Metagenomics test saves woman's sight after mystery infection

The BBC article seems to overstate the uniqueness of the service at Great Ormond Street Hospital. While it’s true that they are the first in the UK to offer a UKAS-accredited clinical metagenomics service (UKAS being the United Kingdom Accreditation Service, which certifies labs to meet medical testing standards like ISO 15189), metagenomics itself is already being used in several other places across the UK.

For example, the Earlham Institute, the University of Oxford, and the UK Health Security Agency are all actively involved in metagenomics research and surveillance.

For example: https://www.phgfoundation.org/blog/metagenomic-sequencing-in...

https://www.earlham.ac.uk/events/nanopore-metagenomics-sampl...

Leptospirosis is very rare (~100 cases/year in the UK?) and typically affects other tissues (She's lucky it seems to have only infected one eye), making it more like a unicorn than a zebra diagnostically. Effective antibiotics are common, but even via IV they might reach not therapeutic levels in the eye.

Metagenomics are particularly good in cases like this where tissue samples are small. These spirochete are too small for light microscopy - probably why the lab missed them.

What I find most interesting about this story that antibiotics weren't given when the patient had persistent inflammation and a clear cause couldn't be identified. It seems like such a common low risk treatment just to try. Especially curious why auto immune was assumed instead.

Crux:

"Metagenomics technology uses cutting-edge genomic sequencing, which can identify all bacteria, fungi or parasites present in a sample by comparing them against a database of millions of pathogens.

[if you] do a separate test for each and every one and if you've got an infection with something that's unexpected, rare or not previously known, you won't find it."

Presumably the issue is that "went swimming in the Amazon" suddenly puts a ton of rare, difficult to identify diseases on the table.

Leptospirosis is known to be both prevalent in tropical areas and to be difficult to positively culture and identify.

> It is now presumed Ellie picked up the bug swimming in the Amazon river in 2018, while on a trip to Ecuador and Colombia.

Don't doctors always ask about international travel when you present with an unknown illness? The exact timeline is difficult to infer from the article but that seems like pretty important detail to overlook.

I'm curious if they initially diagnosed her with uveitis and began treatment based on that. However, I'm surprised there was no mention of consulting an infectious disease specialist.

In Canada, when a complex issue like this arises, it's common to see several different specialists; the testing is typically very thorough, even including some forms of genetic testing. They do everything they can to get you off the steroids, knowing it will cause issues if taken long-term.

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