Highlight: Virtual Issue on Host–Pathogen Interactions and Antimicrobial Drug Resistance

© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. A 2022 Virtual Issue from Genome Biology and Evolution (GBE) highlights recent articles on the evolutionary dynamics of host–pathogen interactions and antimicrobial drug resistance. This topic was the subject of a recent global symposium of the Society for Molecular Biology and Evolution (SMBE) organized by Santiago Castillo-Ramírez from the Universidad Nacional Autónoma de México, Ellen Leffler from the University of Utah, and Azim Ansari from the University of Oxford. This day-long symposium focused on coevolutionary relationships between pathogens and their hosts and the eco-evolutionary genomics of antimicrobial drug resistance. According to Leffler, the co-organizers “had been wanting to organize a symposium on this topic for a while, and even had one planned for SMBE 2020 [which was later canceled due to COVID-19]. We felt that host–pathogen studies were very exciting and in early stages, with a lot of creative research in diverse systems. ” The global symposium, which was held on October 20, 2022, included 4 invited and 12 contributed talks, with the diverse group of speakers hailing from 4 continents. Following the symposium, GBE compiled this Virtual Issue of recent papers to foster further discussion and research on this topic. Host–pathogen interactions and antibiotic resistance dynamics constitute good evolutionary models due to the strong selective pressures involved. As discussed by Jacques Fellay from École Polytechnique Fédérale de Lausanne in the first invited talk of the SMBE symposium, host–pathogen interactions leave signatures on the genomes of both organisms, allowing for interrogation of the coevolutionary forces at play. However, the specific genomic footprints observed may differ among host–pathogen systems due to differences in demographic histories, lifehistory traits, or genome architectures. For example, in their paper on the population genomics of the maize pathogen Ustilago maydis, Schweizer et al. (2021) observed loweraverage genetic diversity compared with other fungal pathogens due to recent strong bottlenecks coinciding with maize domestication. They also found a higher rate of adaptive substitutions in genes located within virulence clusters, highlighting their role in U. maydis evolution. In contrast, in another plant fungal pathogen, the poplar rust fungus, Melampsora larici-populina, Persoons et al. (2022) found little impact of a selective sweep on overall genomic diversity outside of the immediate vicinity of the adaptive locus. This may indicate a “soft” selective sweep in which selection acted on standing variation and/or the impact of recombination in mitigating the loss of diversity. Selective sweeps are not the only genomic signatures exhibited by pathogens adapting to their hosts. A study by Wyka et al. (2021) investigated the plant pathogen Claviceps and found that expansion of transposable elements and tandem gene duplications coincided with increased host range potential and speciation. According to Wyka et al., this indicates that “alterations of genomic architecture and plasticity can substantially influence and shape the evolutionary trajectory of fungal pathogens and their adaptability. ” Consistent with this, Torres et al. (2021) identified polymorphic transposable elements in the fungal plant pathogen Verticillium dahliae that colocalized near pathogenicity-related genes and correlated with high expression levels, suggesting that these elements may impact the evolution of adaptive genomic regions. Although these adaptive forces can increase pathogen virulence, they may come at a cost. A study by Cherry (2020) looked at gene inactivations driven by positive selection in the human pathogen Salmonella enterica. Cherry found that many of these genes were involved in virulence, motility and chemotaxis, biofilm formation, and resistance to antibiotics or toxins, providing a glimpse into the selective trade-offs often faced by pathogens in nature. On the other side of this dynamic are the host genomes, which often exhibit their own unique signatures of host– pathogen interactions. Liu et al. (2020) explored these