ID Week 2018 as seen by an Infection Preventionist

Guest Blogger Barley Chironda (bio below) writes…

IDWeek was held this year from Oct 3 to 7, 2018 in beautiful San Francisco. This was my fourth year in a row attending; having first attended and blogged about my first experience here in 2014. The pressure to offer IDWeek attendees a stellar conference was palpable. A week before, the city of San Francisco had hosted Dream Force. Dream Force is one of the world’s largest tech conventions with over 150,000 attendees. I’m glad to say IDWeek did not disappoint; boasting it’s highest ever attendance of over 8,000 people from over 85 countries. Given its wide and diverse audience, there are many targeted streams that allow a range of topics.

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The first International Conference on Clinical Metagenomics (ICCMg)


Guest blogger Dr Etienne Ruppé (bio below) writes about a new conference in the emerging field of ‘Clinical Metagenomics’. I suspect we are all beginning to dip our toes into this challenging new arena, so I am sure this conference will be useful…   Continue reading

Are spores the secret of the success of FMT in treating recurrent CDI?

Characteristic of the aimes strain of b anthracis is the smooth

I have been following the literature around the use of faecal microbiota transplantation (FMT) for the treatment of recurrent Clostridium difficile infection (CDI). FMT is spectacularly effective but rather crude – and may have some associated risks, not least the possibility of transmissing infectious organisms we have not yet discovered! There is also the issue of administration. Compared with recurrent CDI, a duodenal infusion (aka tube up the backside) isn’t so bad – but an oral delivery would be preferable. The ‘crapsule’ (oral FMT) has been tested and is effective, but it requires a large number of crapsules to reach the required dose. So, the search is on to distill the effective elements of FMT into a format that can be delivered more easily. Some work has been done on exploring various combinations of live bacteria – with variable success.

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Biofilms make the hospital environment far from ‘inanimate’


Anybody doubting that biofilms really do exist on dry hospital surfaces needs to read this study: biofilms are there, they are complex, and they are common. A landmark study by the same Australian Vickery group published in 2012 first identified biofilms on a handful of dry hospital surfaces in an ICU. But this study is far more comprehensive and convincing.

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What’s lurking in the NYC subway? “City-scale metagenomics” brings unprecedented resolution


A remarkable study published last week in Cell Systems has described the ‘environmentome’ of the subway system in NYC. The study has attracted a fair bit of attention in the mainstream press, not least due to claims of Bubonic Plague and Anthrax lurking in the NYC subway system (more on this later)…

The authors took a ‘microbiomic’ approach to characterize the DNA found on surfaces, similar in concept to the Hospital Microbiome Project. Since the collection of microbes in and on our bodies outnumbers our own cells by 10:1, and accounts for up to a third of active molecules in the bloodstream, this sort of approach to microbiology is going to become more and more common.

The study is mind-blowing in many ways, with 1457 samples collected from subways, public parks and alongside a canal. The headline findings are:

  • DNA from pathogens (including Yesinia pestis and B. anthracis and some antibiotic resistant bacteria) were found on some surfaces.
  • Human DNA identified in subway stations mirrors the demographics of the local region.
  • The microbiome of surface in a station is far from stable: hourly sampling over a single day at Penn Station (a busy rail hub) identified considerable ebb and flow in predominant bacterial species.

I have a lingering concern that the techniques available for bioinformatic analysis have not yet caught up with our ability to sequence vast amounts of DNA. Put another way, the identification of bacteria in metagenomic samples is a surpassingly and rather unnervingly approximate science.

In order to identify bacteria in the sample, very many short reads of DNA are produced and then compared with databases. (This results in particular difficulty in distinguishing plasmid from genomic DNA, the subject of a recent post.) Almost half of the DNA identified in the study from New York did not match any known sequences. Furthermore, some of the species identified seem rather unlikely. For example, two of the most common Eukaryotic DNA species identified were the Mountain Pine Beetle and Mediterranean Fruit flies. Now, I’ve spent many-a-weekend in NYC from my time living in Connecticut, and I’ve never seen a Mountain Pine Beetle down there. So, this seems almost certain to be a mis-match with a closely related species due to imperfect databases. And yet when it comes to Y. pestis and B. anthracis, the authors seem more certain that the matches are correct, unlikely as they seem. (There is an acknowledgement in the discussion that these apparent “best hits” may be erroneous.)

Another key limitation is the degree of viability associated with the DNA identified. It could be that much of the DNA is a shadow of ancient contamination that is no longer viable. Whilst the authors did do a small amount of conventional sampling, and did grow some antibiotic resistant bacteria, there is no real sense of how much of the DNA identified is from viable microbes.

Quite a few years ago, I took some similar samples from buses and tube trains in London, and found no MRSA whatsoever and only a few sites grew S. aureus. It would be fascinating to see how a metagenomic analysis of these samples would look. Would there be a vastly different ‘environmentome’ in the London Underground compared with the NYC subway? Probably, but I suspect you wouldn’t find many Mountain Pine Beetles, Y. pestis or B. anthracis in either!

One of the best parts of the study is the accompanying website, which provides an interactive overview of the ‘environmentome’ of NYC: Related to this, an interesting future application of these data is to derive a persons’ recent or ancient geographical location based on their current microbiome. Criminals beware – analysis of the ‘environmentome’ on the sole of your foot could invalidate your alibi!

The authors should be credited for describing the microbial ecology of the NYC subway in unprecedented detail – and this study will serve as a marker in the sand for future approaches to exploring where we fit into our inanimate environment.

Tending the human microbiome

Atomic antibiotics

This isn’t hot off the press (a 2012 review article by Tosh & McDonald) but it’s probably more important now than when first published, given our rapid advances in understanding of the importance of the microbiome in human health over the last year or two.

A couple of clear principles emerge from the review:

  • A happy, healthy human microbiome is characterized by diversity (both in terms of number of different species, and diversity within the species), and composed mainly of bacteria that we’re not familiar with – Fermicutes and Bacteroidetes).
  • Antibiotics have a profound and sustained effect on the human microbiome (even those that are typically associated with no or few side effects). This results in a reduction in both diversity and change in composition, which is bad news for human health. In particular, this leave the gut more open to colonization with unwanted intruders aka antibiotic resistant bacteria.

The future of anti-infective therapy according to Tosh and McDonald is in:

(1)     Developing and using more microbiome-sparing antimicrobial therapy. The idea of ‘selective digestive decontamination’ flies in the face of this objective.

(2)     Developing techniques to maintain and restore indigenous microbiota. A lot of progress has been made here, for example, in the case of faecal microbiota transplantation (FMT) for the treatment of recurrent CDI.

(3)     Discovering and exploiting host protective mechanisms normally afforded by an intact microbiome.

Rather than obliterate our microbiome with overuse of antibiotic “Atomic bombs”, we need to carefully tend individual and collective microbiomes in order to make them resistant to the increasing queue of antibiotic resistant colonizers!

Article citation: Tosh PK, McDonald LC. Infection control in the multidrug-resistant era: tending the human microbiome. Clin Infect Dis 2012;54:707-713.

Image credit: Modified from ‘Mushroom cloud‘.

Journal Roundup August 2014: seeking your input

Fist bumpThe August edition of the Journal of Hosptial Infection Journal Roundup is now available, featuring:

  • A whopping five-fold increase in the detection of CRE in 25 US community hospitals.
  • MALDI-TOF as a new frontier for rapid detection of carbapenemase activity.
  • More on fist bumping instead of hand shaking. (Would you like a fist bump greeting from your doctor? No thanks!)
  • Triclosan-impregnated stitches would be cost-effective if they were only a little bit effective, but turns out they’re not effective at all.
  • The new ‘crAssphage bacteriophage’, C. difficile biofilms, and increasing rates of antibiotic resistance – all in the human gut microbiome.
  • Some hope for Ebola drug and vaccine targets.
  • How to reduce the number of sickies that children take from school (through effective school-based immunization programmes).
  • Thoughtful analysis on S. aureus outbreaks of old with lessons for now.
  • Reviews of CRE mortality, global antibiotic use, microbial hitchhikers, overdiagnosis & overtreatment, useless reporting of science in the mainstream media, and whether biocide use drives biocide resistance.

I’ve written three editions of the Journal of Hosptial Infection Roundup now (June, July and August), so there’s a few examples to review. You can read about my methods for producing the Roundup in the blog accompanying the June edition. I thought that now would be a good time to get some feedback, specifically:

  • Is the title right? A few people have expected it to be an overview of articles in the Journal of Hospital Infection only.
  • Is the length about right? (Do you fall asleep reading it or find yourself begging for more?)
  • Is the depth right? Or would you like to read more about less articles, or less about more articles?

Any feedback that you have would be most appreciated. Please either submit a comment below or email me.

Photo credit: ‘Fist bump’.