Evolving Populations in Biofilms Contain More Persistent Plasmids

Abstract

Bacterial plasmids substantially contribute to the rapid spread of antibiotic resistance, which is a crisis in healthcare today. Coevolution of plasmids and their hosts promotes this spread of resistance by ameliorating the cost of plasmid carriage. However, our knowledge of plasmid–bacteria coevolution is solely based on studies done in well-mixed liquid cultures, even though biofilms represent the main way of bacterial life on Earth and are responsible for most infections. The spatial structure and the heterogeneity provided by biofilms are known to lead to increased genetic diversity as compared with well-mixed liquids. Therefore, we expect that growth in this complex environment could affect the evolutionary trajectories of plasmid–host dyads. We experimentally evolved Shewanella oneidensis MR-1 with plasmid pBP136Gm in biofilms and chemostats and sequenced the genomes of clones and populations. Biofilm populations not only maintained a higher diversity of mutations than chemostat populations but contained a few clones with markedly more persistent plasmids that evolved via multiple distinct trajectories. These included the acquisition of a putative toxin–antitoxin transposon by the plasmid and chromosomal mutations. Some of these genetic changes resulted in loss of plasmid transferability or decrease in plasmid cost. Growth in chemostats led to a higher proportion of variants with decreased plasmid persistence, a phenomenon not detected in biofilms. We suggest that the presence of more stable plasmid–host dyads in biofilms reflects higher genetic diversity and possibly unknown selection pressures. Overall, this study underscores the importance of the mode of growth in the evolution of antibiotic-resistant bacteria.

The distribution of plasmid fitness effects explains plasmid persistence in bacterial communities

“…This is the standard practise in the field, and previous studies have shown that plasmid fitness effects measured in laboratory conditions correlate with those measured in animal models 24 ; however, our results may not be fully representative of pOXA-48 fitness effects in the human gut. Future studies will need to explore more complex in vitro systems 60 , as well as in vivo animal models 61 . Another important limitation of our study is that we modelled bacterial communities with a simple resource competition model that does not consider spatial structure 62 , complex ecological interactions between community members 63 , plasmid-host co-evolution 64 , or differential rates of horizontal transmission 28 .…”

Simulating the Influence of Conjugative-Plasmid Kinetic Values on the Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model

“…In any case, PL3 persists over the long term much more effectively at low segregation levels (such as 10 −5 and 10 −6 ). In the present version of our model, the role of toxin-antitoxin postsegregational killing mechanisms in plasmid stabilization, eventually in synergy with spatial differentiation (biofilms), was not addressed ( 71 , 72 ), but we are signaling here the potential importance of this process in plasmid persistence and spread.…”

Slightly beneficial genes are retained by evolving Horizontal Gene Transfer despite selfish elements

“…Besides investigating the impact of HGT for a range of different fitness effects, we have also shown how spatial structure is a key component for the emergence of HGT of rescuable genes. Both conjugation and transformation have indeed been observed to occur more frequently in biofilms than in well-mixed cultures (Madsen et al, 2012), and plasmids have furthermore been shown to be more persistent in biofilms (Stalder et al, 2020). On the other hand, spatial structure can slow down adaptation in asexual populations because individuals are mostly competing with their related conspecifics (Gordo and Campos, 2006;Habets et al, 2007;Chacón and Harcombe, 2019).…”