Abstract
BackgroundEndemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area.Methods50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypesResultsMLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico β-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group.Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis.ConclusionsOur data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.
Highlights
Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; recent studies suggest an ongoing epidemiological change in this geographical area
The existing body of research on carbapenemresistance mechanisms suggests that the production of K. pneumoniae carbapenemase (KPC) encoded by the plasmidic gene blaKPC is the most common one and its rapid dissemination has typically been caused by the clonal expansion of clonal complex (CC) 258 strains, including ST258 and ST512 [12,13,14,15,16]
The primary aim of this study was to take a current snapshot of the distribution of K. pneumoniae in our geographic area by: 1) characterizing the virulome and resistome of Carbapenem-resistant K. pneumoniae (CR-Kp) clones; 2) assessing the extent to which virulence determinants were carried by CR-Kp and Carbapenem-susceptible K. pneumoniae (CS-Kp); 3) investigating the phylogenetic correlations among samples by Multilocus sequence typing (MLST) in silico and the analysis of core single nucleotide polymorphisms (SNPs)
Summary
Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; recent studies suggest an ongoing epidemiological change in this geographical area. In K. pneumoniae the relation between resistance and virulence is a complex issue since a systematic understanding of its population structure is still lacking [4, 9]. This makes it difficult to perceive the emergence of new clones, what instead could be an advantageous approach to develop epidemiological surveillance programs and avoid outbreaks, of strains which have become resistant to carbapenem (carbapenem-resistant K. pneumoniae, CR-Kp) [9,10,11]. The last European Antimicrobial Resistance Surveillance Network report has confirmed an average prevalence of CR-Kp of up to 33.9%, percentages that make Italy an endemic country for this microorganism [18, 19]
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