Plasmid conjugation drives within-patient plasmid diversity

Grayson, F.; Loman, L.; Nonnenmacher, T.; Pople, D.; Pollard, J.; Patel, B.; Williams, D.; Hounsome, L.; Hopkins, K. L.; Robotham, J. V.; Ledda, A.

doi:10.1101/2024.09.27.615342

bioRxiv · 10.1101/2024.09.27.615342

Plasmid conjugation drives within-patient plasmid diversity

Grayson, F.·Loman, L.·Nonnenmacher, T.·Pople, D.·Pollard, J.·Patel, B.·Williams, D.·Hounsome, L.·Hopkins, K. L.·Robotham, J. V.·Ledda, A.

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Abstract

Plasmids are well known vehicles of antimicrobial resistance (AMR) genes dissemination. Through conjugation, plasmid-encoded AMR genes are spread among neighbouring bacteria, irrespective of their strain or even their species. This process is very concerning from a public health perspective, as plasmid-borne AMR gene outbreaks are often not confined to single species or strains and are therefore more difficult to be fully uncovered. At the moment, the impact of plasmid conjugation on within-patient plasmid diversity is not well understood. In this work we will tackle the role of conjugation on within-patient plasmid diversity using a dataset of carbapenemase-producing Enterobacterales (CPEs). The dataset of 256 sequences from 115 patients was sampled across England over 30 months. Each patient has more than one sequence, with at least one sequence carrying an OXA-48 gene, a well-known plasmid-borne carbapenemase-encoding gene. If more than one sequence carries the OXA-48 gene, they are carried on different bacterial hosts. Using a hybrid de novo-on-reference assembly pipeline, we were able to reconstruct the full OXA-48 plasmid from short read sequencing data for 232 of the 256 sequences. Of the 115 patients, 83 (72%) of patients had an identical OXA-48 plasmid in two or more sequences. Only 2 patients carried very different (>200 SNPs) alleles of the OXA-48 plasmid, probably from separate acquisitions. Our study shows that when more than one bacterial host carrying an OXA-48 plasmid is found in a patient, it is most likely that the same plasmid has been shared via conjugation. The event of separate acquisition of different plasmids in different bacterial hosts is highly unlikely in our dataset. Data StatementWe use data provided by Hopkins et al 2022 [16]. The data can be accessed from the National Center for Biotechnology Information (NCBI) and can be found at Bioproject Accession no. PRJNA788733. None of the data used was synthetically generated. Impact StatementConjugative plasmids are well known vessels of horizontal gene transfer, with a prominent role in the spread of antimicrobial resistance genes among different bacterial species or strains. At the epidemiological level, conjugation combined with sequencing a single colony per patient, results in plasmids outbreaks carrying antimicrobial resistance genes being found in different bacterial species and strains in different patients, potentially eluding surveillance protocols based on same bacterium/same resistance scheme. In this study we analyse within-patient plasmid diversity in a dataset with more than one sequence per patient. Only two patients show clear genomic signs of separate plasmids acquisition, while 83 patients share identical plasmids in different bacterial hosts. This points out to a very strong role of plasmid conjugation in shaping within-patient plasmid diversity.

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Grayson, F., Loman, L., Nonnenmacher, T., Pople, D., Pollard, J., Patel, B., Williams, D., Hounsome, L., Hopkins, K. L., Robotham, J. V., Ledda, A.. 2024-09-29. Plasmid conjugation drives within-patient plasmid diversity. https://doi.org/10.1101/2024.09.27.615342

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