Abstract

Plasmids are extra-chromosomal mobile DNA elements found mostly in bacteria, and often serve as vectors for accumulation and transfer of antibiotic resistance genes (ARGs) within bacterial populations in different environments. Plasmid mediated transfer of ARGs has accounted for the spread of antibiotic resistance within clinically relevant pathogenic bacteria; this has escalated into a global health problem. Plasmids can be classified into several groups based on their genetic incompatibility. The occurrence and distribution by plasmid incompatibility (Inc/rep) groups is not well understood. The study sought to determine the extent of diversity and distribution of different Inc/rep groups that are harbouring ARGs in three different environments broadly classified as natural, host-associated and managed. In this research, DNA sequence data of nearly all known natural plasmids from NCBI databases was used to determine the correlation between plasmid Inc/rep group encoding antibiotic resistance and their source environment. From the metadata, resistance plasmids constitute 1404 (25%) of known natural plasmids; 729 (54%) of which have multidrug resistance (more than 1 resistance gene per plasmid). The majority of antibiotic resistance plasmids were found in host associated environments particularly in human samples from clinical settings. It was also clearly elucidated by the data that the diversity of natural plasmids surpasses the efficiency of polymerase chain reaction (PCR) based replicon typing (PBRT) plasmid identification scheme, which managed to identify 460 (35%) of the resistance plasmids in the dataset. Some major limitation were identified in this study, we recommend that sequence data submission to public databases be improved for future bioinformatics studies that aim to look particularly at evolution of plasmids encoding antibiotic resistance.

Key words: Plasmids, antibiotic resistance genes, polymerase chain reaction (PCR) based replicon typing (PBRT), incompatibility, environment, bioinformatics.