Periodic Reporting for period 3 - PLASREVOLUTION (Understanding the evolution of plasmid-mediated antibiotic resistance in real life scenarios)
Reporting period: 2020-07-01 to 2021-12-31
We first established the ideas and concepts that we wanted to investigate during PLASREVOLUTION by publishing two perspective/opinion pieces in Trends in Microbiology and Science. In parallel, we started all the experimental work, with the main focus of understanding the evolution of plasmid-mediated antibiotic resistance in the Hospital Universitario Ramon y Cajal, which is a large public hospital in Madrid. Specifically, we have focused our efforts in understanding the evolutionary dynamics of the antibiotic resistance plasmid pOXA-48, which is the an extremely prevalent and relevant carbapenem resistance plasmid worldwide. We have performed an extensive series of epidemiological work, molecular analyses and mathematical modelling to characterize the “in-hospital” ecology and evolution of this plasmid, which we detailed below (work belonging to objectives 1 and 2).
First, we have used mechanistic models combining epidemiological data from more than 9,000 patients with whole genome sequence information from 250 enterobacteria clones to characterise the dissemination routes of a pOXA-48-like carbapenemase-encoding plasmid in our hospital setting over a two-year period. Next, we used these epidemiological and molecular analyses to discover events of in vivo compensatory evolution in the gut of hospitalised patients. Finally, we determined the distribution of fitness effects for the antibiotic resistance plasmid pOXA-48 in wild-type, ecologically compatible enterobacterial isolates from the human gut microbiota. The results of these works have produced two manuscripts which have been uploaded to bioRxiv (under review in Nature Microbiology and Nature Communications) and one more manuscript which is currently in preparation. In addition, we have also published a methods paper covering some of the techniques used in these experiments (in Methods in Molecular Biology).
Moreover, we have also experience important progress in objective 3 (plasmid dynamics). Specifically, we uncovered the central role of genetic dominance shaping genetic cargo in plasmids, using antibiotic resistance as a model system. Our results provide a new understanding of how mobile genetic elements evolve and spread, uncovering the neglected influence of genetic dominance on bacterial evolution. As a result, we published a paper on this topic (in PNAS).
In summary, the project is advancing at a good pace and over the next 2.5 years we will continue to accomplish the different objectives we established for PLASREVOLUTION, producing high impact publications as a result.
-Describing the relative importance of between-patient and within-patient spread of pOXA-48-mediated carbapenem resistance in a hospital setting.
-Analysing the in vivo evolution of plasmid-mediated antibiotic resistance in the gut of hospitalised patients.
-Describing the distribution of plasmid fitness effects in wild-type, clinically relevant, enterobacteria isolates.
-Uncovering the central role of genetic dominance shaping genetic cargo and horizontal spread of mobile genetic elements in bacteria.
In the second half of the project we will continue characterising the evolution of plasmid-mediated antibiotic resistance, using animal models to complement the results we have obtained from the patients and the in vitro experiments.