Emergence of ST11-K47 and ST11-K64 hypervirulent carbapenem-resistant <i>Klebsiella pneumoniae</i> in bacterial liver abscesses from China: a molecular, biological, and epidemiological study

Abstract

<b>Background:</b> Multidrug-resistant bacteria, especially those with high virulence, are an emerging problem in clinical settings.<b>Methods:</b> We conducted a multicentre epidemiological and comparative genomic analysis on the evolution, virulence and antimicrobial resistance of carbapenem-resistant <i>Enterobacteriaceae</i> in patients with bacterial liver abscesses from 2012 to 2016.<b>Results:</b> A total of 477 bacterial isolates were collected. <i>Enterobacteriaceae</i> were the main pathogen (89.3%) with <i>K. pneumoniae</i> (52.4%) predominating followed by <i>Escherichia coli</i> (26.8%). All CRKps (3.2%) were of sequence type (ST) 11 and serotypes K47 or K64, and simultaneously possessed acquired <i>bla</i>_KPC-2/<i>bla</i>_KPC-5 and <i>bla</i>_CTX-M-65 together with the multidrug transporter EmrE. Seven Hv-CRKps (five ST11-K47, two ST11-K64) were confirmed by bacteriological test, neutrophil killing assay and <i>Galleria mellonella</i> infection model. Genomic analysis indicated that the emergence of one ST11-K64 Hv-CRKp strain was related to the acquisition of <i>rmpA/rmpA2</i> genes and siderophore gene clusters, while ST11-K47 Hv-CRKp lacked these traditional virulence genes. Further complete genome analysis of one ST11-K47 Hv-CRKp strain, R16, showed that it acquired a rare plasmid (pR16-Hv-CRKp1) carrying <i>bla</i>_KPC-2, <i>bla</i>_SHV-12, <i>bla</i>_TEM-1, <i>bla</i>_CTX-M-65, <i>rmtB</i> and a predicted virulence gene R16_5486 simultaneously.<b>Conclusion:</b> The emergence of the ST11-K47/K64 Hv-CRKps, which are simultaneously multidrug-resistant and hypervirulent, requires urgent control measures to be implemented.