Plasmids are extra-chromosomal mobile DNA elements found 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; meaning that plasmid with similar replication (rep) genes cannot co-exist in the same bacterial cell. Even though ARGs have been detected in samples from clinical and non-clinical environments, their occurrence and distribution within plasmid incompatibility groups is not well understood. The study sought to determine the extent of diversity and distribution of different plasmid incompatibility (Inc/rep) groups that are harbouring ARGs in three different environments broadly classified as natural, host-associated and managed. The hypothesis is stated that antibiotic resistance plasmids of a certain Inc/rep group occur in certain environments with higher frequency than other Inc/rep groups. 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. The majority of antibiotic resistance plasmids were found in host associated environments particularly in human samples from clinical settings. Inc P was the only group clearly associated with all the 3 broad categories of environments. Results suggest no clear or notable variability on the correlation proportions of plasmids of other incompatibility groups being associated with specific environmental sources. The major limitation within this bioinformatics study was the plasmid sequences that were not completely sequenced and those not clearly described in terms of source or isolation. It is recommended that sequence data submission to public sequence databases be improved for future bioinformatics studies that aim to look at evolution of plasmids encoding antibiotic resistance.

Theses (MSc Biology and Biotechnological Sciences),-----Botswana International University of Science and Technology,2018