Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India

Abstract

Klebsiella pneumoniae U25 is a multidrug resistant strain isolated from a tertiary care hospital in Chennai, India. Here, we report the complete annotated genome sequence of strain U25 obtained using PacBio RSII. This is the first report of the whole genome of K. pneumoniaespecies from Chennai. It consists of a single circular chromosome of size 5,491,870-bp and two plasmids of size 211,813 and 172,619-bp. The genes associated with multidrug resistance were identified. The chromosome of U25 was found to have eight antibiotic resistant genes [blaOXA-1,blaSHV-28, aac(6’)1b-cr,catB3, oqxAB, dfrA1]. The plasmid pMGRU25-001 was found to have only one resistant gene (catA1) while plasmid pMGRU25-002 had 20 resistant genes [strAB, aadA1,aac(6’)-Ib, aac(3)-IId,sul1,2, blaTEM-1A,1B,blaOXA-9, blaCTX-M-15,blaSHV-11, cmlA1, erm(B),mph(A)]. A mutation in the porin OmpK36 was identified which is likely to be associated with the intermediate resistance to carbapenems in the absence of carbapenemase genes. U25 is one of the few K. pneumoniaestrains to harbour clustered regularly interspaced short palindromic repeats (CRISPR) systems. Two CRISPR arrays corresponding to Cas3 family helicase were identified in the genome. When compared to K. pneumoniaeNTUHK2044, a transposase gene InsH of IS5-13 was found inserted.

Hypervirulent Klebsiella pneumoniae – clinical and molecular perspectives

“…[119]. Highlighting the diversity amongst isolates, there are examples of rmpAÀ/HMV+ [9,[122][123][124][125], rmpA-/ rmpA2+/HMV+ [10], and rmpA+/HMVÀ [9,118]. Further, in an attempt to identify new biomarkers for clinical testing of hvKp, the string test performed only moderately well as a predictor of cKp versus hvKp [117].…”

Panel strain ofKlebsiella pneumoniaefor beta-lactam antibiotic evaluation: their phenotypic and genotypic characterization

“…Previous studies indicate that K. pneumoniae consists of several large plasmids which carry vast number of ESBLs and carbapenemases genes along with the genes for resistance to aminoglycosides, trimethoprim, sulphonamides, tetracyclyclins and chloramphenicol (Conlan et al, 2016; Paterson, 2000; Tokajian et al, 2015). These plasmids are encoded with wide variety of adhesin-related gene clusters, mobile genetic elements such as conjugation transfer genes such as tra , transposons and insertion sequences which help in adaptive evolution, horizontal gene transfer, thus spreading the antibiotic resistance from one species or genera to another (Liu et al, 2012; Rafiq, Sam & Vaidyanathan, 2016; Ramos et al, 2014). Increased resistance to carbapenems and glycylcycline has also been facilitated by alterations in membrane permeability/potential or altered efflux pumps (Cannatelli et al, 2014; Filgona, Banerjee & Anupurba, 2015; He et al, 2015; Seecoomar, Marmol & Kwon, 2013).…”

Punica Granatum Rind Extract: Antibiotic Potentiator and Efflux Pump Inhibitor of Multidrug Resistant Klebsiella Pneumoniae Clinical Isolates

“…The synergistic interaction with other classes of antibiotics such as cephalosporins, β-lactams, and aminoglycosides was determined for a representative K. pneumoniae strain U25 which showed a 16-fold reduction in MIC of ciprofloxacin and is known to have high efflux activity [17].…”

“…The efflux inhibition activity of PGR ethanol extract and the hexane, butanol and water fractionwasanalyzed by the norfloxacin accumulation assay [14] using a representative K. pneumoniae isolate U25 which is known to have high efflux activity [17]. A well-known EPI CCCP that dissipates the proton gradient was used as a control [20].…”