ABSTRACT
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
ABSTRACT
OBJECTIVES: Klebsiella pneumoniae genomic surveillance in India was performed to understand the spread of antimicrobial resistant genes across the country over 10 years and to delineate environment and clinical K. pneumoniae through comparative genomics approach. METHODS: The genomic data of 153 strains were retrieved from PATRIC. To compare the presence of AMR genes, virulence genes, episomes and their evolutionary relationship in 153 K. pneumoniae genomes, ResFinder, Virulence Factor Database, Plasmid Finder and CSI phylogeny tools were used, respectively. RESULTS: Diverse serotypes were found among the 153 K. pneumoniae isolates, of which K51 (28%) and K64 (21.56%) were majorly found. Most of the K51 isolates belong to ST231 (93.02 %). The number of associated virulence genes (rmpA, magA, entB, ybtS, iutA, allS) appeared to be higher in ST231-KL51 and ST23-KL1 isolates. More than 97% of clinical strains have yersiniabactin, aerobactin genes. Importantly, 98% and 62% of the ESBL and carbapenemase-producing isolates harboured ybtS, iutA, and rmpA, magA genes, respectively. The IncF conjugative plasmids are predominant in K. pneumoniae. The phylogenetic analysis clearly separates the environmental strains from clinical and characterised by uncommon STs and serotypes. CONCLUSION: Our study illustrates K. pneumoniae genomic surveillance in India representing the phylogenetic evolution, STs, AMR, virulence, serotype to provide more attention for immediate treatment and preventing the dissemination of K. pneumoniae.