A bit over two years ago I was a guest blogger at the US Biophysical Society Annual Meeting in Baltimore. I was disappointed by the lack of Tweeting at the conference – there were 208 tweets using the #bps15 hashtag when I wrote a blog post in which I speculated that, one day, there might be a tipping point and Twitter at large conventions would become genuinely useful.

Well, I’ve just returned from ECCMID, which is the European Congress of Clinical Microbiology and Infectious Diseases in Vienna, and it seems we are now there!. For example, on the morning of the last day, there were over 200 tweets per hour which is about 20x the level of Tweeting at BPS15. That is enough activity that it was really worth keeping an eye on the #ECCMID2017 hashtag using TweetDeck whilst sat in talks. It was especially useful when some of the talks were less relevant or interesting.

It isn’t a perfect comparison as ECCMID is a bit bigger than BPS (10,000 v 7,500) and the attendees have different backgrounds (clinical microbiologists v biophysicists), but the difference is so stark that I’d hope the increase applies across all or most large conventions.

Likewise, not everything that I wrote about in my previous post has come to pass. Yes, occasionally people did post links to papers that the speaker had just mentioned (and this is incredibly useful) and yes you got an idea of which sessions were “hot” and interesting in real-time. But the chairs were not, as far as I could see, monitoring twitter (you’d really need a session specific hashtag for that) for questions from the floor) or even tweeting themselves. Also there is a tendency, which I mostly follow as well, to be positive, upbeat and effusive on Twitter so there are lots of posts saying “Professor X is giving an amazing talk in Hall Y!”, rather than “I was a bit disappointed that Professor X just did the same talk as last year in Hall Y”. You’d be forgiven for thinking all the talks were interesting and engaging if you just followed the hashtag Twitter, but of course some talks were poorly delivered or aimed at the wrong audience or were a touch too sycophantic.

So Twitter is now a useful addition to large, international conventions. Jon Otter gave a presentation at ECCMID (which, alas, I missed) on social media use by healthcare professionals and has surveyed that cohort. He found that a bit over 70% of respondents used some form of social media platform, with about 35% using Twitter. To read more, please visit his blog post. By the way, I’ve never met him in person, I only know of this work because … you guessed it, he followed me on Twitter during ECCMID and then I retweeted him during the conference.

That’s what happens.

It is Sunday, I’m in Vienna at the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) congress. As is traditional at all large conventions, I’m sitting on the floor outside one of the halls because the organisers have put one of the most popular sessions (Gram-negative resistance) in one of the smallest rooms. A good time to record some thoughts.

I see a coming paradigm shift away from species to plasmid and, perhaps, resistance genes. Several talks this morning discussed “plasmid outbreaks” in Gram-negatives, where although you see multiple species, what is actually happening is a plasmid is hopping between species. Or worse, resistance genes embedded in a transposon are hopping between plasmids which are themselves hopping between species. The growth and transfer of such beta-lactamase (bla) genes (and probably also mcr-1) will contribute significantly to the growth of antibiotic resistance in the coming years.

This will drive the adoption of using genetics to follow and understand these outbreaks, since culture-based microbiology is species-based and so struggles to sort out what is happening in this sort of situation. Since there are many different genes involved, PCR-based methods will probably not be much help either. Second-generation sequencing (e.g. Illumina), with its relatively short reads will also struggle since it is difficult to tell where a read originates from, although it can tell you if a gene is present or not. That leaves long-read sequencing which is either expensive (e.g. PacBio) or still in development (ONT MinION). So there isn’t yet a cheap, off-the-shelf genetic approach that allows you to sequence bacterial DNA and determine how many and which plasmids are present.

Much of the current whole-genome sequencing effort is focussed on Tuberculosis with good reason: you don’t have to worry about detecting plasmids since there is little horizontal transfer and there is a huge clinical gain to be made in reducing the time to producing an antibiogram. But ultimately, the skills and knowledge here will have to be transferred to Gram-negatives.

So who is going to do it?

The answer to this is, I think, not obvious since there are commercial issues. Basically, any solution will require a sequencing method that produces long reads. The key questions are: (i) will company A who own a long-read sequencing method license it to company B for a “reasonable” amount, if not (ii) will company A develop such a clinical microbiology workflow itself? I worry this will retard the development of a genetics-based microbiology that can follow a resistance-gene or plasmid-mediated outbreak.

You get a very clear illustration of the importance of commercial considerations walking around the Exhibition Hall here at ECCMID; the vast majority of the stands are for diagnostic solutions and there are very few stands marketing antibiotics, even to the point where companies, whose name you would historically associate with antibiotics, appear to only be marketing diagnostics.