Recovering <i>Escherichia coli</i> Plasmids in the Absence of Long-Read Sequencing Data

The incidence of infections caused by multidrug-resistant <i>E. coli</i> strains has risen in the past years. Antibiotic resistance in <i>E. coli</i> is often mediated by acquisition and maintenance of plasmids. The study of <i>E. coli</i> plasmid epidemiology and genomics often requires long-read sequencing information, but recently a number of tools that allow plasmid prediction from short-read data have been developed. Here, we reviewed 25 available plasmid prediction tools and categorized them into binary plasmid/chromosome classification tools and plasmid reconstruction tools. We benchmarked six tools (MOB-suite, plasmidSPAdes, gplas, FishingForPlasmids, HyAsP and SCAPP) that aim to reliably reconstruct distinct plasmids, with a special focus on plasmids carrying antibiotic resistance genes (ARGs) such as extended-spectrum beta-lactamase genes. We found that two thirds (<i>n</i> = 425, 66.3%) of all plasmids were correctly reconstructed by at least one of the six tools, with a range of 92 (14.58%) to 317 (50.23%) correctly predicted plasmids. However, the majority of plasmids that carried antibiotic resistance genes (<i>n</i> = 85, 57.8%) could not be completely recovered as distinct plasmids by any of the tools. MOB-suite was the only tool that was able to correctly reconstruct the majority of plasmids (<i>n</i> = 317, 50.23%), and performed best at reconstructing large plasmids (<i>n</i> = 166, 46.37%) and ARG-plasmids (<i>n</i> = 41, 27.9%), but predictions frequently contained chromosome contamination (40%). In contrast, plasmidSPAdes reconstructed the highest fraction of plasmids smaller than 18 kbp (<i>n</i> = 168, 61.54%). Large ARG-plasmids, however, were frequently merged with sequences derived from distinct replicons. Available bioinformatic tools can provide valuable insight into <i>E. coli</i> plasmids, but also have important limitations. This work will serve as a guideline for selecting the most appropriate plasmid reconstruction tool for studies focusing on <i>E. coli</i> plasmids in the absence of long-read sequencing data.