Interaction of selected alkoxy naringenin oximes with model and bacterial membranes

Naringenin is a flavonoid found in many fruits and herbs, most notably in grapefruits. In recent years, this compound and its derivatives have been of great interest due to their high biological activity, including fungicidal and bactericidal effects, also in relation to multidrug-resistant bacteria. Membrane interactions of naringenin oxime (NO) and its 7-O-alkyl (7-alkoxy) derivatives, such as methyl (7MENO), ethyl (7ETNO), isopropyl (7IPNO), n-butyl (7BUNO) and n-pentyl (7PENO) were studied. Thermotropic properties of model membranes were investigated via differential scanning calorimetry (DSC), the influence on lipid raft mimicking giant unilamellar vesicles (GUVs) via fluorescence microscopy, and membrane permeability via measuring calcein leakage from liposomes. Molecular calculations supplemented the study. The influence of naringenin oximes on two strains of multidrug resistant bacteria: Staphylococcus aureus KJ and Enterococcus faecalis 37VRE was also investigated. In DSC studies all compounds reduced the temperature and enthalpy of main phase transition and caused disappearing of the pretransition. NO was the least active. The reduction in the area of surface domains in GUVs was observed for NO. Compounds NO and 7BUNO resulted in very low secretion of calcein from liposomes (permeability < 3 %). The highest results were observed for 7MENO (88.4 %) and 7IPNO (78.5 %). When bacterial membrane permeability was investigated all compounds caused significant release of propidium iodide from S. aureus (31.6-87.0 % for concentration 128 μg/mL). In the case of E. faecalis, 7ETNO (75.7 %) and NO (28.8 %) were the most active. The rest of the tested compounds showed less activity (permeability < 13.9 %). The strong evidence was observed that antibacterial activity of the tested compounds may be associated with their interaction with bacterial membrane.

A Combination of β-Aescin and Newly Synthesized Alkylamidobetaines as Modern Components Eradicating the Biofilms of Multidrug-Resistant Clinical Strains of Candida glabrata

The current trend in microbiological research aimed at limiting the development of biofilms of multidrug-resistant microorganisms is increasingly towards the search for possible synergistic effects between various compounds. This work presents a combination of a naturally occurring compound, β-aescin, newly synthesized alkylamidobetaines (AABs) with a general structure-CnTMDAB, and antifungal drugs. The research we conducted consists of several stages. The first stage concerns determining biological activity (antifungal) against selected multidrug-resistant strains of Candida glabrata (C. glabrata) with the highest ability to form biofilms. The second stage of this study determined the activity of β-aescin combinations with antifungal compounds and alkylamidobetaines. In the next stage of this study, the ability to eradicate a biofilm on the polystyrene surface of the combination of β-aescin with alkylamidobetaines was examined. It has been shown that the combination of β-aescin and alkylamidobetaine can firmly remove biofilms and reduce their viability. The last stage of this research was to determine the safety regarding the cytotoxicity of both β-aescin and alkylamidobetaines. Previous studies on the fibroblast cell line have shown that C9 alkylamidobetaine can be safely used as a component of anti-biofilm compounds. This research increases the level of knowledge about the practical possibilities of using anti-biofilm compounds in combined therapies against C. glabrata.

Bioactive Compounds from Plant Origin as Natural Antimicrobial Agents for the Treatment of Wound Infections

The rising prevalence of drug-resistant bacteria underscores the need to search for innovative and nature-based solutions. One of the approaches may be the use of plants that constitute a rich source of miscellaneous compounds with a wide range of biological properties. This review explores the antimicrobial activity of seven bioactives and their possible molecular mechanisms of action. Special attention was focused on the antibacterial properties of berberine, catechin, chelerythrine, cinnamaldehyde, ellagic acid, proanthocyanidin, and sanguinarine against Staphylococcus aureus, Enterococcus spp., Klebsiella pneumoniae, Acinetobacter baumannii, Escherichia coli, Serratia marcescens and Pseudomonas aeruginosa. The growing interest in novel therapeutic strategies based on new plant-derived formulations was confirmed by the growing number of articles. Natural products are one of the most promising and intensively examined agents to combat the consequences of the overuse and misuse of classical antibiotics.

Meropenem/Vaborbactam: β-Lactam/β-Lactamase Inhibitor Combination, the Future in Eradicating Multidrug Resistance

Due to the fact that there is a steadily increasing trend in the area of antimicrobial resistance in microorganisms, there is a need to look for new treatment alternatives. One of them is the search for new β-lactamase inhibitors and combining them with β-lactam antibiotics, with the aim of increasing the low-dose efficacy, as well as lowering the resistance potential of bacterial strains. This review presents the positive effect of meropenem in combination with a vaborbactam (MER-VAB). This latest antibiotic-inhibitor combination has found particular use in the treatment of infections with the etiology of carbapenem-resistant Enterobacterales (CRE), Gram-negative bacteria, with a high degree of resistance to available antimicrobial drugs.

Testing Antimicrobial Properties of Human Lactoferrin-Derived Fragments

Lactoferrin, an iron-binding glycoprotein, plays a significant role in the innate immune system, with antibacterial, antivirial, antifungal, anticancer, antioxidant and immunomodulatory functions reported. It is worth emphasizing that not only the whole protein but also its derived fragments possess antimicrobial peptide (AMP) activity. Using AmpGram, a top-performing AMP classifier, we generated three novel human lactoferrin (hLF) fragments: hLF 397-412, hLF 448-464 and hLF 668-683, predicted with high probability as AMPs. For comparative studies, we included hLF 1-11, previously confirmed to kill some bacteria. With the four peptides, we treated three Gram-negative and three Gram-positive bacterial strains. Our results indicate that none of the three new lactoferrin fragments have antimicrobial properties for the bacteria tested, but hLF 1-11 was lethal against Pseudomonas aeruginosa. The addition of serine protease inhibitors with the hLF fragments did not enhance their activity, except for hLF 1-11 against P. aeruginosa, which MIC dropped from 128 to 64 µg/mL. Furthermore, we investigated the impact of EDTA with/without serine protease inhibitors and the hLF peptides on selected bacteria. We stress the importance of reporting non-AMP sequences for the development of next-generation AMP prediction models, which suffer from the lack of experimentally validated negative dataset for training and benchmarking.

Ether Derivatives of Naringenin and Their Oximes as Factors Modulating Bacterial Adhesion

Because of the close connection between adhesion and many vital cellular functions, the search for new compounds modulating the adhesion of bacteria belonging to the intestinal microbiota is a great challenge and a clinical need. Based on our previous studies, we discovered that O-lkyl naringenin derivatives and their oximes exhibit antimicrobial activity against antibiotic-resistant pathogens. The current study was aimed at determining the modulatory effect of these compounds on the adhesion of selected representatives of the intestinal microbiota: Escherichia coli, a commensal representative of the intestinal microbiota, and Enterococcus faecalis, a bacterium that naturally colonizes the intestines but has disease-promoting potential. To better reflect the variety of real-life scenarios, we performed these studies using two different intestinal cell lines: the physiologically functioning ("healthy") 3T3-L1 cell line and the disease-mimicking, cancerous HT-29 line. The study was performed in vitro under static and microfluidic conditions generated by the Bioflux system. We detected the modulatory effect of the tested O-alkyl naringenin derivatives on bacterial adhesion, which was dependent on the cell line studied and was more significant for E. coli than for E. faecalis. In addition, it was noticed that this activity was affected by the concentration of the tested compound and its structure (length of the carbon chain). In summary, O-alkyl naringenin derivatives and their oximes possess a promising modulatory effect on the adhesion of selected representatives of the intestinal microbiota.

Antiproliferative Activity and Impact on Human Gut Microbiota of New O-Alkyl Derivatives of Naringenin and Their Oximes

Naringenin is a 5,7,4′-trihydroxyflavanone naturally occurring mainly in citrus fruits, characterized by a wide spectrum of biological activity. Chemical modifications based on alkylation and oximation in most cases increase its bioactivity. The aim of our research was to evaluate the antiproliferative activity and influence on selected representatives of the human gut microbiota of new synthesized O-alkyl derivatives (A1–A10) and their oximes (B1–B10), which contain hexyl, heptyl, octyl, nonyl and undecyl chains attached to the C-7 or to both the C-7 and C-4′ positions in naringenin. To the best of our knowledge, compounds A3, A4, A6, A8–A10 and B3–B10 have not been described in the scientific literature previously. The anticancer activity was tested on human colon cancer cell line HT-29 and mouse embryo fibroblasts 3T3-L1 using the sulforhodamine B (SRB) and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-2H-tetrazolium bromide (MTT) assays. We also determined the impacts of all compounds on the growth of Gram-positive and Gram-negative bacterial strains, such as Staphylococcus aureus, Enterococcus faecalis and Escherichia coli. The antimicrobial activity was expressed in terms of minimal inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC) values. For 7,4′-di-O-hexylnaringenin (A2), 7-O-undecylnaringenin (A9) and their oximes (B2, B9), which were safe for microbiota (MIC > 512 µg/mL) and almost all characterized by high cytotoxicity against the HT-29 cell line (A2: IC₅₀ > 100 µg/mL; A9: IC₅₀ = 17.85 ± 0.65 µg/mL; B2: IC₅₀ = 49.76 ± 1.63 µg/mL; B9: IC₅₀ = 11.42 ± 1.17 µg/mL), apoptosis assays were performed to elucidate their mechanisms of action. Based on our results, new compound B9 induced an apoptotic process via caspase 3/7 activation, which proved its potential as an anticancer agent.

Testing Antimicrobial Properties of Selected Short Amyloids

Amyloids and antimicrobial peptides (AMPs) have many similarities, e.g., both kill microorganisms by destroying their membranes, form aggregates, and modulate the innate immune system. Given these similarities and the fact that the antimicrobial properties of short amyloids have not yet been investigated, we chose a group of potentially antimicrobial short amyloids to verify their impact on bacterial and eukaryotic cells. We used AmpGram, a best-performing AMP classification model, and selected ten amyloids with the highest AMP probability for our experimental research. Our results indicate that four tested amyloids: VQIVCK, VCIVYK, KCWCFT, and GGYLLG, formed aggregates under the conditions routinely used to evaluate peptide antimicrobial properties, but none of the tested amyloids exhibited antimicrobial or cytotoxic properties. Accordingly, they should be included in the negative datasets to train the next-generation AMP prediction models, based on experimentally confirmed AMP and non-AMP sequences. In the article, we also emphasize the importance of reporting non-AMPs, given that only a handful of such sequences have been officially confirmed.

Naringenin and Its Derivatives-Health-Promoting Phytobiotic against Resistant Bacteria and Fungi in Humans

Naringenin is a trihydroxyflavanone present in large amount in different citrus fruits, e.g., oranges, pomelos, grapefruits, but also in tomatoes, fenugreek and coffee. It has a wide range of pharmacological and biological effects beneficial to human health. Its antioxidant, anti-cancer, anti-inflammatory, antifungal and antimicrobial activity is frequently reported in scientific literature. In this review we presented the current state of knowledge on the antimicrobial activity of naringenin and its natural and synthetic derivatives as a phytobiotic against resistant Gram-positive and Gram-negative bacteria as well as fungi in humans. Most of the data reported here have been obtained from in vitro or in vivo studies. Over the past few years, due to the overuse of antibiotics, the occurrence of bacteria resistant to all available antibiotics has been growing. Therefore, the main focus here is on antibiotic resistant strains, which are a significant, worldwide problem in the treatment of infectious diseases. The situation is so alarming that the WHO has listed microbial resistance to drugs on the list of the 10 most important health problems facing humanity. In addition, based on scientific reports from recent years, we described the potential molecular mechanism of action of these bioflavonoids against pathogenic strains of microorganisms. As plant-derived substances have been pushed out of use with the beginning of the antibiotic era, we hope that this review will contribute to their return as alternative methods of preventing and treating infections in the epoch of drug resistance.

Natural Compounds in the Battle against Microorganisms-Linalool

The purpose of this article is to present recent studies on the antimicrobial properties of linalool, the mechanism of action on cells and detoxification processes. The current trend of employing compounds present in essential oils to support antibiotic therapy is becoming increasingly popular. Naturally occurring monoterpene constituents of essential oils are undergoing detailed studies to understand their detailed effects on the human body, both independently and in doses correlated with currently used pharmaceuticals. One such compound is linalool, which is commonly found in many herbs and is used to flavor black tea. This compound is an excellent fragrance additive for cosmetics, enhancing the preservative effect of the formulations used in them or acting as an anti-inflammatory on mild skin lesions. Previous studies have shown that it is extremely important due to its broad spectrum of biological activities, i.e., antioxidant, anti-inflammatory, anticancer, cardioprotective and antimicrobial. Among opportunistic hospital strains, it is most active against Gram-negative bacteria. The mechanism of action of linalool against microorganisms is still under intensive investigation. One of the key aspects of linalool research is biotransformation, through which its susceptibility to detoxification processes is determined.

Nanoapatites Doped and Co-Doped with Noble Metal Ions as Modern Antibiofilm Materials for Biomedical Applications against Drug-Resistant Clinical Strains of Enterococcus faecalis VRE and Staphylococcus aureus MRSA

The main aim of our research was to investigate antiadhesive and antibiofilm properties of nanocrystalline apatites doped and co-doped with noble metal ions (Ag⁺, Au⁺, and Pd²⁺) against selected drug-resistant strains of Enterococcus faecalis and Staphylococcus aureus. The materials with the structure of apatite (hydroxyapatite, nHAp; hydroxy-chlor-apatites, OH-Cl-Ap) containing 1 mol% and 2 mol% of dopants and co-dopants were successfully obtained by the wet chemistry method. The majority of them contained an additional phase of metallic nanoparticles, in particular, AuNPs and PdNPs, which was confirmed by the XRPD, FTIR, UV–Vis, and SEM–EDS techniques. Extensive microbiological tests of the nanoapatites were carried out determining their MIC, MBC value, and FICI. The antiadhesive and antibiofilm properties of the tested nanoapatites were determined in detail with the use of fluorescence microscopy and computer image analysis. The results showed that almost all tested nanoapatites strongly inhibit adhesion and biofilm production of the tested bacterial strains. Biomaterials have not shown any significant cytotoxic effect on fibroblasts and even increased their survival when co-incubated with bacterial biofilms. Performed analyses confirmed that the nanoapatites doped and co-doped with noble metal ions are safe and excellent antiadhesive and antibiofilm biomaterials with potential use in the future in medical sectors.

Composition and Antimicrobial Activity of Ilex Leaves Water Extracts

Plants from the Ilex genus are known for properties such as antimicrobial and anti-inflammatory activity, can act as antiobesity agents and thus can be helpful in medicine. Some holly species, such as Ilex paraguariensis (widely known in the form of popular beverage: yerba mate), have been investigated, while others have been partially researched or remain unknown. Therefore, we performed qualitative and quantitative phytochemical analyses and screened antimicrobial properties of lesser-studied species (I. aquifolium L., I. aquifolium ‘Argentea Marginata’ and I. × meserveae ‘Blue Angel’). I. paraguariensis was used as a standard species for comparison purposes. Investigations were performed on water extracts due to their expected activity and composition. Antimicrobial research included evaluating minimal inhibitory, bactericidal (Staphylococcus aureus and Escherichia coli) and fungicidal concentration (Candida albicans, Alternaria alternata, Fusarium oxysporum, and Aspergillus niger) of extracts. The influence of the extracts on the production, eradication, and viability of bacterial biofilms was also analysed. It was established that Ilex paraguariensis possesses the richest profile of hydroxycinnamic acids derivatives in terms of component concentration and diversity. Ilex spp., especially I. × meserveae, contain a slightly higher amount of flavonoids and more different flavonoid derivatives than I. paraguariensis. However, the strongest antibacterial activity was shown by I. aquifolium L. and its cultivar ‘Argentea Marginata’ in terms of minimal inhibitory, bactericidal and fungicidal concentration, and biofilm assays. Extracts from both species significantly reduced the biofilm viability of S. aureus as well, which may be of use in the production of multicomponent lavaseptics, antiseptics, diuretics (supporting urinary tract infection therapy) and, due to their action on fungi, additives to growth media for specific fungi. The significant content of saponins enables Ilex extracts to be used as natural emulsifiers, for example, in cosmetics. Moreover, relatively high chlorogenic acid and rutin content may suggest use of Ilex spp. to treat obesity, digestive problems, in chemoprevention, and as preservatives in the food industry.

Antimicrobial O-Alkyl Derivatives of Naringenin and Their Oximes Against Multidrug-Resistant Bacteria

New antimicrobial agents are needed to address infections caused by multidrug-resistant bacteria. Here, we are reporting novel O-alkyl derivatives of naringenin and their oximes, including novel compounds with a naringenin core and O-hexyl chains, showing activity against clinical strains of clarithromycin-resistant Helicobacter pylori, vancomycin-resistant Enterococcus faecalis, methicillin-resistant Staphylococcus aureus, and beta-lactam-resistant Acinetobacter baumannii and Klebsiella pneumoniae. The minimum inhibitory concentrations (MICs), which provide a quantitative measure of antimicrobial activity, were in the low microgram range for the selected compounds. Checkerboard assays for the most active compounds in combination with antibiotics revealed interactions that varied from synergistic to neutral.

The prevalence of mucosa-associated diffusely adherent Escherichia coli in children with inflammatory bowel disease

BACKGROUND

The relationship of diffusely adherent Escherichia coli (DAEC) with pediatric inflammatory bowel disease (IBD) has not been previously studied. Diffusely adherent E. coli are a common cause of long-lasting childhood diarrhea and we postulated that they may induce inflammation of the intestinal mucosa, contributing to the development of IBD in susceptible children.

OBJECTIVES

The aim of the study was to investigate the relationship between DAEC and pediatric IBD, including Crohn's disease (CD) and ulcerative colitis (UC). Diffusely adherent E. coli isolates were also assessed regarding their pathogenicity.

MATERIAL AND METHODS

Diffusely adherent E. coli were screened among 130 E. coli strains isolated from intestinal biopsy specimens from 26 children with IBD using polymerase chain reaction (PCR) with primers specific to the pathotype and adherence assays to HEp-2 cells. Diffusely adherent E. coli were further analyzed for their ability to adhere to and invade polarized Caco-2 cells. The immunomodulatory effect of DAEC on the secretion of tumor necrosis factor α (TNF-α) by human monocyte-derived macrophages (MDM) was assessed using an immunoenzymatic assay.

RESULTS

Diffusely adherent E. coli were recovered from 18 (69.2%) of the 26 intestinal biopsy specimens from both CD and UC patients. Most DAEC isolates carried AfaE3 adhesin, adhered to and were internalized by Caco-2 cells, and induced secretion of elevated levels of TNF-α.

CONCLUSIONS

The study demonstrated the internalization of DAEC by intestinal epithelial cells and their ability to induce secretion of increased level of TNF-α in a Caco-2/macrophage compartmentalized culture. This indicated that the pathovar should be considered a pathobiont inducing inflammation of the intestinal mucosa in pediatric patients with IBD.

Effect of amyloid curli fibrils and curli CsgA monomers from Escherichia coli on in vitro model of intestinal epithelial barrier stimulated with cytokines

Amyloid curli fibrils produced by Escherichia coli are well-known virulence factor influencing E. coli adhesion and biofilm formation. However, the impact of curli on intestinal epithelial barrier stimulated with proinflammatory cytokines is unknown. In the study, we examined the effect of curli produced by nonpathogenic E. coli K-12 and wild-type E. coli EC32 strains, and purified CsgA proteins on differentiated Caco-2 cell monolayers stimulated with a mixture of IL-1β, TNF-α, and INFγ cytokines as a model of 'inflamed intestinal epithelial barrier' in vitro. The results of the study indicated that curliated E. coli adhered better to polarized Caco-2 cells than their curli-deficient mutants and the adherence was further augmented by stimulation of epithelial cells with proinflammatory cytokines. Interestingly, curli reduced internalization but enhanced intracellular survival of the wild-type E. coli strain EC32 within intestinal epithelial cells. Curli-expressing E. coli, as well as purified CsgA proteins, attenuated IL-8 secretion by unstimulated Caco-2 cells, although the effect was barely observed on cytokine-stimulated cells. The findings of the study revealed that curli fibrils are an important virulence factor enabling curliated E. coli to effectively colonize intestinal epithelium especially in individuals with inflammatory intestinal disorders.

Potential of Biocellulose Carrier Impregnated with Essential Oils to Fight Against Biofilms Formed on Hydroxyapatite

In this research, bacterial cellulose (BC), one of the most promising biopolymers of the recent years, was saturated with thyme, eucalyptus and clove essential oils (EOs) and applied against staphylococcal and pseudomonal biofilms formed on hydroxyapatite (HA). BC dressings were thoroughly analyzed with regard to their physical properties. Moreover, the exact composition and ability of particular EO molecules to adhere to HA was assessed. Additionally, cytotoxicity of oil-containing, cellulose-based dressings towards osteoblasts and fibroblasts as well as their impact on reactive oxygen species (ROS) production by macrophages was assessed. The results revealed the high ability of BC dressings to absorb and subsequently release EOs from within their microstructure; the highest number of compounds able to adhere to HA was found in the thyme EO. The eucalyptus EO displayed low, while thyme and clove EOs displayed high cytotoxicity towards fibroblast and osteoblast cell lines. The clove EO displayed the highest eradication ability toward staphylococcal, while the thyme EO against pseudomonal biofilm. Taken together, the results obtained indicate the suitability of EO-saturated BC dressings to eradicate pseudomonal and staphylococcal biofilm on HA surface and moreover, to not trigger reactive oxygen species production by immune system effector cells. However, due to cytotoxic effects of thyme and clove EOs towards cell lines in vitro, the eucalyptus EO-saturated BC dressing is of highest potential to be further applied.

A twelve-year retrospective analysis of prevalence and antimicrobial susceptibility patterns of Ureaplasma spp. and Mycoplasma hominis in the province of Lower Silesia in Poland

OBJECTIVE

Genital mycoplasmas are opportunistic pathogens that have been associated with urogenital infections in humans. Only a few groups of antimicrobials are available for treatment of urogenital tract infections caused by genital mycoplasmas. However, emerging resistance of mycoplasmas to antimicrobial agents has been reported worldwide. The aim of the study was a retrospective analysis of the prevalence and antimicrobial susceptibility patterns of M. hominis and Ureaplasma spp. in patients with urogenital tract infections during a twelve-year period between 2003 and 2015.

STUDY DESIGN

Mycoplasma IST2 test was used for the detection, enumeration, identification and antimicrobial susceptibility testing of genital mycoplasmas in 1182 samples from 778 women and 404 men with genitourinary tract infection. Indicative enumeration in the test determines whether the mycoplasma count in the sample is equal or higher than the threshold set at 10⁴ colony forming units.

RESULTS

A total of 152 (12.8%) samples were found to be positive for genital mycoplasmas. M. hominis was detected only in three samples and Ureaplasma spp. in 141 samples. Both, M. hominis and Ureaplasma spp. were detected in the remaining eight samples. In the analyzed period between 2003 and 2015, a gradually increasing resistance of ureaplasmas to ciprofloxacin and clarithromycin and decreasing resistance to ofloxacin, erythromycin and tetracycline were observed. Pristinamycin, josamycin and doxycycline were most active against Ureaplasma spp. In contrast, fluoroquinolones had the lowest efficacy against Ureaplasma spp. and as many as 116 (82.3%) and 77 (54.6%) of Ureaplasma spp. isolates were resistant to ciprofloxacin and ofloxacin, respectively. M. hominis isolates were uniformly resistant to azithromycin, clarithromycin and erythromycin but susceptible to josamycin, ofloxacin, doxycycline and pristinamycin. One-third of these isolates were resistant to ciprofloxacin and tetracycline.

CONCLUSION

In the study Ureaplasma spp. and M. hominis were detected with relatively low frequency in comparison with other studies however, most of these isolates were resistant to ciprofloxacin indicating the need for better management of ciprofloxacin prescription. Important limitations of Mycoplasma IST2 assay concerning antimicrobial susceptibility testing and divergences between breakpoints in the test and EUCAST guidelines point the need to introduce new methodologies to improve evaluation of resistant strains at our region.

Amyloidogenic motifs revealed by n-gram analysis

Amyloids are proteins associated with several clinical disorders, including Alzheimer's, and Creutzfeldt-Jakob's. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest classifiers. Since the amyloidogenicity may not depend on the exact sequence of amino acids but on their more general properties, we tested 524,284 reduced amino acid alphabets of different lengths (three to six letters) to find the alphabet providing the best performance in cross-validation. The predictor based on this alphabet, called AmyloGram, was benchmarked against the most popular tools for the detection of amyloid peptides using an external data set and obtained the highest values of performance measures (AUC: 0.90, MCC: 0.63). Our results showed sequential patterns in the amyloids which are strongly correlated with hydrophobicity, a tendency to form β-sheets, and lower flexibility of amino acid residues. Among the most informative n-grams of AmyloGram we identified 15 that were previously confirmed experimentally. AmyloGram is available as the web-server: http://smorfland.uni.wroc.pl/shiny/AmyloGram/ and as the R package AmyloGram. R scripts and data used to produce the results of this manuscript are available at http://github.com/michbur/AmyloGramAnalysis .

Relevance of serology for Mycoplasma pneumoniae infection among children with persistent cough

BACKGROUND

Mycoplasma pneumoniae is an important cause of upper and lower respiratory tract infections. Cough and tracheobronchitis are the commonest features of M. pneumoniae infection but diagnosis based on clinical symptoms that may be due to other respiratory pathogens is impossible. Thus laboratory testing for M. pneumoniae is particularly important. Correct and rapid diagnosis of M. pneumoniae infections is of prime importance to introduce appropriate antibiotic treatment.

OBJECTIVES

Evaluation of the incidence of IgM and IgG antibodies specific to M. pneumoniae among children with pneumonia and/or chronic cough.

MATERIAL AND METHODS

Serum samples from 148 children with a history of chronic cough (lasting at least one month), recurrent respiratory tract infections, allergic rhinitis, and/or inflammatory changes on X-chest ray. First, all sera were screened for specific anti-M. pneumoniae antibodies using agglutination test following the detection of specific IgM and IgG anti-M. pneumoniae antibodies using immunoenzymatic assays.

RESULTS

Out of the 148 serum samples, 57 (38.5%) gave positive screening results. However, the presence of M. pneumoniae-specific IgM and/or IgG antibodies was confirmed by immunoenzymatic assays in only 30 (52.6%) of these 57 positive samples. These results indicated that in as many as 27 (47.4%) out of the 57 serum samples screened, false-positive results occurred.

CONCLUSIONS

Evaluation of acute- and convalescent-phase sera is necessary to make possible accurate interpretation of the serological testing results.

Association of untypeable enteropathogenic Escherichia coli (EPEC) strains with persistent diarrhea in children from the region of lower Silesia in Poland

Enteropathogenic Escherichia coli strains (EPEC) carrying the eae gene encoding intimin are divided into typical strains producing bundle forming pili, encoded by the bfpA gene, and atypical strains lacking the gene. In the study typical and atypical EPEC that did not agglutinated with EPEC polyvalent antisera but carrying virulence factors characteristic to other pathogenic E. coli i.e. diffusely adhering and enteroaggregative E. coli were isolated from 24 (43.6%) of 55 children > 10 years old with persistent diarrhea. These results indicated that non-typeable typical and atypical EPEC can contribute to chronic intestinal infections in teenagers.

Virulence genes profiles and phylogenetic origin of Escherichia coli from acute and chronic intestinal diseases revealed by comparative genomic hybridization microarray

The association between Escherichia coli virulence factors and chronic intestinal disorders is mostly unknown. The presented study compared the distribution of virulence genes and phylogroups among E. coli isolated from chronic intestinal disorders such as Crohn's disease and irritable bowel syndrome (IBS) with strains isolated from patients with acute diarrhea as a control group. The presence of 159 virulence genes corresponding to known E. coli pathotypes was determined among 78 E. coli archive strains isolated from IBS, acute diarrhea and Crohn's disease using CGH microarray. E. coli isolated from IBS demonstrated a mosaic of virulence genes specific to enteropathogenic, enterotoxigenic, enterohemorrhagic E. coli strains and Shigella species. In contrast, virulence factors and phylogroups distribution among E. coli isolated from children with acute diarrhea was similar to extraintestinal E. coli strains that probably acquired some virulence genes. The acquisition of virulence genes might have an impact on diarrheagenic potential of these strains. On the other hand, E. coli isolated from children with Crohn's disease seem to be similar to adherent-invasive E. coli strains (AIEC), as it lack most known virulence genes. The presented study showed that these analyzed groups of E. coli strains differed from each other with the respect to the distribution of virulence genes. The differences in gene content support the idea that the participation of E. coli in chronic intestinal diseases is mostly related to virulence potential of these strains.

Characterization of genes associated with internalization of enteroaggregative Escherichia coli

On animal models enteroaggregative Escherichia coli (EAEC) can cause mild, but significant mucosal damage, suggesting the invasive capability of these strains. In the study we investigated the ability of typical, aggR-positive and atypical, aggR-negative EAEC isolates to enter intestinal epithelial Int407 cells in relation to the distribution of genes encoding the putative invasins described among pathogenic E. coli categories. The results demonstrated that regardless of origin and affiliation to typical and atypical EAEC, most isolates examined were internalized by the epithelial cells to different extent. Although as many as 50 (84.3%) EAEC demonstrated a variety of combinations of the aggB, afaD, ipaH and tia genes determined, there was no correlation between the invasion efficiency of these strains and the presence of any particular gene involved in invasion. Most of EAEC examined belonged to phylogenetic group B2 and D.