title: Native California soils are selective reservoirs for multidrug-resistant bacteria.
abstract: Soil bacteria can exhibit extensive antibiotic resistomes and act as reservoirs of important antibiotic resistance traits. However, the geographic sources and evolutionary drivers of resistance traits are poorly understood in these natural settings. We investigated the prevalence, spatial structure and evolutionary drivers of multidrug resistance in natural populations of Bradyrhizobium, a cosmopolitan bacterial lineage that thrives in soil and aquatic systems as well as in plant and human hosts. We genotyped > 400 isolates from plant roots and soils across California and assayed 98 of them for resistance traits against 17 clinically relevant antibiotics. We investigated the geographic and phylogenetic structure of resistance traits, and analysed correlations of resistance with strain abundance, host infection capacity and in vitro fitness. We found: (i) multidrug resistance at all sites, (ii) subsets of resistance traits that are spatially structured and (iii) significant associations between resistance traits and increased strain abundance or host infection capacity. Our results highlight multiple selective factors that can result in the spread of resistance traits in native Bradyrhizobium populations.
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Amanda C
authors.initials: AC
authors.lastname: Hollowell
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Kelsey A
authors.initials: KA
authors.lastname: Gano
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Lopez
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Kareem
authors.initials: K
authors.lastname: Shahin
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: John U
authors.initials: JU
authors.lastname: Regus
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Gleason
authors.affiliation: Department of Anthropology, University of California, Riverside, CA, USA.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Graeter
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Pahua
authors.affiliation: Department of Biology, University of California, Riverside, CA, USA.|Institute for Integrative Genome Biology, University of California, Riverside, CA, USA.
authors.forename: Joel L
authors.initials: JL
authors.lastname: Sachs
mesh_terms: D020369:Bradyrhizobium / Q000187:drug effects* / Q000302:isolation & purification*; D002140:California; D024901:Drug Resistance, Multiple, Bacterial; D005838:Genotype; D018517:Plant Roots / Q000382:microbiology*; D012641:Selection, Genetic; D012988:Soil Microbiology