Abstract
The global spread of Klebsiella pneumoniae producing Klebsiella pneumoniae carbapenemase (KPC) has been mainly associated with the dissemination of high-risk clones. In the last decade, hospital outbreaks involving KPC-producing K. pneumoniae have been predominantly attributed to isolates belonging to clonal group (CG) 258. However, results of recent epidemiological analysis indicate that KPC-producing sequence type (ST) 307, is emerging in different parts of the world and is a candidate to become a prevalent high-risk clone in the near future. Here we show that the ST307 genome encodes genetic features that may provide an advantage in adaptation to the hospital environment and the human host. Sequence analysis revealed novel plasmid-located virulence factors, including a cluster for glycogen synthesis. Glycogen production is considered to be one of the possible adaptive responses to long-term survival and growth in environments outside the host. Chromosomally-encoded virulence traits in the clone comprised fimbriae, an integrative conjugative element carrying the yersiniabactin siderophore, and two different capsular loci. Compared with the ST258 clone, capsulated ST307 isolates showed higher resistance to complement-mediated killing. The acquired genetic features identified in the genome of this new emerging clone may contribute to increased persistence of ST307 in the hospital environment and shed light on its potential epidemiological success.
Highlights
The worldwide spread of carbapenemase-producing Klebsiella pneumoniae (Kp) has become a major threat for healthcare facilities [1]
Half of the isolates (n=12) were selected from 27 ST307 Klebsiella pneumoniae carbapenemase (KPC)-3-Kp isolates collected during the surveillance study performed in March–August 2014 in Palermo [18]; they were representatives of the isolates obtained from the three participating hospitals, and were selected based on slightly different pulsed-field gel electrophoresis (PFGE) patterns identified in the survey [18, 19]
Cluster analysis based on 634 strict core-genome multi locus sequence typing (MLST) genes demonstrated the clear phylogenetic distinction of the ST307 genomes from those of previously analyzed isolates, indicating that they represent a unique sub-lineage of K. pneumoniae very distant from the two ST258 clades, but not unusually divergent from other K. pneumoniae (Fig. 1)
Summary
The worldwide spread of carbapenemase-producing Klebsiella pneumoniae (Kp) has become a major threat for healthcare facilities [1]. This global phenomenon has been mainly associated with the clonal dissemination of high-risk clones. One of the most succesful is the Klebsiella pneumoniae carbapenemase (KPC)-producing Kp (KPC-Kp) sequence type (ST) 258 clone, and its related variants belonging to clonal group 258 (CG258) [2, 3]. KPC-Kp ST307 is a candidate for becoming one of the most clinically relevant clones, since its emergence has been recognized in several countries in the last five years [9,10,11,12]. The acquisition of a KPC enzyme was subsequent to that of CTX-M-15, as deduced from the fact that CTX-M-15-producing Kp ST307 have been previously reported at high frequencies in Italy, Korea, Pakistan and Morocco and in pets from Japan [9,10,11,12,13,14,15]
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