Whole Genome Analysis of the Extensively Drug Resistant Clinical Klebsiella Pneumonia Isolates from the Military Hospital in Vietnam

Background: The over using of antibiotics in hospitals, communities and agriculture has raised drug resistance in Vietnam. Recently, Klebsiella pneumoniae ( K.pneumoniae ) emerged as the main agent causing hospital infections because of the alarming resistance to carbapenem and high mortality. The purpose of this study was to identify the antibiotic resistance pattern, gene carbapenemase expression and mutation that related to drug resistance mechanisms of K.pneumoniae isolated from clinical samples in the Military Hospital 103 in Vietnam. Methods Seventeen extensively drug resistant (XDR) strains were completed whole genome sequence, analyzed by bioinformatics, and confirmed using PCR and Sanger sequence methods. Results K.pneumoniae showed resistance to almost fifteen antibiotics with very high rates of over 70%, only sensitive to colistin 100%. There is a correlation between carpabenem resistance and XDR status in the K.pnemoniae group. Analysis Multilocus sequence typing (MLST) reported the total of 9/17 strains belong to ST15, after that ST11 (4/17), ST656 (2/17), ST 16 (1/17) and ST395 (1/17). Most of the K.pneumoniae isolates harbored the widely distributed ESBL genes, e.g. NDM , SHV , OXA , KPC , TEM and CTX-M , in which, the most prevalent carbapenemase genes were NDM-1 , NDM -4, OXA-48 , OXA-181 and KPC-2 . Especially, two strains demonstrated resistance to a wide range of antibiotics and showed the novel drug resistance gene mutation, namely Pro187Ala in NDM-4 gene and Gly25Ser in KPC-2 gene of MH16-335M and MH17-011M, respectively. Conclusion Our study adds new and significant DNA sequence data on K.pneumoniae strains and demonstrates the value of whole-genome sequencing in characterizing multidrug resistance in clinical isolates.