Abstract
F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.
Highlights
F-type plasmids were found across all four of the genera collected in the dataset: Citrobacter (53 C. freundii), Enterobacter (67: 65 E. cloacae, 2 untyped Enterobacter sp.), Escherichia (471 E. coli), and Klebsiella (135: 61 K. oxytoca, 67 K. pneumoniae and 7 untyped Klebsiella sp.)
Livestock plasmids mostly came from Escherichia (392/ 407), whereas WwTW plasmids had a more uniform distribution over all four genera in line with the greater diversity of genera in WwTW isolates (Fig. 1a)
We considered several statistics to optimise our network threshold: (i) the number of communities detected (Fig. 2a), (ii) the proportion of plasmids recruited into communities (Fig. 2b) and (iii) kernel density estimates (KDEs) of network edge weights stratified by sampling compartment (Fig. 2c)
Summary
F-type plasmids are a diverse group of Enterobacteralesassociated plasmids characterised by their corresponding replicons’ need for DNA gyrase, DnaB, DnaC, DnaG and single-strand binding and DNA polymerase III proteins to replicate [13]. Previous studies of F-type plasmids have often focussed on clinically relevant isolates, often only those encoding ESBLs [16]. They have been limited to studies with smaller sample sizes. Potential seasonal variation was accounted for by sampling over three time-points (TPs) at each site This provided a high-quality dataset of n = 726 plasmids for characterising natural plasmid populations. They are defined as subsets of nodes with dense intra-connections, but sparse inter-connections [23] In our analyses, they represented groups of similar plasmid sequences. We aimed to provide a framework applicable to such studies
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