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Enterobacteriaceae Pangenomes Offer Look at Antimicrobial Resistance Reservoirs in Natural Populations

NEW YORK – By sequencing hundreds of Enterobacteriaceae family bacterial representatives from wastewater and livestock-related sites, investigators in the UK and US profiled pangenome dynamics in the bugs, including antimicrobial resistance (AMR) genes and other features found on chromosomal DNA and plasmids.

For a study in Science Advances on Friday, University of Oxford John Radcliffe Hospital researcher Nicole Stoesser and her colleagues reasoned that studies centered on clinical isolates of Escherichia coli and other Enterobacteriaceae representatives alone may miss clinically relevant pangenome, plasmid, and horizontal gene transfer features in naturally occurring Enterobacteriaceae populations that may act as reservoirs for AMR genes.

The researchers did short- and long-read genome sequencing on more than 550 representatives from the Escherichia genus, along with 274 isolates from non-Escherichia species. The non-clinical isolates — collected and cultured from 14 pig, cattle, or sheep farms or from five wastewater treatment sites in the UK at three points over the year — provided a window into AMR gene patterns and mobile genetic element dynamics within and between Enterobacteriaceae species at these sites.

"Plasmids have a higher burden of AMR genes and insertion sequences, and AMR gene-carrying plasmids show evidence of being under stronger selective pressure," the authors reported, noting that plasmid dynamics appeared to reflect geographical sampling locations as well as the environmental niche considered.

With the 827 high-quality genomes generated for bacteria from Escherichia, Klebsiella, Citrobacter, Enterobacter, and other genera, for example, the team detected nearly 2,300 circularized plasmids, which seemed to vary alongside the genus and environmental niche considered.

The researchers' analyses further suggested that those plasmids were particularly prone to carrying AMR genes and insertion sequences involved in horizontal gene transfer compared with chromosomal sequences in the pangenome and appeared to show signs of selection linked to the environmental niches tested.

"[O]ur study highlights the plastic and dynamic nature of AMR gene dissemination within the pangenome of major Enterobacteriaceae in several important non-clinical niches," the authors reported. "It also demonstrates how robustly evaluating the flow or AMR genes and [mobile genetic elements] across highly diverse and dynamic niches is challenging even with extensive sampling."

"The implications of this for adequately understanding dissemination and selection of AMR genes in a 'One Health' context should not be underestimated," they added.

It remains to be seen whether selective pressures at distinct sites such as farms can whittle down the diverse set of strains and species found there, or whether AMR evolution is distinct at each site, the authors explained, noting that additional research is needed to untangle details of the site-specific distinctions.

Even so, they wrote, "our findings underline the importance of local control strategies for the emergence and spread of AMR beyond clinical settings."