Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

Abstract

Large conjugative plasmids are important drivers of bacterial evolution and contribute significantly to the dissemination of antibiotic resistance. Although plasmid borne multidrug resistance is recognized as one of the main challenges in modern medicine, the adaptive forces shaping the evolution of these plasmids within pathogenic hosts are poorly understood. Here we study plasmid–host adaptations following transfer of a 73 kb conjugative multidrug resistance plasmid to naïve clinical isolates of Klebsiella pneumoniae and Escherichia coli. We use experimental evolution, mathematical modelling and population sequencing to show that the long-term persistence and molecular integrity of the plasmid is highly influenced by multiple factors within a 25 kb plasmid region constituting a host-dependent burden. In the E. coli hosts investigated here, improved plasmid stability readily evolves via IS26 mediated deletions of costly regions from the plasmid backbone, effectively expanding the host-range of the plasmid. Although these adaptations were also beneficial to plasmid persistence in a naïve K. pneumoniae host, they were never observed in this species, indicating that differential evolvability can limit opportunities of plasmid adaptation. While insertion sequences are well known to supply plasmids with adaptive traits, our findings suggest that they also play an important role in plasmid evolution by maintaining the plasticity necessary to alleviate plasmid–host constrains. Further, the observed evolutionary strategy consistently followed by all evolved E. coli lineages exposes a trade-off between horizontal and vertical transmission that may ultimately limit the dissemination potential of clinical multidrug resistance plasmids in these hosts.

Fitness Costs of Plasmids: a Limit to Plasmid Transmission

“…Several reports pinpoint conjugation as a source of plasmid cost for the bacterial host (28,64,65). For example, the fitness cost associated with plasmids R1 and RP4 in E. coli is reduced after the conjugation rate is decreased or abolished by natural selection in an experimental setting (64).…”

“…Also, the expression of plasmid R1 conjugation genes has been shown to activate stress responses in E. coli (65), although it is not clear if this is cause or consequence of the cost of plasmid carriage. Finally, in a recent analysis of the IncN antibiotic resistance plasmid pKP33, Porse and colleagues showed that the loss of the conjugation region reduced the burden associated with plasmid carriage in E. coli (28).…”

“…Plasmids can promote bacterial survival in the presence of antibiotics, but, as we have seen, they can also impose a fitness cost when they enter a new bacterial host. The past few years have witnessed growing interest in the fitness effects of plasmids (21)(22)(23)(24)(25)(26)(27)(28)115), and some of the general principles underlying these effects are now beginning to be identified. However, we still are a long way from understanding the specific molecular basis of these costs or being able to predict plasmid fitness effects in a bacterial host.…”

“…To date, only a handful of studies have investigated the genetic basis of plasmid fitness costs (23,(25)(26)(27)(28) or the transcriptional effects of plasmids on the bacterial host (23,25,113,131). In our experience, the best way to investigate the molecular mechanisms underlying the fitness costs of plasmids is to first obtain a compensated clone from the parental plasmid-carrying strain (22,23).…”

“…The idea underlying this hypothesis is that even if plasmids produce a cost when they first arrive in a new bacterial host, this cost could be alleviated over time through compensatory mutations in the plasmid and/or the host chromosome (20). In recent years, several studies have analyzed the molecular basis of the cost and compensation of plasmids in bacterial populations (21)(22)(23)(24)(25)(26)(27)(28), generating new models of the existence conditions of plasmids (22,24). These studies evaluate a number of selection, transfer, and compensation regimes that could explain plasmid survival in bacterial populations, and have revealed new evidence about the molecular mechanisms underlying the cost of and adaptation to plasmids.…”