An integrated phenotypic and genomic approach to characterize MBL-producing Enterobacterales strains circulating in a Sicilian transplant center

Metallo-β-lactamases (MBLs)-producing Enterobacterales infections represent a serious threat in clinical practice due to high mortality rates associated and the limited therapeutic options available. Given their increased dissemination across Europe and their involvement in hospital outbreaks, further epidemiological investigations are required. Here, we provide a comprehensive characterization, by integrating clinical, genomic, and phenotypic data, of 22 MBL-carrying Enterobacterales strains (17 Klebsiella pneumoniae and 5 Escherichia coli ), isolated from critically ill patients admitted to IRCCS ISMETT from 2021 to 2024. Bacterial antimicrobial susceptibility was evaluated using phenotypic methods. Using a whole-genome sequencing approach, we identified the sequence types (STs) and depicted the resistome and virulome content. This study revealed the circulation of alarming MBL-producing strains in our hospital, with New Delhi MBL (82%), followed by Verona integron-encoded MBL (VIM) (18%). Beyond carbapenem resistance, these strains exhibited high resistance rates to crucial antibiotics, including amikacin (63%), in addition to reduced susceptibility to cefiderocol (50%). Moreover, the emergence of VIM-1 K. pneumoniae isolates resistant to colistin was observed. Genomic analysis revealed the presence of high-risk clones such as K. pneumoniae ST147 and ST512 and E. coli ST648, necessitating vigilant monitoring. The resistome analysis showed widespread co-occurrence of several resistance genes, contributing to the multidrug-resistant (MDR) phenotype. The convergence of resistance and virulence characteristics highlights the urgent need for integrated genomic surveillance and improved measures to control the spread of hypervirulent MDR bacteria. IMPORTANCE The increasing prevalence of metallo-β-lactamase-producing Enterobacterales is a significant healthcare concern. Traditional phenotypic methods, commonly employed in diagnostic labs, are essential for the resistance marker detection and antimicrobial susceptibility testing. Instead, bacterial genetic features, including additional resistance genes and virulence determinants that have significant clinical implications, remain neglected. To overcome this critical gap, an integrated approach, consisting of phenotypic and genomic analyses, is crucial for gaining essential insights that guide both comprehensive patient management and effective epidemiological surveillance. Our findings highlight the importance of antimicrobial stewardship, antimicrobial susceptibility testing, and control measures to limit the spread of high-risk multidrug-resistant bacteria.