Campylobacter is currently the most common cause of acute bacterial diarrhoea in Australia among all the notified enteric pathogens with more than 15,000 cases each year. The incidence of notified campylobacteriosis has steadily increased during the past 15 years from 67.0/100,000 population in 1991 to 121.4/100,000 in 2005, though the factors contributing to this increase had not been studied. Adjusting for under-reporting there are, at this point in time, an estimated 225,000 infections occurring each year in Australia, most of which are sporadic in nature. Much of our knowledge in Australia about risk factors for sporadic disease has been based on overseas literature. Prior to the studies undertaken in this thesis, the epidemiology of Campylobacter infection had not been thoroughly studied in Australia, nor had there been any national studies examining risk factors for locally-acquired infection. The broad aim of this thesis was to examine in depth the descriptive epidemiology of Campylobacter infection in Australia, explore the reasons for the sustained increase in incidence of infection and to identify the major risk factors for locally acquired infection using a multi-centre case-control study design. The descriptive study of the epidemiology of campylobacteriosis in Australia was based on Australian notifiable disease surveillance data collected over a 15-year period between 1991 and 2005. This study described the key epidemiological characteristics of this disease in Australia and identified some significant differences in incidence trends across states and territories and among different age groups which had not been previously reported. The study identified gaps in our knowledge of this disease in Australia and made recommendations for future research including the investigation of factors associated with the decline in incidence of infection among children aged  4 years and further studies to identify age and sex-specific risk factors for infection. The issue of seasonality, transmission routes and infection was addressed and areas for further research were specified including longitudinal studies at a regional level that incorporate a comparison of human, animal and environmental genotypes. This study also provided strong compelling evidence to support the hypothesis that the increase in notification rates in Australia during this period represented a real increase in the incidence of infection and that the main driving force behind this rise has been the ongoing increase in chicken consumption among the Australian public. The multi-centre case-control study, involving 1,714 participants  5 years of age, identified the major foodborne and non-foodborne risk factors for Campylobacter infection among the general population in Australia. This study confirmed that chicken meat is a major source of sporadic infection in this country and is responsible for almost one-third of all cases that occur in the Australian community each year. Other independent risk factors for sporadic infection in Australia included consumption of offal and ownership of domestic dogs or chickens aged  6 months. The Nagelkerke R² value of 16% for the final multivariable model indicated a considerable proportion of our case-patients had unexplained risk factors. The combined population attributable risk (PAR) estimate for the independent foodborne risk factors in this study was 31%, which is considerably less than the 75% to 80% of cases in the general population which are thought to be caused through foodborne transmission. Possible explanations for these results include the likelihood that a proportion of foodborne transmission in Australia occurs through food vehicles other than chicken due to cross-contamination from raw products, and the likelihood that much of the population attributable risk that is unaccountered for, may in fact be due to inherent limitations of study design resulting in systematic errors (information bias) and possibly reduced estimates of effect. The burden of illness among the general population in Australia attributable to different independent risk factors was estimated using a novel method developed specifically for this study. Briefly, community incidence data was coupled with PAR data from the case-control study and simulation techniques were used to: (i) estimate the number of infections attributable to specific risk factors, and (ii) derive credible intervals for these estimates by modeling the uncertainty in each variable component. This model of using case-control data in conjunction with pre-existing surveillance data provides researchers with a simple but robust tool for conducting source attribution studies on enteric pathogens. In conclusion, the studies undertaken in this thesis have made important contributions to our understanding of the epidemiology of sporadic Campylobacter infection in Australia.

Research Doctorate - Doctor of Philosophy (PhD) / The NSW poultry processing industry has gone through an evolution of regulatory change over the past 100 years from an inspection system through to a HACCP-based food safety system audited by the NSW Food Safety Authority (FSA). This required the restructuring of legislation and an understanding of the appropriate microbiological standards by which the FSA could judge the effectiveness of the operator’s processing operation. This microbiological standard was developed following two surveys of the vast majority of registered poultry processors in NSW. These surveys demonstrated the microbiological outcomes that could be achieved by the processors. From this knowledge, a new standard for the levels of Escherichia coli (E. coli) on product were established that were to be used by the operator and the regulator to judge the effectiveness of the operator’s program. Studies into the carriage of Salmonella species on raw poultry in the plant and on the reliability of the microbiological tests being used within the survey and by industry were carried out. They found that there had been a significant reduction in carriage of Salmonella species on raw poultry from 48.6% to 34.2% over two years. The test method utilised in the survey and one utilised by the Australian industry were shown to be able to detect Salmonella Typhimurium at 1-3 CFU per ml of carcase rinse fluid. An examination of E. coli by PCR to determine the likelihood that E. coli carried by NSW poultry were capable of inducing Haemorrhagic Uraemic Syndrome (HUS) found no evidence of shigatoxin producing genes (stx1 or stx2) or enterohaemorrhagic E. coli specific plasmid (ehxA). The attachment factor, intimin (eaeA) was found in E. coli from 93 of 430 carcases (21.6%). Campylobacter species were found on 94% of all carcases in the first survey. A count of Campylobacter species on a series of carcases from one plant found an average of 163 CFU per cm2 on the broiler chickens tested. Because raw poultry carry pathogens from the processing plant into the wider community, the use of two post-chill sanitisers was examined. This study found that it is possible to significantly reduce the number of pathogens being carried by raw poultry. The use of post-chill sanitisers provides a potential means of reducing the risk of foodborne illness arising from the handling of raw poultry and eating undercooked poultry meat.

Freie Universiẗat, Diss., 2006--Berlin. / Dateiformat: zip, Dateien im PDF-Format.

Thesis (M.S.)--Auburn University, 2006. / Abstract. Vita. Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 1996. / Vita. Includes bibliographical references (leaves [141]-172).

München, Techn. Univ., Diss., 2000.

Thesis (M. Sc.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references (p. 169-200). Also available via the World Wide Web.

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.

Submitted by Marco Antônio de Ramos Chagas (mchagas@ufv.br) on 2017-03-28T13:58:36Z No. of bitstreams: 1 texto completo.pdf: 1220110 bytes, checksum: 803118ec7eccfad2cba1645f25679903 (MD5) / Made available in DSpace on 2017-03-28T13:58:36Z (GMT). No. of bitstreams: 1 texto completo.pdf: 1220110 bytes, checksum: 803118ec7eccfad2cba1645f25679903 (MD5) Previous issue date: 2016-12-19 / A carne de frango consiste em uma matriz ideal para a multiplicação de micro- organismos, e, portanto, é associada a numerosas infecções em humanos. Entre as bactérias que mais geram infecções intestinais, a partir do consumo de produtos avícolas, encontra-se a espécie Campylobacter jejuni. O uso indiscriminado de antibióticos na produção animal, pode contribuir na seleção de bactérias resistentes, que podem ser disseminadas durante a produção ou processamento dos alimentos. Desta forma, são necessárias novas alternativas para o controle desse patógeno, como a utilização de bacteriófagos. O objetivo deste trabalho foi isolar, caracterizar e avaliar o efeito de um coquetel de bacteriófagos de forma individual ou associado ao antibiótico enrofloxacina, no controle de C. jejuni, em frangos de corte. Foram isolados seis bacteriófagos (BC2, BC7, BC10, BC14, BC18 e BC19) a partir de fezes de frango coletadas em duas granjas avícolas na região de Viçosa, no Estado de Minas Gerais. Os bacteriófagos foram avaliados quanto à especificidade frente a diferentes cepas bacterianas. Cinco bacteriófagos foram específicos para C. jejuni, e um (bacteriófago BC14) além de apresentar ação lítico nas cepas de C. jejuni, apresentou atividade lítica frente a Salmonella Typhimuium (ATCC 14028) e Escherichia coli (CDC0111ab). A caracterização morfológica de dois bacteriófagos (BC7 e BC14) por meio de Microscopia Eletrônica de Transmissão (MET), evidenciou que os bacteriófagos apresentam cabeça icosáedrica e cauda de tamanho médio, indicando que provavelmente eles são vírus da ordem Caudovirales, família Myoviridae, e subfamília Eucampyvirinae. O coquetel de bacteriófagos foi afetado maiormente quando exposto a pH 2,5 (redução de 6,90) ciclos logarítmicos, e aos sais biliares nas concentrações de (0,3 e 1,0) %, com redução de (0,37 e 0,51) ciclos logarítmicos, respectivamente. Portanto, os animais devem ser previamente tratados com um antiácido como CaCO 3 , a fim de manter a viabilidade dos bacteriófagos no trato gastrointestinal das aves. A sinergia entre os bacteriófagos e a enrofloxacina, levou a redução de 1,08 ciclos logarítmicos de C. jejuni (B12313), e 1,48 ciclos logarítmicos de C. jejuni (IOC/ATCC 33560) nas fezes dos frangos após cinco dias de tratamento. No conteúdo cecal, a redução de C. jejuni (B12313) com tratamento de coquetel de bacteriófagos foi de 2,58 ciclos logarítmicos, e o tratamento com o antibiótico foi de 1,67 ciclos logarítmicos. Nos frangos infectados com C. jejuni (IOC/ATCC 33560), a redução foi de 2,42 ciclos logarítmicos com o uso de coquetel de bacteriófagos, e de 2,51 ciclos logarítmicos com o antibiótico enrofloxacina. Os bacteriófagos são apresentados como uma ferramenta útil na redução do patógeno C. jejuni, antes e após o abate. Mais investigações devem ser feitas com outros antibióticos, com o objetivo de aumentar o conhecimento de sinergia entre bacteriófagos e antibióticos como terapêutico dentro da granja. Em conteúdo cecal, as análises indicaram atuação mais eficiente do coquetel de bacteriófagos isoladamente. Isso indica que o tratamento com fagos seria eficiente no controle da contaminação da carne durante o abate. / Poultry meat, consist of an ideal matrix for the multiplication of microorganisms and thus is a source of numerous infections in humans. Among the bacteria, which generates more intestinal infection from the consumption of poultry products, is the species Campylobacter jejuni. The indiscriminate use of antibiotics in animal production may contribute to the selection of resistant bacteria, which may be disseminated during food production or processing. Therefore, new alternatives are needed to control this pathogen, such as the use of bacteriophages. The objective of this study was to isolate, characterize and evaluate the effect of a cocktail of bacteriophages individually or associated with the antibiotic enrofloxacin, in the control of C. jejuni, in broilers. Six bacteriophages were isolated (BC2, BC7, BC10, BC14, BC18 and BC19) from chicken feces collected from two poultry farms in the region of Viçosa, in the State of Minas Gerais. The bacteriophages were evaluated for specificity against different bacterial strains. The bacteriophage BC14 besides presenting lytic power over the strains of C. jejuni presented lithic activity against Salmonella Typhimuium (ATCC 14028) and Escherichia coli (CDC0111ab). The morphological characterization of two bacteriophages (BC7 e BC14) by transmission electron microscopy (TEM) showed that bacteriophages had icosahedral head and medium-sized tail indicating that they are probably viruses of the order Caudovirales order and Myoviridae family. The bacteriophage cocktail was mostly affected when exposed to pH 2.5 (reduction of 6.90) log 10 units and bile salt in the concentrations of (0.3 and 1.0) %, with a reduction of (0.37 and 0.51) log 10 units respectively. Therefore, animals should be pretreated with an antacid such as CaCO 3 , in order to maintain the viability of bacteriophages in the gastrointestinal tract of birds. A synergy was observed between bacteriophage and enrofloxacin with a reduction of 1,08 log 10 units of C. jejuni (B12313) and 1.48 log 10 units of C. jejuni (IOC/ATCC 33560) in the feces of the chickens after five days of treatment. In the cecal content, the reduction of C. jejuni (B12313) with treatment of bacteriophage cocktail was 2.58 log 10 units, and treatment with the antibiotic was 1.67 log 10 units. In chickens infected with C. jejuni (IOC / ATCC 33560), the reduction was 2.42 log 10 units with the use of bacteriophage cocktail, and 2.51 log 10 units with the antibiotic enrofloxacin. Bacteriophages are presented as a useful tool in the reduction of the C. jejuni pathogen, before and after slaughter. Further investigations should be made with other antibiotics, with the aim of increasing the knowledge of synergy between bacteriophages and antibiotics as a therapeutic process within the farm. In cecal content, the analyzes indicated a more efficient performance of the bacteriophage cocktail alone. This indicates that phage treatment would be effective in controlling meat contamination during slaughter.

Tesis para optar al Grado de Magíster en Ciencias Animales y Veterinarias mención Ciencias Avícolas. / La campilobacteriosis es una enfermedad emergente transmitida por los alimentos y es la principal enfermedad gastrointestinal en seres humanos en países desarrollados. El desarrollo de resistencia de Campylobacter spp. a los antimicrobianos empleados como tratamiento en personas es un problema de salud pública que está relacionado con el uso inadecuado de estos agentes en los sistemas de salud y en la producción animal. Aún se debe esclarecer la patogenia de esta enfermedad y el mecanismo por el que actúan los factores de virulencia que no son completamente conocidos. En el mundo existe escasa información de la prevalencia de genes de virulencia de Campylobacter spp. aislados de pavos y de igual manera poca información de la susceptibilidad antimicrobiana en esta especie. El objetivo de este trabajo fue determinar los perfiles de resistencia a los antimicrobianos: Ciprofloxacino, Tetraciclina, Eritromicina y Gentamicina de 105 cepas de Campylobacter spp. aisladas de sistemas de producción de pavos, empleando la técnica de Kirby Bauer. Se obtuvieron 76 cepas resistentes a Ciprofloxacino y 42 a Tetraciclina. Ninguna cepa fue resistente a Eritromicina ni a Gentamicina. Del total de la cepas resistentes a Tetraciclina, 41 de ellas fueron multiresistentes (Ciprofloxacino y Tetraciclina). Al mismo tiempo las 105 cepas fueron analizadas por PCR en busca de genes de virulencia asociados con adherencia y colonización (cadF, racR, flaA), invasión (ciaB, pldA), producción de toxinas (cdtA, cdtC) y mimetismo del LPS (wlaN). La prevalencia de cadF fue de 64,8%, racR 45,7%, flaA 53,3%, ciaB 24,8%, pldA 36,2%, cdtA 65,7%, cdtC, 61% y wlaN 21%. Los resultados sugieren que existe un potencial patógeno de algunos de los aislamientos y demuestra la necesidad de implementar un plan de vigilancia con el fin de resguardar la Salud Pública. / Campylobacteriosis is an emerging disease transmitted by foods, it is also a main human gastrointestinal disease in developed countries. The evolvement of Campylobacter spp. resistance to antimicrobials used for treatment in humans is a public health problem, related to the inappropriate use of these agents in animal production and health systems. The pathogenesis of this human disease still needs to be elucidated, since the mechanism by which virulence factors act are not completely known. In the world there is insufficient information on the prevalence of the virulence genes of Campylobacter spp. isolated from turkeys, as well as little information on antimicrobial susceptibility in this species. The aim of this study was to determine the antimicrobial resistance profiles to Ciprofloxacin, Tetracycline, Erythromycin and Gentamicin of 105 strains of Campylobacter spp. isolated from turkey production systems using the Kirby-Bauer technique. As a result we found 76 strains resistant to ciprofloxacin, 42 to Tetracycline, moreover Erythromycin and Gentamicin had no antimicrobial resistance. Of the total tetracycline resistant strains 41 of them were multiresistant (Ciprofloxacin and Tetracycline). These 105 strains were analyzed by PCR for genes associated with virulence adhesion and colonization (cadF, racR, flaA), invasion (ciaB, pldA), toxins production (cdtA cdtC) and mimitims of LPS (wlaN). With a prevalence of 64.8% cadF,45.7% racR, 53.3% flaA, 24.8% ciaB, 36.2% pldA, 65.7% cdtA, 61% cdtC and 21% wlaN. The results suggest that there is a pathogen potential of some of the isolates and demonstrates the necessity of implementing a surveillance plan in order to protect public health.