Phenotypic and Genotypic Analysis of Clinical MDR E. Coli

Abstract

World Health Organization listed Escherichia coli as the number one priority pathogen for the development of new antibiotic due to the fast evolution of its pathogenicity and multidrug resistance. Understanding the mechanism behind increasing bacterial antibiotic resistance is as significant as development of new antibiotics. Often, bacterial resistance and virulence attributes are harboured on highly mobile pieces of DNA that can transfer to other bacteria. Prophages, plasmids, transposons and insertion sequences all are mediators of this form of genetic transfer. A case of UTI was reported in PIMS hospital Islamabad contributed by an extended spectrum β-lactamase (ESBL) Escherichia coli exhibiting resistance to Ceftazidime (3rd generation cephalosporin). Phenotypic analysis by antimicrobial susceptibility assay by using Kirby Bayer Disk Diffusion revealed that isolate was resistant against commonly prescribed antibiotics for treatment of urinary tract infection. Isolate was susceptible to carbapenem but resistant against more than three classes of antibiotics suggesting the isolate to be classified as Multidrug Resistant (MDR). Genotypic analysis was done by identification of β-lactamases by PCR revealing the presence of blaCTX-M. Whole Genome Sequencing and downstream analysis were employed for extensive genotypic analysis. Whole Genome Annotation revealed the genome to be ~4.85Mbp having 5095 CDSs, 62 tRNA and 5 rRNA genes. Further downstream analysis exhibited the presence of multiple insertion and mobile elements present along with resistance genes that provide resistance to Sulphonamides, Aminoglycosides, Trimethoprim and Beta-lactams. For long term of infection control it is significant to develop a vaccine against Uropathogenic Escherichia coli which shows susceptibility to few antibiotics. There is no vaccine available against this pathogen up to date. The 3D structure of proposed multi-epitope vaccine was refined and validated using bioinformatics tool. The proposed vaccine is antigenic and stably interacts with TLR-2 and TLR-5.