Résumé
Avaliou-se a circulação de Campylobacter spp. em uma criação de primatas neotropicais macacos-de-cheiro (Saimiri spp.), clinicamente saudáveis, utilizados em investigações biomédicas. A análise foi feita no decorrer de sete anos não consecutivos, de 1995 a 1999, 2002 e 2003. Os resultados revelaram um maior índice de positividade no ano de 1996, em contraste com a ausência do agente em 2003. Os dados sugerem que as alterações realizadas no manejo animal, ao longo deste estudo, foram eficazes para a eliminação do Campylobacter spp. na criação de macacos-de-cheiro, levando os animais a uma melhor qualidade de vida e, consequentemente, obtendo-se um melhor produto para fins de pesquisas.
The circulation of Campylobacter spp. in a breeding colony of clinically healthy neotropical primates squirrel monkeys (Saimiri spp.) used in biomedical investigation was evaluated. Analyses were undertaken during seven non-consecutive years: 1995 to 1999, 2002 and 2003. Results revealed a higher rate of positivity in 1996, in contrast to the absence of the agent in 2003. The data suggest that the changes made in the animal management during this study were effective for the Campylobacter spp. elimination of the squirrel monkeys breeding colony, leading to a better quality of life and, hence, resulting in a better animal for research.
Résumé
The production of nucleic acid sequences by automatic DNA sequencer machines is always associated with some base-calling errors. In order to produce a high-quality DNA sequence from a molecule of interest, researchers normally sequence the same sample many times. Considering base-calling errors as rare events, re-sequencing the same molecule and assembling the reads produced are frequently thought to be a good way to generate reliable sequences. However, a relevant question on this issue is: how many times the sample needs to be re-sequenced to minimize costs and achieve a high-fidelity sequence? We examined how both the number of re-sequenced reads and PHRED trimming parameters affect the accuracy and size of final consensus sequences. Hundreds of single-pool reaction pUC18 reads were generated and assembled into consensus sequences with CAP3 software. Using local alignment against the published pUC18 cloning vector sequence, the position and number of errors in the consensus were identified and stored in MySQL databases. Stringent PHRED trimming parameters proved to be efficient for the reduction of errors; however, this procedure also decreased consensus size. Moreover, re-sequencing did not have a clear effect on the removal of consensus errors, although it was able to slightly increase consensus.