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?
Continue readingWhole genome sequencing
Tracking Outbreaks in Hospitals: Can Genomic Surveillance Help?
A guest post by Dr Alexander Sundermann (bio below) in preparation for tomorrow’s Journal Club on genomic surveillance (register here for that)…
When was the last time you investigated a potential outbreak in your facility? How was it identified—or was it even confirmed as a true outbreak? For years, outbreak detection methods have remained relatively unchanged, relying heavily on observing infection patterns or confirming outbreaks reactively using whole genome sequencing (WGS). But what if we shifted this approach to perform WGS proactively on all infections? This idea is the foundation of our new pre-print study, which evaluates whether WGS surveillance can enable earlier outbreak detection and halt transmission before it spreads.
Continue readingWhole genome sequencing to support IPC has been ‘the future’ for too long
There has been a lot of excitement about the prospects of whole genome sequencing (WGS) to support infection prevention and control in a really meaningful way over the past decade or two. But to me this potential seems largely unfulfilled. WGS remains largely the domain of reference and research laboratories, and has not transitioned effectively to support IPC daily decision making. A recent review highlights the potential of WGS to support IPC, and identifies some of the barriers to be overcome if WGS really is to be a big part of our future in IPC.
Continue readingOn the origin of multidrug-resistant Gram-negative bacteria (MDR-GNB)
The colour of the global crisis of antibiotic resistance is red (if te Gram stain is your reference). In rich countries we have ESBL-producing Enterobacterales (mainly E. coli), but the real problem are carbapenemase-producing strains (Klebsiella, Pseudomonas and Acinetobacter) that are already endemic in lower and middle-income countries. The unanswered question is “where did these resistant bacteria come from”? Animals or bathrooms? Continue reading
What about E. coli ST131 (part 2); is it foodborne?
Last November I blogged on E. coli ST131, frequently portrayed as a pandemic clone, combining hypervirulence, ciprofloxacin resistance and ESBL production. The question is whether the undeniable high prevalence of this bug among clinical isolates results from its virulence and antibiotic resistance or whether it is just a reflection of carriage prevalence in the general population, without any relationship to virulence or resistance. Two recently published studies try to shed new light on the debate; one bringing in chicken retail meat as the source…… Continue reading
What about E. coli ST131?
One of the faces of the global antibiotic resistance crisis is Escherichia coli ST131, frequently portrayed as a pandemic clone, combining hypervirulence, ciprofloxacin resistance and ESBL production. A recent study in Genome Research, a journal you may not read every month, though, sheds a whole new light on this “superbug”. Continue reading
Real-time whole genome sequencing (RT-WGS) & spread of resistant bacteria
At last weeks’ ICPIC I crossed arguments with John Rossen on the question whether RT-WGS helps us to control the spread of resistant bacteria. The setting is the hospital and the definition of RT is “in time to guide essential decision making”. Is RT-WGS a “need-to-have” or a “nice-to-have” thing? Continue reading
It’s transmission doc, but not as we know it
A groundbreaking study just published in PLOS Genetics provides new insight into the transmission dynamics of bacteria in the ICU setting using WGS. The ambitious authors performed WGS on virtually all bacterial isolates from ICUs in a US hospital for a year. The first surprise was that 12% of the bacteria considered clinically relevant were previously undescribed.
The next – and perhaps biggest – surprise was that whilst transmission of the usual suspect pathogens (MRSA, VRE etc) was rare, 9% of the other bacteria were shared by multiple patients, often with overlapping admissions (see the figure below). This suggests that there is a fair bit of transmission going on under the radar in the ICU setting.
Figure: Clonal lineages extending across multiple patients.
This study reminds me of one published in CID a few years ago showing that outbreaks of resistance probably occur regularly and usually undetected across multiple species.
So, is it time to start using WGS for all bacteria identified in the clinical laboratory? Not quite yet I don’t think: the analytical methods have not yet caught up with the sequencing technology. But this study is a glimpse of the future, no doubt about it.
Reflections on Infection Prevention and Control 