Introducing NGS to the clinical microbiology laboratory: an update

One of the most eagerly anticipated presentations to the British Society for Microbial Technology (BSMT) Annual Scientific Conference 2020 was to have been by Adela Medina, describing work using Oxford Nanopore sequencing directly on clinical specimens from patients to identify rapidly any bacteria, fungi or DNA viruses present. Over the past five or so years, there has been increasing mention of DNA sequencing in clinical microbiology laboratories. The introduction of next-generation sequencing (NGS) in clinical microbiology laboratories has increasingly been advocated as a practical approach for the diagnosis of infectious disease as well as tracking outbreaks, typing organisms, and in metagenomic studies.

The ability to rapidly detect non-culturable bacteria and those that take a long time to grow using routine methods in a single test is highly attractive. Improvements in the accuracy of technology and decreasing costs make it an increasingly attractive proposition. Up until now, however, there have been two major obstacles – capital costs remain high, and the need for bioinformatics expertise. These factors have limited the introduction of the technology into the diagnostic clinical microbiology laboratory. Adela Medina’s work used the Oxford Nanopore MinION system, which is a USB-sized cell connected to a laptop or desktop computer. There is even a version that connects to a mobile phone. The use of a disposable cell containing hundreds of pores through which the DNA strands migrate avoids the need for the initial high capital expenditure, which has been one of the two major barriers to adoption.

The advantage of NGS compared with other molecular techniques like 16S polymerase chain reaction (PCR) targeted at a specific gene is that it allows the sequencing and identification of numerous pathogens in a single run and it is ‘agnostic’ (ie there is no need to target specific pathogens, for example by primer selection in advance).