One-year surveillance for hypervirulent Klebsiella pneumoniae detected carbapenem-resistant superbugs

Abstract

Hypervirulent Klebsiella pneumoniae (hvKp) can cause infections in clinically healthy people, such as young and immunocompetent patients. Genes involved in the capsule synthesis or those encoding the siderophores have been adopted as predictors of hvKp. Certain sequence types, such as ST23 and ST86, have been associated with hvKp strains, too. The aim of this study was to investigate the presence of hvKp among 354 K. pneumoniae strains isolated from clinical samples of patients admitted to an Italian 900-bed hospital between 21 May 2021 and April 2022. All the isolates were screened by PCR for the amplification of virulence loci. Whole genome sequencing was performed in strains tested positive for at least one target gene. Thirteen out of 354 (3.7%) were hvKp. Five were wild type and belonged to the hypervirulent clones ST23, ST86, ST5, and ST375 and to the new clone ST6310. Six strains carried the blaKPC gene: three belonged to ST101, two to ST512, and one to ST395. Two isolates were ST147 and carried the blaNDM gene. Although hvKp isolation is not frequent, their presence should be systematically investigated to avoid the spreading of both virulent strains and strains with combined increase in virulence and resistance to antibiotics. PCR-based protocols are essential for surveillance of these strains, which do not always show a recognizable phenotype. Moreover, hvKp strains were isolated also from patients without history of recent foreign travels, indicating an increased spreading of these strains as well as an underestimated of their circulation so far. IMPORTANCE Klebsiella pneumoniae is a healthcare-associated pathogen frequently resistant to antibiotics. Hypervirulent strains of pneumoniae (hvKp) can spread from the primary site of infection to multiple sites causing life-threatening infections also in young otherwise healthy individuals. This study described the isolation of 13 isolates of K. pneumoniae with increased virulence in a large tertiary hospital over a 1-year period. Among them, eight strains were multidrug resistant and hypervirulent. Although these hypervirulent strains are still rare in Italy, their presence is particularly concerning since they can cause difficult-to-treat life-threatening infections. Moreover, not all the hypervirulent isolates were positive by the string test, so hvKp isolates were not always phenotypically detectable. Molecular biology techniques such as PCR amplification and next generation sequencing are therefore necessary for the detection of hvKp isolates, and surveillance programs exploiting molecular techniques are highly desirable.

Multidrug-Resistant Bacteria in Surgical Intensive Care Units: Antibiotic Susceptibility and β-Lactamase Characterization

“…PCRs for plasmid-mediated mcr genes gave negative for in all three colistin resistant strains and therefore the resistance can probably be attributed to the disruption of the mgrB gene as described previously in Italy [55]. ST101, reported in this study in the OXA-48 producing isolate, was previously identified in wastewater K. pneumoniae isolates in Finland [56] and in Italy [57], and in both cases was linked to KPC positivity. OXA-48 was carried by the L type plasmid, reinforcing the hypothesis that the current spread of OXA-48-carrying genes in different species (K. pneumoniae, E. cloacae and E. coli) is mainly the consequence of the diffusion of an epidemic, conjugative plasmid.…”

Molecular Characterization of Klebsiella pneumoniae Clinical Isolates Through Whole-Genome Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes

“…The present study demonstrated a high percentage (>50%) of hvKp strains, which was considerably high compared to a recent study from Italy that noted a hvKP prevalence of 3.7%. This study observed that hypervirulence was associated with ST-23 and ST-86, and ST-147 carried a bla NDM gene [23]. NDM carriage was noticed among ST-147, ST-15, and ST-101 in our study.…”

Screening of Klebsiella pneumoniae subsp. pneumoniae Strains with Multi-Drug Resistance and Virulence Profiles Isolated from an Italian Hospital between 2020 and 2023

“…Given the importance of monitoring the circulation of hvKp that are also MDR [ 13 , 14 , 15 , 36 ], our study also focused on determinants of virulence since the spread of hvKp strains has been observed in specific settings and/or in patients with severe SARS-CoV-2 infections [ 37 , 38 , 39 ]. Overall, we observed a higher number of strains carrying virulence determinants in 2022–2023, although with low scores ( Figure 3 ); only two strains had a virulence score of 4 (due to the acquisition of iuc1 and ybt ), both isolated in 2023, and both belonging to ST101 ( Table 1 and Figure 3 ).…”

“…Moreover, in 2023, one isolate (2023-KPC-Kpn-60) also carried the rmpA2 gene, which is involved in a hypermucosal phenotype, although the string test was negative for this isolate [ 41 ]; this is not surprising, as the performance of the string test has also been shown to be inconsistent in other studies [ 14 , 15 ], highlighting the importance of a combined phenotypic, molecular, and WGS approach even more. Ridom SeqSphere+ software version 9.0.10 2023-09 was used to investigate the presence of clusters of transmission.…”

“…Although hvKp is rarely MDR, the ECDC warned about the possibility that strains of hvKp could become a serious health threat if combined with carbapenem resistance. This threat represents a serious concern for hospital settings, and various surveillance studies have been published, aimed at assessing the prevalence of hvKp in general and, more specifically, of MDR-hvKp [ 13 , 14 , 15 ].…”