Abstract
Background Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing between Enterobacterales causing human infections and those from other niches remains unclear. Studies to date have been small, with dispersed sampling frames, restricted to drug-resistant isolates only, and using incomplete plasmid sequence reconstruction.
Methods We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008-2020 from sites <60km apart in Oxfordshire, UK, and sequenced using short-(Illumina) and long-read (PacBio, Nanopore) approaches to fully reconstruct bacterial genomes.
Findings We analysed 1,458 complete Enterobacterales genomes, including 3,697 circularised plasmids, one-third of which represented novel diversity. Plasmid alignment-free clustering identified 122/247 (49%) closely related clusters containing plasmids found in human BSIs and ≥1 other niche (73/247 [30%] such clusters across human BSI and livestock-associated niches). Seventeen groups of near-identical plasmids (n=84 plasmids) were seen across human BSIs and ≥1 other sampling niche (eight groups across human BSI and livestock-associated niches), including six AMR-gene associated groups. Pangenome-style analyses of the 69 most prolific clusters (n=1,832/3,697 plasmids) revealed shared, core, “backbone” gene sets. Core-gene plasmid phylogenies reflected an intertwined ecology where well-conserved plasmid backbones carried diverse accessory functions, potentially linked to niche adaptation. Closely related plasmids were found across distantly related bacterial lineages and species.
Interpretation We identified significant plasmid diversity, highlighting the challenges in adequately sampling natural plasmid populations. Many genetically related plasmids were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change may be relatively common. Dense, unselected sampling is highly relevant to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the dissemination of plasmid-associated AMR.
Funding This study was funded by the Antimicrobial Resistance Cross-council Initiative supported by the seven research councils and the NIHR, UK.
Evidence before this study We searched PubMed using the search terms (Enterobacterales AND plasmid*) AND (Human OR Animal OR wastewater OR river OR sewage OR environment*) and (Enterobacterales AND plasmid*) AND (“One Health”) to 04/Jul/2022 with no restrictions on start date or language. We identified 221 studies, of which 167 (76%) were investigating Enterobacterales plasmid epidemiology to a lesser or greater extent. 108 (65%) studies analysed >1 Enterobacterales species, 49 (29%) studies investigated >50 isolates, 38 (23%) studies completely reconstructed all genomes being evaluated (20 studies a subset of genomes), 23 (14%) studies sampled across multiple niches, and only seven (4%) studies considered drug- and non-drug-resistant isolates. We identified no large-scale study which considered plasmid epidemiology in several species of drug-resistant and non-resistant Enterobacterales across multiple human and non-human niches.
Added value of this study For the first time, we demonstrate that Enterobacterales plasmid transfer and evolution between geographically proximate niches, including human bloodstream infection and livestock-associated niches, is not uncommon. This includes closely related plasmids associated with AMR, observed across Enterobacterales species and lineages, underscoring the relevance of our findings for “One Health” for AMR management approaches. Our study also highlights that plasmid diversity in Enterobacterales is substantial and undersampled to date.
Implications of all the available evidence Our understanding of Enterobacterales plasmid and AMR epidemiology has been limited by the size and scope of available studies. In the largest systematic study to date, we demonstrate that whilst in some cases niche-/host-associated plasmid structuring exists, multiple Enterobacterales plasmid clusters, including those associated with AMR genes, can disseminate widely.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Overall reorganisation of manuscript with secondary results moved to the Supplementary.