Practical issues in implementing genomics in routine diagnostic microbiology

Practical issues in implementing genomics in routine diagnostic microbiology

Next generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed. As the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, quality control issues for using WGS in microbiology, including the importance of proficiency testing, are discussed. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred will be addressed.