ABSTRACT
Objective To compare three methods for the extraction of mycobacterial DNA.Methods Two commercial DNA extraction kits and an ordinary freeze-thawing method were used to extract DNA from the pure suspensions of three species of Mycobacteria (M.tuberculosis,M.leprae and M.smegmatis) at different densities (1 × 10 to 1 × 105 cells/ml),simulated clinical specimens containing different concentrations of mycobacterial cells (1 × 10 to 1 × 104 cells/ml).The purity and concentration of the extracted DNA were evaluated.Then,PCR was performed to amplify the 16S rRNA region of Mycobacteria.The performance of the three methods was compared by the purity and concentration of extracted DNA as well as the results of PCR.Further more,76 clinical skin specimens suspected to be infected with Mycobacteria were used to further validate the performance of these methods.Results All the extracted DNA samples could be detected by PCR.The highest purity of DNA was obtained by the kit A,followed sequentially by the freeze-thawing method and the kit B.When pure suspensions were used,the detection limit was consistently 1 × 102 cells/ml for all the three methods.With simulated specimens,the detection rate was consistently 100％ for all the three methods at the concentration of 1 × 103 cells/ml,60％ (12/20),55％ (11/20) and 55％ (11/20) for the kit A,kit B and freeze-thawing method respectively at the concentration of 1 × 102 cells/ml.The analysis of clinical specimens showed that the kit B could be used to extract DNA from paraffin-embedded specimens,with the detection rate similar to that of kit A and freeze-thawing method.Conclusions The kit A could rapidly yield high-quality genomic DNA of Mycobacteria by repeated cleaning of columns,and may serve as the optimal method for scientific and clinical studies,and the kit B is suitable for extracting mycobacterial DNA from fresh tissue specimens besides paraffin-embedded specimens.
ABSTRACT
Asymptomatic Plasmodium infection is a new challenge for public health in the American region. The polymerase chain reaction (PCR) is the best method for diagnosing subpatent parasitemias. In endemic areas, blood collection is hampered by geographical distances and deficient transport and storage conditions of the samples. Because DNA extraction from blood collected on filter paper is an efficient method for molecular studies in high parasitemic individuals, we investigated whether the technique could be an alternative for Plasmodium diagnosis among asymptomatic and pauciparasitemic subjects. In this report we compared three different methods (Chelex®-saponin, methanol and TRIS-EDTA) of DNA extraction from blood collected on filter paper from asymptomatic Plasmodium-infected individuals. Polymerase chain reaction assays for detection of Plasmodium species showed the best results when the Chelex®-saponin method was used. Even though the sensitivity of detection was approximately 66% and 31% for P. falciparum and P. vivax, respectively, this method did not show the effectiveness in DNA extraction required for molecular diagnosis of Plasmodium. The development of better methods for extracting DNA from blood collected on filter paper is important for the diagnosis of subpatent malarial infections in remote areas and would contribute to establishing the epidemiology of this form of infection.
Infecção assintomática por Plasmodium é um novo desafio para a saúde pública no Brasil. A reação em cadeia da polimerase (PCR) é o melhor método para detectar baixas parasitemias presentes em pacientes com infecção assintomática. Nas áreas endêmicas, a coleta de sangue total é dificultada pela distancia geográfica, transporte e adequada armazenagem das amostras. A coleta de sangue em papel de filtro pode ser uma alternativa nessas áreas de difícil acesso. Neste estudo foram comparados três diferentes métodos de extração de ADN a partir de papel de filtro usando como controle extração a partir de sangue total. O protocolo Chelex®-Saponina foi o que obteve o melhor resultado quando comparado com os outros três protocolos. No entanto a sensibilidade foi de 66,7% para o P. falciparum e 31,6% para o P. vivax. Conclui-se que em caso de infecção assintomática o papel de filtro não é ainda uma boa alternativa para coleta de amostras.