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.

WGS ICU timeline

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.