whole genome sequencing

Using whole genome sequencing to investigate a Burkholderia ICU outbreak

norvillephillip Uncategorized , , ,

I’ve written this post in preparation for Wednesday’s Journal Club (register here) in collaboration with IPC Partners

Burkholderia are fascinating genus of bacteria which I had the pleasure of doing some post doctoral work on. The ability of the species to innately resist antibiotics and preservatives, as well as prolonged persistence in the environment means the organisms can cause challenges for healthcare organisations and infection prevention and control. I have seen an increasing number of publications in recent years linking outbreaks to contaminated medical devices and even disinfectants (good systematic review here). Therefore this paper published in The Journal of Hospital Infection investigating a Burkholderia cenocepacia outbreak using whole genome sequencing (WGS) grabbed my interest. I have also been interested in the role of WGS in detection and prevention of outbreaks (see a previous IPC Partners by Dr Alex Sundermann) and the potential benefits.  

Design and methods 

  • The outbreak took place in an intensive care unit in Vietnam between May and August 2023 affecting 19 patients 
  • Environmental sampling of high touch surfaces, fluid samples and medical devices was performed 
  • WGS was performed on all available B. cenocepacia complex (Bcc) isolates using Illumina Hiseq platform. In total WGS was performed on 20 clinical isolates and 3 environmental isolates (from used syringes)
  • Prior to investigating with WGS it had been suspected that positive clinical Bcc samples were the result of blood culture contaminants

Key findings

  • Environmental sampling identified 3 B. cenocepacia isolates from separate syringes using to deliver IV fluids 
  • No growth of microorganisms was detected in samples of skin antiseptics, hand sanitizers and ultrasound gel (surprising to me!)
  • WGS confirmed that all B. cenocepacia isolates from clinical and environmental samples belonged to the same sequence type 
  • The isolates carried an array of acquired antimicrobial resistance genes predicted to confer resistance to carbapenems, sulfonamide, and tetracycline
  • The source of the outbreak was not identified but limitations in the preparation and administration of IV fluids were identified 

What this means for IPC

  • WGS can successfully be used to aid hospital outbreak investigation which is particularly relevant for complex bacteria such as Burkholderia, in which traditional detection and typing methods often have low sensitivity
  • WGS can be implemented successfully in low and medium income countries such as Vietnam but requires strong collaboration between IPC, clinical microbiologists and molecular biologists 
  • WGS allowed species identification which is important in this context, as the Bcc complex comprises of more than 22 different species, exhibiting differing epidemiological and pathologic features, and varying susceptibility to antibiotics both in vitro and in vivo. Misidentification may lead to inappropriate antimicrobial therapy. 
  • The study highlights the importance of following aseptic practices and procedures in handling and administration of intravenous medications to avoid bacterial contamination and prevent infection

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

Jon Otter (@jonotter) Contamination , , ,

pathomap

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: pathomap.org. 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.

What’s trending in the infection prevention and control literature? HIS 2012 -> HIS 2014

Jon Otter (@jonotter) Conferences , , , , , , , ,

I was privileged to speak at the Healthcare Infection Society meeting in France today on ‘What’s trending in the infection prevention and control literature? HIS 2012 -> HIS 2014’. You can download my slides here, and view the recording below:

http://youtu.be/k2NsEb_xUZ4

I have always enjoyed attending these light-hearted summary sessions at other conferences, so I hope I struck the right tone. In order to track some of the trends in the infection prevention and control literature since the last HIS conference (in late 2012), I plugged some search terms into Google trends (Figure).

Figure: Google Trends for all search terms (excluding viruses) (2004 to present). Logos and arrows represent the time of the HIS 2012 and HIS 2014 conferences. Search terms: hospital cleaning; carbapenem resistant Enterobacteriaceae, whole genome sequencing, fecal microbiota transplantation. [Note, I had to spell it ‘wrong’ (fecal v faecal) to detect a trend. Blasted Americans.]what's trending google trends

Based on my search terms, there was one infection control trend that trumped all others: Ebola. If I include in with the other Google search terms, it eclipses all others! Whilst trends in Google searches may not necessarily correlate with trends in the infection prevention and control literature, in this case, it is true that the outbreak of Ebola in West Africa has prompted a lot of publications in the literature – and consumed an awful lot of professional time for all who are connected with hospital infection prevention and control! Aside from Ebola, other trends in the infection prevention and control literature that I covered include MERS-CoV, universal vs. targeted interventions, faecal microbiota transplantation, whole genome sequencing, carbapenem-resistant Enterobacteriaceae (CRE), and some aspects of environmental science. Finally, I looked into my crystal ball and predict some of the trends in the infection prevention and control literature by the time HIS 2016 comes around.