Reflections from ECCMID: the pink, the blue, and the new


I’ve recently returned from an enjoyable few days in Amsterdam for ECCMID. I’ve not been to a conference of this scale for a few years; there was a lot of good stuff to choose from so I’ve tried to stick to key updates for the purposes of this reflection!

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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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‘Crapsules’: the cure for Cdiff and more

crapsules brown pills

I gave a talk today at a Pint of Science event entitled “Crapsules: the cure for Cdiff and more”. You can download my slides here. Cdiff infection (CDI) is a nasty disease, usually occurring in those who have taken antibiotics in hospital. It’s characterised by frequent loose stools (often 5 or more movements per day) and frequent recurrence. Around 15-35% of patients with CDI will have a repeat episode. The mainstay treatment for recurrent CDI is antibiotics but the cure rate is poor at around 30%. Remarkably a ‘faecal microbiota transplantation’ (FMT) is way more effective, with a cure rate in excess of 90%.

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How big is C. difficile infection in the USA?

Clostridium-difficileThe New England Journal of Medicine recently published an article evaluating the burden of CDI in the USA. The huge CDC-led initiative collected data from 10 geographically distinct regions, identifying more than 15,000 cases. Around two-thirds of cases were classified as healthcare-associated (although only 25% were hospital-onset). This means that, prima facie, a third of CDI cases were community-associated. I find this proportion difficult to believe: I strongly suspect that many of these cases would have had healthcare-associated risk factors if the team were able to look hard enough. For example, they used a fairly standard 12 week look-back period to evaluate previous hospitalisation, but how would the data look if they’d used 12 months? Also, it’s usually only possible to evaluate previous hospitalisation in a single healthcare system, but many patients commute between various healthcare systems. The authors acknowledge in the discussion that this designation of “community-acquired” may be inaccurate based on the finding from a previous study whether healthcare-associated risk factors were identified in most patients, but only be a detailed phone interview.

Scaling up from the figures from the 10 regions, national estimates were around 500,000 cases and 29,000 deaths due to CDI per annum in the US. This estimate is approximately double previous estimates for the national CDI burden in the USA, probably reflecting the adoption of molecular methods for the detection of CDI. This scaling up included an interesting statistical adjustment to see how prevalence varied depending on how many sites use sensitive molecular methods to detect CDI.

A sub-study included the culture of C. difficile from 1625 patients. More than 15% of stool specimens from patients diagnosed as CDI failed to grow C. difficile, probably illustrating the limitations of culture methods more than anything else. NAP1 (027) represented around half of cases, and was significantly more common in healthcare-associated CDI. I think it’s fair to say that the initial fears that NAP1 was a super-strain have been allayed by the fact that it’s now so common and there hasn’t been a surge in CDI mortality.

Finally, around 21% of healthcare-associated cases suffered at least one recurrence. Thus, there is a real need to the roll out of the uber successful faecal microbiota transplantation for recurrent CDI. In fact, there should be around 70,000 faecal microbiota transplantations each year in the US right now (500,000 x 0.66 x 0.21); I suspect there are far fewer.

‘Crapsules’ spell the end for recurrent Clostridium difficile infection

Faecal microbiota transplantation (FMT) has shown remarkable efficacy for treating recurrent C. difficile infection (CDI). In fact, the randomized controlled trial to evaluate the effectiveness of FMT for recurrent CDI versus treatment with vancomycin was terminated early because FMT was so obviously superior, with a cure rate of more than 90% (see Figure 1, below).

Figure 1: Faecal microbiota transplant for recurrent CDI. Patients with recurrent CDI randomised to FMT (n=16), vancomycin (n=12) or vancomycin + bowel lavage (n=13). Colour scheme chosen carefully.van nood_blog

FMT is crude in every sense. You take donor stool, put it in a blender, sieve it, and deliver it to the recipient’s gut. I had the pleasure of watching a colleague prepare a dose of FMT in our laboratory in London last week. It really is a simple preparation. The delivery of the FMT to the recipient’s gut isn’t so much tricky as it is unpleasant for the recipient, with a tube required for the procedure.

So, could you deliver FMT orally? The answer according to a recent JAMA study is yes. The team from Boston in the US developed specially formulated capsules (aka ‘crapsules’) designed to deliver the FMT to the correct part of the gut. Of the 20 patients with recurrent CDI given a short 2 day course of ‘crapsules’, 14 (70%) resolved. The 6 non-responders were given a second course and 4 of these resolved, resulting in an overall resoluation rate of 90% (18/20). The quality of life benefits are obvious, and spelled out in the reduction in number of daily bowel movements (Figure 2, below). Although this wasn’t an RCT, so the patients knew they were getting the FMT and there could have been a placebo effect, the similarity in the rate of resolution between this study and the van Nood study (Figure 1) is striking.

Figure 2: Median number of bowel movements for 20 patients suffering from recurrent CDI treated with ‘crapsules’.Youngster blog

Oral FMT via ‘crapsules’ takes away the unpleasantness of the delivery for the recipient (if they can get over the ‘gross’ factor). But it doesn’t solve the lingering safety concerns associated with the procedure. We simply don’t have the tools to screen donor stool for problems we don’t yet know about. The experience from delivering hepatitis C virus to haemophiliacs in the 1980s in contaminated blood products from donors is salutary, and close to my heart since one of my good friends is still suffering the consequences of this. But, this risk has to be balanced against the urgent need of patients becoming increasingly desperate with recurrent CDI. If I had recurrent CDI, I’d be joining the queue for FMT.

The real solution to this problem is synthetic FMT. Lots of people are working on this at the moment – check our some of the work by Trevor Lawley on this. I am pretty certain that a simple bacterial cocktail will not make an effective synthetic FMT. There’s huge microbial and non-microbial diversity in the gut contents which will need to be replicated somehow. Clearly, some of this will be redundant, but it will take quite some time to pick through the constituent parts to derive an effective synthetic FMT. But I’m certain it will happen, and probably over the next decade.

Until then, ‘crapsules’ offer an alternative, effective way to deliver FMT, which is remarkably effective for resolving recurrent CDI. But recurrent CDI is just the start. There’s a host of other conditions that could potentially benefit from FMT. It may even be that ‘crapsules’ become a ‘new statin’: “a crapsule a day keeps the bad bugs away”?

Article citationYoungster I, Russell GH, Pindar C, Ziv-Baran T, Sauk J, Hohmann EL. Oral, Capsulized, Frozen Fecal Microbiota Transplantation for Relapsing Clostridium difficile Infection. JAMA 2014; in press.

Christmas 2014 Update

Christmas lights

Now that you have digested your Christmas turkey, I thought that it would be a good time to send out an update. These articles have been posted since the last update:

I’m in a rather reflective mood, so time to remind you of some of the key themes from 2014: Ebola, MERS-CoV, universal vs. targeted interventions, faecal microbiota transplantation (FMT), whole genome sequencing (WGS), carbapenem-resistant Enterobacteriaceae (CRE), and some interesting developments in environmental science. And what will we be still talking about come Christmas 2015? Let’s hope it won’t be Ebola, and I think that WGS will be a lab technique akin to a Vitek machine rather than subject matter for NEJM. But I think we still have ground to cover on whether to go for universal or targeted interventions, FMT, and improving our study designs in infection prevention and control. I can also foresee important studies on the comparative and cost-effectiveness of the various tools at our disposal.

And finally, before I sign off for 2014, a classic BMJ study on why Rudolf’s nose is red (it’s to do with the richly vascularised nasal microcirculation of the reindeer nose, apparently).

Image: Christmas #27.

Selective Digestive Decontamination (SDD) is dead; long live faecal microbiota transplantation (FMT)


Ok, so the title may be a little premature, since this blog relates to a study with a sample size of exactly one. However, I do think it spells the beginning of the end for Selective Digestive Decontamination (SDD), especially when applied to suppress gut colonization with antibiotic-resistant bacteria.

A number of groups have looked at using SDD to ‘decolonise’ carriers of multidrug-resistant Gram-negative bacteria such as CRE. In one study, 20 CRE colonized patients in each arm given gentamicin + polymyxin (SDD arm) or placebo (Control arm). The results were rather modest (see chart below). Plus, SDD has substantial downsides in terms of the potential for developing further antibiotic resistance, and ‘collateral’ damage to the gut microbiota.

Figure: Modest impact of SDD to ‘decolonise’ the gastrointestinal tract of CRE carriers.

Saide-Oldes CRE decol

I’ve been waiting for some data on the effectiveness of faecal microbiota transplantation (FMT) to decolonise carriers of antibiotic resistant bacteria for some time. A case report at ID Week related how the ordeal of a 13 year old girl was ended by a faecal microbiota transplantation. After months of persistent colonization and infection, the impact of a single dose of FMT was startling: CRE carriage was eliminated and there was no further bacterial infection.

One of the push-backs against using FMT more regularly is that it’s a crude (in every sense) and labour-intensive procedure compared with an antibiotic capsule. But that was before the invention of ‘crapsules’ (aka oral FMT). Another ID Week abstract reports the successful delivery of oral FMT using crapsules. (And it’s amazing what great dinner party conversation ‘crapsules’ makes. Try it – you’ll see.)

So, I think it’s time for a cluster randomized trial to compare the impact of SDD and FMT; my money is on FMT!

Image: Barbara Krawcowicz.

Inaugural ‘Journal Roundup’ (June 2014)


I’ve been asked by the Editor of the Journal of Hospital Infection to begin writing a monthly column providing an overview of key updates in the infection prevention and control literature. I’m pleased to say that the first edition (June 2014) is now available on the Journal of Hospital Infection website, and I’m delighted that the Journal Roundup is open access.

I thought it would be useful to outline how I produced this roundup. I began by scanning the tables of contents of the following journals, pulling out articles of interest: AJIC, Ann Intern Med, BMJ, CID, ICHE, JAMA, JAMA Intern Med, JHI, JID, JIP, Lancet, Lancet ID, NEJM. This was easy for the “big five” (Lancet, BMJ, AIM, JAMA and NEJM) because only a handful of articles are directly relevant. It was more tricky for the specialist journals, since all articles are likely to be of interest. I’ve tried to avoid focusing solely on my own research interests, but these doubtless come through. One way to mitigate this in future is for others to provide a Journal Roundup now and then – or at least make some contribution. If you’re interested in this, please do let me know.

Highlights of this inaugural issue include a spike in MERS-CoV cases, coverage of the WHO report on antimicrobial resistance, more evidence that faecal microbiota transplantation works for curing recurrent CDI, the impact of nursing education on patient mortality, individualized antibiotic dosing, CA-MRSA in US Fire Stations, a successful community-based hand hygiene intervention, an outbreak of CRE in Ireland, updated SHEA guidelines for SSI and CDI, the identification of ‘optimum outlier’ (aka ‘positive deviant’) cleaners, a disturbing patient story, an update on the move towards ‘bare below the elbow’ in the US, an overview of the regulatory environment for healthcare apps, conference abstracts from APIC and ECCMID, and the use of Yelp (a customer review website) to identify cases that would otherwise have gone unreported during a foodborne outbreak.

Please feel free to share this with your colleagues, and let me know if you have any thoughts or comments.


Highlights from APIC 2014

APIC 2014I couldn’t make it to APIC this year, but I have picked out a few highlights. More than 300 abstracts were presented so I can only scratch the surface here, but the good news is that they’re all available in an AJIC supplement.

Multidrug-resistant Gram-negative rods

One of the oral presentations was on controlling CRE in Texas (Cifelli et al). The interventions comprised improvements in lab identification and patient electronic tagging, and front-line infection prevention and control practices (dedicated rooms, equipment and staff etc). It’s difficult to know which of these approaches (if any!) made the difference: we still don’t know what works to control CRE.

A group from Louisville explored transmission of CRE in an LTAC (Kelley et al). LTACs have previously been shown to be a hotbed for CRE transmission in some parts of the USA. They found that almost half of patients that acquired CRE were admitted to beds that had been previously occupied by a CRE patient, which brings a new meaning to ‘hotbed!’ This links in with previous studies showing that admission to a room previously occupied by a patient with MDROs is a risk factor for acquisition. It also shows that CRE (K. pneumoniae at least) can survive for long enough on surface to bring indirect transmission via environmental contamination into play.

Definitions and terminology surrounding CRE and MDR-GNR in general are in a state of confusion. Both require urgent clarification. A survey of 79 hospitals by Jadin et al for their definitions of MDR-GNR yielded virtually 79 different definitions! This makes it challenging for facilities to communicate clearly about MDR-GNR, since what qualifies as MDR-GNR may not make the cut in another hospital. And this is not even accounting for variations in lab diagnostics!

A small prevalence survey of CRE carriage in Michigan by Berriel-Cass et al found that 2 (3.8%) of 53 patients were colonized. Neither patient had history of CRE, but one who did have a history of CRE screened negative! It’s difficult to know who is at high risk for CRE carriage, and even more difficult to know how long they will carry it for. However, we probably know enough to conclude that “once positive always positive” is a sensible (if somewhat conservative) approach.

The rest

A fascinating study from Arizona by Sifuentes et al evaluated a hygiene intervention in a LTCF. A number of bacteriophages were used as markers for pathogenic virus transmission and inoculated onto hands and surfaces. The viruses spread rapidly throughout the faculty over a short time period (measured in hours), and a hygiene intervention significantly reduced the level of contamination of hands and surfaces. Most similar work has been performed in the acute setting, so some data from the non-acute setting is particularly welcome. This study illustrates the dynamic interplay between hand and surface contamination. In a way, hands are just another highly mobile fomite that are not disinfected frequently enough!

Jinadatha et al performed a very timely study exploring whether serial passage of bacteria with sub-lethal UV exposure prompts reduced susceptibility to UV. The study demonstrates that 25 serial exposures to UV did not affect bacterial UV susceptibility. However, the study did not explore whether other useful mutations may have occurred in the “survivors”; perhaps this is a job for whole genome sequencing in a follow-up study?

Faecal microbiota transplantation (FMT) is quickly becoming the standard of care for recurrent CDI. A study by Greig et al tells the story of implementing a FMT programme. The literature for FMT are impressive, but the ‘nuts and bolts’ of implementation are challenging. Where do you get the donor stool form? How do you screen the donors? Who performs the procedure? Who pays? Will it work here? Are just some of the questions that need to be negotiated for successfully implementing an FMT programme. The message from this study: it’s worth it – 83% of patients with recurrent CDI had resolved within 30 days.

Finally, I remain rather skeptical that “CA-CDI” is really on the rise. I may have to revise my opinion based on this abstract by Rogers and Rosacker, showing that a community-based educational intervention reduced the rate of CA-CDI!

Perspective from ECCMID Part III: CDI synthetic “repoopulation” (bacteriotherapy) closer than you think & “CA-CDI” still pie in the sky

Bacteriotheraphy for CDI is closer than you think

As our understanding of the importance of a happy, healthy microbiota develops, it seems increasingly clear to me that bacteriotherapy (administration of a controlled multi-species dose of bacteria) is a real prospect for the treatment of CDI (and most likely other conditions). This is illustrated by the dramatic effectiveness of faecal microbiota transplantation (FMT) for recurrent CDI. FMT is pretty crude, in every sense; synthetic FMT would be safer and more palatable. But I hadn’t realized how far the research towards available bacteriotherphy for CDI had advanced. Dr Trever Lawley gave an expert overview of his research programme, which is pointed in this direction.

Dr Lawley began by describing the human microbiota as a fingerprint: it’s consistent and unique. The microbiota is highly organized, to reflect its function, resulting in microenvironments. Antibiotics are like an atomoic bomb, resulting in huge perturbation of the gut microbiota. The idea of bacteriotheraphy to redress the balance is not new. Pioneers of bacteriotherapy (aka “repoopulation”) for CDI date back to at least 1989.

So, which bacteria get the nod to be included in the synthetic mix? It’s not an easy question, since examining the massively populous human microbiota is a daunting prospect and requires the application of novel tools (see Fig 1 of this excellent open-access review for a useful summary of the methods to examine the human microbiota and microbiome). Human trials and mouse model indicate that single species theraphy and probiotics are equivocal at best. These are blunt weapons to complement the nuclear fall out of the antibiotic A bombs! Dr Lawley’s reaseach has found an irreducible minimum of 6 species that are necessary for effective bacteriotherapy (in mice at least). Now all that is required is to find a common growth medium…oh, and do some humans trials!

Another speaker, Dr Cornley, mentioned another approach to preventing CDI: the prophylactic administration of metronidazole. If you’re read my Perspective from ECCMID on Selective Decontamination, you can probably guess which approach I’d choose.

“CA-CDI” still pie in the sky

A number of speakers contributed to the debate on whether “community-acquired” CDI is on the rise. Dr Scott Weese outlined the potential for foodborne risk of CDI, beginning with a ‘disclosure’ that we can all relate to: “I like to eat but I don’t like foodborne illness”! C. difficile is present in food animials (especially young ones) and strains are shared with humans. Rates of carriage are low, but Dr Weese made a good point on cumulative exposure. If 2% of burgers are C. difficile contaminated, I eat C. difficile on my 98th burger (not exactly, but you get the point). Plus, C. difficile spores can survive usual cooking times (which is not so relevant for me: I like my burger meat rare)! The carriage of C. difficile in animals combined with the high carriage of C. difficile in small human animals means that exposure to C. difficile is probably a daily event. But is this a risk? For a healthy 25 year old in the community, probably no. For a haematology inpatient, probably yes.

Dr Marjolein Hensgens considered whether CDI is still primarily nosocomial. The distinction of community vs. hospital onset is easy, but community vs. hospital acquisition is much more challenging and epidemiological disitinctions are approximate at best. For example, in the UK, a “Trust-apportioned” (=hospital acquired) case requires a specimen from an inpatient who has been in the same hospital for at least 4 days. Any readmission (even if they were in the hospital the previous week) is considered “non Trust-apportioned”, but it’s important to remember that this is not the same as “community-acquired”. The fact that the Trust-apportioned and non Trust-apportioned cases track each other so closely in the UK reductions suggests that almost all cases were healthcare-associated (Figure 1).

CA-CDI_2Figure 1: the number of CDI cases reported to Public Health England, defined as “Trust-apportioned” or “non Trust-apportioned” from 2007 onwards.  

An important US study suggested a stepwise increase in CA-CDI. However, this apparent increase could be explained by a number of other factors. Firstly, a high proportion of patients with apparent CA-CDI actually have had healthcare exposoure of some kind if you look hard enough (82% in this study). So this upward trend in “CA-CDI” could very well be HA-CDI with unrecognized healthcare exposures. Secondly, it is difficult to know whether there have been any changes in the number of diarrhoeal stools tested in the community. Infectious diarrohea has always been common in the community, but is rarely tested for CDI. Thirdly, comparing the epidemiology of patients who develop CDI in the community with those who develop CDI in hospitals could result in a misleading picture. A more appropriate comparator would be patients who have non-CDI diarrhea in the community. Finally, does WGS prove that hospital acquisition of CDI is now rare? No, it only proves that transmission from known symptomatic CDI cases is less frequent than you may expect. There are many other sources for hospital acquisition of CDI, not least asymptomatic carriers. We’re surrounded by C. difficile so of course a degree of CA-CDI occurs. But is it increasing? I still think no – or at least, not rapidly due to phase-shift in epideimogogy (that we saw with the emergence of CA-MRSA in the late 1990s).

You can view some other ‘Perspectives from ECCMID’ here.

Image: C. difficile‘ by AJ Cann.