Genomic network analysis of environmental and livestock F-type plasmid populations

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.

A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage

“…Indeed, different genetic content was observed within plasmid clusters, with some clusters containing both AMR and non-AMR plasmids, with most distributed across farms, but some showing a much more restricted niche. The diversity of plasmids present in this dataset has been investigated further elsewhere [25, 55].…”

Enterobacteralesplasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK

“…The remaining 32% (1,193/3,697) of plasmids were unclassified (i.e., connected set with less than 4 plasmids) highlighting the previously unsampled plasmid diversity within our dataset. In total, we found n =67 known PTUs, containing a median 9 plasmids (IQR=4-30, range=1-556), where the largest assigned PTU (556/2,504) was PTU-FE, corresponding to F-type Escherichia plasmids 42, 43 . The proportion of unclassified plasmids was higher in environmental/livestock samples (33%; 385/1,155) versus BSI samples (26%; 485/1,880), emphasising the underrepresentation of non-human plasmids in reference plasmid databases.…”

“…Of these, 31% (13/42) carried the AMR gene bla TEM-1 , and in a range of genetic contexts: n =9/13 bla TEM-1 genes were found within Tn 3 and n =4/13 were carried without a transposase, of which n =2/4 were found with the additional AMR genes aph(6)-Id , aph(3’’)-Ib , and sul2 . AMR genes were disproportionately carried by F-type plasmids (61% [337/550] AMR-carrying cluster plasmids versus 34% [891/2627] of the total clustered plasmids), further underlining their known role in AMR gene dissemination 43, 50, 51 . More broadly, bla TEM-1 was found in 15% (38/247) of clusters over n =292 plasmids, suggesting a diversity of plasmid backgrounds.…”

“…The determination of the plasmid-plasmid network, threshold, and clusters could be achieved with several alternative methodologies. Plasmid networks have previously been constructed by full sequence alignments 87 , annotated genes 88 , and alignment-free Mash distances 43,89,90 .…”

Beyond to the Stable: Role of the Insertion Sequences as Epidemiological Descriptors in Corynebacterium striatum

“…Genomic publications in recent years have reinforced the essential role of the niche in the genomic structure of bacteria ( Matlock et al, 2021 ; Shaw et al, 2021 ). The evolution of bacteria in the different niches is mainly driven by two factors, vertical gene transfer (VGT), and horizontal gene transfer (HGT), due to transduction, transformation, or conjugation events ( Lawrence, 2005 ).…”