Given, C. | Search bioRxiv

bioRxiv2025

ESBL plasmid compatibility with the surrounding microbial community influences ESBL gene survival under CRISPR-antimicrobial targeting

Bacteria often acquire resistance against antibiotics through the transfer of conjugative resistance plasmids. Hence, it is vital to develop strategies to mitigate the dispersal of antimicrobial resistance (AMR). CRISPR-based antimicrobial tools offer a sequence-specific solution to diminish and restrict the dissemination of antimicrobial resistance genes among bacteria. CRICON (CRISPR via conjugation) is an antimicrobial CRISPR tool that has been shown to efficiently reduce multi-resistance when targeting ESBL (Extended Spectrum Beta-Lactamase) harboring plasmids. However, conjugatively delivered genetic elements may be subjected to bacterial defense, lead to resistance development, and revert the efficiency of the CRISPR tools. Here, we studied the evolutionary consequences of four ESBL-harboring Escherichia coli strains targeted by CRICON in a 10-day multispecies microcosm experiment. We show that CRICON reduces the ESBL prevalence within the bacterial community, while the final ESBL persistence depends on the initial community composition. We observed an unexpected survival strategy of an ESBL-plasmid by escaping into a more competitive host species. Further, we show the development of partial resistance against the CRISPR-antimicrobials during the experiment. Our results underline the importance of the ecological and evolutionary factors in multispecies bacterial communities, as they may disrupt the effective use of CRISPR-based antimicrobial strategies via undesired outcomes of targeted therapies against plasmid-bearing multi-resistant bacteria.

microbiology↗

bioRxiv2021

Multi-plasmid clash in a bacterial community: plasmid viability depends on the ecological setting of hosts

Plasmids are genetic elements that disperse horizontally between different strains and species of bacteria and a major factor in the dissemination of virulence factors and antibiotic resistance. Understanding the ecology of plasmids has a notable anthropocentric value and therefore the interactions between bacterial hosts and individual plasmids have been studied in detail. However, bacterial systems often carry multiple genetically distinct plasmids, but dynamics of these multiplasmid "clashes" has remained unstudied. Here, we set to investigate the survival of 11 mobilizable or conjugative plasmids in five different ecological settings. The key incentive was to determine whether plasmid dynamics are reproducible and whether there are trade-offs in plasmid fitness that stem from the ecological situation of their initial hosts. Growth rates and maximum population densities increased in all communities and treatments over the 42-day evolution experiment although plasmid contents at the end varied notably. We show that large multiresistance conferring plasmids are unfit when the community also contains smaller plasmids with fewer resistance genes. This suggests that restraining the use to few antibiotics can make bacterial communities sensitive to others. The hosts also appear to react to the presence of multiple genetically different plasmids by enhancing fimbriae production instead of alleviating costs of individual plasmids. In general, the survivors of the here-studied multi-plasmid clash are significantly affected by the presence or absence of antibiotic selection and plasmid-free hosts of varying fitness. Therefore, these trade-offs in different settings can explain for example why some resistance plasmids have an advantage during a rapid proliferation of antibiotic sensitive pathogen whereas others dominate in alternative situations.

microbiology↗