I’ve just read an enjoyable commentary in Antimicrobial Agents and Chemotherapy exploring barriers and solutions to implementing proactive WGS in IPC. It links in nicely with a post I wrote towards the end of last year along similar lines. So what are the key barriers and how do we overcome them?

The review summarises the barriers as follows:

• Evidence. Both in terms of impact in reducing infection risk and cost effectiveness.
• Financial. There is a substantial implementation cost and an ongoing cost to consider. How does this balance against benefits?
• Infrastructure. There needs to be a laboratory (not every hospital has one!), and space within the lab for additional kit. And staff with sufficient expertise to handle the new approaches and workflows to delivery proactive WGS accurately. An alternative approach is outsourcing the WGS.
• Methods. There is currently no agreed and established methodology for interpreting WGS data in the context of IPC. More than that, there’s not even complete agreement on which sequencing platform to use (long read or short read) and whether WGS should be used reactively or proactively! Then we can throw into the mix the complicating factor of thinking beyond bacteria, and how we handle emerging pathogens.
• Legal & financial. How do we ensure that patient data remains safe and secure, and is used in compliance with legal and research ethics best practice? Also, lots of discussion to be had about how to handle the enhanced resolution of outbreaks and transmission events that will doubtless come from this approach. Will we be overwhelmed with small outbreaks that are not that significant, and divert resource from handling the biggies (that we don’t need proactive WGS to identify)?
• Regulatory. As is always the case, the regulatory position will need to catch up with current best practice, and this will take time.

One very consistent finding of all studies of WGS across large bacterial datasets is the identification of “cryptic” outbreaks i.e. those that have not been identified by standard methods. The numbers of these can often be surprisingly large. For example in one Australian study, 31% of the >2000 bacterial isolates were transmitted – many more than were identified as being part of an outbreak. On the other hand, WGS also helps to discount outbreaks by showing that the isolates are too dissimilar to be explained by cross-transmission.

In preparation for Dr Alexander Sundermann’s (the lead author of this review) Journal Club tomorrow on genomic WGS surveillance (you can register here), I thought it would be interesting to run a poll to let you decide which are the key barriers to implementing proactive WGS in IPS. You can take part in the poll here or by using the QR code below (it will remain open and we’ll look at the results during Journal Club tomorrow). As is always the case when you put together a poll like this, there are a million ways you could phrase the questions and options, but here goes:

“Rank the following as barriers to implementing proactive WGS in IPC”:

• Limited evidence of preventing transmission / infection
• Limited evidence of cost effectiveness
• Too expensive
• Lack of infrastructure
• Lack of expertise
• Lack of defined and agreed methodology