Fast and low-cost WGS to track AMR plasmid flow and forecast outbreaks

Identify the direction of AMR plasmid flow through Whole Genome Sequencing. This will help to design strategies to prevent AMR plasmid circulation. 

Ph.D. Oscar Miguel Rollano-Peñaloza, Primary Investigator, Molecular Microbiology Laboratory, Universidad Catolica Boliviana / Associated Researcher, Universidad Mayor de San Andres.

Antimicrobial resistance (AMR) is primary driven by horizontal genetic transfer of AMR plasmids, which can be  transmitted among bacteria across different habitats. By knowing the spread of AMR plasmids (AMR plasmid flow) within human and environmental settings we could design strategies to prevent AMR plasmid flow and AMR outbreaks. However, a significant challenge arises from the limited knowledge of the AMR extend in LMIC communities.

The highlands of Bolivia exemplify this challenge because Bolivia lacks stewardship of antibiotic sales (antibiotics can be acquired as over-the-counter drugs). Here, the lack of proper wastewater management from large cities has placed significant constrain on downstream communities and ecosystems.

AMR plasmid spread is hypothesized to happen during the overlap of habitats, for example when animals drink from polluted rivers obtaining AMR plasmids. Animals will eventually deposit the AMR plasmids in soils. AMR plasmids can be transmitted to farm animals and its workers. Finally, rivers will be polluted by discharges of infected workers, creating a vicious circle of AMR bacterial infections and AMR plasmid flow. 

Therefore, we are interested to understand the actual impact of one of the most polluted rivers in the world into remote communities at Bolivian highlands.

We believe that in the near future, WGS diagnosis will replace traditional diagnosis, and we hope this study will be one step in this direction. Thus, in the near future tracking of AMR plasmids will be easier and cost-effective benefitting the general public. This work will also contribute to the scientific community by proposing new mechanisms of AMR plasmid flow.

In detail, the Pucarani municipality and its communities will be benefited with the establishment of a baseline for bacterial infections and AMR prevalence. At the moment, there are no projects collecting AMR prevalence at national level and we hope that by showing the feasibility of this kind of projects, we can encourage the Central Government to create AMR surveillances. In order to achieve this, we will work closely with National and local health authorities to improve antibiotic stewardship. For example, promoting the limitation or banning the use of antibiotics as growth promoters in fodder.

During the project we will collaborate closely with the Nursing school located in Pucarani. This collaboration will provide an active feedback to the project and it will engage actively with the communities, through educational workshops as well as collecting epidemiological data.

We aim to create a peer-review publication showing the origin of AMR plasmid flow and its direction with the data obtained from sequencing AMR plasmids.  

The information from this project will also be published and socialized with decission maker entities as the Health ministry in order to improve antibiotic stewardship.

The understanding of the AMR plasmid flow will identify the principal dangers of AMR transmission. Further, this will help to understand the threats that a community faces and will help them to prevent AMR outbreaks.

By visualizing how the invisible threat (the AMR plasmid circulation) is transmitted through different habitats of a community, we will help people to understand the importance of AMR and its spread. 

This example will be scalated to bigger commnunities and eventually cities in order to create awareness on AMR spread. By graphically showing the AMR flow in a small community we will identify the AMR plasmid reservoirs.

Based on the initial information acquired in the Pucarani community, we are planning to deploy a similar setting in a different community along the Seke river to verify the proposed AMR plasmid flow for the Pucarani community. We have chosen the Cohana community because is close to the Seke river and is also in the shore of Titikaka lake, that way we will also incorporate water samples and the effects of the AMR plasmid flow on lakes.

For the 3rd year we will try to identify this setting in a less polluted river, such as the Deasguadero river and the Aguallamaya community. The source of this river has effluents from the Peruvian side and the community as such is close to the Tripartite Bolivia-Peru-Chile border. By analyzing the AMR plasmid flow in this community we will make efforts to internationalize the project and hope that in the near future we can collaborate with colleagues from Peru and Chile.

-We will obtain water samples from the river, soil samples from the river, animal stool samples and AMR samples from then local health center.

-We will have good quality DNA with enough amount to perform WGS.

-We will obtain WGS of AMR plasmid from the 4 habitats with good enough quality to create accurate phylogenetic data.

-We will collect information about AMR outbreaks in the community and assess outbreaks that were not identified or related with bacterial infections.

We have observed that there is profound gap in the education at general level about Biology and Biochemistry. General concepts of microbiology and antibiotics are lacking and therefore to grasp the idea of microorganisms creating diseases is still a difficult one. Further, the education regarding the effect of antibiotics on microbes and the importance of completing treatments still remains as a challenge. Therefore, the main barrier for this solution will be that the educational gap will not allow people from the communities to understand the importance of microbes and its relation with the diseases. Therefore, it might be difficult for them to identify AMR infections and to help to prevent AMR outbreaks.

The poorest communities in Bolivia are at higher risk of AMR outbreaks because of their general lack of knowledge about microbes and AMR. 

LMICs dont have a solid baseline data on AMR. Therefore this type of Challenges provide very much needed support to collect this data. However, our deepest interest is to contribute to the AMR problem worldwide by providing knowledge in a very unique setting which includes remote communities, free-romaing animals and a very polluted river. 

We also believe that this challenge will help to scale this solution to other LMICs and overall improve the AMR plasmid tracking worldwide under the One health perspective. The exposure in this kind of programs will help us to expand our Latin American network to study and surveill AMR plasmids. Finally this way we will raise the awareness of AMR. 

In order to initiate the solution we would like to contact the

Health Ministry and Epidemiological program.

We would like to scale our solution with the following LATAM researchers:

Pasteur Institute, Uruguay. We have already had a short collaboration to study SARS-CoV-2 and because they already have the expertise on working on AMR they can share their experience working in LATAM with AMR.

Universidad Cayetano Heredia, Peru. 

Universidad de Antofagasta, Chile.

It will be interesting to collaborate at a South American level to understanding the AMR plasmid transmission dynamics in a broader scale.