A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain

Abstract

Klebsiella pneumoniae is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of K. pneumoniae is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICEKp, iuc, rmpADC/2) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 K. pneumoniae genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 K. pneumoniae, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.

Characterization of blaNDM-19-producing IncX3 plasmid isolated from carbapenem-resistant Escherichia coli and Klebsiella pneumoniae

“…Only EC21 in our study harbored both IncX3 and IncFII but was also positive for three other plasmids. bla NDM-19 variant, was first detected in an E. coli from Switzerland, having also sequence type ST167 and IncX3 plasmid [ 6 ], while in K. pneumoniae NDM-19 was first linked to ST16; an emergent isolate increasingly associated with outbreaks and carrying many resistance determinants [ 31 ]. To our knowledge, this is the first proven occurrence of bla NDM-19 on an IncX3 plasmid recovered from a clinical setting in Lebanon.…”

Occurrence and mechanisms of tigecycline resistance in carbapenem- and colistin-resistant Klebsiella pneumoniae in Thailand

“…Interestingly, very few studies demonstrated the association between tigecycline resistance and this high-risk clone. Nevertheless, K. pneumoniae ST16 has been reported to accumulate various types of antimicrobial resistance determinants 73 such as bla CTX-M-15 61 , bla KPC 74 , bla NDM-5 60 , bla OXA-48-like 75 , bla NDM-1 and bla OXA-232 62 , 67 , 68 , aac ( 6 ′) -lb-cr 64 , aac ( 6 ′) -lb 67 , qnrS 67 , and mgrB mutation 67 , 69 . In our study, the accumulation of many antimicrobial resistance determinants ( bla CTX-M-15 , bla NDM-1 , bla OXA-232 , aadA1 , aadA2, aac ( 6 ′) -lb-cr , and aac ( 6 ′) -lb ) was also detected in C-C-RKP ST16 isolates.…”

Draft genome sequence of Klebsiella pneumoniae KLEB-33: a convergent biofilm hyperforming multiresistant strain belonging to the emerging ST16 lineage harboring multiple hypervirulence genes

“…The emergence of convergent strains of Klebsiella pneumoniae ( 1 , 2 ), showing multidrug resistance typical of the classic pathotype (cKp) and hypervirulence traits (hvKp pathotype) ( 3 , 4 ), prompted us to make public the draft genome of KLEB-33 (LREC_296), a multiresistant, hypermucoviscous, biofilm-producing convergent strain ( 5 ), harboring multiple hypervirulence genes, belonging to the sequence type ST16 (cgMLST 1705), an emerging high-risk lineage similar to other high-risk lineages spread worldwide, such as ST11 ( 6 ). The phenotypic and genotypic characteristics of this strain ( Table 1 ) make it a strong candidate for use as a model for convergent multidrug-resistant strains of K. pneumoniae , and therefore, the availability of its genomic sequence will be a valuable resource for the scientific community.…”