Molecular Typing, Characterization of Antimicrobial Resistance, Virulence Profiling and Analysis of Whole-Genome Sequence of Clinical Klebsiella pneumoniae Isolates

Abstract

Klebsiella pneumoniae is one of the most important pathogens concerned with multidrug resistance in healthcare-associated infections. The treating of infections caused by this bacterium is complicated due to the emergence and rapid spreading of carbapenem-resistant strains, which are associated with high mortality rates. Recently, several hypervirulent and carbapenemase-producing isolates were reported that make the situation even more complicated. In order to better understand the resistance and virulence mechanisms, and, in turn, to develop effective treatment strategies for the infections caused by multidrug-resistant K. pneumoniae, more comprehensive genomic and phenotypic data are required. Here, we present the first detailed molecular epidemiology report based on second and third generation (long-read) sequencing for the clinical isolates of K. pneumoniae in the Russian Federation. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as the virulence and plasmid profiling for 36 K. pneumoniae isolates. We have revealed 2 new multilocus sequence typing (MLST)-based sequence types, 32 multidrug-resistant (MDR) isolates and 5 colistin-resistant isolates in our samples. Three MDR isolates belonged to a very rare ST377 type. The whole genome sequences and additional data obtained will greatly facilitate further investigations in the field of antimicrobial resistance studies.

Genomic and Phenotypic Analysis of Multidrug-Resistant Acinetobacter baumannii Clinical Isolates Carrying Different Types of CRISPR/Cas Systems

“…The same is observed for CriePir87—it has KL33, while its neighbors with identical ST (ST2) are characterized by KL2. Thus, such a hybrid typing scheme that we have recently applied for K. pneumoniae [ 23 ], proved to be applicable for precise distinguishing of the isolates in clinical settings, which is an important task in epidemiological surveillance and infection prevention.…”

“…In this study we analyzed 12 clinical isolates of A. baumannii which belonged to eight different MLST-based sequence types including the novel ST1487 represented by the isolate CriePir307.We also proposed a hybrid typing scheme (MLST/KL typing) that we recently applied to K. pneumoniae [ 23 ] for better distinguishing of the isolates A. baumannii in clinical settings. Although many typing schemes were already provided for pathogenic bacteria, including the ones based on the nucleotide frequency matrices for genomic sequences [ 32 ], CRISPR sequences [ 33 ], and regular sequences classification [ 34 ], the hybrid typing scheme including MLST, KL, and, possibly, OCL loci seems to be the most promising for the species where all of them are available.…”

Antimicrobial Resistance and Genomic Characterization of OXA-48- and CTX-M-15-Co-Producing Hypervirulent Klebsiella pneumoniae ST23 Recovered from Nosocomial Outbreak

“…Long and short sequencing reads were subjected to hybrid assembly using Unicycler version 0.4.8-beta [22]. Additional processing was performed by custom scripts, as described earlier [23].…”

Gram-Negative Bloodstream Infection: Implications of Antimicrobial Resistance on Clinical Outcomes and Therapy

“…Advancements of whole-genome sequencing (WGS) techniques have contributed to a better understanding of antimicrobial resistance mechanisms and improvement of antimicrobial therapy. Shelenkov and colleagues use WGS to define antimicrobial resistance mechanisms and virulence profiling of predominantly MDR Klebsiella pneumoniae isolates in the Russian Federation [ 27 ]. The incorporation and visualization of genotypic and phenotypic resistance patterns on one platform represents phenomenal work and sets a high standard for future investigations.…”

“…The incorporation and visualization of genotypic and phenotypic resistance patterns on one platform represents phenomenal work and sets a high standard for future investigations. Moreover, the authors describe two new multi-locus sequence typing (MLST)-based sequence types of K. pneumoniae [ 27 ]. In the second basic science article of this Special Issue, Fokam and colleagues examine iron chelation in murine models of systemic inflammation induced by Gram-positive and Gram-negative bacterial toxins [ 28 ].…”