P-233-Biodiversity of mucosa associated microbiome of Crohn's disease patients living in middle western São Paulo State, Brazil

Background: The intestinal microbiome (IM) has extensively been studied in the search for a link of bacteria with the cause of Crohn`s disease (CD). The association might result from the action of a specific pathogen and/or an eventual imbalance in bacterial species composition of the gut. The innumerous virulence associated markers and strategies described for adherent and invasive Escherichia coli (AIEC) have made them putative candidate pathogens for CD. IM of CD patients shows dysbiosis, manifested by the proliferation of bacterial groups such as Enterobacteriaceae and reduction of others such as Lactobacillus and Bifidobacterium. The augmented bacterial population comprising of commensal and/or pathogenic organisms super stimulates the immune system, triggering the inflammatory reactions responsible for the clinical manifestations of the disease. Considering the role played by IM in CD and the multiple variables influencing its species composition, resulting in differences among populations, the objective of this study was to determine the bacterial biodiversity in the mucosa associated microbiome of CD patients from a population not previously subject to this analysis, living in the middle west region of Sao Paulo state. Methods: A total of 4 CD patients and 5 controls subjects attending the Botucatu Medical School of the Sao Paulo State University (UNESP) for routine colonoscopy and who signed an informed consent were included in the study. A number of 2 biopsies, one from the ileum and other from any part of the terminal colon, were taken from each subject and immediately frozen at -70[degrees]C until DNA purification. The bacterial biodiversity was assessed by next generation (ion torrent) sequencing of PCR amplicons of the ribosomal DNA 16S V6 region (16S V6 rDNA). The bacterial identification was performed at the genus level, by alignment of the generated DNA sequences with those available at the ribosomal database project (RDP) website. Results: The overall DNA sequence output was based on an average number of 526,427 reads per run, matching 50 bacterial genus 16SrDNA sequences available at the RDB website, and 22 non matching sequences. Over 95% of the sequences corresponded to taxa belonging to the major phyla: Firmicutes, Bacterioidetes, Proteobacteria and Actinobacteria. Irrespective of the intestinal site analyzed, no case-control differences could be observed in the prevalence of Actinobacteria and Firmicutes. The prevalence of Proteobacteria was higher (40%) in the biopsies of control subjects as compared to that of DC patients (16%). For Bacterioidetes, the higher prevalence was observed among DC patients (33% as opposed to 14,5% in controls). The significance for all comparisons considered a p value < 0,05 in a Chi2 test. No mucosal site specific differences could be observed in IM comparisons of CD and control subjects. Conclusions: The rise in the number of Bacterioidetes observed here among CD patients seems to be in agreement with most of studies published thus far. Yet, the reduction in the number of Proteobacteria along with an apparently unaltered population of Actinobacteria and Firmicutes, which include the so called "beneficial" organisms Bifidobacterium and Lactobacillus were rather surprising. These data suggest that the analyses on the role of IM in CD should consider the multiple variables that may influence its species composition.

Desenvolvimento de um embutido cárneo fermentado, com teores reduzidos de gordura e sais de cura, através da utilização de culturas probióticas

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

The characteristics of VIM-1-producing Klebsiella pneumoniae from South Africa

A study was designed to characterize a carbapenem-resistant Klebsiella pneumoniae (KPSA01) isolated from a patient in Gauteng, South Africa without recent travel outside South Africa. Molecular characterization was done using isoelectric focusing, polymerase chain reaction and sequencing for bla(VIM), bla(IMP), bla(NDM), bla(CTX-Ms), bla(OXAs), bla(TEMs), and bla(SHV), plasmid-mediated quinolone resistance determinants, multilocus sequencing typing, plasmid replicon typing, and addiction factors. KPSA01 produced VIM-1 and belonged to the newly described sequence type ST569. The plasmid that harboured bla(VIM) typed within the narrow host range IncF replicon group, contained the aadA1 gene cassette, and tested positive for the vagCD and ccdAB addiction systems. This is the first report of VIM-1-producing K. pneumoniae outside Europe. It is important that surveillance studies be undertaken in Africa to determine if VIM-1-producing K. pneumoniae are present in significant numbers.

Isolation, selection and characterization of root-associated growth promoting bacteria in Brazil Pine (Araucaria angustifolia)

Araucaria angustifolia, a unique species of this genus that occurs naturally in Brazil, has a high socio-economic and environmental value and is critically endangered of extinction, since it has been submitted to intense predatory exploitation during the last century. Root-associated bacteria from A. angustifolia were isolated, selected and characterized for their biotechnological potential of growth promotion and biocontrol of plant pathogenic fungi. Ninety-seven strains were isolated and subjected to chemical tests. All isolates presented at least one positive feature, characterizing them as potential PGPR. Eighteen isolates produced indole-3-acetic acid (IAA), 27 were able to solubilize inorganic phosphate, 21 isolates were presumable diazotrophs, with pellicle formation in nitrogen-free culture medium, 83 were phosphatases producers, 37 were positive for siderophores and 45 endospore-forming isolates were antagonistic to Fusarium oxysporum, a pathogen of conifers. We also observed the presence of bacterial strains with multiple beneficial mechanisms of action. Analyzing the fatty acid methyl ester (FAME) and partial sequencing of the 16S rRNA gene of these isolates, it was possible to characterize the most effective isolates as belonging to Bacillaceae (9 isolates), Enterobacteriaceae (11) and Pseudomonadaceae (1). As far as we know, this is the first study to include the species Ewingella americana as a PGPR. (C) 2011 Elsevier GmbH. All rights reserved.

Endophytic and rhizospheric enterobacteria isolated from sugar cane have different potentials for producing plant growth-promoting substances

Background and aims Endophytic and rhizospheric environments differ in many respects, leading to the presence of different bacterial communities at each site. However, microorganisms such as enterobacteria can be found both within plants and in the surrounding soil. Bacteria must present differences in the traits that affect such environments in order to successfully colonise them. The present study compared the plant growth-promoting potential of diazotrophic enterobacteria isolated from the rhizosphere and from within surface-disinfected plants. Methods A total of 46 diazotrophic enterobacterial strains (21 rhizospheric and 25 putatively endophytic) belonging to the Klebsiella and Enterobacter genera, which are prevalent in sugar cane plantations, were isolated from the rhizosphere and from surface-disinfected plants. Their ability to synthesise amino acids using combined nitrogen obtained from nitrogen fixation, and their ability to synthesise indole-3-acetic acid (IAA) were determined by high performance liquid chromatography. Endogenous ethylene production by the bacteria was measured using gas chromatography, and biocontrol of phytopathogenic fungi was determined qualitatively using a dual culture technique. Results The putative endophytes released significantly higher amounts of amino acids than the rhizospheric bacteria, whilst the latter produced higher quantities of ethylene and were more actively antagonistic to fungi. Both types of bacteria released similar amounts of IAA. Conclusion Endophytic and rhizospheric bacteria differ in their capacity to release plant growth-promoting substances, which may be a reflection of their adaptations and an indication of their potential impact on their natural environment.

The modified Hodge test is a useful tool for ruling out klebsiella pneumoniae carbapenemase

OBJECTIVE: Enterobacteriaceae bacteria harboring Klebsiella pneumoniae carbapenemase are a serious worldwide threat. The molecular identification of these pathogens is not routine in Brazilian hospitals, and a rapid phenotypic screening test is desirable. This study aims to evaluate the modified Hodge test as a phenotypic screening test for Klebsiella pneumoniae carbapenemase. METHOD: From April 2009 to July 2011, all Enterobacteriaceae bacteria that were not susceptible to ertapenem according to Vitek2 analysis were analyzed with the modified Hodge test. All positive isolates and a random subset of negative isolates were also assayed for the presence of blaKPC. Isolates that were positive in modified Hodge tests were sub-classified as true-positives (E. coli touched the ertapenem disk) or inconclusive (distortion of the inhibition zone of E. coli, but growth did not reach the ertapenem disk). Negative results were defined as samples with no distortion of the inhibition zone around the ertapenem disk. RESULTS: Among the 1521 isolates of Enterobacteriaceae bacteria that were not susceptible to ertapenem, 30% were positive for blaKPC, and 35% were positive according to the modified Hodge test (81% specificity). Under the proposed sub-classification, true positives showed a 98% agreement with the blaKPC results. The negative predictive value of the modified Hodge test for detection was 100%. KPC producers showed high antimicrobial resistance rates, but 90% and 77% of these isolates were susceptible to aminoglycoside and tigecycline, respectively. CONCLUSION: Standardizing the modified Hodge test interpretation may improve the specificity of KPC detection. In this study, negative test results ruled out 100% of the isolates harboring Klebsiella pneumoniae carbapenemase-2. The test may therefore be regarded as a good epidemiological tool.

Colistin Resistance in Escherichia coli and Salmonella enterica Strains Isolated from Swine in Brazil

Reports about acquired resistance to colistin in different bacteria species are increasing, including E. coli of animal origin, but reports of resistance in wild S. enterica of different serotypes from swine are not found in the literature. Results obtained with one hundred and twenty-six E. coli strains from diseased swine and one hundred and twenty-four S. enterica strains from diseased and carrier swine showed a frequency of 6.3% and 21% of colistin-resistant strains, respectively. When comparing the disk diffusion test with the agar dilution test to evaluate the strains, it was confirmed that the disk diffusion test is not recommended to evaluate colistin resistance as described previously. The colistin MIC 90 and MIC 50 values obtained to E. coli were 0.25 mu g/mL and 0.5 mu g/mL, the MIC 90 and MIC 50 to S. enterica were 1 mu g/mL and 8 mu g/mL. Considering the importance of colistin in control of nosocomial human infections with Gram-negative multiresistant bacteria, and the large use of this drug in animal production, the colistin resistance prevalence in enterobacteriaceae of animal origin must be monitored more closely.

The first report of the qnrB19, qnrS1 and aac(6 ')-Ib-cr genes in urinary isolates of ciprofloxacin-resistant Escherichia coli in Brazil

In this study, we investigated the presence of plasmid-mediated quinolone resistance (PMQR) genes among 101 ciprofloxacin-resistant urinary Escherichia coli isolates and searched for mutations in the quinolone-resistance-determining regions (QRDRs) of the DNA gyrase and topoisomerase IV genes in PMQR-carrying isolates. Eight isolates harboured the qnr and aac(6')-Ib-cr genes (3 qnrS1, 1 qnrB19 and 4 aac(6')-Ib-cr). A mutational analysis of the QRDRs in qnr and aac(6')-Ib-cr-positive isolates revealed mutations in gyrA, parC and parE that might be associated with high levels of resistance to quinolones. No mutation was detected in gyrB. Rare gyrA, parC and parE mutations were detected outside of the QRDRs. This is the first report of qnrB19, qnrS1 and aac(6')-Ib-cr-carrying E. coli isolates in Brazil.

The presence of genes encoding for different virulence factors in clonally related Escherichia coli that produce CTX-Ms

Successful international clones have recently emerged among Escherichia coli that produce CTX-M beta-lactamases as important causes of community-onset urinary tract and bloodstream infections. One hundred and seven isolates that belong to sequence types (STs) ST38, ST131, ST405, ST648, and 38 nonrelated CTX-M producing E. coli from Canada and the Netherlands were assigned to phylogenetic groups and tested for the presence of genes encoding for virulence factors (VFs) using established multiplex polymerase chain reaction. The STs E. coli were significantly more resistant to antibiotics-ST38, ST405, and ST648 belonged to phylogenetic group D while ST131 belonged to B2. Secreted autotransporter toxin (sat), aerobactin receptor, and pathogenicity island marker were significantly more common among the STs; the heat-resistant agglutinin (hra) was present in ST38, sat, and uropathogenic-specific protein, and putative adhesin-siderophore receptor was more common in ST131, while outer membrane protease T was present in ST648. ST131 had a significantly higher VF score. In conclusion, the precise role of these VFs remains to be elucidated; however, we have identified certain putative VFs that possibly contribute to the fitness and success of certain sequence types. (C) 2012 Elsevier Inc. All rights reserved.

The modified Hodge test is a useful tool for ruling out Klebsiella pneumoniae carbapenemase

OBJECTIVE: Enterobacteriaceae bacteria harboring Klebsiella pneumoniae carbapenemase are a serious worldwide threat. The molecular identification of these pathogens is not routine in Brazilian hospitals, and a rapid phenotypic screening test is desirable. This study aims to evaluate the modified Hodge test as a phenotypic screening test for Klebsiella pneumoniae carbapenemase. METHOD: From April 2009 to July 2011, all Enterobacteriaceae bacteria that were not susceptible to ertapenem according to Vitek2 analysis were analyzed with the modified Hodge test. All positive isolates and a random subset of negative isolates were also assayed for the presence of blaKPC. Isolates that were positive in modified Hodge tests were sub-classified as true-positives (E. coli touched the ertapenem disk) or inconclusive (distortion of the inhibition zone of E. coli, but growth did not reach the ertapenem disk). Negative results were defined as samples with no distortion of the inhibition zone around the ertapenem disk. RESULTS: Among the 1521 isolates of Enterobacteriaceae bacteria that were not susceptible to ertapenem, 30% were positive for blaKPC, and 35% were positive according to the modified Hodge test (81% specificity). Under the proposed sub-classification, true positives showed a 98% agreement with the blaKPC results. The negative predictive value of the modified Hodge test for detection was 100%. KPC producers showed high antimicrobial resistance rates, but 90% and 77% of these isolates were susceptible to aminoglycoside and tigecycline, respectively. CONCLUSION: Standardizing the modified Hodge test interpretation may improve the specificity of KPC detection. In this study, negative test results ruled out 100% of the isolates harboring Klebsiella pneumoniae carbapenemase 2. The test may therefore be regarded as a good epidemiological tool.

Functional and Genetic characterization of new genomic islands from an E. coli strain associated with neonatal meningitis.

Enterobacteriaceae genomes evolve through mutations, rearrangements and horizontal gene transfer (HGT). The latter evolutionary pathway works through the acquisition DNA (GEI) modules of foreign origin that enhances fitness of the host to a given environment. The genome of E. coli IHE3034, a strain isolated from a case of neonatal meningitis, has recently been sequenced and its subsequent sequence analysis has predicted 18 possible GEIs, of which: 8 have not been previously described, 5 fully meet the pathogenic island definition and at least 10 that seem to be of prophagic origin. In order to study the GEI distribution of our reference strain, we screened for the presence 18 GEIs a panel of 132 strains, representative of E. coli diversity. Also, using an inverse nested PCR approach we identified 9 GEI that can form an extrachromosomal circular intermediate (CI) and their respective attachment sites (att). Further, we set up a qPCR approach that allowed us to determine the excision rates of 5 genomic islands in different growth conditions. Four islands, specific for strains appertaining to the sequence type complex 95 (STC95), have been deleted in order to assess their function in a Dictyostelium discoideum grazing assays. Overall, the distribution data presented here indicate that 16 IHE3034 GEIs are more associated to the STC95 strains. Also the functional and genetic characterization has uncovered that GEI 13, 17 and 19 are involved in the resistance to phagocitation by Dictyostelium d thus suggesting a possible role in the adaptation of the pathogen during certain stages of infection.

Methylierung von anorganischem Quecksilber im Intestinaltrakt des Kompostwurms Eisenia foetida

Im Rahmen dieser Arbeit wurde die Methylierung von Quecksilber in Intestinaltrakt des Kompostwurms Eisenia foetida untersucht. Des Weiteren wurden aerobe und anaerobe Mikroorganismen aus dem Darmtrakt von Eisenia fotida isoliert, identifiziert und auf ihr Potential zur Methylierung von Quecksilber getestet. Die Bestimmung von Methylquecksilber erfolgte mittels GC-ICPMS (Gaschromatographie mit induktiv gekoppelter Plasma-Massenspektrometrie) und GC-AFS (Gaschromatographie- Atomfluoreszenzspektrometrie). Für die GC-ICPMS erfolgte die Quantifizierung des Methylquecksilbers mittels der Isotopenverdünnungsmethode. Die Extraktion des Methylquecksilbers aus dem Wurmgewebe erfolgte durch einen alkalischen Aufschluss mit TMAH (Tetramethylammoniumhydroxid) und anschließender Derivatisierung des Methylquecksilbers durch Natriumtetrapropylborat. Für die Extraktion des gebildeten Methylquecksilbers aus Bakterienkulturen wurde eine Extraktion mit einer methanolischen Kaliumhydroxidlösung verwendet. Wie bei dem Wurmgewebe wurde das Methylqueckilsber ebenfalls mit Natriumtetrapropylborat derivatisiert.rnrnFür die Untersuchung einer in vivo Methylquecksilberbildung in bodenlebenden Invertebraten wurde der Kompostwurm Eisenia foetida als Modellorganismus verwendet. Die Tiere wurden aus einer Kultur in einen Boden überführt, der mit anorganischem Quecksilber versetzt wurde. Nach zehn Tagen Inkubationszeit wurden die Würmer entnommen und das Methylquecksilber extrahiert. Um eine mögliche Methylierung von Quecksilber durch Bodenorganismen auszuschließen wurde sowohl steriles als auch unsteriles Bodenmaterial verwendet. In den Wurmproben aus dem unsterilen Bodenmaterial konnte eine Konzentration an Methylquecksilber von 17,4 ng/g Trockengewicht (Boden ohne Zugabe von Quecksilber) und 62,4 ng/g Trockengewicht (Boden mit Quecksilberzugabe). Bei den Wurmproben aus sterilem Bodenmaterial lag die Konzentration an Methylquecksilber bei 17,2 ng/g Trockengewicht (Boden ohne Zugabe von Quecksilber) und 51,9 ng/g Trockengewicht (Boden mit Quecksilberzugabe).rnrnBei den Bakterienkulturen konnte in Reinkulturen keine Methylierung von Quecksilber nachgewiesen werden. In einer fakultativ anaeroben Mischkultur konnte eine Methylierung von Quecksilber beobachtet werden. Für die Identifizierung der Mikroorganismen wurde die 16s rDNA mittels PCR amplifiziert und anschließend über eine DGGE aufgetrennt. Die Banden wurden ausgeschnitten und sequenziert. Dabei konnten drei Enterobacteriaceen identifiziert werden.rn

The role of bifidobacteria in newborn health and the intestinal microbial balance

Gut microbial acquisition during the early stage of life is an extremely important event since it affects the health status of the host. In this contest the healthy properties of the genus Bifidobacterium have a central function in newborns. The aim of this thesis was to explore the dynamics of the gut microbial colonization in newborns and to suggest possible strategies to maintain or restore a correct balance of gut bacterial population in infants. The first step of this work was to review the most recent studies on the use of probiotics and prebiotics in infants. Secondly, in order to prevent or treat intestinal disorders that may affect newborns, the capability of selected Bifidobacterium strains to reduce the amount of Enterobacteriaceae and against the infant pathogen Streptococcus agalactiae was evaluated in vitro. Furthermore, the ability of several commercial fibers to stimulate selectively the growth of bifidobacterial strains was checked. Finally, the gut microbial composition in the early stage of life in response to the intrapartum antibiotic prophylaxis (IAP) against group B Streptococcus was studied using q-PCR, DGGE and next generation sequencing. The results globally showed that Bifidobacterium breve B632 strain is the best candidate for the use in a synbiotic product coupled to a mixture of two selected prebiotic fibers (galactooligosaccharides and fructooligosaccharides) for gastrointestinal disorders in infants. Moreover, the early gut microbial composition was affected by IAP treatment with infants showing lower counts of Bifidobacterium spp. and Bacteroides spp. coupled to a decrement of biodiversity of bacteria, compared to control infants. These studies have shown that IAP could affect the early intestinal balance in infants and they have paved the way to the definition of new strategies alternative to antibiotic treatment to control GBS infection in pregnant women.

Definition of Food Safety Criteria for Bacteria Food-Borne Pathogens in Ready to Eat products

The aims of this research study is to explore the opportunity to set up Performance Objectives (POs) parameters for specific risks in RTE products to propose for food industries and food authorities. In fact, even if microbiological criteria for Salmonella and Listeria monocytogenes Ready-to-Eat (RTE) products are included in the European Regulation, these parameters are not risk based and no microbiological criteria for Bacillus cereus in RTE products is present. For these reasons the behaviour of Salmonella enterica in RTE mixed salad, the microbiological characteristics in RTE spelt salad, and the definition of POs for Bacillus cereus and Listeria monocytogenes in RTE spelt salad has been assessed. Based on the data produced can be drawn the following conclusions: 1. A rapid growth of Salmonella enterica may occurr in mixed ingredient salads, and strict temperature control during the production chain of the product is critical. 2. Spelt salad is characterized by the presence of high number of Lactic Acid Bacteria. Listeria spp. and Enterobacteriaceae, on the contrary, did not grow during the shlef life, probably due to the relevant metabolic activity of LAB. 3. The use of spelt and cheese compliant with the suggested POs might significantly reduce the incidence of foodborne intoxications due to Bacillus cereus and Listeria monocytogenes and the proportions of recalls, causing huge economic losses for food companies commercializing RTE products. 4. The approach to calculate the POs values and reported in my work can be easily adapted to different food/risk combination as well as to any changes in the formulation of the same food products. 5. The optimized sampling plans in term of number of samples to collect can be derive in order to verify the compliance to POs values selected.

First countrywide survey of third-generation cephalosporin-resistant Escherichia coli from broilers, swine, and cattle in Switzerland

The herd prevalence of third-generation cephalosporin-resistant Escherichia coli (3GC-R-Ec) was determined for broilers (25.0% [95% confidence interval (CI) 17.6-33.7%]), pigs (3.3% [(95% CI 0.4-11.5%]), and cattle (3.9% [95% CI 0.5-13.5%]), using a sampling strategy that was representative of the livestock population slaughtered in Switzerland between October 2010 and April 2011. The 3GC-R-Ec isolates were characterized by the measurement of the MICs of various antibiotics, microarray analyses, analytical isoelectric focusing, polymerase chain reaction and DNA sequencing for bla genes, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. CMY-2 (n = 12), CTX-M-1 (n = 11), SHV-12 (n = 5), TEM-52 (n = 3), CTX-M-15 (n = 2), and CTX-M-3 (n = 1) producers were found. The majority of CMY-2 producers fell into 1 PFGE cluster, which predominantly contained ST61, whereas the CTX-M types were carried by heterogeneous clones of E. coli, as shown by the numerous PFGE profiles and STs that were found. This is the first national Swiss study that focuses on the spread of 3GC-R Enterobacteriaceae among slaughtered animals.