Monitoring antibiotic resistance in hospital environments

Cooperating for the future

‍‍The fight against antibiotic resistance is global, and as such there are numerous initiatives all over the world for monitoring antibiotic resistance in different industries. In clinical settings, we have collectives gathering data on AMR, such as GLASS by the World Health Organization and EARS-Net for the EU region. Similar initiatives are also happening in the agricultural and veterinarian sectors, though usually on a national level. 
The problem that monitoring initiatives face today is in cooperation and communication. In many ways, everyone wants to help but no one truly knows who is responsible for setting major actions in motion. This can easily lead to antibiotic resistance being overlooked and free to run rampant until it is too late and an outbreak occurs. 
We need everyone to connect in the fight against antibiotic resistance, which is why a One Health approach is so important to advocate for.

ARG profiles 

When monitoring an area for antibiotic resistance, clearly defined antibiotic resistance gene (ARG) profiles appear. These profiles give us an overview of what the situation is in the given target area. In this webinar, we get to take a closer look on the ARG profiles of two hospitals and how they differ from each other even though they are located in the same region. 

Not only were the hospitals’ ARG profiles very different from each other, but they were also changing. The same hospital could have two different ARG profiles at different times, sometimes only weeks apart. That is a huge indicator that routine and frequent monitoring is needed so that emerging peaks can be identified and precautionary actions justified.

More than crocodiles in the sewers

Monitoring antibiotic resistance in agri- or aquaculture is quite straightforward as far as sampling goes. However, when monitoring for antibiotic-resistant bacteria in a human population we cannot simply select people at random and start investigating what ARGs they are exposed to. If we want to understand the situation in humans efficiently, sewage is the best bet. However, sewage systems only give a general image of the current situation in the human population, not the environment.
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Yet, the environment plays a very important role in the fight against antibiotic resistance. Environments, both natural and human-impacted, are massive playing fields where organisms are in constant cooperation and conflict, and there is potential for some very nasty ARG-carrying bacteria to emerge.  
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The main thing we can do to mitigate the emergence of potentially dangerous bacteria and stop outbreaks is working on prevention, and monitoring is a major component in that endeavor. 

Methods for monitoring 

In this webinar, we get to hear about four different methods for monitoring antibiotic resistance and their pros and cons. The four methods discussed were: 
-   Selective culturing
-   qPCR
-   Functional metagenomics
-   Shotgun metagenomics 

All of the methods have their situational advantages and are viable options, depending on the research objective. If you are familiar with Resistomap or antibiotic resistance research, you have most likely encountered something called High-Throughput qPCR Smartchip, but what exactly does that mean? The HT-qPCR SmartChip technology by Takara Bio is a type of qPCR method which uses a SmartChip that contains 5184 nano-wells. That means that with all operational standard procedures included, one chip can scan for 384 genes from 4 samples, with the possibility of dividing all the way down to 12 genes from 128 samples. The versatility and cost-efficiency of the HT-qPCR SmartChip technology is the reason why it is the chosen method for monitoring AMR utilized in Resistomap’s services.

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If you would like to review the webinar discussed here for yourself, a recording is available here!