Whole genome sequencing and comparative genome analysis of a local multi-drug resistant uropathogenic Escherichia coli isolate

Abstract

Urinary tract infections (UTIs) are one of the most common non-malignant extra-intestinal infection in urology with 300 million infections occurring annually worldwide. Uropathogenic Escherichia coli (UPEC), a gram-negative, multi drug resistant bacteria is the primary causative agent among the microbial spectrum involved in UTIs. Structural and secreted virulence factors of UPEC mainly contribute to the etiology of UTIs. Over a period of years, there is steady rise in number of UPEC infections in our setup and abuse of antibiotics have ensued in increased antibiotic resistance with subsequent increase in multi-drug resistant (MDR) E.coli strains. However, not much is known about the genetic attributes of different UPEC lineages in Pakistan. For a better understanding of genomic diversity, virulence and resistance determinants a local UPEC isolate was characterized and comparative genome analysis with global strains was carried out. The UPEC isolate U1 is a virulent multi-drug resistant strain with a genome size of 5.2 Mb containing 5376 coding sequences and a total of 389 subsystems. The strain U1 belongs to ST131 and have O25:H4 serogroup. It harbors several resistant determinants, four plasmids (designated as pU1_1, pU1_2, pU1_3 and pU1_4) harboring a TEM-1 resistant gene, 4 complete prophages, 3 miniature inverted repeats, 2 composite transposons, 15 insertion sequences and several virulence genes. Comparative analysis revealed that the strain U1 has a similar resistance and virulence profile reported earlier for strains from Sequence type 131. Moreover phylogenetic analysis revealed that the isolate U1 is evolutionary related to strain UPEC 4_0 and strain O25:bH4 were reported from Sweden and Saudi Arabia respectively. These genetic insights will be helpful for effective control measures against this pathogen, for health care providence as well as research and development (R & D) organizations