Friday, I described the discovery of the gene mcr-1, which is a transmissible colistin resistance gene found on a bacterial plasmid (a plasmid is a mini-chromosome that can move from bacterium to bacterium). This is really bad news, since colistin is the last line of defense against carbapenem-resistance enterobacteriaceae (‘CREs’). Were this plasmid to move into a CRE, we would have no treatment options. For more background, read Maryn McKenna’s post or mine (or both!).
Well, it gets worse. The plasmid sequence and protein sequence of mcr-1 are both available in Genbank, so I looked for mcr-1 elsewhere. The identical protein is not only found in three E. coli from Malaysia isolated in 2013, but it is also found in a Salmonella strain possibly from Portugal in 2011.
I write possibly since there’s no geographic location identification provided in the Genbank record, though the submitting lab is based in Europe and seems to submit samples from Europe. The company ControlVet which provided the sample is a subsidiary of ALS which has locations all over the world including several from Southeast Asia. So it’s quite possible this has spread outside of Southeast Asia–with certainty, we can now push the earliest observed date back two years to 2011.
I’ll end with a point about the failure to record a geographic location–and failure is absolutely appropriate here. Having been around quite a few genomics projects, I’ve heard people grouse about having to make even the most basic metadata (where the sample was from, etc.) publicly available.
Now do you get why this matters? In 2015, if you’re doing medically-relevant microbial genomics, release your fucking metadata. While this appears to be a ‘privately-owned’ strain, all government-funded projects, regardless of country, should require the release of as much information as possible, as long as it doesn’t compromise patient confidentiality.
mcr-1 is a good reason to fight for that policy.
Update: I realize there are some metadata that are very costly to collect. In those cases, some sort of balance needs to be struck between research needs and motivations and public health needs–this is a separate and very long post. That said, there’s no reason not to release the country–or even continent–from which a Salmonella isolate came (XDR TB is perhaps a different matter given identification issues, etc.).
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Getting metadata is like pulling teeth. ReGardless, some content is touchy or legally constrained: the location could identify and thereby compromise cooperativity of entity willing to share samples. Though a value of “not provided” or “witheld” would be better than “unknown”. Its not always possible to share all the metadata, but it would be nice to know the difference between constrained and sloppy indifferent content.
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