ABSTRACT: Commercial swab transport systems are used for collection and transporting of fecal and other microbiological samples. This system must maintain viability and contribute to survival of microorganisms during transport to the laboratory. Four swab transport systems have been compared, eSwab, Σ- Transwab and fecalSwab, all three with flocked swabs, and Copan Venturi Transystem with rayon swabs. The study followed the recommendations from the Clinical Laboratory Standard Institute; document M40-A for recovery of Samonella, Shigella, Yersinia and Neisseria gonorrhoeae after storage for 0, 6, 24, 48 and 72 h at room- (22-25°C) and refrigerated (2-8ºC) temperature. A fecal sample has also been inoculated with Salmonella or Shigella to simulate a fecal sample positive for Salmonella or Shigella. Recovery of all strains was higher with eSwab, Σ- Transwab and fecalswab than with Copan Venturi Transystem stored at both temperatures. A heavy growth was observed with all transport systems after storage for 24, 48 and 72 h at room temperature, except for Neisseria gonorrhoeae, and Shigella. The number of CFU for all strains was constant up to 72 h at refrigerated temperature with Copan Venturi Transystem. In the experiment with fecal sample recovery of Salmonella and Shigella was best with fecalSwab at both storage temperatures. ESwab, Σ- Transwab and fecalSwab are equivalent and can be used as an alternative to Copan Venturi Transystem with better survival of enteric pathogens and Neisseria gonorrhoeae. Fecal samples should be refrigerated in order to avoid heavy overgrowth of fecal flora.

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No. of bitstreams: 2 Dissertação - Fernanda Alves de Brito e Cardoso - 2010.pdf: 3862835 bytes, checksum: bac9d567036b30752cd19dc0042891c0 (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2010-12-14 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / The introduction of the nucleic acid amplification tests (NAATs) was a major breakthrough in the screening for the sexually transmitted diseases (STD) caused by Chlamydia trachomatis and Neisseria gonorrhoeae because they are highly sensitive and they can be used with noninvasive specimens, such as urine. The use of urine has made it far easier to test asymptomatic individuals and has also made it possible to perform epidemiological studies in places other than clinical settings. Many studies have shown also that vaginal swab can be used for detection of both infections, however, just the NAAT Aptima Combo 2 has been cleared by Food and Drug Administration for this specimen use. In Brazil, the most widely used NAAT for the diagnosis of chlamydia and neisseria is the kit Amplicor CT/NG (Roche) and, up to date, there isn’t any study which evaluates the use of vaginal swabs. Objectives: To evaluate the performance of the kit AMPLICOR CT/NG (Roche) in the diagnosis of C. trachomatis and N. gonorrhoeae using urine, endocervical and vaginal swabs and to analyze the agreement of results between the different biological specimens. Methods: The target population was sexually active adolescents and young women between 15 and 24 years from Inhumas, Goias. Socio-demographic and sexual behavior were obtained through a face-to-face interview. The diagnosis was performed by PCR using the AMPLICOR CT/NG (Roche) assay in urine, vaginal swab (VS) and endocervical swab (ES) specimens. For the performance evaluation were calculated the sensitivity, specificity, positive predictive value and negative predictive value. The kappa coefficient was calculated to assess agreement between the samples. It was considered a true-positive result when at least two of three biological samples from the same patient were positive for chlamydia and/or gonococcus. Results:Among the 428 participants the mean age was 19,4 years. The three biological specimens were collected from 309 adolescents (72.2%). Among these, the prevalence rates were 8.7% (IC95% 5,8-12,4) for C. trachomatis and 2.3% (IC95% 0,9-4,6) for N. gonorrhoeae.For chlamydia the sensitivities observed with the different samples were above 80% and specificities exceeding 97% with positive predictive values (PPV) between 78.8% and 84.6% and negative predictive values (VPNs) >98%. For the gonococcus the sensitivities were 42.8% for urine, 71.4% for ES and 100% for VS with specificities >96% for the three samples. The two types of swab showed low PPVs for gonococcus (≈40%) and urine showed PPV of 100%. VPNs were >98%. The agreement of results between specimens was around 94% for the detection of both infections. However, the values of kappa (κ) coefficient ranged from 0.68 to 0.73 for chlamydia, which means substantial agreement between samples. For gonococcal infection, the agreement was slight or fair with κ coefficients ranging from 0.13 to 0.33. Conclusions:The performances of the specimens and the κ values suggest that the vaginal swab appears to be equivalent to urine and endocervical swab for detection of chlamydia and may be suitable for screening studies. The three samples showed different performance in the detection of gonococcus and did not present good agreement of results, suggesting that they are not equivalent in the diagnosis of this infection with the PCR kit used. / A introdução dos testes de amplificação de ácidos nucléicos (NAATs) foi um grande avanço no rastreamento das doenças sexualmente transmissíveis (DST) causadas por Chlamydia trachomatis e Neisseria gonorrhoeae, pois apresentam alta sensibilidade e permitem a utilização de amostras de coleta não invasiva, como a urina. O uso da urina facilitou o diagnóstico em indivíduos assintomáticos e possibilitou a realização de estudos epidemiológicos em locais fora do ambiente clínico. Vários estudos mostram que o swab vaginal também pode ser utilizado na detecção de ambas as infecções, porém a Food and Drug Administration restringe o seu uso apenas pelo NAAT Aptima Combo 2. No Brasil, o NAAT mais utilizado no diagnóstico de clamídia e neisseria é o kit Amplicor CT/NG (Roche) e, até o momento, nenhum estudo avaliou a utilização do swab vaginal. Objetivos:Avaliar o desempenho do kit AMPLICOR CT\NG (Roche) no diagnóstico de C. trachomatis e N. gonorrhoeae empregando urina, swabs endocervical e vaginal e analisar a concordância de resultados entre as diferentes amostras biológicas. Métodos: A população alvo foi constituída de adolescentes e jovens sexualmente ativas, com idade entre 15 e 24 anos, residentes em Inhumas, Goiás. Os dados sócio-demográficos e de comportamento sexual foram obtidos através de entrevista. O diagnóstico foi realizado empregando o kit Amplicor CT/NG (Roche) em amostras de urina, swab endocervical (SE) e swab vaginal (SV). Para avaliação do desempenho foram calculadas a sensibilidade, especificidade, valor preditivo positivo e negativo dos testes. O coeficiente kappa foi calculado para avaliar a concordância entre as amostras. Considerou-se um resultado como verdadeiro-positivo quando pelo menos duas das três amostras biológicas da mesma paciente fossem positivas para clamídia e/ou gonococo. Resultados: Entre as 428 participantes a média de idade foi de 19,4 anos. Os três espécimes biológicos foram coletados de 309 adolescentes (72,2%). Entre estas, as prevalências foram de 8,7% (IC95% 5,8-12,4)para C. trachomatis e de 2,3% (IC95% 0,9-4,6) para N. gonorrhoeae. Para clamídia as sensibilidades observadas com as diferentes amostras foram superiores a 80% e as especificidades superiores a 97%, com valores preditivos positivos (VPPs) entre 78,8% e 84,6% e valores preditivos negativos (VPNs) >98%. Para o gonococo as sensibilidades foram de 42,8% na urina, 71,4% no SE e de 100% no SV com especificidades >96% nas três amostras. Os dois tipos de swab apresentaram baixos VPPs para o gonococo (≈ 40%) e a urina apresentou VPP de 100%. Os VPNs foram >98%. A concordância de resultados da PCR empregando as diferentes amostras foi de cerca de 94% para ambas as infecções. Entretanto, os valores do coeficiente kappa (κ) variaram de 0,68 a 0,73 para clamídia, o que significa concordância substancial entre as amostras. Para a infecção gonocócica, a concordância foi fraca ou razoável com valores de κ variando de 0,13 a 0,33. Conclusões: Os desempenhos das amostras e os valores do κ sugerem que o swab vaginal parece ser equivalente à urina e ao swab endocervical na detecção da clamídia podendo ser recomendado para estudos de triagem. As três amostras diferiram quanto ao desempenho na detecção da infecção gonocócica e não apresentaram boa concordância de resultados sugerindo que não são equivalentes no diagnóstico desta infecção com o kit de PCR utilizado.

Fundamentals of forensic deoxyribonucleic acid (DNA) typing for sexual assault samples require the successful application of a differential extraction. Gynecological swabs containing vaginal epithelial cells and sperm cells are commonly encountered in forensic casework. A priority in sexual assault casework is the identity of the male contributor and in order to identify the male contributor, separation of the vaginal epithelial cells and sperm cells must be achieved. Two considerations when separating the different cell-types from a substrate are cellular elution and purity of the DNA fractions. Maximizing DNA yield is directly proportional to the number of cells eluted off of the swab and the extraction method utilized. The trypsin-ZyGEM extraction method has shown results of increased DNA recovery on liquid mixture samples compared with the standard differential extraction, which uses proteinase K and dithiothreitol (DTT). The trypsin-ZyGEM differential extraction protocol calls for the use of proteases EA1, incorporated in the forensicGEM extraction kit, and trypsin, a serine proteinase that has been discovered to effectively digest the DNA bound protamines in sperm cells. The trypsin-ZyGEM protocol follows a similar preferential lysis procedure to the standard differential extraction; however, everything is incorporated into one tube, therefore, minimizing loss of DNA from transfer techniques in the trypsin-ZyGEM protocol. Initially, epithelial cells are lysed using the forensicGEM enzyme and removed from solution after centrifugation. Samples are subsequently treated with trypsin, digesting sperm cells. The resultant solution contains the sperm cell DNA and other cell components. The standard differential extraction commonly uses a Qiagen silica membrane column to purify DNA away from cellular proteins and other contaminants, ensuring successful downstream DNA testing with the polymerase chain reaction (PCR). However, treatment with the trypsin-ZyGEM method is followed by a second incubation with forensicGEM after sperm cells are lysed with trypsin. Extracted samples can be quantified and followed through to DNA typing. Expanding previous studies and optimizing conditions of the dual enzyme approach were explored in this study for semen samples on cotton swabs. When comparing DNA yields of extracted samples, tris-ethylenediaminetetraacetic acid (TE) buffer recovered more cells from the cotton swabs than phosphate buffered saline (PBS) buffer and Buffer ATL, used in the Qiagen QIAamp® DNA Investigator Kit. Relative to DNA recovery of the standard Qiagen differential protocol, the trypsin-ZyGEM method on the cotton swab samples appeared subpar and could be attributed to ineffective cellular elution. Additionally, carryover DNA into the non-sperm cell fraction was exhibited. Procedures with Accumax, a cell detachment solution, were implemented in an attempt to elute more cells. The resulting DNA yields were significantly lower in the presence of Accumax. Contrastingly, incorporating trypsin directly into the elution TE buffer exhibited significant increases in DNA recovery. The direct lysis of sperm cells on the swabs, rather than the two-phase method of eluting the cells from the swab and subsequently extracting the DNA, proved to be much more effective. The swab remains from the elution and subsequent trypsin-ZyGEM method were re-extracted using the direct lysis method. Whilst comparing DNA yields, it was discovered that approximately 90% of the cellular DNA was retained on the swab after the two-phase extraction method was performed. Experiments utilizing direct lysis with the trypsin-ZyGEM method, the standard Qiagen differential protocol, and the trypsin lysis followed by Qiagen extraction were performed on swab samples comprised of different semen concentrations resulting DNA yields and short tandem repeat (STR) DNA profiles were compared. Results obtained indicated that the trypsin-ZyGEM method provided substantially larger DNA recovery yields and provided full STR profiles to a target mass of 0.0625 ng and average peak height ratios above 60%. Successful implementation of this extraction procedure will require further studies with the addition of epithelial cells on the swab samples to mimic vaginal swab mixture samples. These samples will help to determine purity of the DNA fractions and effects of epithelial cells on the trypsin-ZyGEM protocol. / 2017-11-03T00:00:00Z

Master of Science / Food Science Institute / Daniel Y.C. Fung / There are many different environmental sampling methods that are currently used in the industry. They include swab, sponge, flocked swab, direct agar contact, and M-Vac. Several studies have been conducted to determine the benefits and drawbacks of each method. Sampling methods utilized in this study were the swab, flocked swab, and M-Vac. Three surfaces were utilized in this study: ultra high density polypropylene, 304 stainless steel with a 2B finish, and 304 stainless steel with a 2B finish and a buffed surface. Surfaces sampled were 100 cm2. Prior to inoculation, surfaces were autoclaved for 15 min at 121 °C for sterilization. Surfaces were inoculated by either Listeria monocytogenes or Escherichia coli O157:H7 at a concentration of 9 log10 CFU/ml by painting the inoculum onto the surface with a sterilized paintbrush. Brushes were dipped in inoculum for 2 sec before painting from left to right once and then from up to down once. Brushes were redipped for 2 sec and the painting step was repeated. The same brush was used for all E. coli O157:H7 samples and a different brush was used for all L. monocytogenes samples. Then, the surfaces were allowed to dry for 30 min before sampling took place. Listeria monocytogenes samples were appropriately diluted and plated in duplicate onto Tryptic Soy Agar (TSA) and Modified Oxford Media (MOX). Escherichia coli O157:H7 samples were properly diluted and plated in duplicate onto TSA and MacConkey Sorbital Agar (MSA). After plating, dry surfaces were stained using LIVE/DEAD® BacLight™ Bacterial Viability Kit. The Zeiss LSM 5 Pascal confocal laser scanning electron microscope was used for microscopy images and photographs. Six 1 mm by 1 mm random and representative images were taken of each surface. Viable cell count results show that the sponge sampling method, in general, recovered a higher number of microorganisms. The swab was normally shown to recover the least number of microorganisms. When examining the microscopy images it can be concluded that biofilms are more easily formed with L. monocytogenes than E. coli O157:H7. Imaging also allowed for a visual representation of the remaining organisms that made it appear as if there was actually more bacteria recovery when the M-Vac sampling method was employed than when the sponge method was utilized.

Os médicos veterinários que trabalham com répteis frequentemente são indagados pelos proprietários sobre os tipos de doenças que estes animais podem transmitir, bem como sobre as medidas profiláticas que devem ser implementadas para prevenir a transmissão de doenças. Desta forma, o conhecimento sobre os patógenos que estes animais albergam passa a ser importante para orientação dos proprietários quanto aos cuidados adequados que devem ser adotados com estes animais. Os microrganismos que compõem a microbiota podem se tornar patogênicos para seus hospedeiros quando os mesmos encontram-se debilitados, bem como a eliminação contínua destes microrganismos (pelas fezes, por exemplo) por répteis aparentemente saudáveis ou mesmo doentes, pode representar um importante problema para pessoas que tenham contato com eles. Crianças, idosos e indivíduos imunossuprimidos ou imunocomprometidos são bastante suscetíveis às infecções após manipulação de répteis criados como pet. Considerando-se que os répteis participam de forma crescente do mercado de animais criados como pet, suas características microbiológicas devem ser pesquisadas, visando evitar que eles adoeçam ou venham a óbito devido à ocorrência de doenças infecciosas e não transmitam zoonoses para aqueles que os manipulam. Este trabalho teve como objetivos o estudo da microbiota bacteriana e fúngica presente na cloaca de jabutis (Geochelone carbonária) criados em domicílio e análise do potencial risco a saúde humana. Foram realizados exames microbiológicos de swabs de cloaca de 100 jabutis-piranga visando a pesquisa de bactérias aeróbias, anaeróbias facultativas e fungos filamentosos e leveduras. Foram isolados 18 gêneros de bactérias, 06 gêneros de leveduras e 03 gêneros de fungos filamentosos. Os gêneros de microrganismos isolados com maior freqüência foram: Escherichia sp. (67%), Klebsiella spp. (54%), Bacillus spp. (42%), Candida spp. (42%), Citrobacter spp. (33%), Staphylococcus spp. (29%), Corynebacterium spp. (15%) e Aeromonas spp. (15%), dentre outros com menor freqüência. A freqüência de isolamentos de E. coli (67%) foi semelhante à de Klebsiella spp. (54%) e maior (P<0,05) do que as frequências de isolamentos de todos os outros microrganismos. Todos os microrganismos isolados podem representar risco para a saúde humana, devendo-se atentar para os cuidados com répteis criados como animais pet, particularmente quanto aos aspectos de higiene relacionados aos mesmos, visando assim a prevenção destes riscos. / Veterinarians who work with reptiles are frequently asked by owners about diseases that these animals can transmit, as well about the preventative measures that should be taken to prevent the transmission of diseases. Therefore, knowledge about pathogens that inhabit these animals and represent a potential zoonotic risk are very important in order to allow veterinarians to give proper recommendations about husbandry and preventative methods. Children, elderly people, and imunocompromised individuals are increasingly susceptible to infections after reptile pet manipulation. The microorganisms which form the microbiota can become pathogenic for their host if the host is debilitated. Transmission of these microorganisms from healthy or sick reptiles can be hazardous for people that have contact with them. Considering that reptiles are increasing obtained as pet, their microbiota should be investigated in order to prevent transmission of disease to people who manipulate them. The purposes of this paper were to evaluate the bacterial and fungal microbiota in the companion tortoise (Geochelone carbonaria) and to analyze the potential public health risk. One hundred samples of feaces from cloaca were obtained from jabutis-piranga and microbiological examinations were made for the presence of aerobic and facultative anaerobic bacteria, filamentous fungi and yeasts. Eighteen genus of bacteria, six genus of yeasts, and three genus of fungi were identified. The most frequently isolated genus were: Escherichia sp. (67%), Klebsiella spp. (54%), Bacillus spp. (42%), Candida spp. (42%), Citrobacter spp. (33%), Staphylococcus spp. (29%), Corynebacterium spp. (15%) and Aeromonas spp. (15%). The number of isolated E. coli (67%) was similar to that of Klebsiella sp. (54%), and was greater than (P<0.05) the total number of other species isolated. All isolated microorganisms present a public health risk. Therefore, care should be taken when obtaining these reptiles as pets, especially with regards to husbandry and proper hygiene in order to prevent the risk of contamination with the microbiota.

Os médicos veterinários que trabalham com répteis frequentemente são indagados pelos proprietários sobre os tipos de doenças que estes animais podem transmitir, bem como sobre as medidas profiláticas que devem ser implementadas para prevenir a transmissão de doenças. Desta forma, o conhecimento sobre os patógenos que estes animais albergam passa a ser importante para orientação dos proprietários quanto aos cuidados adequados que devem ser adotados com estes animais. Os microrganismos que compõem a microbiota podem se tornar patogênicos para seus hospedeiros quando os mesmos encontram-se debilitados, bem como a eliminação contínua destes microrganismos (pelas fezes, por exemplo) por répteis aparentemente saudáveis ou mesmo doentes, pode representar um importante problema para pessoas que tenham contato com eles. Crianças, idosos e indivíduos imunossuprimidos ou imunocomprometidos são bastante suscetíveis às infecções após manipulação de répteis criados como pet. Considerando-se que os répteis participam de forma crescente do mercado de animais criados como pet, suas características microbiológicas devem ser pesquisadas, visando evitar que eles adoeçam ou venham a óbito devido à ocorrência de doenças infecciosas e não transmitam zoonoses para aqueles que os manipulam. Este trabalho teve como objetivos o estudo da microbiota bacteriana e fúngica presente na cloaca de jabutis (Geochelone carbonária) criados em domicílio e análise do potencial risco a saúde humana. Foram realizados exames microbiológicos de swabs de cloaca de 100 jabutis-piranga visando a pesquisa de bactérias aeróbias, anaeróbias facultativas e fungos filamentosos e leveduras. Foram isolados 18 gêneros de bactérias, 06 gêneros de leveduras e 03 gêneros de fungos filamentosos. Os gêneros de microrganismos isolados com maior freqüência foram: Escherichia sp. (67%), Klebsiella spp. (54%), Bacillus spp. (42%), Candida spp. (42%), Citrobacter spp. (33%), Staphylococcus spp. (29%), Corynebacterium spp. (15%) e Aeromonas spp. (15%), dentre outros com menor freqüência. A freqüência de isolamentos de E. coli (67%) foi semelhante à de Klebsiella spp. (54%) e maior (P<0,05) do que as frequências de isolamentos de todos os outros microrganismos. Todos os microrganismos isolados podem representar risco para a saúde humana, devendo-se atentar para os cuidados com répteis criados como animais pet, particularmente quanto aos aspectos de higiene relacionados aos mesmos, visando assim a prevenção destes riscos. / Veterinarians who work with reptiles are frequently asked by owners about diseases that these animals can transmit, as well about the preventative measures that should be taken to prevent the transmission of diseases. Therefore, knowledge about pathogens that inhabit these animals and represent a potential zoonotic risk are very important in order to allow veterinarians to give proper recommendations about husbandry and preventative methods. Children, elderly people, and imunocompromised individuals are increasingly susceptible to infections after reptile pet manipulation. The microorganisms which form the microbiota can become pathogenic for their host if the host is debilitated. Transmission of these microorganisms from healthy or sick reptiles can be hazardous for people that have contact with them. Considering that reptiles are increasing obtained as pet, their microbiota should be investigated in order to prevent transmission of disease to people who manipulate them. The purposes of this paper were to evaluate the bacterial and fungal microbiota in the companion tortoise (Geochelone carbonaria) and to analyze the potential public health risk. One hundred samples of feaces from cloaca were obtained from jabutis-piranga and microbiological examinations were made for the presence of aerobic and facultative anaerobic bacteria, filamentous fungi and yeasts. Eighteen genus of bacteria, six genus of yeasts, and three genus of fungi were identified. The most frequently isolated genus were: Escherichia sp. (67%), Klebsiella spp. (54%), Bacillus spp. (42%), Candida spp. (42%), Citrobacter spp. (33%), Staphylococcus spp. (29%), Corynebacterium spp. (15%) and Aeromonas spp. (15%). The number of isolated E. coli (67%) was similar to that of Klebsiella sp. (54%), and was greater than (P<0.05) the total number of other species isolated. All isolated microorganisms present a public health risk. Therefore, care should be taken when obtaining these reptiles as pets, especially with regards to husbandry and proper hygiene in order to prevent the risk of contamination with the microbiota.

Recovering deoxyribose nucleic acid (DNA) from items of evidence can provide critical information in criminal cases. Since the development of the polymerase chain reaction (PCR) and use of short tandem repeats (STR) to create unique profiles from an individual’s genome1, sampling items of evidence for the presence of DNA has become routine. Biological evidentiary specimens are commonly collected at crime scenes as well as sampled from collected items of interest by using a cotton swab which can then be easily stored and tested as needed. However, even with modern advances in technology and methods, large amounts of DNA can be either lost throughout processing or remain on the substrate used for collection of the sample, such as a cotton swab2. While many of the downstream processes of evidence evaluation have been vastly improved through the use of automated procedures, engineered buffers, and commercially available extraction kits, the front-end procedures are typically more technician dependent; it is an area in which opportunities to fine-tune techniques remain. The most recent change to generalized stain recovery occurred after Sweet et al. achieved an increased efficiency of recovery by using what they referred to as the “double swab technique”. The classic method of collection before this time used a single, wet cotton swab. Based on a need to increase the effective collection of DNA from saliva samples, the double swab method was developed. The classic method was modified by using a second, dry swab to collect remaining moisture deposited by the first, wet swab3. To continue the effort to maximize cellular and DNA recovery from cotton swabs the use of trehalose in the cotton swab wetting solution was explored. D-(+)-Trehalose dihydrate is a naturally occurring disaccharide composed of two alpha glucose molecules. An alpha, alpha-1, 1 bond connects the two molecules which lends high resistance to acid hydrolysis, giving the molecule unique properties. Specifically, these properties allow the compound to maintain stability even during exposure to high temperatures and in acidic conditions4,5. In nature, trehalose can be found in plants and small organisms where it is thought to act as a protectant against fluctuations in moisture and temperature. Synthesis and release of trehalose by lower life forms during stressed states shows protective properties to cellular integrity by inhibiting protein denaturation6. The objectives of this study are to investigate the use of trehalose as an additive in DNA collection processes. The experiments examine the ability of trehalose to increase efficiency of cellular release from cotton swabs during the elution step and compares trehalose to other common buffer additives, bovine serum albumin (BSA) and sodium dodecyl sulfate (SDS), when utilized as a pre-treatment or moistening agent on the cotton swab. Two procedures were developed to test the ability of trehalose to increase efficiency of cellular and DNA release from cotton swabs. The first procedure tested trehalose at 0.2 molar (M) and 1 M concentrations as the incubating solution over1 hour and 18 hour time periods after which the cotton swab was eluted using a spin-x insert and centrifugation. Both eluate and cotton swab were then processed using ZyGEM direct lysis and quantified. Quantification results of the eluate and swabs incubated in trehalose solution were not significantly different from controls. However, it is apparent that a large portion of deposited DNA remained on the swabs even after elution and ZyGEM direct lysis. The second procedure tested trehalose against BSA and SDS as treatments to cotton swabs before DNA collection. A pre-treated group (solution was applied to the swab and dried overnight; DNA was deposited to the dried swab) and a moist group (solution was applied and DNA deposited immediately) were tested after deposition of a set volume of saliva cell suspension. Quantification and amplification results of SDS treated samples indicated significant differences of DNA recovery and average peak height of profiles compared to water and buffer controls. Trehalose samples did have some significant improvement in DNA yield; however, the addition of trehalose as a moistening agent for cotton swabs does not prove to be of forensic value.

<i>Mycoplasma bovis</i> is generally considered the causative pathogen associated with Chronic Pneumonia and Polyarthritis Syndrome (CPPS) in feedlot cattle. However, <i>M. bovis</i> virulence may vary between strains as it is also isolated from asympytomatic cattle. The following study aims to determine the prevalence of <i>M. bovis</i> in the respiratory tract of western Canadian cattle using two sampling methods and at two time points following feedlot entry. Three study groups were sampled. In the first group nasal swabs (NS) and bronchoalveolar lavages (BAL) were taken from 36 clincally healthy cattle at the University of Saskatchewan feedlot at both 14 and 90 days on feed (DOF). In a second experiment, NS were taken from 56 animals upon arrival at a commercial feedlot and one week to three months later upon treatment for respiratory disease. Lung and joint tissue swabs were collected at necropsy from a third group of 19 animals with CPPS clinical pathology originating in 10 different western Canadian feedlots. All samples were selectively cultured for <i>Mycoplasma</i> spp. DNA was extracted from isolated putative <i>Mycoplasma</i> colonies and amplified with universal 16S rRNA gene primers for identification. Amplified Fragment Length Polymorphism (AFLP) was used to genetically differentiate <i>M. bovis</i> positive isolates. More <i>M. bovis</i> was isolated from NS than BAL and <i>M. bovis</i> prevalence increased with DOF in the feedlot in both the University of Saskatchewan and commercial feedlot trials. Three genetically distinct clusters (A, B, and C) were isolated from the necropsy group. Two of these clusters were primarily associated with isolates collected from feedlot cattle and one strain was exclusively found in CPPS-associated mortalities. No significance difference in the prevalence of <i>M. bovis</i> strains was observed between different days on feed or sampling methods. It was concluded that either the difference in disease state is a host dependent outcome, due to a multi-factorial disease complex, or the AFLP assay was not sensitive enough to differentiate strains based on virulence.

<i>Mycoplasma bovis</i> is generally considered the causative pathogen associated with Chronic Pneumonia and Polyarthritis Syndrome (CPPS) in feedlot cattle. However, <i>M. bovis</i> virulence may vary between strains as it is also isolated from asympytomatic cattle. The following study aims to determine the prevalence of <i>M. bovis</i> in the respiratory tract of western Canadian cattle using two sampling methods and at two time points following feedlot entry. Three study groups were sampled. In the first group nasal swabs (NS) and bronchoalveolar lavages (BAL) were taken from 36 clincally healthy cattle at the University of Saskatchewan feedlot at both 14 and 90 days on feed (DOF). In a second experiment, NS were taken from 56 animals upon arrival at a commercial feedlot and one week to three months later upon treatment for respiratory disease. Lung and joint tissue swabs were collected at necropsy from a third group of 19 animals with CPPS clinical pathology originating in 10 different western Canadian feedlots. All samples were selectively cultured for <i>Mycoplasma</i> spp. DNA was extracted from isolated putative <i>Mycoplasma</i> colonies and amplified with universal 16S rRNA gene primers for identification. Amplified Fragment Length Polymorphism (AFLP) was used to genetically differentiate <i>M. bovis</i> positive isolates. More <i>M. bovis</i> was isolated from NS than BAL and <i>M. bovis</i> prevalence increased with DOF in the feedlot in both the University of Saskatchewan and commercial feedlot trials. Three genetically distinct clusters (A, B, and C) were isolated from the necropsy group. Two of these clusters were primarily associated with isolates collected from feedlot cattle and one strain was exclusively found in CPPS-associated mortalities. No significance difference in the prevalence of <i>M. bovis</i> strains was observed between different days on feed or sampling methods. It was concluded that either the difference in disease state is a host dependent outcome, due to a multi-factorial disease complex, or the AFLP assay was not sensitive enough to differentiate strains based on virulence.

Submitted by Amanda Silva (amanda.osilva2@ufpe.br) on 2015-03-13T12:24:03Z No. of bitstreams: 2 TESE Maria Edileuza Felinto de Brito.pdf: 11234347 bytes, checksum: 59279dc5f2f890ab0282f55e2fce09d8 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) / Made available in DSpace on 2015-03-13T12:24:03Z (GMT). No. of bitstreams: 2 TESE Maria Edileuza Felinto de Brito.pdf: 11234347 bytes, checksum: 59279dc5f2f890ab0282f55e2fce09d8 (MD5) license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Previous issue date: 2013 / A leishmaniose tegumentar americana (LTA) é uma doença complexa com características clínicas e epidemiológicas que podem variar em cada região. Devido ao seu caráter focal é imprescindível a compreensão da dinâmica da doença em nível local assim como a disponibilidade de métodos de diagnóstico efetivos para a implementação de estratégias de controle e prevenção. A definição de caso é feita através de exames clínicos associados aos dados epidemiológicos e exames laboratoriais. O diagnóstico clínico da LTA é difícil, por assemelhar-se a outras doenças dermatológicas. A confirmação laboratorial baseia-se em análises parasitológicas, imunológicas e moleculares. Um dos pontos críticos do diagnóstico é a coleta das amostras para análise, que emprega métodos invasivos, de difícil operacionalização e desconfortáveis para os pacientes. O estudo propõe avaliar um método de coleta de amostras não invasivo em pacientes de área endêmica em Pernambuco, Brasil para o diagnóstico da LTA. A análise da literatura mostra que a doença é endêmica em todas as regiões geográficas do Estado com maior prevalência na Mata Atlântica ocorrendo surtos esporádicos ocasionais nessa região e no Agreste, disseminando-se para outras áreas e com o aumento da incidência em todo o estado; o principal agente etiológico da LTA em Pernambuco é a Leishmania (Viannia) braziliensis; diversas espécies de flebotomíneos vetores são amplamente distribuídas em todo o território do estado, predominando Lutzomyia whitmani no intra e peridomicílio e L. complexa, L. choti e L. sordelli em remanescentes florestais; roedores silvestres e comensais participam no ciclo de manutenção e transmissão da LTA em Pernambuco. De transmissão vetorial, a LTA também pode ser adquirida como acidente ocupacional pela contaminação com material das lesões dos pacientes e manejo de animais e/ou cultura no laboratório. Dois casos de acidentes ocupacionais por Leishmania spp. foram diagnosticados através de PCR a partir de amostras coletadas por swab, método não invasivo. Estas ocorrências comprovam o potencial de risco em ambiente de laboratório e campo, com a necessidade de rígidos procedimentos de biossegurança nas rotinas diárias. Comparando os resultados das análises em amostras de material de lesões cutâneas de pacientes foi observado que apesar de considerado padrão ouro, apenas 70,6% dos pacientes foram positivos pelo método direto. Pela técnica de PCR tendo como alvo kDNA de minicírculos de Leishmania (Viannia) foi observada uma positividade de 79,5%. A análise estatística para comparação do desempenho das técnicas de coleta de amostras pareadas por swab e biópsia para o diagnóstico da LTA por PCR revelou que a coleta por swab é uma alternativa válida. Os resultados permitem concluir que pela simplicidade da coleta de amostra por swab, associada à alta sensibilidade e especificidade da PCR, o procedimento constitui uma importante contribuição para aperfeiçoamento do diagnóstico e para o sucesso do controle da LTA em áreas endêmicas.