Thoughts On ASM Microbe 2016

And other possibly related things as well, along with various ruminations on my part. Let’s begin:

1. E. coli ST131-fimH30, the clone (‘MLST type’) that causes many ESBL and CRE infections (the only beta-lactams that work against ESBLs are carbapenemes, and, with most CRE, no beta-lactams work. That is, nothing that starts with ceph- or ends with either -penem or -cillin can treat the disease), is a very good commensal organism. One speaker estimated that ten percent of healthy people can be carriers (note that not all of these ST131 will be drug-resistant). Needless to say, this is bad news, because this doesn’t appear to be something circulating in the healthcare system but that is ‘out there.’ It’s going to stick around for a while.

2. Regarding CRE (and ESBLs), most of these are loaded with aminoglycoside-modifying enzymes and are resistant to gentamicin, and not uncommonly amikacin (don’t know much about tobramycin resistance patterns). In some cases, these genes are linked with carbapenem resistance or ESBLs (e.g., on the same plasmid), while others are not. We can’t think about carbapenem resistance (the ‘CR’ in CRE) or ESBLs without considering aminoglycoside resistance.

3. Related to cheery point #2, if you’re a chicken, your world is bathed in a dilute solution of gentamicin. Gentamicin is injected into chicken eggs to protect them after vaccination (the needle punctures the shell, creating an opportunity for infection). Gentamicin resistance really can’t be a hospital-based problem, as gentamicin is used very sparingly.

4. Fluoroquinolone use is bringing back sexy. And by “sexy”, I mean UTI-causing E. coli clones ST69 and ST73 (UTI is urinary tract infections) which had declined in frequency. Apparently, they’ve evolved floroquinolone resistance (ciprofloxacin mostly) in the U.S., and because ciprofloxacin is widely used to treat UTIs here, they’re doing very well for themselves. They may have also have spread to other countries from the U.S.

5. On the clinical diagnostics side, there is a lot of work going on in culture-free diagnostics. These are faster and cheaper than traditional methods, but the downside is that there’s no bacterial isolate that’s kept (or isolated in the first place). This is going to make surveillance much harder. I know that someday we’ll reach the Glorious Metagenomic Singularity where we can accurately, down to the strain level, sequence the pathogenic organisms straight from samples (e.g., blood). As best as I can tell, this will occur sometime before Messianic Return. Probably.

6. As always, clinical diagnostics company Biomerieux had the most ridiculous floor display. This year it involved Beaux Arts lamp posts, park benches, classic bicycles, and a tree. That said, Hologene won the plushest floor carpeting competition this year.

7. At least one group that offers public analysis genomics resources wants to take a harder line: if you want to use their tools, you need to commit to making your data publicly available. Can’t say that I disagree.

8. Boston is late June is much more comfortable weather-wise than D.C.

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