Background: α-Hairpinins are a family of antimicrobial peptides, promising antimicrobial agents, which includes only 12 currently revealed members with proven activity, although their real number is supposed to be much higher. α-Hairpinins are short peptides containing four cysteine residues arranged in a specific Cys-motif. These antimicrobial peptides (AMPs) have a characteristic helix−loop−helix structure with two disulfide bonds. Isolation of α-hairpinins by biochemical methods is cost- and labor-consuming, thus requiring reliable preliminary in silico prediction. Methods: In this study, we developed a special algorithm for the prediction of putative α-hairpinins on the basis of characteristic motifs with four (4C) and six (6C) cysteines deduced from translated plant transcriptome sequences. We integrated this algorithm into the Cysmotif searcher pipeline and then analyzed all transcriptomes available from the One Thousand Plant Transcriptomes project. Results: We predicted more than 2000 putative α-hairpinins belonging to various plant sources including algae, mosses, ferns, and true flowering plants. These data make α-hairpinins one of the ubiquitous antimicrobial peptides, being widespread among various plants. The largest numbers of α-hairpinins were revealed in the Papaveraceae family and in Papaver somniferum in particular. Conclusions: By analyzing the primary structure of α-hairpinins, we concluded that more predicted peptides with the 6C motif are likely to have potent antimicrobial activity in comparison to the ones possessing 4C motifs. In addition, we found 30 α-hairpinin precursors containing from two to eight Cys-rich modules. A striking similarity between some α-hairpinin modules belonging to diverse plants was revealed. These data allowed us to assume that the evolution of α-hairpinin precursors possibly involved changing the number of Cys-rich modules, leading to some missing middle and C-terminal modules, in particular.

Escherichia coli is a commensal and opportunistic bacterium widely distributed around the world in different niches including intestinal of humans and animals, and its extraordinary genome plasticity led to the emergence of pathogenic strains causing a wide range of diseases. E. coli is one of the monitored species in maternity hospitals, being the main etiological agent of urogenital infections, endometriosis, puerperal sepsis, and neonatal diseases. This study presents a comprehensive analysis of E. coli isolates obtained from the maternal birth canal of healthy puerperant women 3–4 days after labor. According to whole genome sequencing data, 31 sequence types and six phylogenetic groups characterized the collection containing 53 isolates. The majority of the isolates belonged to the B2 phylogroup. The data also includes phenotypic and genotypic antibiotic resistance profiles, virulence factors, and plasmid replicons. Phenotypic and genotypic antibiotic resistance testing did not demonstrate extensive drug resistance traits except for two multidrug-resistant E. coli isolates. The pathogenic factors revealed in silico were assessed with respect to CRISPR-element patterns. Multiparametric and correlation analyses were conducted to study the interrelation of different pathoadaptability factors, including antimicrobial resistance and virulence genomic determinants carried by the isolates under investigation. The data presented will serve as a valuable addition to further scientific investigations in the field of bacterial pathoadaptability, especially in studying the role of CRISPR/Cas systems in the E. coli genome plasticity and evolution.

The infections of bacterial origin represent a significant problem to public healthcare worldwide both in clinical and community settings. Recent decade was marked by limiting treatment options for bacterial infections due to growing antimicrobial resistance (AMR) acquired and transferred by various bacterial species, especially the ones causing healthcare-associated infections, which has become a dangerous issue noticed by the World Health Organization. Numerous reports shown that the spread of AMR is often driven by several species-specific lineages usually called the ‘global clones of high risk’. Thus, it is essential to track the isolates belonging to such clones and investigate the mechanisms of their pathogenicity and AMR acquisition. Currently, the whole genome-based analysis is increasingly used for these purposes, including epidemiological surveillance and analysis of mobile elements involved in resistance transfer. However, in spite of the exponential growth of available bacterial genomes, their representation usually lack uniformity and availability of supporting metadata, which creates a bottleneck for such investigations. In this dataset, we provide the results of a comprehensive genomic epidemiology analysis of 61,857 genomes of a dangerous bacterial pathogen Klebsiella pneumoniae. Important typing information including multilocus sequence typing (MLST)-based sequence types (STs), assignment of the isolates to known global clones, capsular (KL) and lipooligosaccharide (O) types, presence of CRISPR-Cas systems, and cgMLST profiles are given, and the presence of AMR and virulence genes within the genomes is also reported. This dataset will be useful for researchers in the field of K. pneumoniae genomic epidemiology, resistance analysis and prevention measure development.

Background: Vancomycin-resistant Enterococcus faecium (VREfm), particularly vanA-positive strains, represents a growing threat in hospital settings worldwide. These bacteria are able to survive under severe environmental conditions, including high temperatures and saline concentrations. High genome plasticity and advanced ability of inheriting antimicrobial resistance determinants defined the success of E. faecium as a hospital pathogen. Methods: This study presents the whole genomic characterization of vanA-positive VREfm isolates, analyzing 10 clinical isolates collected from three tertiary care hospitals in Moscow, Russia. Several typing approaches, including two MLST schemes and cgMLST profiles, were used to elucidate the relationship between the isolates. Phylogenetic analysis placed the isolates in context with global VREfm populations, demonstrating both local clonal expansion and possible international connections. Phenotypic and genomic antimicrobial resistance profiles were obtained, as well as data regarding the repertoire of virulence factors and plasmid content. Results: Whole genome sequencing revealed that all isolates belonged to the clinically significant CC17 lineage, specifically sequence types ST80 and ST552. Notably, two isolates possessed truncated Tn1546-type transposons lacking vanY and vanZ genes, representing a potentially emerging variant of the vanA operon in Russian clinical settings. A plasmid carrying a truncated vanA operon was reconstructed using long-read sequencing. Conclusions: The study highlights the utility of genomic investigation for tracking resistance mechanisms and strain dissemination, providing crucial baseline data for epidemiological surveillance of infections caused by VREfm in Russia. These findings emphasize the need for continued genomic monitoring to understand the evolution and spread of antimicrobial resistance in clinically important enterococcal lineages.

ESKAPE bacteria are a major global threat due to their rapid antibiotic resistance acquisition and severe healthcare-associated infections. Effective countermeasures require epidemiological surveillance and resistance transmission studies, particularly for antimicrobial-resistant (AMR) colonization in intensive care unit (ICU) patients. Whole-genome sequencing (WGS) provides critical information on resistance spread and mechanisms. In the provided protocol, rectal and oropharyngeal swabs, or endotracheal aspirate/bronchoalveolar lavage for intubated patients, are collected at ICU admission and twice weekly. Patient interviews and medical records identify risk factors for resistant microflora. Samples undergo cultivation, species identification, antibiotic susceptibility testing, and DNA extraction. Sequencing is performed using second- and third-generation platforms, with selected isolates subject to hybrid genome assembly. Resistance genes, virulence factors, and typing profiles (MLST, cgMLST) are determined. This protocol characterizes the ICU patient colonization by AMR pathogens, including species distribution, phenotypic and genotypic resistance profiles, clonal structure, and temporal changes. It estimates detection frequency and colonization patterns at each locus, identifies key risk factors, including prior community or inter-facility exposure, and analyzes associations between risk factors and admission colonization. The study aims to estimate AMR infection risk and severity in ICU patients through the comprehensive analysis of colonization dynamics, resistance patterns, and clonal characteristics using WGS data on pathogen composition and AMR trends.

Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a critical public health threat because infections caused by this pathogen are associated with high morbidity, mortality, and limited effective therapeutic options. Whilst the majority of studies have concentrated on inter-patient bacterial transmission, within-host genomic analysis offers unprecedented resolution for tracking dynamic clone predominance, plasmid rearrangements, and microevolution under clinical selection pressures. Methods and Results: Whole-genome sequencing (WGS) of nine isolates recovered from oral and rectal swabs revealed an exceptional case of CRKP clonal turnover in an intensive care unit (ICU) patient. Three distinct high-risk clones were identified during the 18 days of surveillance: an initial ST101 (Clonal Group (CG) 101) strain (days 1–7) followed by concurrent colonization with ST395 (carrying bla_NDM-5) and ST512 lineages (both CG258, days 11–18). Conclusions: This study describes a rare instance of within-host heterogeneity of CRKP, involving three distinct STs spanning two CGs. Whole-genome analysis revealed potential structural rearrangements of resistance- and virulence-associated plasmids between coexisting lineages. These genomic shifts likely reflect rapid adaptation under the intense selective pressure of broad-spectrum antibiotic therapy, culminating in the persistence of a less virulent yet multidrug-resistant ST512 clone and a favorable clinical outcome with patient recovery.