“Metagenomic disruption of the diagnostic microbiology lab”

I am 50 now, so I only have another 25-30 years of my working career left. So much to do in so little time!

I often wonder what the microbiology lab will look like on my last day at work. (I have posted on this before). Possibly a more interesting question is how I will look on my last day at work…

I am interested in how metagenomic approaches are going to disrupt the diagnostic microbiology lab and whether this will eventually become a mainstay of microbiological diagnosis, and eventually consign the agar plate to the museum.

The strangely named “shotgun metagenomic sequencing” involves sequencing all genes present in a clinical sample thus allowing identification of pathogens, and (as a bonus) their associated resistance genes and pathogenicity factors.

It sounds relatively straightforward, but there are certain challenges that one needs to be aware of.

  • Sensitivity:- Unlike PCR, the process does not involve an amplification step, therefore it may not be as sensitive as other currently existing methodology. In addition, if the sample contains a lot of human DNA, or DNA from non-pathogens, then the pathogen can be “drowned out” in the testing process. (stoichiometric ratios). Methods to enhance pathogen and suppress non-pathogen/host nucleic acid during the sequencing process are in development to mitigate this issue, but it is a work in progress.
  • Turnaround Time:- Traditional sequencing can take 1-2 weeks when you add the time for the various steps; extraction, library preparation, sequencing and bioinformatic analysis. This is still slow compared to current culture-based and PCR methodology. Newer Real-time sequencing techniques such as Oxford Nanopore can potentially reduce this turnaround down to a couple of days.
  • Cost:- Cost is coming down, and depending on what sequencing platform you use, can be anything from a hundred dollars to a few hundred dollars per sample. The cost will almost certainly come down further but we are still some way from the cost of a couple of agar plates.
  • Bioinformatic analysis and validation thereof:- The bioinformatic analysis of genetic sequences remains somewhat foreign to most microbiologists. Slowly but surely automated bio-informatic pipelines are being developed which automates this step for an increasing number of pathogens. However, validation of these pipelines is laborious and difficult and requires the input of specialist bioinformaticians.

There are now metagenomic assays commercially available in several areas, the most promising possibly being metagenomic analysis of CSF samples for infective causes of meningo-encephalitis. But it is still only a small niche area of the market, and it has a long way to go before becoming mainstream.

If you look at MALDI-TOF, it took approximately 25 years from the technology becoming available, until being widely adopted in clinical microbiology labs. The reason it has been so successful is because it is fast, accurate, cost-efficient and scalable. I think metagenomic sequencing will take just as long. Operationalisation of exciting technology is a protracted and somewhat painful process…

So, on my last day at work, around about 2050, I think metagenomics will be commonplace in most reasonable sized diagnostic microbiology laboratories. But I have a feeling that the tried and trusted agar plate will still be around… 


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