The aim of this study was to compare the prevalence of different virulence factor (VF) genes in extended-spectrum beta-lactamase (ESBL) producingEscherichia colistrains isolated from the Baltic Sea region. A total of 432 strains of phenotypically ESBL positiveE. coliwere collected from 20 institutions located in Estonia, Latvia, Lithuania, and the region of St. Petersburg in Russia from January to May 2012 and analyzed for phylogenetic group and prevalence of 23 VF genes. The strains were collected from clinical material (urine, blood, wound, and respiratory tract). Bacterial isolates were compared according to phylogenetic group, clinical material, and geographical origin. Most of the VF genes were concentrated within phylogenetic group B2 and/or D. When comparing strains isolated from different countries, it was found that strains originating from Estonia and Latvia belonged mainly to group B2 and strains from Lithuania and Russia mainly to groups B2 and D. The P-fimbrial adhesin genepapEFwas more prevalent in Russian strains, colicin genecvaCin Lithuanian strains, and capsular genekpsMTIIin Latvian strains; serum resistant genetraTwas less prevalent in Estonian strains. The regional differences of VF genes remained statistically significant after taking into account the phylogenetic distribution in the countries.

The Сomamonas genus, described in 1985, included one species — Сomamonas terrigena. At present, the Сomamonas genus includes 21 species. The ability of Comamonas to survive in environmental objects (samples of water, soil and plants), including hospital environment and medical equipment, allows them to be considered as opportunistic microorganisms. The purpose of the research was to study the biological properties and antimicrobial susceptibility of Сomamonas kerstersii strains isolated from fecal samples of healthy people living in Saint Petersburg (Russian Federation) and the Republic of Guinea. The study was carried out in the laboratory of enteric infections of the St. Petersburg Pasteur Institute. 1532 fecal samples were obtained from residents of St. Petersburg and 46 samples from residents of the Republic of Guinea. The generic and species identification of the isolated microorganisms was carried out using routine biochemical tests, the NEFERM test24 commercial test system (MIKROLATEST, Erba Rus, Russia) and Vitek 2 Compact (BioMerieux). The difficult for identification microorganisms were studied by MALDI-TOF mass spectrometry, on a “Microflex LRF” mass-spectrometer. Antimicrobial susceptibility was determined by the gradient method with MICEvaluator™ (OXOID, UK) on Müller– Hinton agar (Russia). In the intestine microbiota of 1532 St. Petersburg residents among the opportunistic microorganisms two strains of С. kerstersii were isolated (0.13%). In a survey of 46 residents of the Republic of Guinea in 8 cases (17.4%) С. kerstersii were isolated. The identification of C. kerstersii strains using various methods and biochemical tests has shown different results: routine biochemical tests allowed the strains to be assigned to the group of non-fermenting gram-negative bacteria; NEFERM test24 kit identified all strains as С. testosteroni; VITEC 2 referred all strains to С. testosteroni; using mass spectrometry with a coincidence ratio of 2.19–2.33, all strains were identified as С. kerstersii. It should be taken into account that the С. kerstersii bacteria cannot be identified by the tests of NEFERM test24 kit and the GN VITEC 2 card, since only the С. testosteroni is represented in the databases of both methods. The taxonomic base of mass spectrometry includes reference spectra of five species of Сomamonas from 21 known ones, including С. kerstersii. Strains isolated from the inhabitants of the Republic of Guinea were unsusceptible to at least one tested antibiotic: ciprofloxacin (4 strains), tetracycline (5 strains) and trimethoprim/sulfamethoxazole (5 strains), almost all strains being simultaneously unsusceptible to several antibio tics: ciprofloxacin and trimethoprim/sulfamethoxazole (2 strains), tetracycline and trimethoprim/sulfamethoxazole (2 strains), ciprofloxacin and tetracycline (1 strain). One strain was unsusceptible to ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole.

Background/Objectives: The high prevalence of fluoroquinolone-resistant E. coli in healthy children represents a significant public-health risk, facilitating the spread of antimicrobial resistance and increasing the potential for difficult-to-treat extraintestinal infections with severe clinical outcomes. This study aimed to investigate the prevalence of fluoroquinolone resistance in multidrug-resistant E. coli isolated from presumptively healthy children in St. Petersburg, Russia, with a particular focus on fluoroquinolone resistance determinants. Methods: Phenotypic AST was performed on 307 E. coli isolates from fecal pediatric samples, comprising 230 isolates from 2012 to 2013 and 77 isolates from 2021 to 2022. A subset (n = 47) of MDR isolates underwent whole-genome sequencing. Results: The frequency of MDR E. coli strains rose significantly from 15.7% to 32.5% over the study period. The most significant increases in resistance among E. coli strains were to third-generation cephalosporins (CTX, CTZ) and fluoroquinolones (CIP), rising fourfold over a decade. Based on phenotypic resistance profiles of MDR E. coli to quinolones, the highest resistance rates were observed for MFX (80.9%) followed by NAL (74.5%), LVX (44.7%) and CIP (40.4%). Genotypic analysis revealed distinct pathways: low-level NAL resistance required only an S83 mutation in gyrA, whereas low-level MFX resistance was predominantly conferred by a plasmid-borne qnr gene. In contrast, resistance to CIP and LVX involved at least three QRDR mutations: S83L and D87N/Y in gyrA, and S80I in parC. Notably, our study showed the predominance of the ST131 and ST38 clones in E. coli isolated from pediatric samples. Conclusions: Our findings suggest that the efficacy of moxifloxacin for empirical treatment of infections caused by MDR E. coli might be severely compromised. Overall, the current study highlights that the pediatric gut microbiota serves as a reservoir for resistant E. coli with the expansion of multidrug-resistant clones independently of direct antibiotic selection pressure.

The gut microbiota of healthy people, living in different regions, may vary considerably. The article presents the results of comparative qualitative and quantitative study of the intestine aerobic and anaerobic microbiota of residents of the Republic of Guinea (46) and Russia (60). The content of microorganisms (Enterobacteriaceae, Enterococcus spp., Lactobacillus spp., Bifidobacterium spp., Staphylococcus spp., Candida spp., non-fermentative gram-negative bacteria and others) in 1.0 gram of faeces was determined by bacteriological methods. Generic and species identification was performed using Vitek 2 Compact (bioMerieux, France), tube biochemical tests and MALDI-TОF mass spectrometry (Bruker Daltonics, Germany). Pearson χ2 criterion, p 0.05 and Fisher’s exact test (medstatistica.ru) were used to assess the differences in the compared groups. 95% confidence intervals were calculated by the method of Wilson. Microbiological disorders were characterized by a decrease in the number of obligate microorganisms, an increase in the number of facultative (opportunistic) microorganisms (above 106 CFU/g) and the emergence of their associations. Dysbiotic disorders were identified in both compared groups: in 100% patients from Republic of Guinea (95% CI:92.3–100) and in 86.7% patients from St. Petersburg (95% CI:75.8–93.1). Severe degree of microbiota disorders in the residents of the Republic of Guinea was revealed at 19.6% (95% CI:10.7–33.2), in group of residents of St. Petersburg in 9.6% (95% CI:4.2–20.6). In both groups the microbiota disorders of third degree were detected less frequently, compared with the microbiota disorders of second degree. The study has found no significant differences in the content of obligate bacteria (Bifidobacterium spp. and Lactobacillus spp.), however, significant differences in the species composition of the facultative part of the microbiota were revealed. The residents of the Republic of Guinea had “atypical” E. coli (lactosonegative and hemolytic) and non-fermenting gram-negative bacteria Comamonas kerstersii more frequently. Opportunistic microorganism associations have been found in 30.4% of the residents of the Republic of Guinea (95% CI:19.1–44.8) and 18.3% of residents of St. Petersburg (95% CI:10.6–29.9). Opportunistic microorganism associations from the residents of the Republic of Guinea always contained Staphylococcus aureus. It is necessary to conduct further research on a bigger population to access the differences in the compared groups in Staphylococcus aureus and Hafnia alvei.

Recent studies have shown that bacterial resistance existed long before antimicrobials were used in medicine, and not only pathogens are resistant to antibiotics. 511 strains of E. coli isolated from the intestinal microbiota of children aged 1 month to 17 years living in St. Petersburg were studied: the susceptibility to 15 antibiotics was determined by the disk diffusion method, as well as the susceptibility to 6 commercial bacteriophages produced by «Microgen» (Russia). The b-lactamase genes of molecular families TEM, SHV, OXA, and CTX-M were detected by multiplex PCR. 39,3% E. coli isolates were resistant to one or more antimicrobial classes. The proportion of multidrug resistant isolates (resistant to 3 or more classes) was 16,6%. Multidrug resistance to clinically significant antimicrobial classes (extended-spectrum cephalosporins (ESC) + fluoroquinolones + aminoglycosides) was detected in 0,8% isolates. Resistance to aminopenicillins was detected in 29,5%, ESC - 11,2%, fluoroquinolones - 13,3%, tetracycline - 20,0%, chloramphenicol - 9,8%, aminoglycosides - 2,5% isolates. b-lactam resistance was due to the beta-lactamase production: to ampicillin - the molecular family TEM (81,9%), ESC - the CTX-M molecular family (87,7%) CTX-M1 - (66%) and CTX-M9 groups (34%). 43,5% multidrug resistant E. coli isolates were susceptible to at least one of the six commercial bacteriophages produced by «Microgen». The study showed that the intestinal microbiota of children is an important reservoir of E. coli resistant (including multidrug resistance) to various classes of antibiotics, and bacteriophage therapy is an alternative method for eradication of antibiotic-resistant E. coli.

Background/Objectives: Non-typhoidal Salmonella (NTS) is one of the most common causative agents of food poisoning in Vietnam, and contaminated livestock meat poses a major risk to human health. The present study aims to provide the genetic characteristics of NTS with a particular focus on antimicrobial resistance and determine phylogenetic relationships between isolates from different sources in Southern Vietnam based on whole-genome sequencing (WGS) data. Methods: A total of 49 NTS isolates from pork/broiler meat, pigs, chickens, and humans were collected in Ho Chi Minh City and four provinces of Southern Vietnam. Phenotypic antimicrobial susceptibility testing (AST) and WGS for all isolates were performed. Results: As a result, 14 different serotypes were identified, among which S. Typhimurium and its monophasic variant were the dominant serotypes for human and pig sources. All chicken samples belonged to S. Indiana, whereas S. Infantis predominated in broiler meat. AST results revealed that 98% of isolates were multidrug resistant. NTS strains isolated from poultry and pigs exhibited resistance to the highest priority antimicrobials—quinolones and polymyxin, as well as to β-lactams, aminoglycosides, tetracycline, and sulfonamide, which are considered to be critical for the treatment of severe diseases. Conclusions: The results highlight the utmost importance of issues related to the selection, spreading, and transmission of multi-resistant strains from animals to humans.