Comparative study of virulence potential, phylogenetic origin, CRISPR-Cas regions and drug resistance of Escherichia coli isolates from urine and other clinical materials

IntroductionUrinary tract infections (UTI), among which the main etiological factor is uropathogenic Escherichia coli (UPEC, E. coli), remain an important issue for clinicians. The aim of the study was to demonstrate clear differences in the pathogenic properties of urine-derived E. coli compared to other extraintestinal E. coli clinical isolates (derived from: blood, lower respiratory tracts, sputum, reproductive tract, body fluids, perianal pus, other pus, wound, postoperative wound and other sources).MethodsThe collection of 784 E. coli isolates was collected from various materials of hospitalized patients. They were analyzed in terms of virulence-associated genes (papC, sfaD/sfaE, cnf1, usp., fimG/H, hlyA), belonging to phylogenetic groups and the presence of CRISPR-Cas regions using PCR. In addition, the epidemiological data and the antibiotic resistance profiles provided by the hospital’s microbiology department were included for statistical analyses.ResultsUrine-derived E. coli showed significantly greater virulence potential compared to other isolates, but they were generally unremarkable in terms of drug resistance. The isolates most often belonged to phylogenetic group B2. Drug resistance was negatively correlated with CRISPR 2 presence and high average virulence score, but positively correlated with CRISPR 4 presence. To the best of our knowledge, we are the first to report significant differences in sputum-derived isolates—they revealed the lowest virulence potential and, at the same time, the highest drug resistance.DiscussionIn conclusion, we demonstrated significant differences of urinary-derived E. coli compared to other clinical E. coli isolates. We would like to suggest excluding penicillins from use in E. coli infection at this time and monitoring strains with a high pathogenicity potential

Analysis of uropathogenic Escherichia coli biofilm formation under different growth conditions

The ability to form different types of biofilm enables bacteria to survive in a harsh or toxic environment. Different structures of biofilms are related to different surfaces and environment of bacterial growth. The aim of this study was analysis of the biofilm formation of 115 clinical uropathogenic Escherichia coli strains under different growth conditions: surface for biofilm formation, medium composition and time of incubation. The biofilm formation after 24 h, 48 h, 72 h and 96 h was determined spectrophotometrically (A531) after crystal violet staining and it was correlated with bacterial growth (A600). The live and dead cells in biofilm structures was also observed on the glass surface by an epi-fluorescence microscope. Additionally, the presence of rpoS, sdiA and rscA genes was analyzed. The statistical significance was estimated by paired T-test. The observed biofilms were different for each particular strain. The biofilm formation was the highest in the rich medium (LB) after 24 h and its level hasn't changed in time. When biofilm level was compared to bacterial growth (relative biofilm) - it was higher in a minimal medium in comparison to enriched medium. These results suggest that most of the bacterial cells prefer to live in a biofilm community under the difficult environmental conditions. Moreover, biofilm formation on polyurethane surface did not correlate with biofilm formation on glass. It suggests that mechanisms of biofilm formation can be correlated with other bacterial properties. This phenomenon may explain different types of biofilm formation among one species and even one pathotype - uropathogenic Escherichia coli

The use of infrared spectroscopy and artificial neural networks for detection of uropathogenic Escherichia coli strains' susceptibility to cephalothin

Background & Aims: Infrared spectroscopy is an increasingly common method for bacterial strains' testing. For the analysis of bacterial IR spectra, advanced mathematical methods such as artificial neural networks must be used. The combination of these two methods has been used previously to analyze taxonomic affiliation of bacteria. The aim of this study was the classification of Escherichia coli strains in terms of susceptibility/resistance to cephalothin on the basis of their infrared spectra. The infrared spectra of 109 uropathogenic E. coli strains were measured. These data are used for classification of E. coli strains by using designed artificial neural networks. Results: The most efficient artificial neural networks classify the E. coli sensitive/resistant strains with an error of 5%. Conclusions: Bacteria can be classified in terms of their antibiotic susceptibility by using infrared spectroscopy and artificial neural networks

Ciprofloxacin, amoxicillin, and aminoglycosides stimulate genetic and phenotypic changes in uropathogenic Escherichia coli strains

Antibiotic therapy and its consequences in bacterial and human aspects are widely investigated. Despite this, the emergence of new multidrug resistant bacteria is still a current problem. The scope of our work included the observation of changes among uropathogenic Escherichia coli strains after the treatment with a subinhibitory concentration of different antibiotics. The sensitive strains with or without virulence factors were incubated with amoxicillin, ciprofloxacin, gentamycin, or tobramycin. After each passage, the E. coli derivatives were compared to their wild types based on their susceptibility profiles, virulence genes, biofilm formations and the fingerprint profiles of PCR products amplified with using the (N)(6)(CGG)(4) primer. It turned out that antibiotics caused significant changes in the repertoire of bacterial virulence and biofilm formation, corresponding to acquired cross-resistance. The genomic changes among the studied bacteria were reflected in the changed profiles of the CGG-PCR products. In conclusion, the inappropriate application of antibiotics may cause a rapid rise of Multidrug Resistant (MDR) strains and give bacteria a chance to modulate their own pathogenicity. This phenomenon has been easily observed among uropathogenic E. coli strains and it is one of the main reasons for recurrent infections of the urinary tract

The effects of nickel(II) complexes with imidazole derivatives on pyocyanin and pyoverdine production by Pseudomonas aeruginosa strains isolated from cystic fibrosis

Pseudomonas aeruginosa infection is problematic in patients with cystic fibrosis (CF). P. aeruginosa secretes a diversity of pigments, such as pyocyanin and pyoverdine. The aim of this study was to evaluate the effects of complexes of nickel(II) ([Ni(iaa)2(H2O)2]·H2O (iaa = imidazole-4-acetate anion), [Ni(1-allim)6](NO3)2 (1-allim = 1-allylimidazole) and NiCl2 on pyocyanin and pyoverdine production by 23 strains of P. aeruginosa isolated from cystic fibrosis under growth conditions specific for the CF respiratory system. The antibacterial effects and biophysical properties of the tested substances were measured by spectrofluorometric techniques, as well as by laser interferometry, confocal and atomic force microscopy. The cytotoxic properties of all compounds were measured by Annexin/IP assay against A549 cells. All tested compounds have no effect on pyocyanin production and decrease the pyoverdine secretion in about 40% of tested P. aeruginosa strains at non-cytotoxic range of concentrations. Imidazole-4-acetate anion and 1-allylimidazole have good diffusion properties in the mature P. aeruginosa PAO1 biofilm. In conclusion, the tested nickel(II) complexes do not have clinical implications in P. aeruginosa eradication in cystic fibrosis. The diffusion properties of 1-allylimidazole and imidazole-4-acetate and their lack of effect on A549 cells suggest that they might be considered for chemical synthesis with other transition metals

The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19

Abstract Background The evolution of SARS-CoV-2 has been observed from the very beginning of the fight against COVID-19, some mutations are indicators of potentially dangerous variants of the virus. However, there is no clear association between the genetic variants of SARS-CoV-2 and the severity of COVID-19. We aimed to analyze the genetic variability of RdRp in correlation with different courses of COVID-19. Results The prospective study included 77 samples of SARS-CoV-2 isolated from outpatients (1st degree of severity) and hospitalized patients (2nd, 3rd and 4th degree of severity). The retrospective analyses included 15,898,266 cases of SARS-CoV-2 genome sequences deposited in the GISAID repository. Single-nucleotide variants were identified based on the four sequenced amplified fragments of SARS-CoV-2. The analysis of the results was performed using appropriate statistical methods, with p  T, 14697C > T, 15096 T > C, and 15279C > T), while the 15240C > T mutation was common among strains isolated from outpatients. The selected mutations were searched worldwide in the GISAID database, their presence was correlated with the severity of COVID-19. Conclusion Identified mutations have the potential to be used to assess the increased risk of hospitalization in COVID-19 positive patients. Experimental studies and extensive epidemiological data are needed to investigate the association between individual mutations and the severity of COVID-19

Additional file 1 of The RdRp genotyping of SARS-CoV-2 isolated from patients with different clinical spectrum of COVID-19

Supplementary material 1