Enteroaggregative E. coli on LigerCat

Reading Jon Eisen’s blog this week I was rather taken with this post about LigerCat. LigerCat is an online tool that searches pubmed for whatever you ask it to, and displays a cloud of the MeSH terms (keywords attached to articles) associated with the pubmed results. It also shows a neat bar chart of article counts by year.

Since I’ve just been introduced to enteroaggregative E. coli thanks to the German E. coli outbreak, I thought I’d search for “Enteroaggregative E. coli”… this is the result.

I think this shows quite nicely that (at least according to the literature) this organism is defined by adhesion, normally associated with diarrhea in children and babies and commonly tested for by PCR.

According to this it was first described as enteroaggregative E. coli in 1989 and has been the subject of some attention, but not a lot, ever since (~15 articles per year):

The picture is quite different for “Shiga toxin, most associated with E. coli O157 and hemolytic-uremic syndrome, with first mention in 1942 and a mass of interest since the 1980s, now with >200 papers each year:

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One thought on “Enteroaggregative E. coli on LigerCat

  1. Thanks for posting this — I hadn’t seen LigorCat before and already I’m addicted. PubMed per se has too fussy a search function and so I had been using url-delimited google. Here I started one with Shiga Toxin 2 and then added Hemolytic-Uremic Syndrome + Cattle Diseases, obtaining 5 articles.

    Next I tried the LigorCat blastp sequence search feature on the expression-critical third Q component of the shiga toxin system in our favorite strain, which is conveniently provided and satisfactorily annotated for the final BGI assembly by era7.

    From the resulting mesh cloud, I selected Shiga Toxin 2 + Transcription, Genetic which resulted in 11 on-topic articles, though not critical 2009 PNAS article that era7 provides.

    Entrez can do this too having learned some very clever tricks this spring, including the ability to launch a non-redundant set of PubMed articles from long lists of GenBank accessions, that is, stripping accessions from blast searches to the desired divergence depth.

    From my perspective (as the original annotator of K-12), the two breakthroughs in literature search are realtime citation counts (articles that people in the field found worthy) and foward citations (into intro and discussion sections of the very latest articles) which LigorCat could probably do well.

    Here the 12 month block on open source at for-profit journals is a great hindrance to getting up to speed on ever-shifting topics — a rather harsh business model given people dying all around you. So three cheers for crowdsourcing.

    >Q TY-2482_chr E coli O103:H2 transcription antiterminator activity
    MRDIRQVLERWGAWAANNHEDVTWSPIAAGFKRLIPEKVKSRPQCCDDDAMIICGCMARLNRNNSDLHDLLV
    DYYVLGETFMALARKHGCSDTCIGKRLHKAEGIVEGMLMMLGVRLEMDRYVERELPGGRTSVFYQRKNSLRS

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