The world is increasingly controlled by machine learning and deep learning. Deep neural networks are becoming powerful, encroaching on many tasks in computer vision system areas previously seen as the unique domain of humans, such as image classification, object detection, semantic segmentation, and instance segmentation. The success of a deep learning model at a specific application is determined by a sequence of choices, like what kind of deep neural network will be used, what data to be fed into the deep model, and what manners will be adopted to train a deep model. The goal of this work is to design a practical, lightweight image classification model built and trained from scratch which serves as an assistant to researchers and users to recognize if a small bug is a tick. Some of the images used in this work were collected by specialists using a microscope in the Laboratory of Medical Zoology (LMZ) at the University of Massachusetts Amherst. The following techniques are used in this work. We generated four datasets by collecting 53,150 images of small bugs and cleaning the data by deleting images with low quality. Both preprocessed images and augmented images were used in the training and validation processes. Initially, we proposed the use of five lightweight CNNs. We trained each network on the same training dataset and evaluated them using the same validation dataset. After comparing these five architectures, we chose the one with the best performance, named TickNet. We compared TickNet and five other classical image classification architectures used for large-scale image recognition tasks. We determined TickNet outperforms the five classical networks in model size, number of parameters, testing time on both a CPU and GPU with a tradeoff in testing accuracy. We deployed applications on an Android mobile phone to do binary classifications and four-class image classifications to conclude the research. Disclaimer: This work or any part of it should not be used as guidance or instruction regarding the diagnosis, care, or treatment of tick-borne diseases or supersede existing guidance.

Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.Tick saliva contains a lot of biological active substances helping them to succesfully complete their feeding which is neccesary for their next development. Both proteinaceous and non-proteinaceous molecules including protease inhibitors are present in tick saliva. The biggest family of these proteases are serpins. Serpins are involved in many biological processes as blood coagulation, fibrinolysis, apoptosis or inflammation. The aim of this diploma work was to determine expression profiles of 10 serpins from nymphs of Ixodes ricinus fed for different times using quantitative real time PCR. For chosen genes (IRS 10, IRS 20) dsRNA for silencing of the gene was prepared and using RNA interference the role of these genes during tick (I. ricinus nymphs) feeding and transmission of Borrelia afzelii spirochetes, a vector of Lyme borreliosis, was evaluated.

Ticks are of global interest as the pathogens they spread can cause diseases that are of importance to both human health and economies. In Scotland, the most populous tick species is the sheep tick Ixodes ricinus, which is the vector of pathogens causing diseases such as Lyme borreliosis and Louping-ill. Recently, both the density and spread of I. ricinus ticks have grown across much of Europe, including Scotland, increasing disease risk. Due to the nature of the tick lifecycle they are particularly dependent on environmental factors, including temperature and habitat type. Because of this, the recent increase in tick-borne disease risk is believed to be linked to climate change. Many mathematical models have been used to explore the interactions between ticks and factors within their environments; this thesis begins by presenting a thorough review of previous modelling of tick and tick-borne pathogen dynamics, identifying current knowledge gaps. The main body of this thesis introduces an original mathematical modelling framework with the aim to further our understanding of the impact of climate change on tick-borne disease risk. This modelling framework takes into account how key environmental factors influence the I. ricinus lifecycle, and is used to create predictions of how I. ricinus density and disease risk will change across Scotland under future climate warming scenarios. These predictions are mapped using Geographical Information System software to give a clear spatial representation of the model predictions. It was found that as temperatures increase, so to do I. ricinus densities, as well as Louping-ill and Lyme borreliosis risk. These results give a strong indication of the disease risk implications of any changes to the Scottish environment, and so have the potential to inform policy-making. Additionally, the models identify areas of possible future research.

In this paper, I will show how applying a spatially explicit context to an existing environmental health surveillance framework is vital for more complete surveillance of disease, and for disease prevention and intervention strategies. As a case study to test the viability of a spatial approach to this existing framework, the risk of human exposure to Lyme disease will be estimated. This spatially explicit framework divides the surveillance process into three components: hazard surveillance, exposure surveillance, and outcome surveillance. The components will be used both collectively and individually, to assess exposure risk to infected ticks. By utilizing all surveillance components, I will identify different areas of risk which would not have been identified otherwise. Hazard surveillance uses maximum entropy modeling and geographically weighted regression analysis to create spatial models that predict the geographic distribution of ticks in Texas. Exposure surveillance uses GIS methods to estimate the risk of human exposures to infected ticks, resulting in a map that predicts the likelihood of human-tick interactions across Texas, using LandScan 2008TM population data. Lastly, outcome surveillance uses kernel density estimation-based methods to describe and analyze the spatial patterns of tick-borne diseases, which results in a continuous map that reflects disease rates based on population location. Data for this study was obtained from the Texas Department of Health Services and the University of North Texas Health Science Center. The data includes disease data on Lyme disease from 2004-2008, and the tick distribution estimates are based on field collections across Texas from 2004-2008.

Fästingburet encefalitvirus (TBEV) är ett RNA-virus som tillhör genuset flavivirus. Vid en TBEV-infektion är feber, trötthet, allmänpåverkan samt huvudvärk och muskelvärk vanligt förekommande symtom. Viruset överförs via saliven från fästingar under de första minuterna efter fästingbett. TBEV-IgM och ibland även TBEV-IgG återfinns i serum då symtom i centrala nervsystemet (CNS) yttrar sig i den andra fasen av sjukdomsförloppet. De senaste åren har prevalensen av fästingburen encefalit (TBE) ökat. Sedan 2017 har över 300 fall av TBE rapporterats årligen i Sverige. Laterala flödesanalyser (lateral flow assays, LFA) är billiga, enkla, snabba och baseras på portabla instrument som används bland annat inom biomedicinsk vetenskap. ReaScan® TBE IgM från det finska företaget Reagena är ett snabbtest, baserat på LFA-tekniken, för detektion av TBE-specifika IgM-antikroppar i humant serum och likvor. Syftet med studien var att undersöka om ReaScan® TBE IgM kan användas för att diagnostisera TBE på laboratoriet för Klinisk Mikrobiologi på länssjukhuset i Kalmar. Metodens prestanda undersöktes genom att analysera totalt 23 serumprover, 13 prover från TBE-patienter och 10 prover från icke-TBE-patienter. Sensitiviteten uppskattades genom att analysera 13 serumprover där förekomst av TBE-antikroppar sedan tidigare konfirmerats. Specificiteten uppskattades genom att analysera 10 serumprover från patienter utan känd TBEV-infektion. Den diagnostiska sensitiviteten respektive specificiteten beräknades till 100 %. På grund av den begränsade storleken på undersökningsmaterialet är dock den beräknade sensitiviteten och specificiteten ej helt tillförlitlig. Metodens prestanda ansågs vara tillräckligt god för att den skall kunna användas som en screening-metod för TBEV-IgM-antikroppar på laboratoriet för Klinisk Mikrobiologi på länssjukhuset i Kalmar. / Tick-borne encephalitis virus (TBEV) is an RNA virus that belongs to the genus flavivirus. Symptoms that commonly present during a TBEV infection include headaches, muscle pains, fever and malaise. The virus is transmitted with the saliva from ticks during the first minutes of their blood meal. TBEV-IgM and sometimes TBEV-IgG antibodies can be detected in the patient’s serum when central nervous system (CNS) symptoms present in the second phase of the disease. Over the last couple of years, the prevalence of tick-borne encephalitis (TBE) has increased. Since 2017 over 300 cases of TBE are reported every year in Sweden. Lateral flow assays (LFA) is the technology behind inexpensive, simple, quick and portable instruments that are used within the biomedical science field among others. ReaScan® TBE IgM developed by the Finnish company Reagena is a rapid test, based on the LFA technique, used for the detection of TBEV specific IgM antibodies in human serum and cerebrospinal fluid. The trial aimed to evaluate whether ReaScan® TBE IgM could be used to diagnose TBE at the laboratory of Clinical microbiology at the County hospital in Kalmar. The performance of the test was determined by analysing a total of 23 serum samples, 13 of which consisted of samples from patients with a previously confirmed TBE diagnosis and 10 samples from patients with no known TBEV infection. The diagnostic sensitivity and specificity were both determined to be 100 %. Due to the limited sample size, the calculated sensitivity and specificity are not particularly reliable.  The performance of the test was satisfactory and it could be used as a screening method for the detection of TBEV IgM antibodies at the department of Clinical microbiology at Kalmar County Hospital.

The public health and veterinary importance of Gulf Coast ticks, Amblyomma maculatum Koch (1844) have become more apparent during the last several decades. In addition, new records of this three-host ixodid tick presently show a geographic distribution throughout much of the southern United States. Rickettsia parkeri, a spotted fever group rickettsia (SFGR) that is commonly found infecting the Gulf Coast tick, was only recently recognized as a human pathogen. Over the last decade, more than 20 human cases of disease caused by R. parkeri have been recognized in the Americas, all of which were similar in presentation to mild Rocky Mountain spotted fever. In addition, a novel, poorly characterized SFGR, “Candidatus Rickettsia andeanae”, was recently identified in A. maculatum from Peru, United States, Chile and Argentina. As the recognition of R. parkeri as a pathogen and “Ca. R. andeanae” as an additional SFGR in A. maculatum only recently occurred, a general gap exists in our understanding of the biology of these SFGRs. The overall objective of this dissertation was to contribute to our knowledge of SFGR infecting A. maculatum. In Chapter 3, we present a prevalence study of R. parkeri, and “Ca. R. andeanae” in A. maculatum from Mississippi where we detected 15.2% R. parkeri-singly infected ticks and 3.1% total “Ca. R. andeanae” infected ticks of which 1.7% were co-infected with R. parkeri. In Chapter 4, we discuss finding four genetically different populations of A. maculatum from Mississippi infected with a homogenous population of R. parkeri, using Single Strand Conformation Polymorphism analysis. Those initial data relating to “Ca. R. andeanae” provided a foundation for studies described in Chapters 5 and 6. We report the first morphological study of “Ca. R. andeanae” using transmission electron microscopy in Chapter 5 and isolation of this SFGR in ,A. maculatum cell co-culture in Chapter 6. We anticipate that results presented in this dissertation will contribute to our understanding of the ecology of ,A. maculatum as a vector for the human pathogen, R. parkeri, and increase the current understanding of both R. parkeri and “Ca. R. andeanae” in A. maculatum.

Cette thèse est une investigation de l'écologie et de l'épidémiologie spatiale fine de la tique à pattes noires (Ixodes scapularis) et du risque associé aux pathogènes transmis par cette tique dans une forêt du sud du Québec, au Canada. Sous l’influence de changements climatiques et environnementaux, la répartition spatiale de cette tique s’étend actuellement à travers la province, et son abondance augmente dans la plupart des régions. Il en résulte une préoccupation croissante en matière de santé publique liée à l'émergence de maladies transmises par les tiques (MTT) dans la province. Ainsi, plusieurs besoins de recherche ont vu le jour, y compris l’amélioration de la compréhension des facteurs dictant où et quand le risque émergera, et l’identification des composantes sur lesquelles les autorités régionales, locales et les individus pourraient agir afin réduire ce risque. Le site d’étude pour ce projet était le parc National du Mont-Saint-Bruno. De 2016 à 2018, à 32 sites répartis dans les habitats forestiers du parc, les tiques ont été collectées par la technique de la flanelle, la communauté d’hôtes de la tique a été inventoriée (grands et petits mammifères, et oiseaux nicheurs) et les micro-habitats ont été caractérisés (en termes de structure, de composition et de conditions microclimatiques). La densité des tiques dans la zone d’étude était particulièrement élevée par rapport aux autres régions environnantes. Les analyses spatiales ont montré des patrons d’abondance des tiques, persistants sur trois ans, avec un effet significatif des conditions locales de températures et d’humidité relatives. Un effet significatif de la densité du stade de développement précédent lors de l’année précédente a également été noté, suggérant une dispersion lente des tiques par les hôtes et une dynamique d’invasion caractérisée par plusieurs évènements d’introduction et d’expansion opérant à une échelle locale. En 2017 et 2018, un dispositif d’échantillonnage plus extensif a visé la communauté d’hôtes des stades immatures d’I. scapularis, afin de documenter le rôle de ces espèces dans la circulation des agents pathogènes. 849 oiseaux nicheurs appartenant à 50 espèces et 694 petits mammifères appartenant à 4 espèces ont été examinés pour la présence des tiques et des pathogènes. Les souris à pattes blanches (Peromyscus leucopus) contribuaient à la majorité (80%) des cas d’infection des nymphes par Borrelia burgdorferi dans l’échantillon, alors que les 20% restants étaient attribuables à des oiseaux. Ce résultat confirme la proposition de certains auteurs à savoir que l’importance des hôtes alternatifs (autres que P. leucopus) aient été sous-estimée dans les études précédentes, et souligne l’importance de poursuivre les travaux pour documenter l’impact de ces hôtes dans l’épidémiologie des MTT. Finalement, la caractérisation des patrons de risque associés aux MTT dans la zone d’étude a été complétée par un échantillonnage de l’intensité d’utilisation des sentiers par les visiteurs du parc en 2017 et 2018. D’abord, les prélèvements de tiques dans l’environnement et sur les hôtes ont permis de détecter la présence de trois pathogènes représentant un risque de santé publique pour la population locale, soit en ordre du plus au moins prévalent : B. burgdorferi, Anaplasma phagocytophyllum et Borrelia miyamotoi. Ensuite, l’intégration des patrons spatiaux de l’utilisation du parc par les visiteurs a mis en évidence le rôle des facteurs comportementaux des utilisateurs et des attributs du paysage local dans la détermination des patrons de risque de contacts entre les visiteurs et les nymphes infectées par B. burgdorferi. Le risque de contact était associé à certaines périodes et zones de forte fréquentation du parc, mais pas aux indicateurs locaux de fragmentation de l'habitat, comme le suggèrent d'autres études. En outre, les zones où la densité de la couverture forestière et des points d'intérêt (infrastructures) étaient les plus élevés présentaient les niveaux de risque les plus élevés. Cette thèse contribue à l’avancement des connaissances fondamentales reliées à la biologie des tiques, aux relations écologiques entre ces ectoparasites et leurs hôtes et à l’écologie des pathogènes qu’elles transmettent. Ces connaissances trouveront de multiples applications concrètes, principalement dans le domaine de la santé publique où elles permettront notamment de parfaire les outils existants d’évaluation du risque et de prévention des MTT. En reliant l’écologie à la santé publique, cette thèse répond à un besoin de recherche et de développement d’expertise qui devient de plus en plus important dans le contexte actuel des changements climatiques et de l’émergence des maladies zoonotiques qui s’en trouvent facilitées au Canada. / This thesis is an investigation of the ecology and fine-scale spatial epidemiology of the blacklegged tick (Ixodes scapularis) and the risk associated with pathogens transmitted by this tick in a forest of southern Quebec, Canada. Under the influence of climate and environmental changes, the spatial distribution of this tick is currently expanding across the province, and its abundance is increasing in most regions. This has resulted in a growing public health threat associated with the emergence of tick-borne diseases (TBDs) in the province. Thus, several research needs have emerged, including improving understanding of the factors determining where and when risk will arise, and identifying what regional and local health authorities and individuals can do to reduce that risk. The study site for this project was Mont-Saint-Bruno National Park. From 2016 to 2018, at 32 sites distributed in the park's forest habitats, ticks were collected by drag sampling, the host community was inventoried (large and small mammals, and nesting birds), and microhabitats were characterized (in terms of structure, composition, and microclimatic conditions). The density of ticks in the study area was particularly high compared to other surrounding areas. Spatial analyses showed patterns of tick abundance, persistent over three years, with a significant effect of local microclimatic conditions (relative temperature and humidity). A significant effect of the density of the previous developmental stage in the previous year was also noted, suggesting slow host dispersal of ticks and invasion dynamics characterized by several introduction and expansion events operating at a local scale. In 2017 and 2018, a more extensive sampling scheme targeted the host community of immature stages of I. scapularis, to document the role of these species in pathogen circulation. 849 breeding birds belonging to 50 species and 694 small mammals belonging to 4 species were examined for the presence of ticks and pathogens. White-footed mice (Peromyscus leucopus) contributed to the majority (80%) of Borrelia burgdorferi nymph infections in the sample, while the remaining 20% were attributable to birds. This result confirms the suggestion by some authors that the importance of alternative hosts (other than P. leucopus) may have been underestimated in previous studies and underscores the importance of further work to document the impact of these hosts in the epidemiology of TBDs. Finally, characterization of risk patterns associated with TBDs in the study area was completed by sampling trail use by park visitors in 2017 and 2018. First, the analysis of ticks collected from the environment and on hosts demonstrated the presence of three pathogens representing a public health risk to the local population, in order from the most to the least prevalent: B. burgdorferi, Anaplasma phagocytophyllum and Borrelia miyamotoi. Second, integration of spatial patterns of visitor use of the park highlighted the role of visitor behaviour and local landscape attributes in determining patterns of risk of contact between visitors and B. burgdorferi-infected nymphs. Risk was associated with certain times and areas of increased park use, but not with local indicators of habitat fragmentation, in contrast with the results of previous studies. In addition, areas with the highest densities of forest cover and points of interest (infrastructure) had the highest levels of risk. This thesis contributes to the advancement of fundamental knowledge related to the biology of ticks, the ecological relationships between these ectoparasites and their hosts, and the ecology of the pathogens they transmit. This knowledge will have multiple applications, mainly in the field of public health, where it will allow the refinement of existing tools for risk assessment and prevention of TBDs. By linking ecology to public health, this thesis responds to a need for research and development of expertise that is becoming increasingly important in the current context of climate change and the emergence of zoonotic diseases that it facilitates in Canada.

No description available.

Poucos são os estudos acerca da saúde de onças-pintadas em vida livre. Visando obter melhores parâmetros para avaliação clínica desta espécie ameaçada de extinção, foram realizados exame clínico, hemograma, perfil bioquímico e acompanhamento de 10 onças-pintadas da região de Corumbá, no Pantanal do Mato Grosso do Sul. Além disso, buscando obter informações sobre o possível papel da espécie como suscetível, hospedeira ou sentinela de patógenos de importância em saúde pública e animal, amostras destas 10 onças foram testadas através de métodos sorológicos para verificar contato com vírus rábico, Rickettsia spp. e Ehrlichia canis. As amostras das onças e os carrapatos que as parasitavam no momento das capturas foram testados por reação em cadeia pela polimerase para a família Anaplasmataceae e os gêneros Rickettsia, Borrelia, Coxiella, Hepatozoon e Babesia. Este é o primeiro estudo a relatar os valores de hemograma e perfil bioquímico de uma população de onças-pintadas de vida livre. Dois animais, assintomáticos, apresentaram baixo título sorológico para o vírus da raiva, sugerindo contato da espécie com este patógeno. Todas as onças capturadas foram consideradas soropositivas para Rickettsia spp., e Rickettsia parkeri foi sequenciada a partir de um Amblyomma triste que estava parasitando um dos animais. Foi descoberta uma possível nova espécie do gênero Ehrlichia através do sequenciamento de DNA obtido de um Amblyomma triste e um Amblyomma cajenense que estavam parasitando onças. Quatro onças-pintadas foram consideradas soropositivas para Ehrlichia canis, possivelmente uma reação cruzada com esta outra espécie. Todas as onças-pintadas avaliadas neste estudo apresentaram DNA de Cytauxzoon sp., com 98% de similaridade a C. felis, em amostras sanguíneas. Todas as onças avaliadas neste estudo apresentaram DNA de Hepatozoon sp., com 98% de similaridade a H. felis, em amostras sanguíneas. As onças apresentavam boas condições de saúde geral. / Few studies have been conducted to investigate the health of free-ranging jaguars. In order to obtain better parameters for clinical evaluation of this endangered species, clinical exams, hemogram, biochemical tests and ecological monitoring were done for 10 jaguars in the Pantanal region - Corumbá City, Mato Grosso do Sul State. This project also evaluated the possible role of this species as susceptible, host or sentinel for pathogens of public and/or animal health importance, testing samples from these animals by serological methods to rabies virus, Rickettsia spp. and Ehrlichia canis. All samples and all ticks collected from the jaguars were also tested by polymerase chain reaction to the Anaplasmataceae family and the genera Rickettsia, Borrelia, Coxiella, Hepatozoon and Babesia. This is the first report of hemograms and biochemical profile of a free-ranging jaguar population. Two asymptomatic animals presented low seropositivity for rabies virus, suggesting contact with this pathogen. All jaguars were considered seropositive for Rickettsia spp., and Rickettsia parkeri was sequenced from an Amblyomma triste that was parasitizing one of the animals. A possible new species of the genus Ehrlichia has been identified by DNA sequencing obtained from an Amblyomma triste and an Amblyomma cajenense that were parasitizing jaguars. Four jaguars were considered seropositive for Ehrlichia canis, possibly a cross-reaction with this other species. All jaguars evaluated in this study presented DNA fragments of Cytauxzoon sp., 98% similarity to C. felis in blood samples. In addition, all jaguars presented DNA fragments of Hepatozoon sp., 98% similarity to H. felis in blood samples. In general, these jaguars presented good health.

Em janeiro de 2005, foram coletados 31 carrapatos adultos da espécie Amblyomma triste em uma propriedade rural da CESP, localizada no município de Paulicéia, Estado de São Paulo. Três carrapatos foram positivos para o teste de hemolinfa, demonstrando estruturas compatíveis com riquétsias no interior de hemócitos. Dois desses carrapatos foram submetidos à tentativa de isolamento de riquétsias em células Vero, através da técnica de Shell vial. Um isolado foi obtido com sucesso, estando já estabelecido em cultivo celular, com várias passagens e partidas congeladas. Do restante do carrapato utilizado para este isolamento, foi extraído o DNA e este foi submetido a PCR para um fragmento do gene ompA de Rickettsia spp. Foi realizada a caracterização molecular do isolado, através do sequenciamento genético de quatro genes de Rickettsia spp: gltA, htrA, ompA e ompB e os genes apresentaram 99,8 a 100% de identidade com as seqüências correspondentes de Rickettsia parkeri no GenBank. Todos os 31 carrapatos tiveram o DNA extraído, sendo processados pela PCR para um fragmento do gene gltA e para um fragmento do gene ompA. Três (9,7%) foram positivos a PCR para o gene gltA e os mesmos 3 carrapatos foram positivos para o ompA, sendo exatamente os 3 carrapatos previamente positivos ao teste de hemolinfa). O material amplificado destes 3 carrapatos para o fragmento de gene ompA foi processado para o sequenciamento automático de nucleotídeos resultando em 100% de identidade com a seqüência correspondente de Rickettsia parkeri no GenBank. Este trabalho relata pela primeira vez a bactéria R. parkeri no Brasil, o que foi confirmado pelo isolamento do agente em cultivo de células / In January 2005, 31 adult free-living ticks of the species Amblyomma triste were collected in the CESP rural farm located in the city of Paulicéia, state of São Paulo, Brazil. In the laboratory, 3 of these ticks were positive by the hemolymph test, showing structures compatible with Rickettsia within the hemocytes. Attempts to isolate Rickettsia were performed in two hemolymph-positive ticks by the Shell-vial technique. One isolate was successful obtained, being established in Vero cell culture, with several passages performed. DNA extracted from infected cells was submitted to PCR targeting fragments of four Rickettsia genes: gltA, htrA, ompA and ompB. DNA sequences obtained from PCR products of these four genes showed 99.8 to 100% of similarity with corresponding sequences of Rickettsia parkeri in the Genbank. DNA was extracted from all 31 ticks and processed by PCR targeting a fragment of the rickettsial gltA gene and a fragment of ompA gene. Three (9.7%) ticks were positive for both genes, being the same ticks previously positive by the hemolymph test. PCR products of these ticks were sequenced, being 100% identical to the corresponding sequence of Rickettsia parkeri in GenBanK. This study perfoms the first report of R. parkeri in Brazil, confirmed by the isolation of the agent in cell culture