEV), para confirmação de Enterococcus spp e detecção de cepas resistentes. Procedeu-se igualmente a observação da morfologia, características tintoriais, bioquímicas e moleculares. O número máximo de Enterococcus spp. encontrado foi de 2,6 × 105 e 1,70 × 105 UFC/g de fezes do ambiente e dos animais, respectivamente. Na caracterização bioquímica espécies mais prevalentes foram: Enterococcus faecalis e Vagococcus fluvialis. No ABEV, houve crescimento de colônias VRE em 33 das 84 amostras de ovinos-caprinos e em 21 das 48 amostras ambientais, representando, respectivamente 46,7% e 29,3% das amostras analisadas. A análise por multiplex PCR das 54 cepas VRE obtidas indicaram que 23 (43%), 22 (41%), 2 (3,5%) e 2 (3,5%) foram positivas, respectivamente, para os genes vanC2/C3, vanC1, vanA e vanB, sendo que para 5,3% dos isolados nenhum produto foi amplificado, sugerindo a possível ocorrência de genes dos demais grupos van conhecidos entre os isolados. Os resultados obtidos indicam, de forma inédita no país, a circulação de VRE em propriedades produtoras de ovinos e caprinos, sem ocorrência de manifestações clínicas aparentes nos animais, porém com possíveis riscos à saúde dos produtores e profissionais envolvidos, bem como a eventuais consumidores. / Demands for sanitary conditions in animal farming have been increasing progressively given the need to combine productivity and high quality products to support increasingly demanding consumer markets. In this context, antimicrobial drugs used in prevention as well as in therapy remain as the control strategy for several pathogenic microorganisms, not important only in animal production but also in human health, although restrictions for the indiscriminate use of these drugs have been intensified. However, the excessive use of these products has been associated to the selection of resistant microorganisms in production areas. On the other hand, investigation on strains of public health importance circulating in animal herds is still limited in Brazil. Enterococcus genus bacteria, usually present in animal and human gastrointestinal microbiota, are environmental indicators of fecal contamination and have become a concerning subject in public and veterinary health given the occurrence of strains resistant to vancomycin (VRE). The present study aimed to isolate, quantify and characterize VRE present in stool samples of sheep and goats from several farms in the center-east and northeast regions of São Paulo State. Swabs collected one hundred and thirty-two stool samples either directly from the animal\'s rectum or from the ground. Samples were plated onto m-Enterococcus agar plates and subcultivated in Bile esculin agar with 6 µg/mL of vancomycin (BEAV) to confirm Enterococcus spp and detect resistant samples. Colonies were identified by colonial morphology, Gram\'s staining, biochemical, and molecular profile. The highest colony count was equal to 2.6 × 105 and 1.7 × 105 CFU/g of feces from environmental and animal samples, respectively. Regarding biochemical characterization, Enterococcus faecalis e Vagococcus fluvialis were the most prevalent species. VRE was detected on BEAV in 33 out of 84 sheep-goat samples and in 21 out of 48 ambient samples, indicating a positivity rate of 46.7% and 29.3% respectively in the investigated samples. Analysis by multiplex PCR of the obtained 54 VRE strains indicated that 23 (43%), 22 (41%) 2 (3.5%) and 2 (3.5%) were positive, respectively, for the vanC2/C3, vanC1, vanA and vanB genes, and no product was amplified for 5.3% of the isolates, suggesting the possible occurrence of other known van gene groups among the isolates. The results obtained in this study indicate, for the first time in the studied areas, the circulation of VRE in sheep and goat farms, with no occurrence of apparent clinical signs in the animals, but with possible health risks to the farmers and workers involved, as well as potential consumers.

As exigências das condições higiênico-sanitárias na produção de animais de interesse zootécnico vêm aumentando progressivamente dada à necessidade de aliar-se produtividade a produtos de alta qualidade para atender a mercados consumidores cada vez mais exigentes. Nesse sentido, a utilização de antimicrobianos, tanto na profilaxia como na terapêutica, permanece como estratégia de controle para vários microrganismos patogênicos, de importância não apenas para a produção animal como também para a saúde humana, ainda que restrições ao uso indiscriminado desses produtos têm se intensificado. Não obstante, o uso excessivo desses produtos está associado à seleção de microrganismos resistentes nas áreas de produção. Por outro lado, investigações sobre circulação de cepas resistentes em rebanhos animais, até então restritas a populações humanas, ainda permanecem limitadas no Brasil. Bactérias do gênero Enterococcus, integrantes usuais da microbiota gastrointestinal animal e humana, são indicadoras ambientais de contaminação fecal e tem-se tornado objeto de preocupação em saúde pública e veterinária dada a ocorrência de cepas resistentes à vancomicina (VRE). O presente trabalho teve como objetivo isolar, quantificar e caracterizar VRE presentes em amostras fecais de ovinos oriundos de pequenas propriedades das regiões centro-leste e nordeste do estado de São Paulo. Para tanto, 132 amostras fecais foram coletadas diretamente do reto dos animais ou do piso das instalações. As amostras foram semeadas em ágar m-Enterococcus e subcultivadas em Ágar Bile Esculina acrescido de 6 µg/mL de vancomicina (ABEV), para confirmação de Enterococcus spp e detecção de cepas resistentes. Procedeu-se igualmente a observação da morfologia, características tintoriais, bioquímicas e moleculares. O número máximo de Enterococcus spp. encontrado foi de 2,6 × 105 e 1,70 × 105 UFC/g de fezes do ambiente e dos animais, respectivamente. Na caracterização bioquímica espécies mais prevalentes foram: Enterococcus faecalis e Vagococcus fluvialis. No ABEV, houve crescimento de colônias VRE em 33 das 84 amostras de ovinos-caprinos e em 21 das 48 amostras ambientais, representando, respectivamente 46,7% e 29,3% das amostras analisadas. A análise por multiplex PCR das 54 cepas VRE obtidas indicaram que 23 (43%), 22 (41%), 2 (3,5%) e 2 (3,5%) foram positivas, respectivamente, para os genes vanC2/C3, vanC1, vanA e vanB, sendo que para 5,3% dos isolados nenhum produto foi amplificado, sugerindo a possível ocorrência de genes dos demais grupos van conhecidos entre os isolados. Os resultados obtidos indicam, de forma inédita no país, a circulação de VRE em propriedades produtoras de ovinos e caprinos, sem ocorrência de manifestações clínicas aparentes nos animais, porém com possíveis riscos à saúde dos produtores e profissionais envolvidos, bem como a eventuais consumidores. / Demands for sanitary conditions in animal farming have been increasing progressively given the need to combine productivity and high quality products to support increasingly demanding consumer markets. In this context, antimicrobial drugs used in prevention as well as in therapy remain as the control strategy for several pathogenic microorganisms, not important only in animal production but also in human health, although restrictions for the indiscriminate use of these drugs have been intensified. However, the excessive use of these products has been associated to the selection of resistant microorganisms in production areas. On the other hand, investigation on strains of public health importance circulating in animal herds is still limited in Brazil. Enterococcus genus bacteria, usually present in animal and human gastrointestinal microbiota, are environmental indicators of fecal contamination and have become a concerning subject in public and veterinary health given the occurrence of strains resistant to vancomycin (VRE). The present study aimed to isolate, quantify and characterize VRE present in stool samples of sheep and goats from several farms in the center-east and northeast regions of São Paulo State. Swabs collected one hundred and thirty-two stool samples either directly from the animal\'s rectum or from the ground. Samples were plated onto m-Enterococcus agar plates and subcultivated in Bile esculin agar with 6 µg/mL of vancomycin (BEAV) to confirm Enterococcus spp and detect resistant samples. Colonies were identified by colonial morphology, Gram\'s staining, biochemical, and molecular profile. The highest colony count was equal to 2.6 × 105 and 1.7 × 105 CFU/g of feces from environmental and animal samples, respectively. Regarding biochemical characterization, Enterococcus faecalis e Vagococcus fluvialis were the most prevalent species. VRE was detected on BEAV in 33 out of 84 sheep-goat samples and in 21 out of 48 ambient samples, indicating a positivity rate of 46.7% and 29.3% respectively in the investigated samples. Analysis by multiplex PCR of the obtained 54 VRE strains indicated that 23 (43%), 22 (41%) 2 (3.5%) and 2 (3.5%) were positive, respectively, for the vanC2/C3, vanC1, vanA and vanB genes, and no product was amplified for 5.3% of the isolates, suggesting the possible occurrence of other known van gene groups among the isolates. The results obtained in this study indicate, for the first time in the studied areas, the circulation of VRE in sheep and goat farms, with no occurrence of apparent clinical signs in the animals, but with possible health risks to the farmers and workers involved, as well as potential consumers.

Antibiotic resistant pathogens, such as methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE), are an increasing burden on healthcare systems. Hospital acquired infections with these organisms leads to higher morbidity and mortality compared with the sensitive strains of the same species and both VRE and MRSA are on the rise worldwide including in Australian hospitals. Emerging community infectious diseases are also having an impact on hospitals. The Severe Acute Respiratory Syndrome virus (SARS Co-V) was noted for its propensity to spread throughout hospitals, and was contained largely through social distancing interventions including hospital isolation. A detailed understanding of the transmission of these and other emerging pathogens is crucial for their containment. The statistical inference and mathematical models used in this thesis aim to improve understanding of pathogen transmission by estimating the transmission rates of contagions and predicting the impact of interventions. Datasets used for these studies come from the Princess Alexandra Hospital in Brisbane, Australia and Shanxi province, mainland China. Epidemiological data on infection outbreaks are challenging to analyse due to the censored nature of infection transmission events. Most datasets record the time on symptom onset, but the transmission time is not observable. There are many ways of managing censored data, in this study we use Bayesian inference, with transmission times incorporated into the augmented dataset as latent variables. Hospital infection surveillance data is often much less detailed that data collected for epidemiological studies, often consisting of serial incidence or prevalence of patient colonisation with a resistant pathogen without individual patient event histories. Despite the lack of detailed data, transmission characteristics can be inferred from such a dataset using structured HiddenMarkovModels (HMMs). Each new transmission in an epidemic increases the infection pressure on those remaining susceptible, hence infection outbreak data are serially dependent. Statistical methods that assume independence of infection events are misleading and prone to over-estimating the impact of infection control interventions. Structured mathematical models that include transmission pressure are essential. Mathematical models can also give insights into the potential impact of interventions. The complex interaction of different infection control strategies, and their likely impact on transmission can be predicted using mathematical models. This dissertation uses modified or novel mathematical models that are specific to the pathogen and dataset being analysed. The first study estimates MRSA transmission in an Intensive Care Unit, using a structured four compartment model, Bayesian inference and a piecewise hazard methods. The model predicts the impact of interventions, such as changes to staff/patient ratios, ward size and decolonisation. A comparison of results of the stochastic and deterministic model is made and reason for differences given. The second study constructs a Hidden Markov Model to describe longitudinal data on weekly VRE prevalence. Transmission is assumed to be either from patient to patient cross-transmission or sporadic (independent of cross-transmission) and parameters for each mode of acquisition are estimated from the data. The third study develops a new model with a compartment representing an environmental reservoir. Parameters for the model are gathered from literature sources and the implications of the environmental reservoir are explored. The fourth study uses a modified Susceptible-Exposed-Infectious-Removed (SEIR) model to analyse data from a SARS outbreak in Shanxi province, China. Infectivity is determined before and after interventions as well as separately for hospitalised and community symptomatic SARS cases. Model diagnostics including sensitivity analysis, model comparison and bootstrapping are implemented.

En ökad utbredning av vankomycinresistenta enterokocker (VRE) har setts i Sverige sedan 2007. Bakteriemi orsakad av VRE är mycket svårbehandlad, varför snabbare tillförlitlig resistensdiagnostik är betydelsefullt för att minska dödlighet, vårdtider, vårdkostnader och belastning på sjukvårdssystemet. På mikrobiologilaboratoriet, Region Jönköpings län (RJL), tar idag identifiering av fenotypisk vankomycinresistens vid optimala förhållanden 6 timmar, räknat från att enterokocker konstaterats växa i blodet. Resistensgenerna vanA och vanB, som bland andra orsakar vankomycinresistens hos enterokocker, kan genetiskt verifieras med loop-mediated isothermal amplification men tar idag upp till ett dygn då bakteriekolonier används som analysmaterial i arbetsrutinen på molekylärbiologilaboratoriet, RJL. Syftet med studien var att utvärdera bakteriepellet som analysmaterial för genetisk identifiering av vanA och vanB, på Genie® II Mk2 med eazyplex® VRE basic, hos enterokocker från positiva blododlingar. För att utvärdera bakteriepellet som analysmaterial analyserades isolat av Enterococcus faecium (n=17) och Enterococcus faecalis (n=5) från bakteriepellets tillverkade från simulerade positiva blododlingar med eazyplex® VRE basic på Genie® II Mk2, varpå resultaten jämfördes mot isolatens faktiska närvaro/frånvaro av vanA/vanB. Samstämmigheten av de uppmätta- och de förväntade resultaten var fullständig, vilket indikerar att bakteriepellet med hög tillförlitlighet kan användas som analysmaterial till eazyplex® VRE basic för att påvisa vanA och vanB hos enterokocker i blododlingar. / An increased prevalence of vancomycin-resistant enterococci (VRE) has been observed in Sweden since 2007. Treating bacteremia caused by VRE is difficult, which is why faster, and reliable resistance diagnostics are important. At the Microbiology laboratory, Region Jönköping County, the identification of phenotypic vancomycin resistance under optimal conditions takes 6 hours from when growth of enterococci in blood is determined. The genes vanA and vanB, which among others cause vancomycin resistance, can be genetically verified by loop-mediated isothermal amplification, but takes up to one day since bacterial colonies are used as analysis material. The aim of the study was to evaluate bacterial pellet as an analytical material for genetic identification of vanA and vanB, on Genie® II Mk2 with eazyplex® VRE basic, in enterococci from positive blood cultures. To evaluate the bacterial pellet, isolates of Enterococcus faecium (n=17) and Enterococcus faecalis (n=5) from bacterial pellets made from simulated positive blood cultures were analyzed with eazyplex® VRE basic on the Genie® II Mk2, and the results were compared to the actual presence/absence of vanA/vanB in the isolates. The complete coherence between the expected and measured results indicates that the bacterial pellet can be used as an analytical material for eazyplex® VRE basic.