Niche and local geography shape the pangenome of wastewater- and livestock-associatedEnterobacteriaceae

Abstract

Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes1,2, where genes move intra- and inter-species via horizontal gene transfer3. These species can cause clinical infections4,5 as well as persist environmentally6,7. Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates8,9, the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828 Enterobacteriaceae, including 553 Escherichia spp. and 275 non-Escherichia species with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing on E. coli, we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.

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

“…This comprises a subset of the entire REHAB dataset, which overall contains n = 2293 circularised plasmids recovered from n = 828 isolates. This dataset is described in more detail [21].…”

“…We recovered n = 726 circularised plasmids containing an F-type replicon (see Table S1) from a large dataset of highquality Enterobacterales genomes, obtained by hybrid assembly using both short-read (Illumina, 150 bp pairedend) and long-read (PacBio or Nanopore) sequencing of cultured isolates [21]. These isolates were collected over three TPs in 2017 from a region of south-central England, UK.…”

“…All participating farmers provided written consent for participation. Specific details on farm recruitment and sampling procedure can be found in [21] and Anjum et al (paper in preparation).…”

“…Further, they have been limited to studies with smaller sample sizes. Here, we analyse hundreds of F-type plasmids drawn from a survey of environmental diversity in Enterobacterales, sampled in 2017 from a region of South-Central England, UK [21]. Sampling was from livestock (cattle, pig and sheep), and from influent, effluent and upstream/downstream waterways surrounding wastewater treatment works (collectively termed WwTWs).…”

Role of the mobilome in the global dissemination of the carbapenem resistance geneblaNDM

“…Gene dissemination is a fundamentally spatial process. Despite being theoretically mobile, in practice most plasmids may be both strongly host-constrained (Acman et al, 2020) and associated with particular locations or environmental niches (Shaw et al, 2020). All in all, this could be hinting at the existence of plasmid niches: settings to which particular plasmids are more adapted.…”