E. coli
mikethemadbiologist | June 9, 2011Or maybe wild-ass speculation. As the data continue to come in about the E. coli outbreak in Germany caused by E. coli O104:H4 HUSEC041 (well, everything but the public health and epidemiological data which are a contradictory, incoherent mess), it appears that one of the things that has made this strain so dangerous is its ability to make Shiga-like toxin--a compound that stops cells from making proteins cells--the mechanism is similar to that of the biowarfare agent ricin (Note: there are several different Shiga-like toxins; for clarity, since it's not germane to this post, I'll lump…
tsmith | June 9, 2011Maryn McKenna has a great update today on the E. coli situation, looking at where we are as far as unanswered questions about the outbreak and the strain. It's been a messy day; more evidence seems to point to the sprout farm, but CIDRAP also notes that another contaminated cucumber was found in the compost bin of a family sickened by the bacterium (this one had the correct serotype--O104), but it's impossible to tell at this point whether the cucumber was the source of that bacterium or it ended up there from one of the sickened family members. Twists and turns abound in this investigation…
tsmith | June 6, 2011Well, Sunday the said we'd have some results on the sprout tests for E. coli O104:H4. Well, so far the results are negative.
The 1st tests from a north German farm suspected of being the source
of an _E. coli_ [O104:H4] outbreak are negative, officials say. Of 40 samples from the farm being examined, they said 23 tested negative.
Officials had said earlier that bean sprouts produced at the farm in Uelzen, south of Hamburg, were the most likely cause of the outbreak. The outbreak, which began 3 weeks ago and is concentrated in Hamburg, has left 22 people dead. Initially, German officials had…
mikethemadbiologist | June 6, 2011After Friday's post, I've held off on writing much about the German E. coli outbreak, often referred to by its serotype, O104:H4, or as HUSEC041 (HUS stands for hemolytic uremic syndrome). Having had the weekend to digest some of the ongoing analysis and news reports, here are some additional thoughts:
1) The multilocus sequence type (MLST) of this outbreak is definitely ST678. This means this outbreak strain is related to an older strain found in 2001 that caused disease. A new, improved assembly released by BGI yields a perfect match to ST678. In addition, there is independent…
mikethemadbiologist | June 5, 2011...and I can't blame them. The recent and ongoing E. coli outbreak which began in Germany was originally claimed to have been traced to Spanish cucumbers. Erm, not so much:
German agricultural authorities on Sunday identified locally grown bean sprouts as the likely cause of an E. coli outbreak that has killed 22 people and sickened hundreds in Europe.
The Lower Saxony agriculture ministry was sending an alert Sunday warning people to stop eating the sprouts, which are often used in mixed salads, ministry spokesman Gert Hahne told The Associated Press.
"Bean sprouts have been identified as…
tsmith | June 5, 2011The E. coli story is moving quickly. A news report out today suggests that sprouts might be the culprit (though it should be emphasized that the outbreak strain hasn't been isolated from these vegetables yet):
Mr Lindemann said epidemiological studies all seemed to point to the plant nursery in Uelzen in the state of Lower Saxony, about 100km (62m) south of Hamburg - though official tests had not yet shown the presence of the bacteria there.
"Further evidence has emerged which points to a plant nursery in Uelzen as the source of the EHEC cases, or at least one of the sources," he said.
"The…
tsmith | June 3, 2011Mike has has a great new post up looking at some molecular analyses of the current European outbreak strain. For anyone who hasn't been paying close attention to what's happening across the pond, there's an ongoing outbreak of enterohemorrhagic E. coli (EHEC)--the type of E. coli that includes O157:H7, which has been associated with outbreaks of disease associated with food. The most infamous outbreak was the 1993 Jack-in-the-Box disaster, associated with undercooked hamburgers contaminated with the organism, but there have also been outbreaks associated with contaminated vegetables (such as…
ksnyder | June 3, 2011In news that may shake the cranberry juice industry to its core, new atomic-level "snapshots" reveal how bacteria such as E. coli produce and secrete sticky appendages called pili, which help the microbes attach to and infect human bladder cells.
These crystal structures -- produced at the National Synchrotron Light Source (NSLS) at Brookhaven Lab and the European Synchrotron Radiation Facility in Grenoble, France -- unravel a complex choreography of protein-protein interactions that will aid in the design of new antibacterial drugs. Finding ways to interfere with pili formation could help…
mikethemadbiologist | June 3, 2011...in Europe. I'll get to that in a moment. You've probably heard of the E. coli outbreak sweeping through Germany and now other European countries that has caused over one thousand cases of hemolytic uremic syndrome ('HUS'). What's odd is that the initial reports are calling this a novel hybrid or some new strain of E. coli.
BGI has done some sequencing using Ion Torrent of one of these isolates, and Nick Loman assembled the data. Without getting too technical, the genome is actually in about 3,000 pieces, but with those data (and thanks to Nick for assembling them and releasing them) I…
lborkowski | June 2, 2011In Germany, 17 people have died and more than 1,500 sickened by a particularly virulent strain of E. coli. Der Spiegel explains that this rare E. coli serotype, O104:H4, is especially virulent; after infection by as few as 100 bacteria, many patients develop hemolytic uremic syndrome, which can result in kidney failure and even death. Cucumbers imported from Spain were initially blamed, although it turns out that the cucumbers' strain of E. coli is not the one implicated in the outbreak. Investigators are racing to identify the source of the infections while hospitals care for those who've…
mikethemadbiologist | May 26, 2011A seminal discovery of modern biology was Joshua Lederberg's demonstration that bacteria can swap genes through a process known as bacterial recombination. Not only is recombination the mechanism by which antibiotic resistance genes are transferred, but it's also been turned into a useful tool for genetically manipulating E. coli, which has led to so many things, including the industrial synthesis of insulin; it's also a key tool--and at one time--the key tool for molecular genetics.
So while working my way through Population Genetics of Bacteria: A Tribute to Thomas S. Whittam, I came…
mikethemadbiologist | April 5, 2011Nick Loman listed the fifty most sequenced bacterial genomes according to NCBI. A reader at Nick's blog came up with an improved list--one that reflects the genomes for which we actually have data (depending on who is doing the sequencing, a project will be registered with NCBI, often months before any sequencing is done). Here's the 'improved' top twenty:
173 Escherichia coli
82 Salmonella enterica
78 Staphylococcus aureus
69 Propionibacterium acnes
56 Streptococcus pneumoniae
56 Enterococcus faecalis
45 Bacillus cereus
42 Mycobacterium tuberculosis
36 Vibrio cholerae
29 Pseudomonas…
mikethemadbiologist | March 9, 2011Consider this the post wherein I channel my Inner ERV. During the last week, I've come across a couple sensationalist article about E. coli and Staphylococcus aureus being found on common surfaces. Here's one article about shopping carts and E. coli:
Researchers from the University of Arizona swabbed shopping cart handles in four states looking for bacterial contamination. Of the 85 carts examined, 72 percent turned out to have a marker for fecal bacteria.
The researchers took a closer look at the samples from 36 carts and discovered Escherichia coli, more commonly known as E. coli, on 50…
mikethemadbiologist | February 8, 2011Lest there be any doubt that I'm not as nuts in real life as I am on the blog, here's a slide I used yesterday during a full-blown fancy-schmancy professional talk:
Just saying.
For context, read this post (IT HAZ SCIENTISMZ!!).
mikethemadbiologist | December 6, 2010I don't see the need to redescribe the recent paper about the discovery of bacteria that can might replace, in extremis, phosphorus with arsenic, which was overhyped by NASA, was poorly covered by most journalists, and which has compromising methodological problems (for good coverage, read here, here, and here; and snark). But what the paper does demonstrate is the importance of culturing microorganisms, knowledge about which is becoming rapidly lost by younger scientists.
With the advent of DNA-based, culture-independent techniques, where we can look at the DNA and RNA of microbes without…
mikethemadbiologist | November 9, 2010If you haven't heard, there's a new antibiotic resistance gene, NDM-1, which stands for New Delhi metallo-beta-lactamase-1. This gene has been found in Gram-negative Enterobacteriaceae (E. coli and Klebsiella), and confers resistance to every penicillin derivative. Like the KPC genes, this gene is found on miniature chromosomes that also carry other resistance genes, making this organism resistant to just about everything we can throw at it.
By way of Maryn McKenna, we find this nice ATCC chart which shows just how bad one of these bacteria can be:
All those "R"s mean that drug doesn't…
mikethemadbiologist | June 23, 2010When I first saw the title of this PloSOne article, "Unauthorized Horizontal Spread in the Laboratory Environment: The Tactics of Lula, a Temperate Lambdoid Bacteriophage of Escherichia coli", I thought, "Hunh?!? You can actually publish articles about laboratory contamination?", but it's actually a very interesting article. In short, the article describes the discovery of a bacteriophage ('phage')--a bacterial virus--that is very well suited for survival and spread in microbiology laboratories.
To be successful, Lula faces several problems:
1) It has to successfully hide from researchers…
mpendergrast | June 21, 2010Mark Pendergrast writes: To kick off this book club discussion of Inside the Outbreaks, I thought I would explain briefly how I came to write the book and then suggest some possible topics for discussion.
The origin of the book goes back to an email I got in 2004 from my old high school and college friend, Andy Vernon, who wrote that I should consider writing the history of the EIS. I emailed back to say that I was honored, but what was the EIS? I had never heard of it. I knew Andy worked on tuberculosis at the CDC, but I didn't know that he had been a state-based EIS officer from 1978…
mikethemadbiologist | May 4, 2010If you want the short version, Superbug: The Fatal Menace of MRSA is a must read. While I have a couple minor quibbles (more about those in a bit), they don't detract from either the importance or the style of this book. While there has been a lot written about methicillin resistant Staphylococcus aureus (MRSA) that describes how awful these infections can be, unlike most authors, McKenna makes it clear that this epidemic arose and persists because of human error.
Rather than throwing our hands up and proclaiming doom and gloom--although there is a fair bit of that (and rightly so)--McKenna…
mikethemadbiologist | April 1, 2010When I'm not fighting the forces of evil or calling idiots who desperately need my help fucking morons, I'm doing various genomics-related things. One of the things I'm involved with is a project to sequence a bunch of commensal (not associated with disease) E. coli. When most people think of the genus Escherichia, they think of a single species, E. coli. But a recent paper describes five new lineages (clades) of Escherichia that, while found mostly in the environment, are also found in humans (and, yes, we're sequencing ten of these). Here's how they're related to each other:
UPMGA…