Made available in DSpace on 2016-08-10T10:38:28Z (GMT). No. of bitstreams: 1 GERUSA CRISTHINY DA PAIXAO RONCATO.pdf: 1739734 bytes, checksum: e31f127c33ebfe10748de3fa7c77d454 (MD5) Previous issue date: 2011-04-14 / Genital infection by human papillomavirus (HPV) is considered the sexually transmitted disease most prevalent among the population. The man has represented an important role as virus reservoir and transmitter. Most HPV-infected men are asymptomatic. The HPV infection prevalence in young males is poorly understood and few studies are available. This study aim was to evaluate the HPV prevalence in a group of young adults, ages 18 and 25, male, living in the City of Leopoldo de Bulhões-GO. For viral genome detection, was used the polymerase chain reaction (PCR) technique with primers PGMY09/11 Line Blot. Descriptive statistics and their frequencies was performed for the variables related to socio-demographic and behavioral features in the group of asymptomatic men for HPV infection. To investigate the possible associations between related factors and the infection, univariate analysis was performed by chi-square test with Yates correction. The study involved a population of 57 asymptomatic men aged between 18 and 25 years old living in the city of Leopoldo de Bulhões-GO, selected at the Jose Francisco Vargas Health Center. Among the study group behavioral characteristics, 43.9% of subjects were single and 56.1% were married. The individual s age who initiated sexual activity was approximately 15 years old. All subjects were informed about the study and signed a free and clear consent form. The HPV infection prevalence in the study group was 31.6%. HPV infection was significantly associated with marital status and partner s number, in other words, infection was more prevalent among unmarried individuals (56%) who did not have a steady partner (57.1%). As for condom use and early sexual activity, HPV infection was not significantly associated. Our results demonstrate that a man behavioral factor represents a significant risk for HPV infection association / A infecção genital pelo papilomavírus humano (HPV) é considerada a doença sexualmente transmissível de maior prevalência na população mundial. O homem tem apresentado um importante papel como reservatório e o transmissor desse vírus. A maioria dos homens infectados pelo HPV são assintomáticos. A prevalência da infecção pelo HPV em jovens do sexo masculino é pouco conhecida e apenas alguns estudos encontram-se disponíveis. O objetivo deste trabalho foi avaliar a prevalência do HPV em um grupo de adultos jovens, com idades entre 18 e 25 anos, do sexo masculino, residentes no Município de Leopoldo de Bulhões-GO. Para a detecção do genoma viral utilizou a reação em cadeia da polimerase (PCR), utilizando a técnica com primers PGMY09/11. A estatística descritiva com suas respectivas freqüências foi realizada para as variáveis relativas às características sócio-demográficas, comportamentais no grupo de homens assintomáticos para infecção pelo HPV. Para investigar as possíveis associações entre os fatores relacionados e a infecção realizou-se análise univariada, pelo teste do qui-quadrado com correção de Yates, selecionados no Centro de Saúde José Franscisco Vargas. Dentre as características comportamentais do grupo estudado 43,9% dos indivíduos eram solteiros e 56,1% eram casados. A idade de início da atividade sexual foi de aproximadamente 15 anos. Todos os indivíduos foram informados sobre o estudo e assinaram o termo de consentimento livre e esclarecido. A prevalência da infecção pelo HPV no grupo estudado foi de 31,6%. A infecção pelo HPV esteve significativamente associada ao estado civil e ao número de parceiras, ou seja, a infecção foi mais prevalente nos indivíduos solteiros (56%) e que não apresentaram parceira fixa (57,1%). Quanto ao uso do preservativo e o início da atividade sexual a infecção pelo HPV não esteve significativamente associada. Nossos resultados demonstraram que fatores comportamentais do homem representam uma associação com risco significativo para a infecção pelo HPV

A Laringotraqueíte Infecciosa (LTI) é uma doença respiratória altamente contagiosa, que acomete principalmente galinhas, é causada por um Gallid herpesvirus tipo 1. As aves infectam-se através do trato respiratório e por via ocular, sendo as aves com infecção clínica as principais transmissoras do vírus. Outras fontes de transmissão são as aves com infecções latentes, materiais de cama e fômites contaminados. Os sinais clínicos geralmente aparecem entre 6 a 12 dias da exposição natural e em infecções experimentais entre 4 a 7 dias pós infecção (p.i). Na forma subclínica pode-se observar uma leve traqueíte mucoide, sinusite, conjuntivite, com morbidade variável e baixa mortalidade. Na forma severa, as aves apresentam depressão, dispneia, espirros, corrimento nasal, conjuntivite, expectoração de secreção sanguinolenta. A taxa de morbidade é alta, comprometendo 100% do lote e a mortalidade pode ocorrer em até 70% do plantel, embora taxas de 10 a 20% sejam as mais frequentes. O agente causador desta doença pode ser propagado na membrana corio-alantóide (MCA) de embriões de frango em desenvolvimento e replicado em células de rim de frangos adultos, como também, em uma variedade de células epiteliais de embrião como do rim, do fígado e do pulmão. Existem vários procedimentos para o diagnóstico da LTI como: a observação de sinais clínicos, a observação de lesões macroscópicas e lesões histopatológicas e o uso de técnicas moleculares como: RFLP, PCR e PCR em tempo real. Como a PCR em tempo real apresenta uma maior sensibilidade quando comparada com outros métodos de diagnóstico, permite quantificar o número de cópias amplificadas do genoma viral, assim como, a diferenciação da doença na fase aguda ou crônica, reduzindo o número de possíveis falsos positivos, esta foi usada para a detecção deste vírus. O objetivo deste trabalho foi isolar o VLTI em ovos embrionados, descrever as lesões macroscópicas causadas pelo vírus, detectar o vírus pela reação de PCR em tempo real, usando como alvo da reação o gene ICP4, padronizar uma reação de PCR em Tempo Real usando a glicoproteína E como alvo da reação e propor o seu uso no diagnóstico de rotina. / The Infectious Laryngotracheitis (ILT) is a highly contagious respiratory disease that affects mainly chickens; caused by a Gallid herpesvirus type 1. Infect birds, by the respiratory tract and by the ocular route, the birds with clinical infection the main transmission of the virus. Other transmission sources are birds with latent infections, bedding materials and contaminated fomites. Clinical signs generally appear between 6 to 12 days exposure of the natural and in experimental infections between 4 and 7 days post infection (p.i). In subclinical form can observe a slight mucoid tracheitis, sinusitis, conjunctivitis, variable morbidity and low mortality. In the severe form, the birds present depression, dyspnea, sneezing, nasal discharge, conjunctivitis, expectoration of bloody discharge. The morbidity rate is high, impairing the lot 100% and mortality may occur in up to 70% of the flock, although 10 to 20% rates are the most frequent. The causative agent of this disease can be propagated in chorioallantoic membrane (CAM) of chicken embryos develop and replicated in adult chicken kidney cells as well as in a variety of epithelial-cell embryo as kidney, liver and lung. There are several procedures for the diagnosis of LTI as observation of clinical signs, observation of gross lesions and histopathological lesions, and the use of molecular techniques as RFLP, PCR and real time PCR. As the real-time PCR has greater sensitivity compared to other diagnostic methods to quantify the number of amplified copies of the viral genome, as well as the differentiation of the disease in the acute or chronic phase, reducing the number of potential false positives, this was used for detection of virus. The objective of this study was to isolate the VLTI in embryonated eggs, describe macroscopic lesions caused by the virus, detect the virus by PCR reaction in real time, using as a target of reaction the ICP4 gene, standardize a PCR reaction in real time using the glycoprotein E as a target of reaction and propose their use in routine diagnosis.

Made available in DSpace on 2016-09-27T13:39:59Z (GMT). No. of bitstreams: 0 Previous issue date: 2015-10-29. Added 1 bitstream(s) on 2016-09-27T13:45:07Z : No. of bitstreams: 1 000870610.pdf: 912715 bytes, checksum: fd85044be54e4bd25cdd15279986ef8a (MD5) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Until now, the disease caused by the canine coronavirus (CCoV) was not fully elucidated, the CCoV role in the pathogenesis of the illness is not quite established. Only after the SARS (Severe Acute Respiratory Syndrome) appearance in human beings caused by a coronavirus in 2002, isolated of a wild mammal, many studies were developed with coronavirus of different species in search of circulating variants. Few studies had reported the presence of CCoV and his variability's in Brazil. Viral enteritis are responsible by high morbidity taxes and mortality in the small animals clinic and, although there are several etiologic agents described, the CCoV and the CPV are not yet considered a major cause of acute gastroenteritis pathogens in young dogs. For the present study, were collected 100 stool samples from dogs attended in a veterinary hospital routine with clinical signs of gastroenteritis (hemorrhagic or not). The CCoV and CPV RNA were amplified in the tested samples. Some of the by-products from the CPV amplification were purified, sequenced, aligned and subjected to the GenBank for the detection of CPV-2c and characterization of CCoV. The CCoV was present in 6% of the analyzed samples, while CPV-2a was identified in 43% of samples and CPV-2b in 18% of the total. A sample pool submitted to the sequencing and filogenetic analysis identified the CPV-2c, reveling that the new variant is already present in Araçatuba - SP. The phylogenetic analyses for CCoV revealed that the studied samples belong to the Subtype CCoV-IIa (pantropic), strengthening the agent identification importance in the canine population, once that the actual available vaccines don't have the new variants so that the dogs from Brazil are susceptible to severe outbreaks, as described in other countries. / FAPESP: 2013/249514

Resumo:Até o momento, a doença causada pelo coronavirus canino (CCoV) não foi totalmente elucidada, e o papel que o CCoV desempenha na patogenia da enfermidade não está bem estabelecido. Somente após o aparecimento da SARS (Síndrome Respiratória Aguda) em seres humanos causada por um coronavirus em 2002 isolado de um mamífero selvagem, foram desenvolvidos vários estudos com coronavirus de diversas espécies na busca de variantes circulantes. Poucos estudos têm reportado a presença dos CCoV e suas variabilidades no Brasil. Enterites virais são responsáveis por altas taxas de morbidade e mortalidade na clínica de pequenos animais e, embora existam diversos agentes etiológicos descritos, o CCoV e o CPV ainda são considerados uns dos principais patógenos causadores de gastroenterite aguda em cães jovens. Para o presente estudo, foram colhidas 100 amostras de fezes de cães atendidos em uma rotina hospitalar veterinária com sinais clínicos de gastroenterite (hemorrágica ou não). Foram amplificados RNA do CCoV e o DNA do CPV nas amostras testadas. Alguns dos produtos da amplificação para CPV foram purificados, sequenciados, alinhados e submetidos ao GenBank para detecção do CPV-2c e caracterização do CCoV. O CCoV mostrou-se presente em 6% das amostras analisadas, enquanto o CPV-2a foi identificado em 43% das amostras e o CPV- 2b em 18% do total. Um pool de amostras submetidas ao sequenciamento e análise filogenética identificou o CPV-2c, revelando que a nova variante já está presente em Araçatuba - SP. A análise filogenética para o CCoV evidenciou que as amostras analisadas pertencem ao subtipo CCoV-IIa (pantrópica), reforçando a importância da identificação desse agente na população canina, uma vez que as vacinas disponíveis atualmente não possuem as novas variantes e de modo que os cães do Brasil estão susceptíveis a graves surtos, como já descritos em outros países / Abstract:Until now, the disease caused by the canine coronavirus (CCoV) was not fully elucidated, the CCoV role in the pathogenesis of the illness is not quite established. Only after the SARS (Severe Acute Respiratory Syndrome) appearance in human beings caused by a coronavirus in 2002, isolated of a wild mammal, many studies were developed with coronavirus of different species in search of circulating variants. Few studies had reported the presence of CCoV and his variability's in Brazil. Viral enteritis are responsible by high morbidity taxes and mortality in the small animals clinic and, although there are several etiologic agents described, the CCoV and the CPV are not yet considered a major cause of acute gastroenteritis pathogens in young dogs. For the present study, were collected 100 stool samples from dogs attended in a veterinary hospital routine with clinical signs of gastroenteritis (hemorrhagic or not). The CCoV and CPV RNA were amplified in the tested samples. Some of the by-products from the CPV amplification were purified, sequenced, aligned and subjected to the GenBank for the detection of CPV-2c and characterization of CCoV. The CCoV was present in 6% of the analyzed samples, while CPV-2a was identified in 43% of samples and CPV-2b in 18% of the total. A sample pool submitted to the sequencing and filogenetic analysis identified the CPV-2c, reveling that the new variant is already present in Araçatuba - SP. The phylogenetic analyses for CCoV revealed that the studied samples belong to the Subtype CCoV-IIa (pantropic), strengthening the agent identification importance in the canine population, once that the actual available vaccines don't have the new variants so that the dogs from Brazil are susceptible to severe outbreaks, as described in other countries. / Orientador:Tereza Cristina Cardoso da Silva / Banca:Roberto Gameiro de Carvalho / Banca:Andrea Fontes Garcia / Mestre

Submitted by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-08T12:17:08Z No. of bitstreams: 2 Dissertação - João Paulo Gomes de Sousa - 2017.pdf: 1886122 bytes, checksum: 3663c656c9cf7fc3f9f9b7cecfcfc03d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-12-08T12:17:43Z (GMT) No. of bitstreams: 2 Dissertação - João Paulo Gomes de Sousa - 2017.pdf: 1886122 bytes, checksum: 3663c656c9cf7fc3f9f9b7cecfcfc03d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-12-08T12:17:43Z (GMT). No. of bitstreams: 2 Dissertação - João Paulo Gomes de Sousa - 2017.pdf: 1886122 bytes, checksum: 3663c656c9cf7fc3f9f9b7cecfcfc03d (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-11-13 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The human metapneumovirus, first discovered and described in 2001, has been related to infections in the upper and lower respiratory tract, in all age groups, with severe cases frequently associated with children under five years old, elderlies and immune-compromised people. The present study aims to investigate the occurrence of hMPV in the pediatric population attended in the pediatry referral hospital, in the city of Goiânia - Goiás, evaluating symptomatic and asymptomatic patients. During the period of may/2014 and may/2015 251 nasal swab samples were collected from kids with age up to six years old, with respiratory infection symptoms or asymptomatic. The viral RNA was extracted using the QIAamp cador pathogen mini kit, and the extraction products were submitted to the reverse transcription reaction. The cDNA was submited a nested-PCR using specific primers to the amplification of a conserved region corresponded to the M gene. It was observed a global positivity index for the hMPV of 14.7% (37/251). In the group of children with respiratory infection, the positivity index was 16.6%, however, a significant index was also observed among asymptomatic children (12.3%). Analysis regarding the sample collection period did not show a statistically significant difference, reinforcing literature data that describe the circulation of this pathogen all year long. In Brazil there are few studies regarding the epidemiology of hMPV infections, being this the first report of hMPV occurrence in midwest, contributing to a better understanding of the role played by hMPV in the context of respiratory tract infections. / O Metapneumovírus Humano (hMPV), descoberto e descrito em 2001, vem sendo relacionado a infecções no trato respiratório superior e inferior, em todas as faixas etárias, com quadros graves mais frequentemente associados a crianças menores que cinco anos, idosos e imunocomprometidos. O presente estudo teve como objetivo investigar a ocorrência do hMPV em população pediátrica atendida em hospital de referência pediátrica do município de Goiânia-Goiás, avaliando pacientes sintomáticos e assintomáticos. Para isso, durante o período de maio/2014 a maio/2015 foram coletadas 251 amostras de swab nasal de crianças com idade inferior a seis anos de idade, apresentando quadro de infecção respiratória ou assintomáticas para a mesma. O RNA viral foi extraído utilizando o Kit QIAamp® cador® Pathogen Mini Kit e os produtos de extração foram submetidos à reação de transcrição reversa. A partir do DNA complementar obtido foi realizada uma nested-PCR utilizando iniciadores específicos para amplificação de uma região conservada correspondente ao gene M. Do total de amostras investigadas, foi observado um índice global de positividade para o hMPV de 14,7% (37/251). No grupo de crianças com quadro de infecção respiratória o índice de positividade foi de 16,6%, entretanto índice significativo também foi observado entre crianças assintomáticas (12,3%). Análise em relação ao período de coleta não demonstrou diferença estatisticamente significativa, reforçando dados da literatura que descrevem a circulação deste agente durante todo o ano. No Brasil, existem poucos estudos a respeito da epidemiologia das infecções por hMPV, sendo este o primeiro relato de ocorrência do hMPV na região centro-oeste, contribuindo para uma melhor compreensão do papel deste agente no contexto das infecções do trato respiratório.

Submitted by Cássia Santos (cassia.bcufg@gmail.com) on 2017-03-24T12:53:45Z No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2017-03-24T13:02:10Z (GMT) No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2017-03-24T13:02:10Z (GMT). No. of bitstreams: 2 Dissertação - Geisiane Alves Rocha - 2017.pdf: 2262501 bytes, checksum: 07907cdfd4fccd850c41b5d258f6f6a5 (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-20 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / To understand how new viruses arise in agriculture, the interface zones between native systems and cultivated areas become an interesting object of study. The small number of studies focused on the detection of viruses, mainly with RNA genomes, in cerrado tree species in the interface zones is due to the difficulty of extracting quality nucleic acids for the necessary analysis. In the case of DNA viruses, such as begomovirus, to date there have been no reports on tree species in this type of vegetation. Begomovirus are among the main pathogens in different cultures in Brazil. However, in soybeans, one of the main crops in the country, these viruses are not among the most important pathogens for the culture, however, it is of great importance to identify different hosts of these viruses and in which environments they occur to know their diversity. The objective of this study was to detect and identify begomovirus in cerrado native trees and cultivated soybean plants near native vegetation areas, as well as to establish an efficient RNA extraction protocol for cerrado species in order to facilitate future related research with these plants. For begomovirus detection, samples of 30 tree species were collected from two areas of cerrado, in soybean the sampling was carried out in three areas of the Escola de Agronomia da Universidade Federal de Goiás - Regional Goiânia - planted with different cultivars. For all samples, DNA extraction was performed using a modified CTAB method and the detection was done by means of PCR using primers PAL1v1978 and PAR1c496. For the extraction of RNA, four methods were tested for Xylopia aromatica and Piper arboreum: TRIzol® reagent (method 1), TRIzol® reagent with modifications (method 2) and two methods using CTAB buffer (methods 3 and 4) that present differences in buffers composition in each method. The one that presented the best results was tested to obtain purified RNA of five cerrado tree species. Method 4 was chosen because of its best absorbance ratio (A260 / A280) when compared to the other methods. The RT-PCR of the RNA extracted from five species of cerrado areas showed good results after RNA extraction performed by method 4, qualifying this method as appropriate to obtain quality RNA for the molecular analysis of cerrado species. In the detection of begomovirus in 30 tree species of the cerrado, only Cardiopetalum calophyllum was positive. This is the first report of begomovirus in Brazilian cerrado tree species. The presence of two begomovirus species, Sida micrantha mosaic virus (SimMV) and Tomato severe rugose virus (ToSRV), were detected in one of the areas in the soybean sampled in the areas of the Escola de Agronomia. The ToSRV species was not previously reported in soybean and presents great potential to become an important pathogen for this crop and also for uncultivated plants, since this virus causes great losses in other crops, mainly tomato, and it has been demonstrated that its host range has increased in recent years. / Para se entender como novos vírus surgem na agricultura, as zonas de interface entre os sistemas nativos e as áreas cultivadas tornam-se um interessante objeto de estudo. O pequeno número de estudos focados na detecção de vírus, principalmente de RNA, em espécies arbóreas do cerrado nas zonas de interface é devido à dificuldade de extração de ácidos nucleicos de qualidade para análises necessárias. No caso dos vírus de DNA, como os begomovírus, até o momento não haviam relatos em espécies arbóreas nesse tipo de vegetação. Os begomovírus estão entre os principais patógenos em diferentes culturas no Brasil, entretanto em soja, uma das principais culturas do país, esses vírus não estão entre os patógenos mais importantes para cultura, porém, é de grande importância identificar diferentes hospedeiras desses vírus e em que ambientes ocorrem para conhecer sua diversidade. Assim, o objetivo geral do trabalho foi detectar e identificar begomovírus em espécies arbóreas nativas do cerrado e em plantas de soja cultivadas próximas a áreas de vegetação nativa e também estabelecer protocolo de extração de RNA eficiente para espécies do cerrado com intuito de facilitar pesquisas futuras relacionadas com essas plantas. Para detecção de begomovírus, amostras de 30 espécies arbóreas foram coletadas de duas áreas de cerrado, em soja a amostragem foi realizada em três áreas da Escola de Agronomia da Universidade Federal de Goiás – Regional Goiânia – plantadas com diferentes cultivares. Para todas as amostras foi realizada a extração de DNA através de um método CTAB (Brometo de cetil trimetil amônio) modificado e a detecção foi feita por meio de PCR (Reação em cadeia da polimerase) utilizando os primers PAL1v1978 e PAR1c496. Para extração de RNA foram testados quatro métodos a partir de folhas de Xylopia aromatica e Piper arboreum: reagente TRIzol® (método 1), reagente TRIzol® com modificações (método 2) e dois métodos utilizando tampão CTAB (métodos 3 e 4) que possuem diferenças nos tampões utilizados em cada método. O que apresentou os melhores resultados foi testado para a obtenção de RNA purificado de cinco espécies arbóreas de cerrado. O método 4 foi escolhido devido aos seus melhores resultados na razão de absorbância (A260 / A280) quando comparado aos outros métodos. A RT-PCR do RNA extraído de cinco espécies de áreas de cerrado mostrou bons resultados após a extração de RNA realizada pelo método 4, qualificando este método como apropriado para obtenção de RNA de qualidade para análise molecular de espécies do cerrado. Na detecção de begomovírus em 30 espécies arbóreas do cerrado, apenas Cardiopetalum calophyllum foi positiva. Este é o primeiro relato de begomovírus em espécie arbórea do cerrado brasileiro. Na soja, as plantas sintomáticas amostradas nas áreas da Escola de Agronomia foram positivas, sendo que em uma das áreas foi detectada a presença de duas espécies de begomovírus: Sida micrantha mosaic virus (SimMV) e Tomato severe rugose virus (ToSRV). A espécie ToSRV não foi relatada anteriormente em soja e apresenta grande potencial para se tornar um importante patógeno para essa cultura e também para plantas não cultivadas, já que esse vírus causa grandes perdas em outras culturas, principalmente tomateiro, e tem sido demonstrado que sua gama de hospedeiras tem aumentado nos últimos anos.

The zoonosis Q fever is caused by the obligate intracellular bacterium Coxiella burnetii. Besides the main transmission route via inhalation of contaminated aerosols, ticks are discussed as vectors since the first isolation of the pathogen from a Dermacentor andersonii tick. The rare detection of C. burnetii in ticks and the difficult differentiation of C. burnetii from Coxiella-like endosymbionts (CLEs) are questioning the relevance of ticks in the epidemiology of Q fever. In this review, literature databases were systematically searched for recent prevalence studies concerning C. burnetii in ticks in Europe and experimental studies evaluating the vector competence of tick species. A total of 72 prevalence studies were included and evaluated regarding DNA detection methods and collectionmethods, country, and tested tick species. Specimens ofmore than 25 different tick species were collected in 23 European countries. Overall, an average prevalence of 4.8% was determined. However, in half of the studies, no Coxiella-DNA was detected. In Southern European countries, a significantly higher prevalence was observed, possibly related to the abundance of different tick species here, namely Hyalomma spp. and Rhipicephalus spp. In comparison, a similar proportion of studies used ticks sampled by flagging and dragging or tick collection from animals, under 30% of the total tick samples derived from the latter. There was no significant difference in the various target genes used for the molecular test. In most of the studies, no distinction was made between C. burnetii and CLEs. The application of specific detection methods and the confirmation of positive results are crucial to determine the role of ticks in Q fever transmission. Only two studies were available, which assessed the vector competence of ticks for C. burnetii in the last 20 years, demonstrating the need for further research.

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La revue de la littérature montre que la pulpe dentaire est une source utile pour le diagnostic des bactériémies, y compris en paléomicrobiologie. Les précédents travaux en paléomicrobiologie réalisés dans le laboratoire ont tous mis en évidence une amplification possible de courts ou très courts fragments d'ADN bactérien partant de l'hypothèse que l'ADN ancien est fragmenté. Dans le premier travail, le modèle expérimental de dégradation de l'ADN des macrophages murins J774 et de Mycobacterium smegmatis par la chaleur sèche à 90°C a montré une différence statistiquement significative (p < 0.05) entre la vitesse de fragmentation de l'ADN bactérien et eucaryote. Ces résultats suggèrent que les diagnostics paléomicrobiologiques peuvent détecter des fragments plus longs d'ADN bactérien à partir des échantillons anciens. Dans un deuxième travail, un système de détection rapide de 7 agents pathogènes par PCR multiplex en temps réel a été utilisé pour détecter ces pathogènes suspectés à partir de la pulpe dentaire de 1192 dents anciennes collectées dans 12 charniers dont un localisé à Douai (1710 – 1712). Après la détection de Bartonella quintana dans ce charnier, les PCRs en temps réel emboîtées ultra-sensibles et la «PCR suicide» ont été utilisées pour confirmer la présence de Rickettsia prowazekii souche Madrid E génotype B dans 6/55 pulpes dentaires (11%) collectées de 6/21 squelettes (28.6%) de soldats à Douai. Ces résultats supportent l'hypothèse que le typhus a été introduit en Europe par les soldats espagnols au retour des conquêtes en Amérique. / Reviewing the literature shows that dental pulp is a useful source for bacteremic and paleomicrobiological diagnoses. In the first work, an experimental model of DNA degradation of the murine macrophage cell line J774 and Mycobacterium smegmatis by exposure to 90°C dry heat showed a statistically significant difference (p < 0.05) of fragmentation level between bacterial and eukaryotic DNA. These results suggest that paleomicrobiological diagnosis can detect more large fragments of bacterial DNA from ancient buried specimens. In the second work, a system of rapid detection of seven pathogens by multiplex real-time PCR was used for detecting suspected pathogens from dental pulp of 1192 ancient teeth collected from 12 multiple burials including a mass grave in Douai, 1710 – 1712. After the Bartonella quintana detection in this site, real-time nested PCR and ultra-sensitive “suicide PCR” were used to confirm the presence of Rickettsia prowazekii strain Madrid E genotype B in 6/55 dental pulp specimens collected from 6/21 (29%) skeletons of soldiers buried in Douai.These results support the hypothesis that typhus was imported into Europe by Spanish soldiers from America. In the last work, DNA extracted from 5 dental pulp specimens collected from multiple burials at Issoudun, 17th – 18th centuries, was analyzed by pyrosequencing which detected Yersinia pestis sequences in the metagenome. For paleomicrobiology, pyrosequencing is a sensitive technic which can be used as baseline test to detect both suspected and unexpected pathogens from ancient specimens. We named this new approach «paleometagenomics».

Every gas molecule has a unique absorption spectrum that can be captured using optical spectroscopy to identify an unknown sample's composition. Frequency combs systems can provide an extremely broad mid-infrared spectrum that is very useful for molecular detection. A degenerate optical parametric oscillator (OPO) was built to generate the down-converted and shifted frequency comb spectrum. This system utilizes an ultra-short pulse 1.56µm pump laser and a never before used orientation patterned gallium-phosphide crystal. Periodically polled lithium niobate (PPLN), Gallium Arsenide (GaAs) and Gallium Phosphide are all crystals used to accomplish this task. GaP, in comparison to PPLN, has (i) a larger nonlinear coefficient, (ii) much deeper infrared transparency, and (iii) smaller group dispersion – to allow for achieving broad spectral coverage. GaP also has a larger band gap than GaAs; therefore it can still be pumped with a standard telecom C-band laser. An octave-wide spanning frequency comb system was achieved and the characterization of the system is presented. This system is specifically designed to be compact and portable for initial experimental testing in the applications of medical breath analysis and combustion gas investigation.