Plasmids of the urinary microbiota

Abstract

Studies of the last decade have identified a phylogenetically diverse community of bacteria within the urinary tract of individuals with and without urinary symptoms. Mobile genetic elements (MGEs), including plasmids and phages, within this niche have only recently begun to be explored. These MGEs can expand metabolic capacity and increase virulence, as well as confer antibiotic resistance. As such, they have the potential to contribute to urinary symptoms. While plasmids for some of the bacterial taxa found within the urinary microbiota (urobiome) have been well characterized, many urinary species are under-studied with few genomes sequenced to date. Using a two-pronged bioinformatic approach, we have conducted a comprehensive investigation of the plasmid content of urinary isolates representative of 102 species. The bioinformatic tools plasmidSPAdes and Recycler were used in tandem to identify plasmid sequences from raw short-read sequence data followed by manual curation. In total, we identified 603 high-confidence plasmid sequences in 20 different genera of the urobiome. In total, 70 % of these high-confidence plasmids exhibit sequence similarity to plasmid sequences from the gut. This observation is primarily driven by plasmids from E. coli , which is found in both anatomical niches. To confirm our bioinformatic predictions, long-read sequencing was performed for 23 of the E. coli isolates in addition to two E. coli strains that were sequenced as part of a prior study. Overall, 66.95 % of these predictions were confirmed highlighting the strengths and weaknesses of current bioinformatic tools. Future studies of the urobiome, especially concerning under-studied species in the urobiome, should employ long-read sequencing to expand the catalogue of plasmids for this niche.

Genomic analyses of an Escherichia coli and Klebsiella pneumoniae urinary tract co‐infection using long‐read nanopore sequencing

“…Our results using long‐read sequencing technology, further expand the known plasmid content from multiple bacterial strains occupying the urobiome. In line with a previous report that investigated plasmid content from urinary isolates, similar or identical plasmids were found to be shared between urobiome isolates from different genera, including a 1546‐bp plasmid sequence found in two E. coli and one K. pneumoniae strain (Johnson et al, 2022). Shared plasmid sequences were also found between E. coli and Nosocomiicoccus ampullae, Staphylococcus aureus and Staphylococcus epidermidis , and Alloscardovia omnicolens and Lactobacillus gasseri (Johnson et al, 2022).…”