Hospitals spawn antibiotic resistant bacteria

06 August 2019

Interview with 

Sophia David, Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute


Klebsiella pneumonaie is what’s known as an opportunistic pathogen. It’s a bacterium that can cause infection in vulnerable people, resulting in skin, blood and respiratory problems. Klebsiella strains resistant to a group of so called “last line antibiotics” called carbapenems are spreading through hospitals in Europe. The estimated number of deaths in Europe due to these antibiotic resistant infections increased from about 300 in 2007 to over 2000 by 2015. Sophia David, from the Wellcome Sanger Institute, has been studying this spread by analysing the genetics of 1,700 patient samples from 32 European countries. She took Katie Haylor through the work they'd done...

Sophia - So the key finding from our study is that the majority of carbapenem-resistant Klebsiella pneumoniae infections in Europe were a result of transmission within hospitals. And we also showed that transmission between hospitals, particularly those that were close by and in the same country, also played a significant role in the spread of these bacteria.

Katie - And is it correct then that you can infer those relationships because you know about the relatedness between these different strains?

Sophia - Yes exactly. So where we find that two samples are very closely related in terms of their genetic code, and they also originate from patients that were treated in the same hospital, that gives us a very strong indication that transmission likely occurred within that hospital.

Katie - So why are these carbapenem-resistant strains of Klebsiella pneumoniae spreading through hospitals?

Sophia - Within hospitals a relatively high usage of antibiotics creates a selection pressure, whereby the bacteria that are the most resistant to antibiotics will be the most likely to survive in this kind of environment.

Katie - So they're the fittest essentially.

Sophia - Exactly, so that they are the fittest in this type of environment.

Katie - These strains that are spreading between people, would that suggest that perhaps hygiene or infection control may be partly a cause?

Sophia - Yes exactly. So the finding here suggests improving infection control, hygiene measures, more carefully monitoring patients when they get referred from one hospital to another; those sorts of measures could have a key impact. I should emphasize that the number of infections with these very resistant types of bacteria are still very low.

Katie - How long does it take before you would be sure that somebody has a carbapenem-resistant strain of this type of an infection?

Sophia - So typically it would take a hospital probably a few days from taking a sample from a patient and then getting a result back from the lab. That really is a goal within the community, is for the development of rapid tests that instead of taking days, we could get a result within hours. And it could be that whole genome sequencing will play a major role here. But at the moment we still need to grow the bacteria in a lab. That's really the major limiting factor before we can then go and do DNA sequencing.

Katie - In terms of immediate implications there's the infection control side of things; we need more antibiotics I guess, new ones coming through the pipeline. Longer term, could you envisage a situation where a hospital are already aware of the top five antibiotic-resistant strains to watch out for any given week, for example?

Sophia - Yes exactly. So instead of there just being a small number of sequencing hubs as there are at the moment, I envisage these being much more widespread, and indeed hospitals be able to undertake their own sequencing and analysis. Yes indeed they will be aware of the circulating strains in their area and will then be able to, for example, flag up new strains that they haven't seen before. So there is still work to be done in order to get to that point.


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