Background: Klebsiella pneumoniae, a member of the ESKAPE group of bacterial pathogens, has developed multi-antimicrobial resistance (AMR), including resistance to carbapenems, which has increased alarmingly due to the acquisition of carbapenemase genes located on specific plasmids. Methods: Four clinical K. pneumoniae isolates were collected from four patients of a neuro-intensive care unit in Moscow, Russia, during the point prevalence survey. The AMR phenotype was estimated using the Vitec-2 instrument, and whole genome sequencing (WGS) was done using Illumina and Nanopore technologies. Results: All strains were resistant to beta-lactams, nitrofurans, fluoroquinolones, sulfonamides, aminoglycosides, and tetracyclines. WGS analysis revealed that all strains were closely related to K. pneumoniae ST39, capsular type K-23, with 99.99% chromosome identity. The novelty of the study is the description of the strains carrying simultaneously three large plasmids of the IncHI1B, IncC, and IncFIB groups carrying the carbapenemase genes of three types, bla_OXA-48, bla_NDM-1, and bla_KPC-2, respectively. The first of them, highly identical in all strains, was a hybrid plasmid that combined two regions of the resistance genes (bla_OXA-48 and bla_TEM-1 + bla_CTX-M-15 + bla_OXA-1 + catB + qnrS1 + int1) and a region of the virulence genes (iucABCD, iutA, terC, and rmpA2::IS110). Conclusion: The spread of K. pneumoniae strains carrying multiple plasmids conferring resistance even to last-resort antibiotics is of great clinical concern.

Acinetobacter baumannii is one of the significant healthcare-associated meningitis agents characterized by multidrug resistance and a high mortality risk. Thirty-seven A. baumannii strains were isolated from thirty-seven patients of Moscow neuro-ICU with meningitis in 2013–2020. The death rate was 37.8%. Strain susceptibility to antimicrobials was determined on the Vitek-2 instrument. Whole-genome sequencing was conducted using Illumina technology; the sequence types (ST), capsular types (KL), lipooligosaccharide outer core locus (OCL), antimicrobial resistance genes, and virulence genes were identified. The prevalent ST was ST2, belonging to the international clone IC2, and rarer, ST1, ST19, ST45, ST78, ST106, and ST400, with prevalence of KL9 and OCL1. Twenty-nine strains belonged to multidrug-resistant (MDR) and eight extensively drug-resistant (XDR) categories. Genes conferring resistance to beta-lactams (bla_PER, bla_GES, bla_ADC, bla_CARB, bla_CTX-M, bla_TEM, and bla_OXA-types), aminoglycosides (aac, aad, ant, aph, and arm), tetracyclines (tet), macrolides (msr and mph), phenicols (cml, cat, and flo), sulfonamides (dfr and sul), rifampin (arr), and antiseptics (qac) were identified. Virulence genes of nine groups (Adherence, Biofilm formation, Enzymes, Immune evasion, Iron uptake, Regulation, Serum resistance, Stress adaptation, and Antiphagocytosis) were detected. The study highlights the heterogeneity in genetic clones, antimicrobial resistance, and virulence genes variability among the agents of A. baumannii meningitis, with the prevalence of the dominant international clone IC2.

Hybrid diarrheagenic E. coli strains combining genetic markers belonging to different pathotypes have emerged worldwide and have been reported as a public health concern. The most well-known hybrid strain of enteroaggregative hemorrhagic E. coli is E. coli O104:H4 strain, which was an agent of a serious outbreak of acute gastroenteritis and hemolytic uremic syndrome (HUS) in Germany in 2011. A case of intestinal infection with HUS in St. Petersburg (Russian Federation) occurred in July 2018. E. coli strain SCPM-O-B-9427 was obtained from the rectal swab of the patient with HUS. It was determined as O181:H4-, stx2-, and aggR-positive and belonged to the phylogenetic group B2. The complete genome assembly of the strain SCPM-O-B-9427 contained one chromosome and five plasmids, including the plasmid coding an aggregative adherence fimbriae I. MLST analysis showed that the strain SCPM-O-B-9427 belonged to ST678, and like E. coli O104:H4 strains, 2011C-3493 caused the German outbreak in 2011, and 2009EL-2050 was isolated in the Republic of Georgia in 2009. Comparison of three strains showed almost the same structure of their chromosomes: the plasmids pAA and the stx2a phages are very similar, but they have distinct sets of the plasmids and some unique regions in the chromosomes.

Klebsiella pneumoniae is one of the most significant nosocomial pathogens and an important cause of human infections worldwide. The microorganism is capable of producing different capsular polysaccharides (CPSs), which are the primary receptors for capsule-specific K. pneumoniae bacteriophages encoding tailspike proteins (TSPs) with polysaccharide-degrading activity. In this study, the novel virulent Przondovirus phage Adeo was isolated and characterized. The phage was able to infect K. pneumoniae strain with a K39 capsular polysaccharide structure. The morphology, biological properties, stability, and genomic organization of Adeo were studied. Comparative genomic and phylogenetic analyses were performed to establish the relationship between the phage and other bacterial viruses. The gene encoding TSP Adeo_gp48 was identified and cloned. Recombinant depolymerase lacking the N-terminal part was expressed, purified, and formed an opaque zone of CPS depolymerization on the K39 K. pneumoniae bacterial lawns. The structural and phylogenetic similarities of Adeo’s TSP to other phage-encoded depolymerases were discussed.

Background. Streptococcus pyogenes (group A streptococcus, GAS) is a significant human bacterial pathogen causing a wide range of diseases, from upper respiratory tract infections to severe invasive forms. The increase in incidence in the post-COVID-19 period and the spread of hypervirulent clonal lineages, including M1UK (emm1 genotype), highlight the need for molecular genetic surveillance. Aim. To characterize the clonal structure, virulome and resistome of S. pyogenes strains isolated from hospitalized children and to assess their phenotypic antimicrobial susceptibility. Materials and methods. A total of 67 S. pyogenes strains isolated in 2023–2024 from hospitalized patients aged 0–17 years were studied. Identification was performed by MALDI-TOF mass spectrometry. Antimicrobial susceptibility testing was carried out by serial dilution methods. Whole-genome sequencing, genome assembly were performed. Bioinformatic analysis included emm typing, multilocus sequence typing, detection of virulence and antimicrobial resistance genes, and phylogenetic analysis. Results. Fourteen emm types and 19 sequence types were identified. The predominant clonal lineages were emm6/ST382 (16.4%), emm2/ST55 (14.9%), emm3/ST15 and emm75/ST49 (10.4% each). A strong association between emm and sequence types was observed (p 0.001; Cramer's V = 1.0). One strain of the M1UK lineage was identified among emm1/ST28 isolates. The virulence genes sagA, slo, mf/spd and speB were detected in all strains, while hylP was found in 86.6%. Among superantigen genes, speG (89.6%) and speC (68.7%) were most frequent. All strains were susceptible to β-lactams, clindamycin, linezolid, vancomycin. Resistance to erythromycin and tetracycline was detected in 4.5% and 14.9% of strains, respectively, and was predominantly associated with the mef(A)/msr(D) and tetM genes. Conclusion. S. pyogenes strains isolated from hospitalized children are characterized by genetic heterogeneity, a pronounced clonal structure, and genotype-specific distribution of superantigen genes. The results confirm the importance of whole-genome sequencing for monitoring the clonal structure, virulome and resistome of S. pyogenes within molecular epidemiological surveillance of GAS infections.