Call for a quality standard for sequence-based assays in clinical microbiology: necessity for quality assessment of sequences used in microbial identification and typing.

摘要

Subsequent to the early days of radioisotope sequencing, DNA sequencing technologies have evolved rapidly, giving rise to techniques that are more sensitive and rapid and provide longer sequence reads. These incremental improvements in technology and in the automation of modern sequencing platforms have resulted in applications of DNA sequencing across virtually all biological science disciplines. In microbiology, this has led to a significant increase in the number of available complete microbial and viral genome sequences and, consequently, to increasing use of DNA sequence analysis in clinical microbiology laboratories, where the results may be influential on consequent patient management. The evolution of Sanger-based technologies is now being complemented by the revolution of second- and third-generation sequencing technologies that, potentially, could provide whole-microbial-genome analysis at the clinical bench and have a greater, more direct impact on patient and outbreak management. While the technologies have continued to evolve, common standards for the description of DNA sequence data quality still do not exist. Further, utilization of DNA sequence data requires comparison with other similar sequence data held in private or public databases. Similarly, there is no process for the accreditation of these databases and the analyses that they provide to ensure that they are fit for purpose. We strongly urge that action is required to address this.