The relationship between phylogenetic groups and antibiotic susceptibility patterns of Escherichia coli strains isolated from feces and urine of patients with acute or recurrent urinary tract infection

Background and Objectives: B2 and D have been mentioned as the most common phylogenetic groups among uropatho- genic Escherichia coli. However, there is still controversy about the importance of these phylo-groups. This study was con- ducted to investigate the probable relation between these groups and antibiotic resistance patterns of E. coli isolates derived from urine and feces of the patients with acute or recurrent UTI. Materials and Methods: 10 isolates were recovered from urine and feces samples of patients with different phases of UTI in whom E. coli was causative pathogen. Biochemical fingerprinting was performed to classify the isolates and select their appropriate representatives. Phylogenetic grouping was performed using multiplex PCR, and antibiotic resistance was deter- mined by disk diffusion method. Results: Five-hundred-sixty E. coli isolates were derived from 56 UTI patients (27 acute, 29 recurrent). Among them, 261 isolates were selected using biochemical fingerprinting. All the isolates were sensitive to imipenem and nitrofurantoin. Com- pared to other phylo-groups, the isolates in group D showed considerably different frequencies in acute vs. recurrent phase of UTI, in urine vs. stool samples, in males vs. females, and in- vs. out-patients. They were more resistant to the antibiotics (except norfloxacin), and in contrast to others, this was seen more in acute UTI, especially in urine samples. Multi-drug resistance pattern was also meaningfully higher in group D. Conclusion: Although phylo-groups B2 and D of E. coli bacteria are more responsible for UTI, group D isolates seem to be more resistant and probably more virulent, even than the ones from group B2.

High-Throughput Biochemical Fingerprinting of Oleaginous Aurantiochytrium sp. Strains by Fourier Transform Infrared Spectroscopy (FT-IR) for Lipid and Carbohydrate Productions

The traditional biochemical methods for analyzing cellular composition of oleaginous microorganisms are time-consuming, polluting, and expensive. In the present study, an FT-IR method was used to analyze the cellular composition of the marine oleaginous protist Aurantiochytrium sp. during various research processes, such as strains screening, medium optimization, and fermentation, and was evaluated as a green, low-cost, high throughput, and accurate method compared with the traditional methods. A total of 109 Aurantiochytrium sp. strains were screened for lipid and carbohydrate production and the best results were found for the strains No. 6 and No. 32. The yields and productivities could reach up to 47.2 g/L and 0.72 g/L/h for lipid, 21.6 g/L and 0.33 g/L/h for docosahexaenoic acid (DHA) in the strain No. 6, and 15.4 g/L and 0.18 g/L/h for carbohydrate in the strain No. 32, under the optimal conditions, respectively. These results confirmed potentials of the two Aurantiochytrium sp. strains for lipid, DHA, and carbohydrate productions at industrial scales. The FT-IR method in this study will facilitate research on the oleaginous Aurantiochytrium sp., and the obtained two strains for lipid and carbohydrate productions will provide the foundations for their applications in medical, food, and feed industries.

PhytoAuthent: Molecular authentication of complex herbal food supplements for safety and efficacy

The PhytoAuthent project was structured to gather, test, develop and apply, in real life case scenarios, molecular techniques, such as biochemical fingerprinting and DNA sequence-based methods, for plant identification of constituents in complex herbal products. The project had a strong focus on applied aspects like protecting consumers from health risks associated with product substitution and contamination of herbal products.

Characteristics of own collection of Pseudomonas aeruginosa clinical strains, hosts of bacteriophages

Introduction: The paper presents the phenotypic and molecular characteristics of the collection of 18 P. aeruginosa clinical isolates used as host indicators to study the lytic range of 12 phages against P. aeruginosa. Methods: The phages host ranges were assayed by spot tests. Phenotypic characteristics of strains was investigated by the API 20NE biochemical fingerprinting, oxidase tests, the production of pyocyanin, fluorescein and L-arginine dihydrolase. Resistance profiles were analyzed. The PCR method and sequencing were used to study the distribution the genes of alkaline protease (aprA), exotoxin A (exoA), elastase B (lasB), exotoxins (exoS/T/U/Y), phenazine modyfing genes (phzM, phzS) and to identify selected β-lactamases (blaGES, blaIMP, blaKPC, blaOXA-2, blaOXA-10, blaPER, blaSPM-1, blaSHV, blaTEM, blaVIM). Additionaly, the genetic diversity was investigated by PFGE.116 M. Brzychczy-Włoch i inni Nr 2-4 Results: Twenteen newly isolated P. aeruginosa phages were found to lyse 100% of the analyzed strains. Phages PAR_3 and PAR_10 exhibited the highest lytic activity against isolates, lysing, 77,8% strains tested. The other phages, PAR_9 and PAR_12, presented generally weaker activity against bacteria, lysing respectively, 50% and 44,4% of tested strains. AprA, exoA, phzM, phzS were presented in all strains; lasB in 77,8%. The most frequentlycombination of egzoenzyme genes S+/T+/U-/Y+ in 78% isolates was remarked. In collection, 18 different resistance profiles were observed and 44% isolates were classified as MDR. The blaGES was the most prevalent gene (44%), followed by blaSPM-1 and blaTEM detected in 17% and 11,1% isolates, respectively. BlaOXA-2 was detected in only 5,5% of all isolates. In PFGE method, 18 singletons (A-S) were identified. No relationship between resistance, virulence and PFGE groups was found. Conclusion: In summarize, all phages infect multiple host species and showed a broad lytic spectrum. All bacteria tested were infected by multiple phages and displayed a wide range of susceptibility. In general, we observed a high degree of genetic diversity and individuality of the studied P. aeruginosa collection, bacteriophage hosts.

Enterococci populations of a metropolitan river after an extreme flood event: prevalence, persistence and virulence determinants

We investigated the prevalence, persistence and virulence determinants of enterococci populations in water samples collected over three rounds following an extreme flood event in a metropolitan river. Enterococci (n = 482) were typed using the high resolution biochemical fingerprinting method (PhP typing) and grouped into common (C) or single (S) biochemical phenotypes (BPTs). In all, 23 C-BPTs (72.6% of isolates) were found across the sites. A representative isolate of each C-BPT was identified to the species level and tested for the presence of seven virulence genes (VGs), biofilm formation and resistance to 14 antibiotics. The enterococci concentrations in samples collected during the first two rounds were above national recreational water guidelines. By round three, enterococci concentrations decreased significantly (P < 0.05). However, 11 C-BPTs (55.5% of isolates) persisted across all sampling rounds. E. casseliflavus and E. mundtii were the most common enterococci populations comprising of >57% of all isolates. Ten of the 11 most dominant C-BPTs were resistant to multiple antibiotics and harboured one or more VGs. The high prevalence of antibiotic resistance and VGs among enterococci isolates in this catchment not only provides them with niche advantages but also poses a risk to public health.