The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli

The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.

Bacterial diversity in soil in response to different plans, phosphate fertilizers and liming

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

MICROBIOLOGICAL CONTAMINATION of A HEMODIALYSIS CENTER WATER DISTRIBUTION SYSTEM

The microbiological monitoring of the water used for hemodialysis is extremely important, especially because of the debilitated immune system of patients suffering from chronic renal insufficiency. To investigate the occurrence and species diversity of bacteria in waters, water samples were collected monthly from a hemodialysis center in upstate São Paulo and tap water samples at the terminal sites of the distribution system was sampled repeatedly (22 times) at each of five points in the distribution system; a further 36 samples were taken from cannulae in 19 hemodialysis machines that were ready for the next patient, four samples from the reuse system and 13 from the water storage system. To identify bacteria, samples were filtered through 0.22 mu m-pore membranes; for mycobacteria, 0.45 mu m pores were used. Conventional microbiological and molecular methods were used in the analysis. Bacteria were isolated from the distribution system (128 isolates), kidney machine water (43) and reuse system (3). Among these isolates, 32 were Gram-positive rods, 120 Gram-negative rods, 20 Gram-positive cocci and 11 mycobacteria. We propose the continual monitoring of the water supplies in hemodialysis centers and the adoption of effective prophylactic measures that minimize the exposure of these immunodeficient patients to contaminated sources of water.

Honey consumption in the state of São Paulo: a risk to human health?

Infantile botulism was recognized in 1976 as a paralyzing disease caused by the ingestion of viable spores that would germinate and colonize the intestinal tract of infants, with local production and absorption of Clostridium botulinum toxin. The possible origins of botulinic spores are dust and honey, which has been identified as a dietary risk factor for infantile botulism. The objectives of the present study were to investigate 100 honey samples obtained in the state of São Paulo (Brazil) in terms of incidence of botulinic spores and of microbiologic quality, in agreement with Decree 367/9. All 100 samples analysed were negative for the presence of Salmonella, Shigella, total coliforms. C botulinum spores were present in 3 samples (3%) and molds and yeasts, in 64 samples (64%), but only 25 (25%) exceeded established criteria, with counts ranging from zero to 1.5 x 10(5) CFU/g. The presence of small sporogenic Gram-positive rods was observed in 42 (42%) of the 100 samples tested but these bacteria were not identified. (C) 2003 Elsevier Ltd. All rights reserved.

Efficacy of antibiotic therapy for peritoneal dialysis-associated peritonitis: a proportional meta-analysis

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Biological Hydrogen production from environmental sample in tropical countries

The hydrogen gas is regarded as clean and renewable energy source, since it generates only water during combustion when used as fuel. It shows 2.75 times more energy content than any hydrocarbon and it can be converted into electrical, mechanical energy or heat. Inoculum sources have been successfully tested for hydrogen biological production in temperate climate countries as sludge treatment plants sewage, sludge treatment plant wastewater, landfill sample, among others. However, hydrogen biologic production with inoculum from environmental samples such as sediment reservoirs, especially in tropical countries like Brazil, is rarely investigated. Reservoirs and fresh water lake sediment may contain conditions for the survival of a wide variety of microorganisms which use different carbon sources mainly glucose and xylose, in the fermentation. Glucose is an easily biodegradable, present in most of the industrial effluents and can be obtained abundantly from agricultural wastes. A wide variety of wastewater resulting from agriculture, industry and pulp and paper processed from wood may contain xylose in its constitution. Such effluent contains glucose and xylose concentrations of about 2 g/L. In this sense, this work verified hydrogen biological production in anaerobic batch reactor (1L), at 37 ° C, initial pH 5.5, headspace with N2 (100%), Del Nery medium, vitamins and peptone (1 g/L), fed separately with glucose (2g/L) and xylose (2 g/L). The inoculum was taken from environmental sample (sediment reservoir Itupararanga - Ibiúna - SP-Brazil). It was previously purified in serial dilutions at H2 generation (10-5, 10-7, 10-10), and heat treated (90º C - 10 min) later to inhibited the H2 consumers. The maximum H2 generations obtained in both tests were observed at 552 h, as described below. At the reactors fed with glucose and xylose were observed, respectively, 9.1 and 8.6 mmol H2/L, biomass growth (0.2 and 0.2 nm); consumption of sugar concentrations 53.6% (1.1 glucose g/L) and 90.5% (1.8 xylose g/L); acetic acid generation (124.7 mg/L and 82.7 mg/L), butyric acid (134.0 mg/L and 230.4 mg/L) and there wasn’t methane generation in the reactors. Microscopic analysis of biomass in anaerobic reactors showed the predominance of Gram positive rods and rods with endospores, whose morphology is characteristic of H2-generating bacteria, in both tests. These species were selected from the natural environment. In DGGE analysis performed difference were observed between populations from inoculum and in tests. This analysis confirmed that some species of bacteria were selected which remained under the conditions imposed on the experiment. The efficiency of the pre-treatment of inoculum and the imposition of pH 5.5 inhibited methane-producing microorganisms and the consumers of H2. Therefore, the experimental conditions imposed allowed the attainment of bacterial consortium of producer H2 taken from an environmental sample with concentration of xylose and glucose similar to the ones of the industrial effluents.

Evidence-based medicine: an update on treatments for peritoneal dialysis-related peritonitis

Peritonitis continues to be a major complication of peritoneal dialysis (PD), and adequate treatment is crucial for a favorable outcome. There is no consensus regarding the optimal therapeutic regimen, and few prospective controlled studies have been published. The objective of this manuscript is to review the results of PD peritonitis treatment reported in narrative reviews, systematic reviews, and proportional meta-analyses. Two narrative reviews, the only existing systematic review and its update published between 1991 and 2014 were included. In addition, we reported the results of a proportional meta-analysis published by our group. Results from systematic reviews of randomized control trials (RCT) and quasi-RCT were not able to identify any optimal antimicrobial treatment, but glycopeptide regimens were more likely to achieve a complete cure than a first generation cephalosporin. Compared to urokinase, simultaneous catheter removal and replacement resulted in better outcomes. Continuous and intermittent IP antibiotic use had similar outcomes. Intraperitoneal antibiotics were superior to intravenous antibiotics in reducing treatment failure. In the proportional meta-analysis of RCTs and the case series, the resolution rate (86%) of ceftazidime plus glycopeptide as initial treatment was significantly higher than first generation cephalosporin plus aminoglycosides (66%) and glycopeptides plus aminoglycosides (75%). Other comparisons of regimens used for either initial treatment or treatment of gram-positive rods or gram-negative rods did not show statistically significant differences. The superiority of a combination of a glycopeptide and a third generation cephalosporin was also reported by a narrative review study published in 1991, which reported an 88% resolution rate.

Staphylococcus spp., Enterobacteriaceae and Pseudomonadaceae oral isolates from Brazilian HIV-positive patients. Correlation with CD4 cell counts and viral load

The aim was to evaluate the presence of Staphylococcus spp., Enterobacteriaceae and Pseudomonadaceae in the oral cavities of HIV-positive patients. Forty-five individuals diagnosed as HIV-positive by ELISA and Western-blot, and under anti-retroviral therapy for at least 1 year, were included in the study. The control group constituted 45 systemically healthy individuals matched to the HIV patients to gender, age and oral conditions. Oral rinses were collected and isolates were identified by API system. Counts of microorganisms from HIV and control groups were compared statistically by a Mann-Whitney test (alpha = 5%). The percentages of individuals positive for staphylococci were similar between the groups (p = 0.764), whereas for Gram-negative rods, a higher percentage was observed amongst HIV-positive (p = 0.001).There was no difference in Staphylococcus counts between HIV and control groups (p = 0.1008). Counts were lower in the oral cavities of patients with low viral load (p = 0.021), and no difference was observed in relation to CD4 counts (p = 0.929). Staphylococcus aureus was the most frequently isolated species in HIV group, and Staphylococcus epidermidis was the prevalent species in the control group. Significantly higher numbers of enteric bacteria and pseudomonas were detected in the oral cavities of the HIV group than in the control (p = 0.0001). Enterobacter cloacae was the most frequently isolated species in both groups. Counts of enteric bacteria and pseudomonas were significantly lower in patients with low CD4 counts (p = 0.011); however, there was no difference relating to viral load. It may be concluded that HIV group showed greater species diversity and a higher prevalence of Enterobacteriaceae/Pseudomonadaceae. (C) 2011 Elsevier Ltd. All rights reserved.

Morfologia e quantificação da microbiota intestinal do curimbatá (Prochilodus lineatus) e do cascudo cinza (Pterygoplichthys anisitsi) cultivados em cativeiro

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Evaluation of the in vitro activity of cefepime compared to other broad-spectrum cephalosporins against clinical isolates from eighteen Brazilian hospitals by using the Etest

The in vitro activity of cefepime was compared to that of ceftazidime, ceftriaxone, and cefotaxime in a multicenter study involving 10 clinical microbiology laboratories and clinical isolates from 18 Brazilian hospitals from 7 cities (4 states). A total of 982 isolates consecutively collected between December 1995 and March 1996 were susceptibility tested by using Etest and following the NCCLS procedures for agar diffusion tests. The cefepime spectrum was broader than that of the other broad-spectrum cephalosporins against both Gram-negative rods and Gram-positive cocci. Cefepime tons particularly move active against Enterobacter sp. (MIC90, 2 mu g/ml), Serratia sp. (MIC90, 2 mu g/ml) and oxacillin-susceptible Staphylococcus aureus (MIC90, 3 mu g/ml). Against Pseudomonas aeruginosa, cefepime (MIC90 16 mu g/ml) was slightly more active than ceftazidime (MIC90 32 mu g/ml) and 8- to 16-fold more active than ceftriaxone or cefotaxime (MIC90 >256 mu g/ml). Our results show that nosocomial bacteria, especially Gram-negative rods, have a high rate of cephalosporin resistance in Brazil. However, part of these resistant bacteria remains susceptible to cefepime. The Etest was shown to be an excellent method for multicenter studies of the in vitro evaluation of new antimicrobial agents. (C) 1997 Elsevier B.V.

Antibiotic 26-deoxylaidlomycin isolated from Streptomyces sp. Ar386 from Brazilian soil

An actinomycete strain (Ar386) was isolated from the soil of the Araraquara regio, SP, Brazil. The strain, named Streptomyces jacareensis, formed irregular rayed, rugose, grayish-white mycelium with sinuous, branched hyphae carrying rare isolated spores; assimilated glucose, galactose, inositol, ribose, maltose, sucrose, melibiose and starch but not mannitol, rhamnose, arabinose, xylose, lactose and raffinose; and contained LL- diaminopimelic acid in its cell wall. An antibiotic active against Gram- positive bacteria, which was characterized as being 26-deoxylaidlomycin and which may have application against poultry coccidiosis, was isolated from cultures of the strain. This was the first isolation of this antibiotic from a microorganism of the genus Streptomyces and also the first isolation of this antibiotic in Brazil.

The diagnostic value of Gram stain for initial identification of the etiologic agent of peritonitis in CAPD patients

Objective: To evaluate the effectiveness of the Gram stain in the initial diagnosis of the etiologic agent of peritonitis in continuous ambulatory peritoneal dialysis (CAPD). Design: Retrospective study analyzing the sensitivity (S), specificity (SS), positive predictive value (+PV), and negative predictive value (-PV) of the Gram stain relating to the results of cultures in 149 episodes of peritonitis in CAPD. The data were analyzed in two studies. In the first, only the cases with detection of a single agent by Gram stain were taken (Study 1). In the second, only the cases with two agents in Gram stain were evaluated (Study 2). Setting: Dialysis Unit and Laboratory of Microbiology of a tertiary medical center. Patients: Sixty-three patients on regular CAPD who presented one or more episodes of peritonitis from May 1992 to May 1995. Results: The positivity of Gram stain was 93.2% and the sensitivity was 95.7%. The values of S, SS, +PV, and -PV were respectively: 94.9%, 53.5%, 68.3%, and 90.9% for gram-positive cocci and 83.3%, 98.8%, 95.2%, and 95.6% for gram-negative bacilli. The association of gram-positive cocci plus gram-negative bacilli were predictive of growth of both in 6.8%, growth of gram-positive cocci in 13.7%, and growth of gram-negative bacilli in 72.5%. Conclusions: The Gram stain is a method of great value in the initial diagnosis of the etiologic agent of peritonitis in CAPD, especially for gram-negative bacilli.