Mitigating PCR /Amplicon Contamination in a High Risk High Burden Mycobacterial Reference Laboratory in a Resource Limited Setting

Abstract

Background: Nucleic acid amplification techniques have become important machineries in the diagnosis of several diseases in clinical laboratories. PCR contamination/Amplicon Contamination leading to false positivity remains a major concern in these laboratories. Prevention of these contaminations in establishing these Molecular Biology Laboratories has been very crucial over the years. Though closed system PCRs has substantial reduction in the PCR contamination rates the conventional probe based hybridization methods continues to show occurrence of contamination for various reasons. The Study involved checking the crucial parameters as well as the probable candidates of causing the contamination at a high burden setting. Bringing out the most effective interventions in controlling PCR contaminations for future endeavors stood as a priority. The study explored the efficacies of different sets of interventions contributed in the process of reducing the contaminants.Materials and Methods: The detection of the contaminating PCR products or amplicons or contaminating organism is done by the Genotype MTBDR plus V2 kits (Hains Life Sciences) based on DNA strip technologyResults: The pre and post cleaning as well as cleaning of the working surfaces was able to bring down the mean contamination percentage by 36.5%. The combined effect of the cleaning of the work surfaces, the automated pipetting devices and the AC machines along with it filters were able bring down the mean contamination percentage to 53.5% reducing the rate contamination nearly to between 94.6% (mean percentage contamination was 56.5% at the control run).