Genome Annotation and Comparative Genome Analysis of Klebsiella pneumoniae Strain KP3 isolated from Patient

Abstract

Klebsiella pneumoniae is a gram-negative, nosocomial bacteria reported to be the second most common causative agent of Urinary tract infections. UTIs are one of the most common extra-intestinal infections occurring across the world. About 300 million infections are reported worldwide annually. Virulence factors of K. pneumoniae contribute in causing UTIs. Over the period abuse of antibiotics has developed multi drug resistant leading to the rise in number of different infections including UTIs caused by K. pneumoniae in Pakistan. In depth genomic studies need to be conducted to learn more about such strains. In this study, a local isolate of K. pneumoniae KP3 was characterized, gone through pangenome and comparative genome analysis with global strains to get the insights of the genetic diversity, resistance, and virulence profile among K. pneumoniae strains across the world. The local isolate KP3 was identified to be multi-drug resistant virulent strain with a genome size of 4.9Mb having 5067 coding sequences. The strain carried many resistance genes as TEM-1, tolC, CRP etc. responsible for causing resistance against tetracycline, rifamycin, phenicol, fluoroquinolone etc., more than hundred virulence factors including rmpA, rcsA hlyE,, pgaC etc and five plasmids two of which harbor resistance genes for Carbapenems and β-Lactams. MLST analysis showed KP3 belongs to ST5. Pangenome analysis of selected 47 strains identified 14,520 genes with 343 core genes, 2061 accessory genes and 11,364 unique genes indicating an open pangenome system and a close relation to a strain KpC5 from USA. Comparative analysis exhibited KP3 had a unique resistance and virulence profile which is somewhat related to other strains in causing UTIs. Furthermore, phylogenetic analysis revealed that KP3 is evolutionarily related to the reference genome HS11286 of K. pneumoniae and a UTI causing strain ATCCBAA_2146 from USA. This genetic information will be helpful in future for effective control of this MDR pathogen and develop targeted therapeutics.