The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a new threat to healthcare. In this study, we analyzed nine CR-hvKp isolates of different sequence-types (ST) recovered from patients with nosocomial infections in two hospitals in Saint Petersburg. Whole-genome sequencing showed that eight of them harbored large mosaic plasmids carrying resistance to carbapenems and hypervirulence simultaneously, and four different types of hybrid plasmids were identified. BLAST analysis showed a high identity with two hybrid plasmids originating in the UK and Czech Republic. We demonstrated that hybrid plasmids emerged due to the acquisition of resistance genes by virulent plasmids. Moreover, one of the hybrid plasmids carried a novel New Delhi metallo-beta-lactamase (NDM) variant, differing from NDM-1 by one amino acid substitution (D130N), which did not provide significant evolutionary advantages compared to NDM-1. The discovery of structurally similar plasmids in geographically distant regions suggests that the actual distribution of hybrid plasmids carrying virulence and resistance genes is much wider than expected.

Since 2018, Klebsiella pneumoniae isolates have been described in Russia, demonstrating the convergence of hypervirulent properties and multiple antibiotic resistance. The problem of the Klebsiella hypervirulent pathotype has been actualized relatively recently that was progressively described in the 1980s in the Pacific region. These Klebsiella spp. can cause serious community-acquired infections in healthy people, which fundamentally differs from the classic Klebsiella pathotype initially preserving sensitivity to most antibacterial drugs. In 20182020, there were reported detection of hypervirulent K. pneumoniae isolates in the Russian Federation. Like multiple resistance, hypervirulence is associated with the acquiring additional genetic material and formation of genetic lineages that effectively support such acquired determinants. For a long time, it was believed that the convergence of multiple resistance and hypervirulence is unlikely due to a large genetic burden as well as different ecological strategies in same species. The spread of hypervirulent strains, primarily in the Asian region, is associated with the conserved plasmids of the pLVPK group. The conservatism of both the originally discovered virulence plasmids (such as pLVPK and pK2044) and the genetic lineages associated with them (mainly CG23) is probably determined by the absence of a gene cluster responsible for conjugation in these plasmids. The driver of the spread of non-conjugative plasmids with determinants of hypervirulence is clonal spread, not horizontal gene transfer. Nevertheless, after a sufficiently long period of circulation of plasmids bearing markers of hypervirulence (described since 1986) in Klebsiella, a relatively limited number of genetic lineages, there were events of mobilization of the determinants of hypervirulence and, as a consequence, the inclusion in horizontal gene transfer in the population (described cases in 2016 ), which led to a sharp increase in the number of genetic lineages and variants of genetic platforms carrying hypervirulence genes. In Russia, first cases of hv-MDR-Kpn were described in 2018 in Moscow based on analyzing collection of Klebsiella isolated in 20122016. In 2020 and 2021, similar cases were described in St. Petersburg. In case of repeated pessimistic scenario observed over the last decade due to spread of carbapenemases, effectiveness of health care will be more than substantially harmed.

Vancomycin and daptomycin are first-line drugs for the treatment of complicated methicillin-resistant Staphylococcus aureus (MRSA) infections, including bacteremia. However, their effectiveness is limited not only by their resistance to each antibiotic but also by their associated resistance to both drugs. It is unknown whether novel lipoglycopeptides can overcome this associated resistance. Resistant derivatives from five S. aureus strains were obtained during adaptive laboratory evolution with vancomycin and daptomycin. Both parental and derivative strains were subjected to susceptibility testing, population analysis profiles, measurements of growth rate and autolytic activity, and whole-genome sequencing. Regardless of whether vancomycin or daptomycin was selected, most of the derivatives were characterized by a reduced susceptibility to daptomycin, vancomycin, telavancin, dalbavancin, and oritavancin. Resistance to induced autolysis was observed in all derivatives. Daptomycin resistance was associated with a significant reduction in growth rate. Resistance to vancomycin was mainly associated with mutations in the genes responsible for cell wall biosynthesis, and resistance to daptomycin was associated with mutations in the genes responsible for phospholipid biosynthesis and glycerol metabolism. However, mutations in walK and mprF were detected in derivatives selected for both antibiotics.

The minimal inhibitory concentration (MIC) is conventionally used to define in vitro levels of susceptibility or resistance of a specific bacterial strain to an antibiotic and to predict its clinical efficacy. Along with MIC, other measures of bacteria resistance exist: the MIC determined at high bacterial inocula (MIC_HI) that allow the estimation of the occurrence of inoculum effect (IE) and the mutant prevention concentration, MPC. Together, MIC, MIC_HI and MPC represent the bacterial “resistance profile”. In this paper, we provide a comprehensive analysis of such profiles of K. pneumoniae strains that differ by meropenem susceptibility, ability to produce carbapenemases and specific carbapenemase types. In addition, we have analyzed inter-relations between the MIC, MIC_HI and MPC for each tested K. pneumoniae strain. Low IE probability was detected with carbapenemase-non-producing K. pneumoniae, and high IE probability was detected with those that were carbapenemase-producing. MICs did not correlate with the MPCs; significant correlation was observed between the MIC_HIs and the MPCs, indicating that these bacteria/antibiotic characteristics display similar resistance properties of a given bacterial strain. To determine the possible resistance-related risk due to a given K. pneumoniae strain, we propose determining the MIC_HI. This can more or less predict the MPC value of the particular strain.