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Molecular testing is an ever-evolving world for the most common infectious diseases, including respiratory and gastrointestinal pathogens detection. While microbiology laboratories are pivotal in the detection and identification of infectious diseases, the microbiology lab environment is rapidly changing. Conventional methods are being reevaluated as innovative test methodologies emerge. The challenges for conventional methods include inability to detect some coinfections, delay time to results, and false negatives due to poor sensitivity. A molecular approach that uses the PCR technology has the potential to increase the specificity and sensitivity of pathogen detection in polymicrobial samples.