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

• Published in: Memórias do Instituto Oswaldo Cruz 2016-02, Vol.111 (2), p.144-146
• Main Authors: Rafiq, Zumaana, Sam, Nithin, Vaidyanathan, Rama
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; beta-Lactamases - genetics; Biofilms; carbapenem resistant OMPK36 porin mutant; Clustered Regularly Interspaced Short Palindromic Repeats - genetics; CRISPR; Databases, Genetic; Drug Resistance, Multiple, Bacterial - genetics; Genome Announcement and Highlights; Genome, Bacterial - genetics; Genotyping Techniques - methods; Humans; India; Klebsiella Infections - urine; Klebsiella pneumoniae - classification; Klebsiella pneumoniae - genetics; Klebsiella pneumoniae - physiology; Klebsiella pneumoniae genome sequence; multidrug resistant; PARASITOLOGY; Sequence Analysis, DNA; TROPICAL MEDICINE
• ISSN: 1678-8060; 0074-0276; 1678-8060; 0074-0276
• DOI: 10.1590/0074-02760150423

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. pneumoniae species 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. pneumoniae strains 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. pneumoniae NTUHK2044, a transposase gene InsH of IS5-13 was found inserted.