Abstract
Plasmids are infectious double stranded DNA molecules that are found within bacteria. Horizontal gene transfer promotes successful spread of different types of plasmids within or among bacteria species, making their detection an important task for guiding clinical treatment. We used whole genome sequenced data to determine the prevalence of plasmid replicons in clinical bacterial isolates, the presence of resistance and virulence genes in plasmids, and the relationship between resistance and virulence genes within each plasmid. All bacterial sequences were de novo assembled using Unicycler before extraction of plasmids. Assembly graphs were submitted to Gplas+plasflow for plasmid prediction. The predicted plasmid components were validated using PlasmidFinder.
A total of 159 (56.2%) out of 283 bacterial isolates were found to carry plasmids, with E. coli, K. pneumoniae and S. aureus being the most prevalent plasmid carriers. A total of 27 (87.1%) combined plasmids were found to carry both resistance and virulence genes compared to 4 (12.9%) single plasmids. No statistically significant correlation was found between the number of antimicrobial resistance and virulence genes in plasmids (r =-0.25, p > 0.05). Our findings show a relatively high proportion of plasmid-carrying isolates suggesting selection pressure due to antibiotic use in the hospital. Co-occurrence of antibiotic resistance and virulence genes in clinical isolates is a public health relevant problem needing attention.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
The revised version of the manuscript has the following updates: (A) Name of authors Frank Moller Aarestrup corrected to be Frank M. Aarestrup (FM)and Elingarami Sauli Nkya corrected to be Elingarami Sauli (line 8). (B) Abstract section - A space is inserted in the word "aureusbeing" (line 31) - (C) Results section - On study population description, the word "eight" is inserted between twenty and patients (line 116). - Description of Table 1. particularly "Patient hospital transfer" variable on category "No", 34.44% is approximated to be one decimal place 34.4% and 3 (2.3%) missed identification included as shown in Table 1. (D) Discussion section - "which" is inserted between "in and "P.mirabilis" - A sentence "The study findings are consistent with other studies conducted in Canada, Greece and Mexico" with no citation is deleted because of duplication (line 233-234). - The author name is added in 45 citation as not previous included (line 258). Note: The lines numbers in brackets are the references in the previous version of the manuscript.