Resolving the plasmid paradox: costs and benefits of horizontal gene transfer in a community context

Horizontal gene transfer (HGT) is a central evolutionary process enhancing genome diversification and rapid adaptation of species to new environmental conditions. Mobile genetic elements (MGE) facilitate genetic exchange between species through HGT by carrying accessory gene cargos encoding beneficial traits such as resistance to metals and antibiotics. MGE-mediated transfer of antibiotic resistance genes between species in natural microbial communities has contributed to the global spread of antibiotic resistance. It is therefore essential to understand the ecological drivers of the maintenance and transmission of MGEs in bacterial communities. Here I use conjugative plasmids as an example MGE to study the ecological and evolutionary dynamics of plasmids in bacterial populations and communities across a range of environments. First, I demonstrate that plasmids selected in a single-host environment evolved host specialism due to fitness trade-offs, whereas plasmids evolved in a multi-host environment could overcome this trade-off to evolve host-generalism. Secondly, I show that the costs and benefits of plasmid carriage and the long-term dynamics of the plasmid and the mercury resistance transposon it encodes varied extensively between diverse species of Pseudomonas. I next show that plasmid maintenance was facilitated by compensatory evolution to ameliorate the cost of plasmid carriage. Compensatory loci varied between species, with parallel mutations targeting different regulatory and biosynthetic pathways in each species. Lastly, I examine the effect of community structure on plasmid dynamics in simple bacterial communities. When plasmids were carried by proficient plasmid-donor species this led to higher plasmid abundance at the community-level, while in diverse communities, plasmid transmission could be impeded through the dilution effect, limiting plasmid spread. This thesis demonstrates that plasmid dynamics in bacterial communities are determined by the combination of ecological and evolutionary processes, depending on the selective environment, the structure of the bacterial community and variation among species in their proficiency to host plasmids and to undergo compensatory evolution to ameliorate their costs. These data highlight the importance of studying plasmid dynamics in a community-context

The proficiency of the original host species determines community-level plasmid dynamics

Plasmids are common in natural bacterial communities, facilitating bacterial evolution via horizontal gene transfer. Bacterial species vary in their proficiency to host plasmids: Whereas plasmids are stably maintained in some species regardless of selection for plasmid-encoded genes, in other species, even beneficial plasmids are rapidly lost. It is, however, unclear how this variation in host proficiency affects plasmid persistence in communities. Here, we test this using multispecies bacterial soil communities comprising species varying in their proficiency to host a large conjugative mercury resistance plasmid, pQBR103. The plasmid reached higher community-level abundance where beneficial and when introduced to the community in a more proficient host species. Proficient plasmid host species were also better able to disseminate the plasmid to a wider diversity of host species. These findings suggest that the dynamics of plasmids in natural bacterial communities depend not only upon the plasmid's attributes and the selective environment, but also upon the proficiency of their host species

The dilution effect limits plasmid horizontal transmission in multispecies bacterial communities.

By transferring ecologically important traits between species, plasmids drive genomic divergence and evolutionary innovation in their bacterial hosts. Bacterial communities are often diverse and contain multiple coexisting plasmids, but the dynamics of plasmids in multi-species communities are poorly understood. Here, we show, using experimental multi-species communities containing two plasmids, that bacterial diversity limits the horizontal transmission of plasmids due to the 'dilution effect'; this is an epidemiological phenomenon whereby living alongside less proficient host species reduces the expected infection risk for a focal host species. In addition, plasmid horizontal transmission was also affected by plasmid diversity, such that the rate of plasmid conjugation was reduced from co-infected host cells carrying both plasmids. In diverse microbial communities, plasmid spread may be limited by the dilution effect and plasmid-plasmid interactions, reducing the rate of horizontal transmission

Ecological and evolutionary mechanisms driving within-patient emergence of antimicrobial resistance

The ecological and evolutionary mechanisms of antimicrobial resistance (AMR) emergence within patients and how these vary across bacterial infections are poorly understood. Increasingly widespread use of pathogen genome sequencing in the clinic enables a deeper understanding of these processes. In this Review, we explore the clinical evidence to support four major mechanisms of within-patient AMR emergence in bacteria: spontaneous resistance mutations; in situ horizontal gene transfer of resistance genes; selection of pre-existing resistance; and immigration of resistant lineages. Within-patient AMR emergence occurs across a wide range of host niches and bacterial species, but the importance of each mechanism varies between bacterial species and infection sites within the body. We identify potential drivers of such differences and discuss how ecological and evolutionary analysis could be embedded within clinical trials of antimicrobials, which are powerful but underused tools for understanding why these mechanisms vary between pathogens, infections and individuals. Ultimately, improving understanding of how host niche, bacterial species and antibiotic mode of action combine to govern the ecological and evolutionary mechanism of AMR emergence in patients will enable more predictive and personalized diagnosis and antimicrobial therapies

Multi-host environments select for host-generalist conjugative plasmids

BACKGROUND: Conjugative plasmids play an important role in bacterial evolution by transferring ecologically important genes within and between species. A key limit on interspecific horizontal gene transfer is plasmid host range. Here, we experimentally test the effect of single and multi-host environments on the host-range evolution of a large conjugative mercury resistance plasmid, pQBR57. Specifically, pQBR57 was conjugated between strains of a single host species, either P. fluorescens or P. putida, or alternating between P. fluorescens and P. putida. Crucially, the bacterial hosts were not permitted to evolve allowing us to observe plasmid evolutionary responses in isolation. RESULTS: In all treatments plasmids evolved higher conjugation rates over time. Plasmids evolved in single-host environments adapted to their host bacterial species becoming less costly, but in the case of P. fluorescens-adapted plasmids, became costlier in P. putida, suggesting an evolutionary trade-off. When evolved in the multi-host environment plasmids adapted to P. fluorescens without a higher cost in P. putida. CONCLUSION: Whereas evolution in a single-host environment selected for host-specialist plasmids due to a fitness trade-off, this trade-off could be circumvented in the multi-host environment, leading to the evolution of host-generalist plasmids