Soil amended with manure has been implicated as a source of produce contamination leading to foodborne gastrointestinal-disease outbreaks. While current composting guidelines require temperatures ≥ 55°C for 3 days to destroy bacterial pathogens, these requirements have not been evaluated for all pathogens. Investigation of parasite survival in manure required development of a flow cytometry method integrating the cell-impermeant viability dye SytoX for simultaneous quantification and viability assessment of Cryptosporidium and Giardia oocysts/cysts. Further studies will be required to apply this method to investigate thermal reduction in parasites. Studies conducted with bacterial pathogens indicated that E. coli O157:H7 survived longer than other pathogens at 50°C to 55°C. Listeria monocytogenes survived significantly better in chicken manure compared to cow manure at 50°C to 55°C. Results suggest composting guidelines are adequate for bacterial pathogen reduction; however, testing for E. coli O157 along with Salmonella may increase confidence in compost safety.

Statens veterinärmedicinska anstalt, SVA, is a government agency that works for better animal and human health with a primary focus on infectious animal diseases. One of their projects involves tracking the spread of Campylobacter infection in broilers and the occurrence of antimicrobial resistance in these bacteria. A pipeline was developed to contribute to making the analysis of Whole Genome Sequencing (WGS) data from Campylobacter more effective. This was done by changing the currently used pipeline’s programming language from Perl to Python and adding the possibility to run multiple analyses in parallel. With parallelization, the time for running multiple analyses was reduced compared to running them sequentially, even if it was not as fast in practice as in theory. It also did not work as well when running parallel analyses of different strains compared to identical strains. Furthermore, different attributes of the pipeline were changed or added to improve the pipeline and a database comparison was performed in order to suggest the best ones for future use. VFDB, CARD, and MEGARes were suggested as appropriate databases to use in future WGS analysis of Campylobacter. Due to a lack of resources and technical difficulties, some of the requested attributes for the pipeline could not be implemented, such as the tool Pilon and the inclusion of MLST and cgMLST analysis. Nonetheless, the pipeline is well structured, has most of the requested tools, and is easy to run. With some minor improvements, the pipeline will be a useful tool for SVA and their project.

Over 3.7 million people are in high risk of coastal flooding and live within 1 mile of high tide in the US alone. The Atlantic coast is one of the most vulnerable areas due to its low elevation, large population, and economic importance (Bray, et. al, 2016). Coastal municipalities in the region of Southeast Florida, such as the cities of Miami, Miami Beach, Fort Lauderdale, etc., are at especial risk from coastal flooding related to sea level rise. The US National Climate Assessment has named Miami, Florida as the economically most vulnerable city impacted by this sea level rise in the world (Melillo et. al, 2014). Virtually all coastal communities in Southeast Florida are now experiencing increased incidents of coastal tidal flooding and coastal storm flooding related to sea level rise. This has led to a variety of responses by coastal communities in how to address this issue. In the case of the City of Miami Beach, the city has [CS1] come up with an ambitious but expensive plan to help combat the increased urban coastal flooding that is now occurring multiple times a year. They invested over 500 million dollars into replacing the increasingly less-effective gravity-based drainage system with a pump-based system (Bray, et. al, 2016). With these influences, we hypothesized that microbial communities would significantly differ between three years (2014-2016) and that the potential pathogens would increase over the past years . Genetic analyses of the 16S rRNA V4 region yielded a total of 77,346 unique bacterial OTUs from a total of 96 samples collected monthly for three years from 2014-2016. The most abundant OTU within the whole sample set was New.ReferenceOTU407 or Arcobacter in the Campylobacter family with an overall abundance of 0.008232535481%.The second most abundant organism in the sample set was Bacillus, or OTUNew.CleanUp.ReferenceOTU121132, with an overall abundance of .007797807097%. Bacillusmay cause many more foodborne illness than is known and one main reason that there is not more reported cases is because people do not seek medical attention (FDA 2012). The remaining pathogens except for Serratia, Pleisomonas, and Cronobacter were all with an abundance over .001%, with Salmonella, Yersinia,andListeria not being identified at all within the data set. By showing that genetic signatures for this bacterium, especially Arcobacter,was present in more than half of the samples stresses the importance of better understanding of the microbial population within South Florida waters and how to prevent or reduce future outbreaks by making sure the water is treated correctly before use, and to better identify potential exposure sources in water.

Campylobacteriosis is a leading foodborne illness worldwide, primarily caused by Campylobacter jejuni (C. jejuni) which is associated with poultry consumption. The emergence of antibiotic resistance has emphasized the need for alternative strategies to control C. jejuni colonization in poultry. To assess the prevalence of C. jejuni in poultry, 270 cloacal swab samples were collected from broilers raised under No-Antibiotics Ever system. Among these samples, 16.3% were identified as C. jejuni positive. Notably, these isolates exhibited a diverse range of virulence factors and antimicrobial resistance genes, with 61.36% of isolates showing hyper-motile and 20.45% demonstrating multidrug resistance. Following isolation, whole genome sequencing was conducted on four selected strains using a hybrid sequencing approach. Subsequently, the complete genomes of these C. jejuni strains were analyzed to identify vaccine candidates using reverse vaccinology. Three conserved potential vaccine candidates were identified as suitable targets for vaccine development, namely phospholipase A (PldA), TonB dependent transporter (ChuA), and cytolethal distending toxin (CdtB). Furthermore, the gene expression of these candidates was examined in four C. jejuni strains during host-pathogen interactions using avian macrophage cell line HD11. Significant upregulation of all three candidate genes were observed in the four tested C. jejuni strains during interaction with host cells, indicating their crucial role in C. jejuni infection. Additionally, the expression of immune genes was evaluated in avian macrophage cells to understand the immune responses during C. jejuni infection. The infection resulted in the upregulation of toll-like receptor genes (TLR-4), pro-inflammatory genes (IL-1β, IFN-γ, IL-6, IL-8L1), anti-inflammatory gene (IL-10), and iNOS2 gene expression. The observed immune response demonstrates the potential of C. jejuni to induce host immunity for protection. In conclusion, our study identifies three conserved potential vaccine candidates and provides insights into the immune responses induced by C. jejuni infection in avian macrophage cells. These findings are crucial for the development of an effective vaccine against C. jejuni, aiming to reduce C. jejuni transmission through poultry consumption and the risk of human infection.

Direkter Tierkontakt gehört zu den wirkungsvollsten Elementen des Besuchererlebnisses in Zoologischen Gärten. In Streichelzoos hat der Zoobesucher unkontrollierten und unmittelbaren Kontakt mit kleinen Wiederkäuern und insbesondere mit Ziegen. Diese Anlagen können ein Zoonoserisiko darstellen, da Ziegen asymptomatische Träger von verschiedenen zoonotischen Krankheitserregern sein können und in der Vergangenheit bereits Übertragungen auf den Menschen nach Kontakt mit Streicheltieren nachgewiesen wurden. Es sollte das Vorkommen ausgewählter zoonotischer Pathogene (Shigatoxin-produzierende Escherichia coli (STEC), Coxiella burnetii, Campylobacter spp., Arcobacter spp., Salmonella spp., Yersinia spp., Enterobacteriaceae mit beta-Laktamasen mit breitem Wirkungsspektrum (ESBL), Methicillin-resistente Staphylococcus aureus (MRSA) und Dermatophyten) bei klinisch gesunden Ziegen in Streichelzoos Zoologischer Gärten in Deutschland untersucht werden. Aus 21 Herden in 14 tiergärtnerischen Einrichtungen in Deutschland wurden 300 klinisch gesunde Ziegen im Rahmen tierärztlicher Routineuntersuchungen beprobt. Der Nachweis von STEC und Salmonella spp. wurde aus Rektaltupfern über die Anzucht auf GCG-Agar versucht. Für Escherichia coli verdächtige Kulturen wurden auf Blutagar überführt und auf ausgewählte Virulenzgene per PCR untersucht. In der Folge wurde eine Serotypisierung vorgenommen. Nach Coxiella burnetii wurde in Vaginaltupfern der 230 weiblichen Tieren der Studie mittels einer real-time PCR (qPCR) gesucht. Campylobacter spp. und Arcobacter spp. aus Rektaltupfern wurden nach Isolation über Selektivnährböden unter mirkoaerophilen Bedingungen jeweils per Multiplex-PCR und qPCR auf Artebene bestimmt. Rektaltupfer wurden nach einer Kälteanreicherung mit folgender Anzucht auf Selektivnährböden auf Yersinia spp. untersucht. Nach Anzucht über einen ESBL-Selektivagar auf Basis von Rektaltupfern wurden verdächtige Kolonien mit einem VITEK-System artbestimmt und auf mögliche Antibiotikaresistenzen untersucht. Beta-Lactamase-Gene wurden mittels PCR identifiziert. Das aus Nasentupfern stammende Untersuchungsmaterial zum MRSA-Nachweis wurde nach Anreicherung einer Kultur auf einem Selektivnährboden zugeführt. Eventuelle Kolonien wurden auf einen Blutagar transferriert und danach per MALDI-TOF massenspektrometrisch untersucht. Positive Proben wurden durch PCR-Microarray untersucht. Mit einer modifizierten Mackenzie-Brush- Methode gewonnene Hautschuppen wurden über einen Pilzagar und einen selektiven Dermatophytenagar untersucht. Demographische Korrelationen zum Auftreten von Campylobacter spp. wurden mit einem exakten Test nach Fisher evaluiert. Campylobacter spp. wurden bei 22,7 %, STEC bei 20,0 % und Arcobacter spp. bei 1,7 % der 300 getesteten Ziegen nach der Kultur aus Rektaltupfern und der folgenden PCR nachgewiesen. Die Prävalenz von Campylobacter spp. war bei juvenilen höher als bei adulten Tieren (53,0 % gegenüber 14.1 %; p<0,0001). Ein Isolat der Art Escherichia fergusonii trug phänotypisch Hinweise auf eine ESBL, die durch den Nachweis des Gens blaCTX-M-1 bestätigt wurde. Aus den Nasentupfern von 20,7 % der beprobten Ziegen konnte Staphylococcus aureus kultiviert werden, darunter auch ein mecC-positiver MRSA. Weder Salmonella spp. noch Yersinia spp. fanden sich in der Stichprobe und auch der Nachweis von Dermatophyten gelang bei einer häufigen Überwucherung durch ubiquitäre Pilze (19,3 %) nicht. Unter den 230 weiblichen Ziegen der Studie gab es bei zwei Tieren positive PCR- Signale für Coxiella burnetii, die nach ausgiebiger Nachbeprobung und epidemiologischer Prüfung als falsch-positiv gewertet werden mussten. Grundsätzlich muss vom Vorhandensein einiger Zoonoseerreger in Ziegenbeständen in Streichelzoos ausgegangen werden, da Campylobacter spp. und STEC regelmäßig in der Stichprobe auftraten. Damit sollte das Risiko der Übertragung zoonotischer Bakterien von Ziegen auf Zoobesucher beim Betrieb entsprechender Anlagen Berücksichtigung finden. Angemessene Informationen und Einrichtungen zum Waschen der Hände und zur Handdesinfektion sollten in jedem Fall zur Verfügung gestellt werden. Zum genaueren Verständnis des vermehrten Auftretens von Campylobacter spp. bei jungen Ziegen sind weitere Untersuchungen notwendig. Die Identifikation von asymptomatischen Ziegen mit einer Dermatophyteninfektion bedarf einer modifizierten Technik.:1 Einleitung 1 2 Literaturübersicht 3 2.1 Geschichte und tiergärtnerische Bedeutung des Streichelzoos 3 2.2 Ausgewählte Zoonoseerreger bei Ziegen 4 2.2.1 Shigatoxin-bildende Escherichia coli 4 2.2.1.1 Erreger 4 2.2.1.2 Bedeutung bei der Ziege 5 2.2.1.3 Bedeutung beim Menschen 5 2.2.2 Coxiella burnetii 5 2.2.2.1 Erreger 5 2.2.2.2 Bedeutung bei der Ziege 6 2.2.2.3 Bedeutung beim Menschen 7 2.2.3 Campylobacter spp. 7 2.2.3.1 Erreger 7 2.2.3.2 Bedeutung bei der Ziege 8 2.2.3.3 Bedeutung beim Menschen 8 2.2.4 Arcobacter spp. 9 2.2.4.1 Erreger 9 2.2.4.2 Bedeutung bei der Ziege 9 2.2.4.3 Bedeutung beim Menschen 10 2.2.5 Salmonella spp. 10 2.2.5.1 Erreger 10 2.2.5.2 Bedeutung bei der Ziege 11 2.2.5.3 Bedeutung beim Menschen 11 2.2.6 Yersinia spp. 12 2.2.6.1 Erreger 12 2.2.6.2 Bedeutung bei der Ziege 12 2.2.6.3 Bedeutung beim Menschen 13 2.2.7 beta-Laktamasen mit breitem Wirkungsspektrum 13 2.2.7.1 Erreger 13 2.2.7.2 Bedeutung bei der Ziege 14 2.2.7.3 Bedeutung beim Menschen 14 2.2.8 Methicillin-resistente Staphylococcus aureus 15 2.2.8.1 Erreger 15 2.2.8.2 Bedeutung bei der Ziege 15 2.2.8.3 Bedeutung beim Menschen 16 2.2.9 Dermatophyten 16 2.2.9.1 Erreger 16 2.2.9.2 Bedeutung bei der Ziege 17 2.2.9.3 Bedeutung beim Menschen 17 3 Veröffentlichung 19 3.1 Stellungnahme zum Eigenanteil an den Arbeiten an der Publikation 19 3.2 Publikation 20 4 Diskussion 31 5 Zusammenfassung 35 6 Summary 37 7 Literaturverzeichnis 39 8 Danksagung

Chez les bactéries à chromosomes circulaires, le crossing-over introduit par la recombinaison homologue peut conduire à des échanges de chromatides soeurs. Des nombres impairs de ces échanges aboutissent à la dimérisation des deux chromatides nouvellement répliquées compromettant ainsi leur ségrégation. Par conséquent, la plupart des bactéries utilisent le système de recombinaison spécifique de site Xer pour convertir les dimères de chromosomes et de plasmides en monomères stables. Ce système comporte deux recombinases de la famille Tyrosine recombinase, XerC et XerD, agissant sur le site dif. Cependant, quelques ε-protéobactéries n’ont besoin que d'une seule recombinase XerH agissant sur un site difH. Il parait intéressant d’étudier le système de recombinaison XerH de Campylobacter jejuni, surtout que l'augmentation spectaculaire de l'incidence de campylobactériose est alarmante. Cette étude vise à mieux comprendre comment la protéine XerH catalyse la réaction de recombinaison au niveau du site difH en mettant en évidence les séquences indispensables pour la liaison et le clivage. Grâce à ces expériences, nous avons pu confirmer que XerH est capable de se lier à la séquence entière difH; XerH est capable de cliver les deux brins supérieurs et inférieurs de difH avec une réaction plus efficace au niveau du brin inférieur; les nucléotides conservés du site de liaison sont indispensables pour la réaction de liaison; la modification de la longueur de l’espaceur améliore la réaction de liaison et de clivage et les modifications apportées au site de clivage prédit ont aboli la réaction de liaison et affecté la réaction de clivage au niveau du brin supérieur et inférieur du site difH. Ces expériences aideront à comprendre comment la recombinase XerH/difH contrôle la résolution des dimères chromosomiques chez Campylobacter jejuni en identifiant les séquences et les facteurs indispensables pour qu’un certain système soit fiable. Notre étude représente un pas vers l’avant pour comprendre un mécanisme important chez un agent pathogène ayant un grand impact sur la santé publique. / In bacteria with circular chromosomes, cross-over induced by homologous recombination can lead to sister chromatid exchanges, odd numbers of these exchanges result in dimerization of the two newly replicated chromatids compromising their segregation. Therefore, most bacteria use the Xer site-specific recombination system to convert chromosomal and plasmid dimers into stable monomers. This system involves two recombinases of the Tyrosine recombinase family, XerC and XerD, acting at the dif site. However, some ε-proteobacteria require only one XerH recombinase acting on a difH site. It seems interesting to study the XerH recombination system of Campylobacter jejuni, especially since the dramatic increase in the incidence of campylobacteriosis is alarming. This study aims to better understand how the XerH protein catalyzes the recombination reaction at the difH site by identifying the sequences required for binding as well as the factors regulating this reaction. As a result of these experiments, we were able to confirm that XerH is able to bind to the entire difH sequence; it is able to cleave both the top and bottom strands of difH with a more efficient reaction at the bottom strand; The conserved nucleotides in the binding site are essential for the binding reaction, modification of the spacer length improves the binding and cleavage reaction, and modifications in the predicted cleavage site abolished the binding reaction and affected the cleavage reaction at both the top and bottom strands of the difH site.. These experiments will help to understand how the XerH/difH recombinase controls the resolution of chromosomal dimers in Campylobacter jejuni by identifying the essential sequences and factors required for a certain system to be reliable. Our study represents a step forward in understanding an important mechanism in a pathogen with great impact on public health.

Campylobacter enteritis in humans is primarily associated with C. jejuni/coli infection. Other species cause campylobacteriosis relatively infrequently; while this could be attributed to bias in diagnostic methods, the pathogenicity of non-jejuni/coli Campylobacter spp. such as C. upsaliensis and C. helveticus (isolated from dogs and cats) is uncertain. Galleria mellonella larvae are suitable models of the mammalian innate immune system and have been applied to C. jejuni studies. This study compared the pathogenicity of C. jejuni, C. upsaliensis, and C. helveticus isolates. Larvae inoculated with either C. upsaliensis or C. helveticus showed significantly higher survival than those inoculated with C. jejuni. All three Campylobacter species induced indistinguishable histopathological changes in the larvae. C. jejuni could be isolated from inoculated larvae up to eight days post-inoculation whereas C. upsaliensis and C. helveticus could only be isolated in the first two days. There was a significant variation in the hazard rate between batches of larvae, in Campylobacter strains, and in biological replicates as random effects, and in species and bacterial dose as fixed effects. The Galleria model is applicable to other Campylobacter spp. as well as C. jejuni, but may be subject to significant variation with all Campylobacter species. While C. upsaliensis and C. helveticus cannot be considered non-pathogenic, they are significantly less pathogenic than C. jejuni.

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Understanding the transmission dynamics of infectious diseases is important to well-informed public health policy, responsive infection control and individual patient management. The on-going revolution in whole-genome sequencing provides unprecedented resolution for detecting evidence of recent transmission and characterising population-level transmission dynamics. In this thesis, I develop and apply evolutionary approaches to investigating transmission, focusing on three globally important pathogens. Hepatitis C virus (HCV) is a major cause of liver disease affecting 150 million people and killing 350,000 annually. I conducted a meta-analysis of twentieth-century HCV epidemics, finding that the age of the epidemic can be predicted by genetic diversity. Using the coalescent, I fitted classic susceptible-infected (SI), susceptible-infected-susceptible (SIS) and susceptible-infected-recovered (SIR) epidemiological models. Most epidemics showed signatures of SI dynamics, but three, from Argentina, Hong Kong and Thailand, revealed complex SIR dynamics. Norovirus is the leading viral cause of diarrhoea, estimated to cost the NHS around £115 million annually. I analysed whole norovirus genomes via a stochastic transmission model, finding that up to 86% of hospital infection was attributable to transmission from another patient in the hospital. In contrast, the rate of new introductions to hospital by infected patients was extremely low (<0.0001%), underlining the importance of ward management during outbreaks. Campylobacter is the most commonly identified cause of bacterial gastroenteritis worldwide. I developed a zoonotic transmission model based on phylogeography approaches to test whether three strains previously associated with multiple host species were in fact aggregates of strongly host-restricted sub-strains, or genuine generalists. Members of the same strain isolated from different host species were often more closely related than those isolated from the same host species. I estimated 419, 389 and 31 zoonotic transmissions in ST-21, ST-45 and ST-828 respectively, strongly supporting the hypothesis that these strains are adapted to a generalist lifestyle.