Eucalypt Extracts Prepared by a No-Waste Method and Their 3D-Printed Dosage Forms Show Antimicrobial and Anti-Inflammatory Activity.

The pharmaceutical industry usually utilizes either hydrophobic or hydrophilic substances extracted from raw plant materials to prepare a final product. However, the waste products from the plant material still contain biologically active components with the opposite solubility. The aim of this study was to enhance the comprehensive usability of plant materials by developing a new no-waste extraction method for eucalypt leaves and by investigating the phytochemical and pharmacological properties of eucalypt extracts and their 3D-printed dosage forms. The present extraction method enabled us to prepare both hydrophobic soft extracts and hydrophilic (aqueous) dry extracts. We identified a total of 28 terpenes in the hydrophobic soft extract. In the hydrophilic dry extract, a total of 57 substances were identified, and 26 of them were successfully isolated. The eucalypt extracts studied showed significant antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis, Candida albicans, Corynebacterium diphtheriae gravis, and Corynebacterium diphtheriae mitis. The anti-inflammatory activity of the dry extract was studied using a formalin-induced-edema model in mice. The maximum anti-exudative effect of the dry extract was 61.5% at a dose of 20 mg/kg. Composite gels of polyethylene oxide (PEO) and eucalypt extract were developed, and the key process parameters for semi-solid extrusion (SSE) 3D printing of such gels were verified. The SSE 3D-printed preparations of novel synergistically acting eucalypt extracts could have uses in antimicrobial and anti-inflammatory medicinal applications.

Unveiling the etiology of peritonsillar abscess using next generation sequencing.

BACKGROUND: Peritonsillar abscess (PTA) is a severe deep neck space infection with an insufficiently characterized bacterial etiology. We aimed to reveal the bacteria associated with PTA applying next generation sequencing (NGS). Tonsil biopsies and pus samples of 91 PTA patients were analysed applying NGS method. RESULTS: Over 400 genera and 800 species belonging to 34 phyla were revealed. The most abundant species in both sample types were Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. When present, S. pyogenes was normally a predominant species, although it was recovered as a minor population in some samples dominated by F. nucleatum and occasionally F. necrophorum. S. pyogenes and F. necrophorum were the predominant species (> 10% in a community) in 28 (31%) pus samples, while F. nucleatum in 21 (23%) and S. anginosus in 8 (9%) pus samples. We observed no substantial differences between the microbial findings in pus and tonsil biopsies. CONCLUSIONS: The most probable causative agents of PTA according to our NGS-study include Streptococcus pyogenes, Fusobacterium necrophorum and Fusobacterium nucleatum. Some other streptococci (S. anginosus) and anaerobes (Prevotella, Porphyromonas) may contribute to the infection as well. Pus of the peritonsillar abscess is more representative specimen for microbiological examination than the tonsillar tissue. Our results are important in the context of optimizing the handling of the PTA patients.

Aerobic vaginitis in the third trimester and its impact on pregnancy outcomes.

BACKGROUND: Aerobic vaginitis (AV) is a vaginal inflammation characterized by disruption of the lactobacillus microbiota and increased counts of different aerobic bacteria. AV may result in severe complications, especially during pregnancy, including preterm delivery, neonatal and maternal infections. This study aimed to determine the prevalence of AV in the third trimester of pregnancy, and the relationship between AV and pregnancy outcomes.  METHODS: A cross-sectional descriptive study included 323 pregnant women attending for routine antenatal care in the Hue University Hospital. Vaginal samples collected at the third trimester of pregnancy were evaluated for AV according to the scoring system of Donders and cultured for identification of predominant bacteria. Pregnancy was followed to its end, and pregnancy outcomes were recorded for both mothers and infants. RESULTS: The proportion of pregnant women diagnosed with AV in the third trimester was found to be 15.5%, with the vast majority of the cases (84%) displaying the light AV and 16% the moderate AV. The vaginal cultures in the women with AV revealed most frequently Streptococcus agalactiae (6%), followed by Enterococcus spp (4%), Staphylococcus aureus (4%), and Acinetobacter baumannii (2%). In addition, AV during the last trimester of pregnancy was associated with an increased risk of puerperal sepsis (OR 8.65, 95% CI: 1.41-53.16, p = 0.020) and there was a slightly increased risk for neonatal infections, which was statistically insignificant. CONCLUSIONS: The proportion of AV is relatively high in Vietnamese pregnant women. Since it is associated with an increased risk of puerperal sepsis, it needs to be diagnosed and treated before delivery.

Comparative Analysis of Gut Microbiota in Centenarians and Young People: Impact of Eating Habits and Childhood Living Environment.

The composition of centenarians' gut microbiota has consistently been used as a model for healthy aging studies. However, there is an incomplete understanding of how childhood living conditions and eating habits affect the development and composition of gastrointestinal microbiota in centenarians with good cognitive functions. We compared the gut microbiota as well as the living and eating habits of the oldest-old group and the young people group. The richness and diversity of microbiota and the abundance of hereditary and environmental microbes were higher in people with longevity than young people. People with longevity ate more potatoes and cereal products. In their childhood, they had more exposure to farm animals and did not have sewers compared with young people. Young people's gut microbiota contained more butyrate-producing bacteria and bacteria that characterized an animal-based Western diet. These results expand our understanding of the effects of childhood environment and diet on the development and stability of the microbiota in people with longevity.

Effect of erythritol and xylitol on Streptococcus pyogenes causing peritonsillar abscesses.

Polyols are effective against caries-causing streptococci but the effect on oropharynx-derived pyogenic streptococci is not well characterised. We aimed to study the effect of erythritol (ERY) and xylitol (XYL) against Streptococcus pyogenes isolated from peritonsillar abscesses (PTA). We used 31 clinical isolates and 5 throat culture collection strains. Inhibition of bacterial growth by polyols at 2.5%, 5% and 10% concentrations was studied and the results were scored. Amylase levels in PTA pus were compared to polyol effectivity scores (PES). Growth curves of four S. pyogenes isolates were analysed. Our study showed that XYL was more effective than ERY inhibiting 71-97% and 48-84% of isolates, respectively, depending of concentrations. 48% of clinical and all throat strains were inhibited by polyols in all concentrations (PES 3). PES was negative or zero in 26% of the isolates in the presence of ERY and in 19% of XYL. ERY enhanced the growth of S. pyogenes isolated from pus with high amylase levels. Polyols in all concentrations inhibited the growth in exponential phase. In conclusion, ERY and XYL are potent growth inhibitors of S. pyogenes isolated from PTA. Therefore, ERY and XYL may have potential in preventing PTA in the patients with frequent tonsillitis episodes.

Exploration of singular and synergistic effect of xylitol and erythritol on causative agents of dental caries.

Non-cariogenic sweet substances, like sugar alcohols, are used to decrease the risk of caries by reducing the growth of dental plaque. The aim of our study was to reveal the impact of xylitol and erythritol on the growth and biofilm formation of cariogenic bacteria including as a novelty, set of clinical mutans streptococci and Scardovia wiggsiae and to assess the possible synergistic influence of these polyols. We found both xylitol and erythritol to express high growth inhibition effect on cariogenic bacteria. In synergistic effect experiments, 10% polyol combination with excess of erythritol was found to be more effective against growth of Streptococcus mutans and the combination with excess of xylitol more effective against growth of Streptococcus sobrinus and S. wiggsiae. In biofilm inhibition experiments, solutions of 10% polyols in different combinations and 15% single polyols were equally effective against mutans streptococci. At the same time, higher biofilm formation of S. wiggsiae compared to experiments without polyols was detected in different polyol concentrations for up to 34%. In conclusion, both erythritol and xylitol as well as their combinations inhibit the growth of different cariogenic bacteria. Biofilm formation of mutans streptococci is also strongly inhibited. When applying polyols in caries prophylaxis, it is relevant to consider that the profile of pathogens in a particular patient may influence the effect of polyols used.

Phenotypic and Molecular Epidemiology of ESBL-, AmpC-, and Carbapenemase-Producing Escherichia coli in Northern and Eastern Europe.

Extended-spectrum beta-lactamases (ESBL) and AmpC producing-Escherichia coli have spread worldwide, but data about ESBL-producing-E. coli in the Northern and Eastern regions of Europe is scant. The aim of this study has been to describe the phenotypical and molecular epidemiology of different ESBL/AmpC/Carbapenemases genes in E. coli strains isolated from the Baltic States (Estonia, Latvia, and Lithuania), Norway and St. Petersburg (Russia), and to determine the predominant multilocus sequence type and single nucleotide polymorphisms diversity of E. coli isolates deduced by whole genome sequencing (WGS). A total of 10,780 clinical E. coli strains were screened for reduced sensitivity to third-generation cephalosporins. They were collected from 21 hospitals located in Estonia, Latvia, Lithuania, Norway and St. Petersburg during a 5 month period in 2012. The overall prevalence of ESBL/AmpC strains was 4.7% by phenotypical test and 3.9% by sequencing. We found more strains with the ESBL/AmpC phenotype and genotype in St. Petersburg and Latvia than other countries. Of phenotypic E. coli strains, 85% contained confirmed ESBL genes (including bla CTX-M, bla TEM- 29, bla TEM- 71), AmpC genes (bla CMY- 59, bla ACT- 12 / - 15 / - 20, bla ESC- 6, bla FEC- 1, bla DHA- 1), or carbapenemase genes (bla NDM- 1). bla CTX-M- 1, bla CTX-M - 14 and bla CTX-M- 15 were found in all countries, but bla CTX-M- 15 prevalence was higher in Latvia than in St. Petersburg (Russia), Estonia, Norway and Lithuania. The dominating AmpC genes were bla CMY- 59 in the Baltic States and Norway, and bla DHA- 1 in St. Petersburg. E. coli strains belonged to 83 different sequence types, of which the most prevalent was ST131 (40%). In conclusion, we generally found low ESBL/AmpC/Carbapenemase prevalence in E. coli strains isolated in Northern/Eastern Europe. However, several inter-country differences in distribution of particular genes and multilocus sequence types were found.

Application of Molecular Methods for Carbapenemase Detection.

This study has evaluated the correlation between different carbapenemases detection methods on carbapenem non-susceptible Klebsiella pneumoniae strains from Northern and Eastern Europe; 31 institutions in 9 countries participated in the research project, namely Finland, Estonia, Latvia, Lithuania, Russia, St. Petersburg, Poland, Belarus, Ukraine, and Georgia. During the research program, a total of 5,001 clinical K. pneumoniae isolates were screened for any carbapenem non-susceptibility by the disk diffusion method, Vitek 2 or Phoenix system following the EUCAST guideline on detection of resistance mechanisms, version 1.0. Strains isolated from outpatients and hospitalized patients from April 2015 to June 2015 were included. All types of samples (blood, pus, urine, etc.) excluding fecal screening or fecal colonization samples have been represented. In total, 171 carbapenemase screening-positive K. pneumoniae isolates (3.42%) were found and characterized. Several methods were used for detection of carbapenemases production, including Luminex assay (PCR and hybridization), whole genome sequencing, MALDI-TOF based Imipenem degradation assay, and immunochromatography testing. Minimal inhibitory concentration determination for Meropenem by agar-based gradient method was also used. Finally, 83 K. pneumoniae strains were carbapenemase negative by all confirmation methods (49.4% of all screening-positive ones), 74 - positive by three methods (44.0%), 8 - positive by two methods (4.8%) and 3 - positive by only one method (1.8%). The sensitivity of the tests was 96.3% for Whole genome sequencing and MALDI-TOF assay (both three undetected cases), and 95.1% for Luminex-Carba (4 undetected cases). The most commonly detected carbapenemases were NDM (n = 54) and OXA-48 (n = 26), followed by KPC-2, VIM-5, and OXA-72 (one case of each). Our results showed that different types of carbapenemases can be detected in the countries involved in the project. The sensitivity of our methods for carbapenemase detection (including screening as a first step and further confirmation tests) was >95%, but we would recommend using different methods to increase the sensitivity of detection and make it more precise.

High level bacterial contamination of secondary school students' mobile phones.

INTRODUCTION: While contamination of mobile phones in the hospital has been found to be common in several studies, little information about bacterial abundance on phones used in the community is available. Our aim was to quantitatively determine the bacterial contamination of secondary school students' mobile phones. METHODS: Altogether 27 mobile phones were studied. The contact plate method and microbial identification using MALDI-TOF mass spectrometer were used for culture studies. Quantitative PCR reaction for detection of universal 16S rRNA, Enterococcus faecalis 16S rRNA and Escherichia coli allantoin permease were performed, and the presence of tetracycline (tetA, tetB, tetM), erythromycin (ermB) and sulphonamide (sul1) resistance genes was assessed. RESULTS: We found a high median bacterial count on secondary school students' mobile phones (10.5 CFU/cm2) and a median of 17,032 bacterial 16S rRNA gene copies per phone. Potentially pathogenic microbes (Staphylococcus aureus, Acinetobacter spp., Pseudomonas spp., Bacillus cereus and Neisseria flavescens) were found among dominant microbes more often on phones with higher percentage of E. faecalis in total bacterial 16S rRNA. No differences in contamination level or dominating bacterial species between phone owner's gender and between phone types (touch screen/keypad) were found. No antibiotic resistance genes were detected on mobile phone surfaces. CONCLUSION: Quantitative study methods revealed high level bacterial contamination of secondary school students' mobile phones.

StrainSeeker: fast identification of bacterial strains from raw sequencing reads using user-provided guide trees.

BACKGROUND: Fast, accurate and high-throughput identification of bacterial isolates is in great demand. The present work was conducted to investigate the possibility of identifying isolates from unassembled next-generation sequencing reads using custom-made guide trees. RESULTS: A tool named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables the identification of bacterial isolates in 1-2 min. It uses a novel algorithm, which analyses the observed and expected fractions of node-specific k-mers to test the presence of each node in the sample. This allows StrainSeeker to determine where the isolate branches off the guide tree and assign it to a clade whereas other tools assign each read to a reference genome. Using a dataset of 100 Escherichia coli isolates, we demonstrate that StrainSeeker can predict the clades of E. coli with 92% accuracy and correct tree branch assignment with 98% accuracy. Twenty-five thousand Illumina HiSeq reads are sufficient for identification of the strain. CONCLUSION: StrainSeeker is a software program that identifies bacterial isolates by assigning them to nodes or leaves of a custom-made guide tree. StrainSeeker's web interface and pre-computed guide trees are available at http://bioinfo.ut.ee/strainseeker. Source code is stored at GitHub: https://github.com/bioinfo-ut/StrainSeeker.

Proactive Approach for Safe Use of Antimicrobial Coatings in Healthcare Settings: Opinion of the COST Action Network AMiCI.

Infections and infectious diseases are considered a major challenge to human health in healthcare units worldwide. This opinion paper was initiated by EU COST Action network AMiCI (AntiMicrobial Coating Innovations) and focuses on scientific information essential for weighing the risks and benefits of antimicrobial surfaces in healthcare settings. Particular attention is drawn on nanomaterial-based antimicrobial surfaces in frequently-touched areas in healthcare settings and the potential of these nano-enabled coatings to induce (eco)toxicological hazard and antimicrobial resistance. Possibilities to minimize those risks e.g., at the level of safe-by-design are demonstrated.

First report of Wohlfahrtiimonas chitiniclastica from soft tissue and bone infection at an unusually high northern latitude.

Wohlfahrtiimonas chitiniclastica is a rare human pathogen mostly associated with parasitic flies. This is the report on W. chitiniclastica infection in the soft tissue and bone at a 58°N latitude in the northern temperate climate zone. The importance of correct identification of clinically relevant bacteria is highlighted.

Differences in extended-spectrum beta-lactamase producing Escherichia coli virulence factor genes in the Baltic Sea region.

The aim of this study was to compare the prevalence of different virulence factor (VF) genes in extended-spectrum beta-lactamase (ESBL) producing Escherichia coli strains isolated from the Baltic Sea region. A total of 432 strains of phenotypically ESBL positive E. coli were 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 gene papEF was more prevalent in Russian strains, colicin gene cvaC in Lithuanian strains, and capsular gene kpsMTII in Latvian strains; serum resistant gene traT was less prevalent in Estonian strains. The regional differences of VF genes remained statistically significant after taking into account the phylogenetic distribution in the countries.

Detection of carbapenemase-producing enterobacteriaceae in the baltic countries and st. Petersburg area.

The spread of carbapenemase-producing Enterobacteriaceae is a global problem; however, no exact data on the epidemiology of carbapenemase in the Baltic countries and St. Petersburg area is available. We aimed to evaluate the epidemiology of carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Baltic States and St. Petersburg, Russia, and to compare the different methods for carbapenemase detection. From January to May 2012, all K. pneumoniae (n = 1983) and E. coli (n = 7774) clinical isolates from 20 institutions in Estonia, Latvia, Lithuania, and St. Petersburg, Russia were screened for carbapenem susceptibility. The IMP, VIM, GIM, NDM, KPC, and OXA-48 genes were detected using real-time PCR and the ability to hydrolyze ertapenem was determined using MALDI-TOF MS. Seventy-seven strains were found to be carbapenem nonsusceptible. From these, 15 K. pneumoniae strains hydrolyzed ertapenem and carried the bla NDM gene. All of these strains carried integron 1 and most carried integron 3 as well as genes of the CTX-M-1 group. No carbapenemase-producing E. coli or K. pneumoniae strains were found in Estonia, Latvia, or Lithuania; however, NDM-positive K. pneumoniae was present in the hospital in St. Petersburg, Russia. A MALDI-TOF MS-based assay is a suitable and cost-effective method for the initial confirmation of carbapenemase production.

The Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections.

The aim of our study was to characterize the phylogenetic groups of Escherichia coli, antibiotic resistance, and containment of class 1 integrons in the first attack of pyelonephritis and in subsequent recurrences in young children. Altogether, 89 urine E. coli isolates from 41 children with urinary tract infection (UTI) were studied for prevalence and persistence of phylogenetic groups by pulsed-field gel electrophoresis (PFGE), antibacterial resistance by minimal inhibitory concentrations (MIC) and class 1 integrons by PCR. Phylogenetic group B2 was most common (57%), followed by D (20%), A (18%) and B1 (5%). Overall resistance to betalactams was 61%, trimethoprim-sulfamethoxazole 28%, and was not associated with phylogenetic groups. According to PFGE, the same clonal strain persisted in 77% of patients. The persistence was detected most often in phylogenetic group B2 (70%). Phylogenetic group B2 more often contained class 1 integrons than group A. Integron positive strains had higher MIC values of cefuroxime, cefotaxime, and gentamicin. In conclusion, phylogenetic group B2 was the most common cause of the first episode of pyelonephritis, as well as in case of the persistence of the same strain and contained frequently class 1 integrons in childhood recurrent UTI. An overall frequent betalactam resistance was equally distributed among phylogenetic groups.

In vitro synergy of oxacillin and gentamicin against coagulase-negative staphylococci from blood cultures of neonates with late-onset sepsis.

Coagulase-negative staphylococci (CoNS) are the leading cause of late-onset sepsis (LOS) in neonates. Increasing resistance of CoNS to beta-lactams and aminoglycosides has led to widespread use of vancomycin, which in turn may lead to resistance to vancomycin. Thus, combination therapy of LOS has been advocated. We aimed to determine the interaction of oxacillin and gentamicin against CoNS. In 2005, 34 isolates of oxacillin- and gentamicin-resistant CoNS were obtained from blood samples of neonates with LOS. Combination effect was tested using the checkerboard method, E-test with the other antibiotic incorporated in the medium (E-test-1) and two E-test strips placed in a cross-formation (E-test-2). Of 34 isolates 61.8%, 53% and 73.5% revealed synergy or an additive effect when tested by the checkerboard method, E-test-1 and E-test-2, respectively. Results of all three tests were concordant for six (17.6%) isolates, four showing synergy, and two indifference. Our in vitro results support that combination therapy with penicillinase-resistant penicillin and aminoglycoside can be an alternative to vancomycin.

Quantification of Clostridium difficile in antibiotic-associated-diarrhea patients.

Comparing culture- and non-culture-based methods for quantifying Clostridium difficile in antibiotic-associated-diarrhea patients, we found that the real-time PCR method correlated well with quantitative culture and was more sensitive. A positive association between the population levels of C. difficile and the presence of its toxins was found.

Intestinal lactoflora in Estonian and Norwegian patients with antibiotic associated diarrhea.

The disruption of intestinal microbiota is an important risk factor for the development of Clostridium difficile caused antibiotic associated diarrhea (AAD). The role of intestinal lactoflora in protection against C. difficile is unclear. Fecal samples (n = 74) from AAD patients were investigated for C. difficile and lactobacilli by culture and real-time PCR. Lactobacilli were identified by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) and sequencing of 16S rRNA. In C. difficile negative cases we found somewhat higher counts of intestinal Lactobacilli (5.02 vs. 2.15 CFU log(10)/g; p = 0.053) by culture and more frequently Lactobacillus plantarum (33.3% vs. 9.4%; p = 0.03) as compared with positive ones. Results of total counts of lactobacilli comparing Estonian and Norwegian samples were conflicting by culture and PCR. We found higher colonization of Norwegian AAD patients with L. plantarum (21% vs. 5%, p = 0.053) and Estonians with Lactobacillus gasseri (19% vs. 2%, p = 0.023). Particular lactobacilli (e.g. L. plantarum) may have a role in protection against C. difficile, whereas the meaning of total counts of lactobacilli remains questionable. In different persons and nations, different lactobacilli species may have a protective role against C. difficile.

The occurrence of antimicrobial resistance and class 1 integrons among commensal Escherichia coli isolates from infants and elderly persons.

BACKGROUND: The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals. METHODS: One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR. RESULTS: Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical interventions, we found a higher resistance and frequency of integrons in strains from hospitalized elderly persons compared with non-hospitalized ones. Children treated with antibiotics had strains with higher MIC values (when compared with antibiotic-naive ones), but the integron-bearing in strains was similar. In most cases, the differences in resistance between the groups (integron-positive and negative strains separately) were higher than the differences between integron-positive and negative strains within the groups. CONCLUSION: The prevalence of integrons in commensal E. coli strains in persons without previous medical intervention depended on age. The resistance of integron-carrying and non-carrying strains is more dependent on influencing factors (hospitalization and antibiotic administration) in particular groups than merely the presence or absence of integrons.