Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis

Abstract

The emergence of carbapenem-resistant Klebsiella pneumoniae poses a significant threat to public health. In this study, we aimed to investigate the distribution and genetic diversity of plasmids carrying beta-lactamase resistance determinants in a collection of carbapenem-resistant K. pneumoniae blood isolates. Blood isolates of carbapenem-resistant K. pneumoniae bacteremia were collected and identified. Whole-genome sequencing, assembly and analysis were performed for the prediction of antimicrobial resistance determinants. Plasmidome analysis was also performed. Our plasmidome analysis revealed two major plasmid groups, IncFII/IncR and IncC, as key players in the dissemination of carbapenem resistance among carbapenem-resistant K. pneumoniae. Notably, plasmids within the same group exhibited conservation of encapsulated genes, suggesting that these plasmid groups may serve as conservative carriers of carbapenem-resistant determinants. Additionally, we investigated the evolution and expansion of IS26 integrons in carbapenem-resistant K. pneumoniae isolates using long-read sequencing. Our findings revealed the evolution and expansion of IS26 structure, which may have contributed to the development of carbapenem resistance in these strains. Our findings indicate that IncC group plasmids are associated with the endemic occurrence of carbapenem-resistant K. pneumoniae, highlighting the need for targeted interventions to control its spread. Although our study focuses on the endemic presence of carbapenem-resistant K. pneumoniae, it is important to note that carbapenem-resistant K. pneumoniae is indeed a global problem, with cases reported in multiple regions worldwide. Further research is necessary to better understand the factors driving the worldwide dissemination of carbapenem-resistant K. pneumoniae and to develop effective strategies for its prevention and control.

Comparative Genomic Analysis Reveals Emergence of ST-231 and ST-395 Klebsiella pneumoniae Strains Associated with High Transmissibility of blaKPC Plasmids

“…Out of the total 50 isolates of K. pneumoniae, 24 isolates were analyzed by WGS, including the 7 isolates which were successful in conjugation. Sixteen of these isolates were positive for the variable regions ( Kp 5,7,10,11,15,16,21,28,37,40,42,43,44,45,46,and 49) and two isolates showed bands with an unexpected size for the intI3 gene (Kp 4 and Kp 22). According to previous studies, these bands could be variants of integrase genes [35].…”

“…Integrons, for example, are semi-mobile platforms that recognize and capture mobile gene cassettes and transform them to usable genes by ensuring their appropriate expression [8][9][10]. They are located on different MGEs, such as plasmids, transposons, and pathogenicity islands (PAIs), which enable their movement between different bacteria [11,12]. A number of studies showed that most K. pneumoniae clinical isolates carried class 1 integrons, whereas class 2 integrons were only present in 1-2% of the isolates and rarely harbored class 3 integron [13].…”

“…Bar chart representing the percentage of trans-conjugation efficiency of K. pneumoniae isolates as donors and E. coli HB101 as a recipient.Out of the total 50 isolates of K. pneumoniae, 24 isolates were analyzed by WGS, including the 7 isolates which were successful in conjugation. Sixteen of these isolates were positive for the variable regions (Kp 5,7,10,11,15,16,21,28,37,40,42,43,44,45,46,and 49) and two isolates showed bands with an unexpected size for the intI3 gene (Kp 4 and…”

Multi-approach methods to predict cryptic carbapenem resistance mechanisms in Klebsiella pneumoniae detected in Central Italy

“…Carbapenem resistance, however, does not only depend on the presence of carbapenemases genes but may also be conferred by the combination of alternative mechanisms, such as the action of ESBL or AmpC enzymes, together with decreased membrane permeability and/or the over-expression of efflux pumps ( Goessens et al, 2013 ; Guerra et al, 2014 ; van Boxtel et al, 2016 ; Tseng et al, 2023 ).…”