Niger's AMR outbreak sheds light on where superbugs thrive

Now, back to Kirsty Sands, whom we heard from earlier at the Ineos Oxford Institute for antimicrobial research. She has been looking at severely malnourished young children hospitalised in Niger and found that 3 in 4 of them were colonised with highly drug resistant bacteria, a situation which arose through significant spread between them in hospital…

Kirsty - We collected samples from just under 1,400 children. All of them were below the age of five. We collected rectal swabs as a less invasive tool for us to screen the gut microbiome. We were really interested in trying to understand what bacteria were colonising within the gut and inferring whether or not this could be a risk for ongoing infection and ongoing transfer to other children and into the environment. We began by culturing them to have a look at what was growing from these samples. To complement our work, we also used some genetic approaches, and some whole genome sequencing, to understand the genomic traits of different bacteria.

Chris - And was this just done once when the kids first came in, or did you look multiple times?

Kirsty - Multiple times. This was a study that progressed over time. We collected the first swabs when the patients were admitted and then we collected samples throughout their hospital stay for those children that were quite unwell, and then for everybody we also collected a swab at patient discharge. This gave us the ability to look at those different environments, so whether the bacteria were present at the beginning or whether they picked up particular drug-resistant bacteria during their stay.

Chris - When you give people antibiotics you can drive the development of resistance to those antibiotics - but also they could be picking up resistant bacteria from other kids who are in the environment. So I suppose there are two sources through which resistance could flow here?

Kirsty - Yes, absolutely there are. I think one of the most important aspects is to be able to understand whether the resistance is within the bacteria itself in terms of the core gene, or whether it's being carried on what we call plasmids, which are mobile, often circular structures that the bacteria can pick up and pass on in many different situations. And in our study, that’s what we found - the bacteria had these plasmids with antibiotic resistance genes.

Chris - So does that argue then that because these kids are being put on antibiotics, there is a risk that they’re going to acquire resistance from the environment they’re in? And did you find that was happening - that there was a spread of resistant forms around these children as they were hospitalised?

Kirsty - We did, in large numbers unfortunately. Some children were colonised with these drug-resistant bacteria at the beginning. However, over two-thirds of the patients that were negative for a particular drug-resistant E. coli on admission became colonised by the time we collected the sample at patient discharge. This suggests that within that environment and within that time frame, they are picking up this bacteria from somewhere. It’s quite a concerning finding in the fact that in a short space of time extremely vulnerable patients - who of course are admitted to a treatment facility for a very good reason - are leaving the treatment facility carrying a drug-resistant E. coli that may well go on to pose a threat to the wider community.

Chris - So what should we do about it? Do we know that they do actually pose a threat and they're going to carry on hanging on to those resistant forms, is there evidence of onward harm?

Kirsty - There is evidence of onward harm more widely. We have to think that these bacteria, you know, because they can persist in different environments, they can be found, different samples, different sources, there's always this possibility of an ongoing concern. I think, following this project, it would be really important to know whether the same bacteria we found colonising the children was found within the treatment facility. This would really drive the need for access to more suitable and sustainable infection prevention and control strategies. It would be essential to know how long these children remained colonised for and how long that potential threat exists in the community.

Chris - Right now, of course, we’ve got serious problems in the Middle East, and it almost looks like we’re going to have history repeating itself - based on what you found in Niger - in Gaza.

Kirsty - Yes, absolutely. We are seeing all the same problems. There's a huge shortage of food, which will increase the levels and numbers of malnutrition in children in particular. A large amount of overcrowding. It’s a very, very tough situation, which would then mean that there are limited resources and access to clean, safe drinking water. Hygiene and sanitation will be very difficult to maintain. What this really means is that we will see an increase in drug-resistant bacteria and we will see an increase in the spread of these bacteria across people, across the environment, and this may well be a broader threat to other countries.