Publications

isolation, selection and biodegradation profile of phenol degrading bacteria from oil contaminated soil.	in the present study, an aerobic bacterial strains ocs-a and ocs- b were isolated from an oil contaminated soil. the strains were identified to be citrobacter freundi and proteus mirabilis according to morphological, physiological and biochemical characteristics. the strains were able to degrade about 90% of 100 mg/l phenol within 80 h as sole carbon and energy source. the lag phase increased with increase in phenol concentration. determination of metabolic intermediate 2-hms, was done which ind ...	2011	21643832
mouldy feed, mycotoxins and shiga toxin - producing escherichia coli colonization associated with jejunal hemorrhage syndrome in beef cattle.	abstract: background: both o157 and non-o157 shiga toxin - producing escherichia coli (stecs) cause serious human disease outbreaks through the consumption of contaminated foods. cattle are considered the main reservoir but it is unclear how stecs affect mature animals. neonatal calves are the susceptible age class for stec infections causing severe enteritis. in an earlier study, we determined that mycotoxins and stecs were part of the disease complex for dairy cattle with jejunal hemorrhage sy ...	2011	21639911
three-dimensional structures of noncovalent complexes of citrobacter freundii methionine γ-lyase with substrates.	crystal structures of citrobacter freundii methionine γ-lyase complexes with the substrates of γ- (l-1-amino-3-methylthiopropylphosphinic acid) and β- (s-ethyl-l-cysteine) elimination reactions and the competitive inhibitor l-norleucine have been determined at 1.45, 1.8, and 1.63 å resolution, respectively. all three amino acids occupy the active site of the enzyme but do not form a covalent bond with pyridoxal 5'-phosphate. hydrophobic interactions between the active site residues and the side ...	2011	21639836
the influence of environmental bacteria in freshwater stingray wound-healing.	invasion by bacteria can influence the course of healing of wounds acquired in aquatic environment. in this study, the bacteria present in potamotrygonmotoro stingray mucus and in the alto paraná river water were identified, and their ability to induce tissue injury and resist antibiotics was determined. biochemical identification analysis showed that 97% of all bacterial isolates were gram negative, aeromonas spp., enterobacter cloacae and citrobacter freundii being the species most prevalent. ...	2011	21635911
practical approach for reliable detection of ampc beta-lactamase-producing enterobacteriaceae.	in this prospective study all enterobacteriaceae isolates (n = 2,129) recovered in the clinical microbiology laboratory during october 2009 to april 2010 were analyzed for ampc production. clinical and laboratory standards institute (clsi) cefoxitin and cefotetan susceptibility breakpoints and clsi critical esbl diameters were used to screen for potential ampc producers. in total, 305 isolates (211 potential ampc producers and 94 ampc screen-negative isolates as a control group) were further ana ...	2011	21632895
the utility of matrix assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms) following introduction for routine laboratory bacterial identification.	maldi-tof ms was evaluated prospectively in a diagnostic laboratory. 927 organisms were tested in triplicate; 2351/2781 (85%) species and 2681/2781 (96%) genus identifications were correct. known issues such as the misidentification of α-haemolytic streptococci as streptococcus pneumonia were easily corrected. identifications cost $aud0.45 per isolate and were available in minutes. maldi-tof ms is rapid, accurate and inexpensive.	2011	21632894
ctx-m-14 beta-lactamase-producing citrobacter freundii isolated in venezuela.	abstract: a clinical isolate of c. freundii with reduced susceptibility to extended-spectrum beta-lactams from a woman with cystocele associated with recurrent urinary tract infection was analyzed. susceptibility tests, double disk synergy tests (ddst) and enzymatic activity by the agar iodometric method suggested the presence of esbls. conjugation experiments revealed the presence of a large conjugative plasmid (plm07/20) with an exclusive frepb replicon type (incf/fib). pcr analysis and sequen ...	2011	21627834
experimental alveolitis in rats: microbiological, acute phase response and histometric characterization of delayed alveolar healing.	the pathogenesis of alveolitis is not well known and therefore experimental situations that mimic some features of this disease should be developed.	2011	21625744
new delhi metallo-ss-lactamase-1: local acquisition in ontario, canada, and challenges in detection.	new delhi metallo-ß-lactamase-1 (ndm-1) is a recently identified metallo-ß-lactamase that confers resistance to carbapenems and all other ß-lactam antibiotics, with the exception of aztreonam. ndm-1 is also associated with resistance to many other classes of antibiotics. the enzyme was first identified in organisms isolated from a patient in sweden who had previously received medical treatment in india, but it is now recognized as endemic throughout india and pakistan and has spread worldwide. t ...	2011	21624908
redetermination of methyl 3,4-o-isopropyl-idene-β-d-fucopyran-oside monohydrate.	in the title compound, c(10)h(18)o(5)·h(2)o, the fucopyran-oside ring adopts a chair conformation. the crystal packing is stabilized by inter-molecular o-h⋯o and c-h⋯o hydrogen bonds together with intra-molecular o⋯o [2.2936 (8) å] and inter-molecular o⋯o [2.7140 (8)-2.829 (3) å] short contacts. the mol-ecules are linked together to form an infinite chain along the a axis. this structure has been solved previously but with no r-values [spiers (1931). z. kristallogr. kristallgeom. kristallphys. k ...	2009	21583828
dissemination of blakpc-2 by the spread of cc258-klebsiella pneumoniae clones (st258, st11, st437) and plasmids (incfii, incn, incl/m) among enterobacteriaceae species in brazil.	this study reports the spread of bla(kpc-2) in são paulo and rio de janeiro states facilitated by globally spread cc258-k. pneumoniae clones (st258, st11, st437) and a diversity of plasmids (incfii, incn, incl/m, two untypeable plasmids carrying tn4401a or tn4401b) successfully disseminated among enterobacteriaceae species (enterobacter cloacae, serratia marcescens and citrobacter freundii). it also constitutes the first description of st258 in brazil which was associated with a nosocomial hospi ...	2011	21576442
new noncovalent inhibitors of penicillin-binding proteins from penicillin-resistant bacteria.	penicillin-binding proteins (pbps) are well known and validated targets for antibacterial therapy. the most important clinically used inhibitors of pbps β-lactams inhibit transpeptidase activity of pbps by forming a covalent penicilloyl-enzyme complex that blocks the normal transpeptidation reaction; this finally results in bacterial death. in some resistant bacteria the resistance is acquired by active-site distortion of pbps, which lowers their acylation efficiency for β-lactams. to address th ...	2011	21573060
identification of neutrophil granule glycoproteins as lewisx-containing ligands cleared by the scavenger receptor c-type lectin.	the scavenger receptor c-type lectin (srcl) is a glycan-binding receptor that has the capacity to mediate endocytosis of glycoproteins carrying terminal lewis(x) groups (galβ1-4(fucα1-3)glcnac). a screen for glycoprotein ligands for srcl using affinity chromatography on immobilized srcl followed by mass spectrometry-based proteomic analysis revealed that soluble glycoproteins from secondary granules of neutrophils, including lactoferrin and matrix metalloproteinases 8 and 9, are major ligands. b ...	2011	21561871
antimicrobial resistance in urinary tract pathogens in canada from 2007 to 2009: canward surveillance study.	from january 2007 to december 2009 an annual canadian national surveillance study (canward) tested 2943 urinary culture pathogens for antimicrobial susceptibilities following clinical and laboratory standards institute (clsi) guidelines. the most frequently isolated urinary pathogens (n, % of all isolates) were escherichia coli (1581, 54%), enterococci (410, 14%), klebsiella pneumoniae (274, 9%), proteus mirabilis (122, 4%), pseudomonas aeruginosa (100, 3%), and staphylococcus aureus (80, 3%). r ...	2011	21537027
effects of bacterial microflora of the lower digestive tract of free-range waterfowl on influenza virus activation.	proteolytic cleavage activation of influenza hemagglutinin (ha0) is required for cell entry via receptor mediated endocytosis. despite numerous studies describing bacterial protease mediated influenza a viral activation in mammals, very little is known about the role of intestinal bacterial flora of birds in hemagglutinin cleavage/activation. therefore, the cloaca of wild waterfowl was examined for 1) representative bacterial types and 2) their ability to cleave in 'trypsin-like' manner the prec ...	2011	21531837
in vitro inhibition of citrobacter freundii, a red-leg syndrome associated pathogen in raniculture, by indigenous lactococcus lactis crl 1584.	red-leg syndrome (rls) is one of the main infectious diseases that cause economic losses in lithobates catesbeianus hatcheries, citrobacter freundii being an etiological agent. treatment or prevention with therapeutics or chemicals results in modifications of the indigenous microbiota, development of antibiotic resistance, presence of their residues in food and enhancement of production costs. thus, probiotics could be used as an alternative therapy. lactic acid bacteria are part of the indigeno ...	2011	21531092
identification and characterisation of a novel adhesin ifp in yersinia pseudotuberculosis.	abstract:	2011	21527009
engineering microbial factories for synthesis of value-added products.	microorganisms have become an increasingly important platform for the production of drugs, chemicals, and biofuels from renewable resources. advances in protein engineering, metabolic engineering, and synthetic biology enable redesigning microbial cellular networks and fine-tuning physiological capabilities, thus generating industrially viable strains for the production of natural and unnatural value-added compounds. in this review, we describe the recent progress on engineering microbial factor ...	2011	21526386
phenotypic detection of broad-spectrum beta-lactamases in microbiological practice.	background: enterobacteriaceae producing esbl and ampc enzymes can be associated with failure of antibiotic therapy and related morbidity and mortality. their routine detection in microbiology laboratories is still a problem. the aim of this study was to compare the sensitivity of selected phenotypic methods.<br /> material/methods: a total of 106 strains of the enterobacteriaceae family were tested, in which molecular biology methods confirmed the presence of genes encoding esbl or ampc. in esb ...	2011	21525803
rapid detection of viable salmonella in produce by coupling propidium monoazide with loop-mediated isothermal amplification (pma-lamp).	recent outbreaks linked to salmonella-contaminated produce heightened the need to develop simple, rapid, and accurate detection methods, particularly those capable of determining cell viability. in this study, we examined a novel strategy for the rapid detection and quantification of viable salmonella in produce by coupling a simple propidium monoazide sample treatment with loop-mediated isothermal amplification (pma-lamp). we first designed and optimized a lamp assay targeting salmonella. secon ...	2011	21498750
mechanistic evaluation of mela α-galactosidase from citrobacter freundii: a family 4 glycosyl hydrolase in which oxidation is rate-limiting.	the mela gene from citrobacter freundii, which encodes a glycosyl hydrolase family 4 (gh4) α-galactosidase, has been cloned and expressed in escherichia coli. the recombinant enzyme catalyzes the hydrolysis of phenyl α-galactosides via a redox elimination-addition mechanism involving oxidation of the hydroxyl group at c-3 and elimination of phenol across the c-1-c-2 bond to give an enzyme-bound glycal intermediate. for optimal activity, the mela enzyme requires two cofactors, nad(+) and mn(2+), ...	2011	21495656
peracetylated 4-fluoro-glucosamine reduces the content and repertoire of n- and o-glycans without direct incorporation.	prior studies have shown that treatment with peracetylated 4-fluorinated analog of glucosamine (4-f-glcnac) elicits anti-skin inflammatory activity by ablating n-acetyllactosamine (lacnac), sialyl lewis x (slex) and related lectin ligands on effector leukocytes. based on anti-slex antibody and lectin probing experiments on 4-f-glcnac-treated leukocytes, it was hypothesized that 4-f-glcnac inhibited slex formation by incorporating into lacnac and blocking addition of galactose or fucose at carbon ...	2011	21493714
co-colonization with multiple different species of multidrug-resistant gram-negative bacteria.	the characteristics of co-colonization with multiple different species of multidrug-resistant gram-negative bacteria (mdrgn) have not been fully elucidated. quantifying the prevalence of co-colonization and those patients at higher risk of co-colonization may have important implications for strategies aimed at limiting the spread of mdrgn.	2011	21492962
citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux.	citrobacter rodentium is a natural mouse pathogen that causes attaching and effacing (a/e) lesions. it shares a common virulence strategy with the clinically significant human a/e pathogens enteropathogenic e. coli (epec) and enterohaemorrhagic e. coli (ehec) and is widely used to model this route of pathogenesis. we previously reported the complete genome sequence of c. rodentium icc168, where we found that the genome displayed many characteristics of a newly evolved pathogen. in this study, th ...	2011	21490962
effects of gender and seasonal variation on the prevalence of bacterial septicemia among young children in benin city, nigeria.	to determine the effects of gender and seasonal variations on the prevalence of bacterial septicaemia among children 5 years and younger, and to identify the bacterial agents responsible for septicaemia and their antibiotic susceptibility profiles.	2009	21483524
microbiology of animal bite wound infections.	the microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. bacteria may also originate from the victim's own skin or the physical environment at the time of injury. our review has focused on bite wound infections in ...	2011	21482724
molecular characterization of the glycerol-oxidative pathway of clostridium butyricum vpi 1718.	the glycerol oxidative pathway of clostridium butyricum vpi 1718 plays an important role in glycerol dissimilation. we isolated, sequenced, and characterized the region coding for the glycerol oxidation pathway. five open reading frames (orfs) were identified: dhar, encoding a putative transcriptional regulator; dhad (1,142 bp), encoding a glycerol dehydrogenase; and dhak (995 bp), dhal (629 bp), and dham (386 bp), encoding a phosphoenolpyruvate (pep)-dependent dihydroxyacetone (dha) kinase enzy ...	2011	21478343
a prebiotic, celmanax™, decreases escherichia coli o157:h7 colonization of bovine cells and feed-associated cytotoxicity in vitro.	abstract:	2011	21473767
pyogenic liver abscess: an audit of 10 years' experience.	to describe our own experience with pyogenic liver abscesses over the past 10 years and investigate the risk factors associated with failure of initial percutaneous therapy.	2011	21472130
practical disk-based method for detection of escherichia coli clinical isolates producing the fluoroquinolone-modifying enzyme aac(6')-ib-cr.		2011	21471342
bordetella petrii infection with long-lasting persistence in human.	we report the repeated isolation of bordetella petrii in the sputum of a 79-year-old female patient with diffuse bronchiectasis and persistence of the bacterium for >1 year. the patient was first hospitalized due to dyspnea, which developed into severe cough with purulent sputum that yielded b. petrii on culture. after this first episode, the patient was hospitalized an additional 4 times with bronchorrhea symptoms. the isolates collected were analyzed by using biochemical, genotypic, and proteo ...	2011	21470449
new treatment options against gram-negative organisms.		2011	21457501
complete sequencing of pndm-hk encoding ndm-1 carbapenemase from a multidrug-resistant escherichia coli strain isolated in hong kong.	the emergence of plasmid-mediated carbapenemases, such as ndm-1 in enterobacteriaceae is a major public health issue. since they mediate resistance to virtually all ß-lactam antibiotics and there is often co-resistance to other antibiotic classes, the therapeutic options for infections caused by these organisms are very limited.	2011	21445317
comparative evaluation of a chromogenic agar medium, the modified hodge test, and a battery of meropenem-inhibitor discs for detection of carbapenemase activity in enterobacteriaceae.	three phenotypic methods (modified hodge test, chromogenic agar, and meropenem discs combined with specific inhibitors) used for the detection of carbapenemase activity were tested on a panel of characterized enterobacteriaceae expressing various β-lactamase mechanisms. overall, the meropenem-plus-inhibitor approach was more sensitive and specific than the other methods, despite its limitation of being unable to detect class d carbapenemases.	2011	21430097
bacterial hand contamination and transfer after use of contaminated bulk-soap-refillable dispensers.	bulk-soap-refillable dispensers are prone to extrinsic bacterial contamination, and recent studies demonstrated that approximately one in four dispensers in public restrooms are contaminated. the purpose of this study was to quantify bacterial hand contamination and transfer after use of contaminated soap under controlled laboratory and in-use conditions in a community setting. under laboratory conditions using liquid soap experimentally contaminated with 7.51 log(10) cfu/ml of serratia marcesce ...	2011	21421792
gastrointestinal flora and gastrointestinal status in children with autism--comparisons to typical children and correlation with autism severity.	children with autism have often been reported to have gastrointestinal problems that are more frequent and more severe than in children from the general population.	2011	21410934
exploring sequence requirements for c3/c4 carboxylate recognition in the pseudomonas aeruginosa cephalosporinase: insights into plasticity of the ampc ß-lactamase.	in pseudomonas aeruginosa, the chromosomally encoded class c cephalosporinase (ampc ß-lactamase) is often responsible for high-level resistance to ß-lactam antibiotics. despite years of study of these important ß-lactamases, knowledge regarding how amino acid sequence dictates function of the ampc pseudomonas-derived cephalosporinase (pdc) remains scarce. insights into structure-function relationships are crucial to the design of both ß-lactams and high-affinity inhibitors. in order to understan ...	2011	21404358
utilization of biodiesel by-products for biogas production.	this contribution reviews the possibility of using the by-products from biodiesel production as substrates for anaerobic digestion and production of biogas. the process of biodiesel production is predominantly carried out by catalyzed transesterification. besides desired methylesters, this reaction provides also few other products, including crude glycerol, oil-pressed cakes, and washing water. crude glycerol or g-phase is heavier separate liquid phase, composed mainly by glycerol. a couple of s ...	2011	21403868
molecular basis of macrolide, triamilide, and lincosamide resistance in pasteurella multocida from bovine respiratory disease.	the mechanism of macrolide-triamilide resistance in pasteurella multocida has been unknown. during whole-genome sequencing of a multiresistant bovine p. multocida isolate, three new resistance genes, the rrna methylase gene erm(42), the macrolide transporter gene msr(e), and the macrolide phosphotransferase gene mph(e), were detected. the three genes were pcr amplified, cloned into suitable plasmid vectors, and shown to confer either macrolide-lincosamide resistance [erm(42)] or macrolide-triami ...	2011	21402855
evolution and spread of a multidrug-resistant proteus mirabilis clone with chromosomal ampc-type cephalosporinases in europe.	proteus mirabilis isolates obtained in 1999 to 2008 from three european countries were analyzed; all carried chromosomal ampc-type cephalosporinase bla(cmy) genes from a citrobacter freundii origin (bla(cmy-2)-like genes). isolates from poland harbored several bla(cmy) genes (bla(cmy-4), bla(cmy-12), bla(cmy-14), bla(cmy-15), and bla(cmy-38) and the new gene bla(cmy-45)), while isolates from italy and greece harbored bla(cmy-16) only. earlier isolates with bla(cmy-4) or bla(cmy-12), recovered in ...	2011	21402851
in vivo regulation of the vi antigen in salmonella and induction of immune responses with an in vivo-inducible promoter.	salmonella enterica serovar typhi, the agent of typhoid fever in humans, expresses the surface vi polysaccharide antigen that contributes to virulence. however, vi expression can also be detrimental to some key steps of s. typhi infectivity, for example, invasion, and vi is the target of protective immune responses. we used a strain of s. typhimurium carrying the whole salmonella pathogenicity island 7 (spi-7) to monitor in vivo vi expression within phagocytic cells of mice at different times af ...	2011	21402763
evaluation of antimicrobial susceptibility for +¦-lactams against clinical isolates from 51 medical centers in japan (2008).	this antimicrobial resistance surveillance study was performed in 51 medical centers in japan over an 11-year period. the susceptibilities of 4228 strains including escherichia coli (491 strains), klebsiella spp. (462 strains), enterobacter spp. (459 strains), citrobacter freundii (358 strains), indole-positive proteus spp. (386 strains), serratia spp. (443 strains), acinetobacter spp. (327 strains), pseudomonas aeruginosa (473 strains), oxacillin-susceptible staphylococcus aureus (481 strains), ...	2011	21396543
molecular docking analysis of new generation cephalosporins interactions with recently known shv-variants.	extended-spectrum-β-lactamases (esbls), constitutes the growing class of betalactamses, these are enzymes produced by bacteria which impart resistance against advanced-generation-cephalosporins. shv enzymes are among the most prevalent esbls. the mode of molecular interactions of recent shv-variants to advanced generation cephalosporins has not been reported yet. this is the first time we are reporting the insilico study of these recent variants with new generation cephaosporins. homology models ...	2011	21383920
isolation of lactobacillus salivarius 1077 (nrrl b-50053) and characterization of its bacteriocin, including the antimicrobial activity spectrum.	lactobacillus salivarius 1077 (nrrl b-50053) was isolated from poultry intestinal materials, and in vitro anti-campylobacter jejuni activity was demonstrated. the isolate was then used for bacteriocin production and its enrichment. the protein content of the cell-free supernatant from the spent medium was precipitated by ammonium sulfate and dialyzed to produce the crude antimicrobial preparation. a typical bacteriocin-like response of sensitivity to proteolytic enzymes and resistance to lysozym ...	2011	21378051
ribonucleases and bacterial virulence.	bacterial stress responses provide them the opportunity to survive hostile environments, proliferate and potentially cause diseases in humans and animals. the way in which pathogenic bacteria interact with host immune cells triggers a complicated series of events that include rapid genetic re-programming in response to the various host conditions encountered. viewed in this light, the bacterial host-cell induced stress response (hcisr) is similar to any other well-characterized environmental str ...	2010	21375713
aminoglycoside resistance rates, phenotypes, and mechanisms of gram-negative bacteria from infected patients in upper egypt.	with the re-emergence of older antibiotics as valuable choices for treatment of serious infections, we studied the aminoglycoside resistance of gram-negative bacteria isolated from patients with ear, urinary tract, skin, and gastrointestinal tract infections at minia university hospital in egypt. escherichia coli (mainly from urinary tract and gastrointestinal tract infections) was the most prevalent isolate (28.57%), followed by pseudomonas aeruginosa (25.7%) (mainly from ear discharge and skin ...	2011	21359143
canadian practice guidelines for surgical intra-abdominal infections.		2010	21358883
novel carbon-carbon bond formations for biocatalysis.	carbon-carbon bond formation is the key transformation in organic synthesis to set up the carbon backbone of organic molecules. however, only a limited number of enzymatic c-c bond forming reactions have been applied in biocatalytic organic synthesis. recently, further name reactions have been accomplished for the first time employing enzymes on a preparative scale, for instance the stetter and pictet-spengler reaction or oxidative c-c bond formation. furthermore, novel enzymatic c-c bond formin ...	2011	21354781
modified real-time pcr for detecting, differentiating, and quantifying ureaplasma urealyticum and ureaplasma parvum.	we evaluated a previously described quantitative real-time pcr (qpcr) for quantifying and differentiating ureaplasma parvum and u. urealyticum. because of nonspecific reactions with staphylococcus aureus dna in the u. parvum pcr, we developed a modified qpcr and designed new primers. these oligonucleotides eradicated cross-reactions, indicating higher specificity. the detection limits of the qpcr were determined at 1 and 3 colony-forming units/ml for u. parvum and u. urealyticum, respectively. t ...	2011	21354056
in vitro activity of ceftobiprole against frequently encountered aerobic and facultative gram-positive and gram-negative bacterial pathogens: results of the canward 2007-2009 study.	the in vitro activity of ceftobiprole was evaluated against 15 011 clinical isolates obtained from patients in canadian hospitals between 2007 and 2009. all staphylococcus aureus were susceptible to ceftobiprole (mic(90)'s for methicillin-susceptible staphylococcus aureus and methicillin-resistant staphylococcus aureus of = 1 µg/ml and 2 µg/ml, respectively). ceftobiprole was active against penicillin-susceptible streptococcus pneumoniae (mic(90), = 0.06 µg/ml), penicillin-resistant streptococcu ...	2011	21353964
bacteriocinogeny in experimental pigs treated with indomethacin and escherichia coli nissle.	to evaluate bacteriocinogeny in short-term high-dose indomethacin administration with or without probiotic escherichia coli nissle 1917 (ecn) in experimental pigs.	2011	21350709
distribution of genes encoding nucleoid-associated protein homologs in plasmids.	bacterial nucleoid-associated proteins (naps) form nucleoprotein complexes and influence the expression of genes. recent studies have shown that some plasmids carry genes encoding nap homologs, which play important roles in transcriptional regulation networks between plasmids and host chromosomes. in this study, we determined the distributions of the well-known naps fis, h-ns, hu, ihf, and lrp and the newly found naps mvat and ndpa among the whole-sequenced 1382 plasmids found in gram-negative b ...	2011	21350637
prevalence of pseudomonas aeruginosa in post-operative wound infection in a referral hospital in haryana, india.	the objective of our study was to determine the prevalence of pseudomonas aeruginosa in the isolates of postoperative wound and its susceptibility pattern to commonly used antibiotics.	2010	21346900
diarrheagenic escherichia coli in acute gastroenteritis in infants in north-west italy.	enteropathogenic escherichia coli may cause diarrhoea in infancy, but it is not routinely detected and regarded as a major causative agent. the aim of the present study was to estimate the incidence of enteropathogenic e. coli infection and to investigate its epidemiology and pathogenesis from faecal specimens in infants hospitalized for acute gastroenteritis. between march 2008 and june 2009, faecal samples were collected and examined to recognize diarrhoeal aetiology, especially for e. coli, b ...	2011	21344146
akara ogbomoso: microbiological examination and identification of hazards and critical control points.	akara ogbomoso was examined toward the establishment of hazard analysis and critical control point (haccp). the akara was produced in residential buildings with the attendant consequence of contamination. there was ample growth of aerobes, coliforms, staphylococci, shigella and yeast/mold from the samples, water and cowpea pastes. microbial contaminations occur through the processing, which can be corrected through education by adopting good hygienic and manufacturing practices. the critical con ...	2010	21339157
molecular characterization of antimicrobial resistance in gram-negative bacteria isolated from bovine mastitis in egypt.	the aim of this study was to characterize the genetic basis of multidrug resistance in gram-negative bacteria isolated from bovine mastitis cases in egypt. multidrug resistance phenotypes were found in 34 of 112 (30.4%) gram-negative bacterial isolates, which harbored at least one antimicrobial resistance gene. the most prevalent multidrug-resistant (mdr) species were enterobacter cloacae (8 isolates, 7.1%), klebsiella pneumoniae (7 isolates, 6.3%), klebsiella oxytoca (7 isolates, 6.3%), escheri ...	2011	21338385
biofilm formation by and thermal niche and virulence characteristics of escherichia spp.	in order to better understand the ecological and virulence characteristics of the various clades of escherichia, in vitro and in vivo experiments were undertaken. members of the recently described cryptic clades of escherichia (clades iii, iv, and v) were found to have an enhanced ability to form biofilms compared to strains of escherichia coli, e. fergusonii, or e. albertii. members of the cryptic clades were also able to replicate at a lower temperature (5°c versus 11°c) than strains of the na ...	2011	21335385
isolation of a selected microbial consortium capable of degrading methyl parathion and p-nitrophenol from a contaminated soil site.	a bacterial consortium with the ability to degrade methyl parathion and p-nitrophenol, using these compounds as the only carbon source, was obtained by selective enrichment in a medium with methyl parathion. samples were taken from moravia, medellin; an area that is highly contaminated, owing to the fact that it was used as a garbage dump from 1974 to 1982. acinetobacter sp, pseudomonas putida, bacillus sp, pseudomonas aeruginosa citrobacter freundii, stenotrophomonas sp, flavobacterium sp, prot ...	2011	21328125
evaluation of a dna microarray (check-mdr ct102) for rapid detection of tem, shv, and ctx-m extended-spectrum β-lactamases and of kpc, oxa-48, vim, imp, and ndm-1 carbapenemases.	the check-mdr ct102 microarray, aimed at identifying bacteria producing extended-spectrum β-lactamase (esbl) (shv, tem, and ctx-m) and carbapenemase (kpc, oxa-48, vim, imp, and ndm-1), was evaluated on a total of 144 gram-negative strains expressing various β-lactamases. the sensitivity and specificity were 100% for most tested genes, suggesting that this assay allows accurate identification of common esbl and carbapenemase producers from bacterial cultures.	2011	21325547
bacterial species associated with sound and botrytis-infected grapes from a greek vineyard.	grape bacterial microbiota plays central roles in the quality of grapes and wine, yet its diversity remains poorly described. in the present study, bacterial species associated with sound and botrytis-infected grapes of two cultivars originating from the same vineyard were assessed. isolates were identified by pcr-denaturing gradient gel electrophoresis (pcr-dgge) and sequence analysis of partial 16s rrna gene. comparable counts were recorded between botrytis-infected and sound grape samples. in ...	2011	21315469
antimicrobial resistance of aerobes and facultative anaerobes isolated from the oral cavity.	this study evaluated the resistance to antimicrobials of aerobes and facultative anaerobes isolated from patients wearing complete dentures, patients with gingivitis and periodontitis, and periodontally health subjects.	2010	21308284
first report of performance of the versant ct/gc dna 1.0 assay (kpcr) for detection of chlamydia trachomatis and neisseria gonorrhoeae.	we evaluated the analytical, work flow, and clinical performance of the versant ct/gc dna 1.0 assay (versant ct/gc assay, where "ct" represents chlamydia trachomatis and "gc" represents neisseria gonorrhoeae). the assay simultaneously detects chlamydia trachomatis and neisseria gonorrhoeae in swab and first-catch urine (fcu) specimens. the limit of detection (lod) was determined to be 342 copies/ml for c. trachomatis and 137 copies/ml for gc. the versant ct/gc assay detected 15 c. trachomatis se ...	2011	21307209
citrobacter freundii infection after acute necrotizing pancreatitis in a patient with a pancreatic pseudocyst: a case report.		2011	21299889
antimicrobial susceptibility and multiplex pcr screening of ampc genes from isolates of enterobacter cloacae, citrobacter freundii, and serratia marcescens.	the emergence of multiple drug resistance in enterobacteriaceae is of particular concern. the aim of this study was to evaluate the antimicrobial susceptibility and screen for the ampc gene in three members of the enterobacteriaceae family (enterobacter cloacae, citrobacter freundii, and serratia marcescens) found at taichung veterans general hospital during the past 5 years using multiplex polymerase chain reaction (pcr).	2010	21291844
rapid identification of gram-negative bacteria with and without ctx-m extended-spectrum ß-lactamase from positive blood culture bottles by pcr followed by microchip gel electrophoresis.	we evaluated the usefulness of pcr analysis of the 16s-23s rrna gene internal transcribed spacer (its) and the ctx-m extended-spectrum ß-lactamase (esbl) followed by microchip gel electrophoresis (mge) for direct identification and ctx-m detection of gram-negative bacteria (gnb) from positive blood culture bottles. of 251 gnb isolated from blood cultures containing a single bacterium, 225 (90%) were correctly identified at the species level directly from positive blood culture bottles by compari ...	2011	21289149
incidence of fever and bacteriemia following flexible fiberoptic bronchoscopy: a prospective study.	the latest american heart association (aha) statement for preventing infectious endocarditis, has not recommended prophylactic antibiotic therapy prior to fiberoptic bronchoscopy (fb) except for patients with preexisting predisposing cardiac conditions. our aim was to determine the incidence of bacteriemia and fever following fb in our experience and compare with those which have been mentioned in aha guideline as well as other studies. venous blood of 85 consecutive patients was evaluated for b ...	2010	21287478
lactobacillus reuteri-produced cyclic dipeptides quench agr-mediated expression of toxic shock syndrome toxin-1 in staphylococci.	the production of the staphylococcal exotoxin toxic shock syndrome toxin-1 (tsst-1) by staphylococcus aureus has been associated with essentially all cases of menstruation-associated toxic shock syndrome (tss). in this work, we show that the human vaginal isolate lactobacillus reuteri rc-14 produces small signaling molecules that are able to interfere with the staphylococcal quorum-sensing system agr, a key regulator of virulence genes, and repress the expression of tsst-1 in s. aureus mn8, a pr ...	2011	21282650
identification of genes essential for prey-independent growth of bdellovibrio bacteriovorus hd100.	bdellovibrio bacteriovorus hd100 is an obligate predatory bacterium that attacks and invades gram-negative bacteria. the predator requires living bacteria to survive as growth and replication take place inside the bacterial prey. it is possible to isolate mutants that grow and replicate outside prey bacteria. such mutants are designated host or prey independent, and their nutritional requirements vary. some mutants are saprophytic and require prey extracts for extracellular growth, whereas other ...	2011	21278289
concentrations of procalcitonin and c-reactive protein, white blood cell count, and the immature-to-total neutrophil ratio in the blood of neonates with nosocomial infections: gram-negative bacilli vs coagulase-negative staphylococci.	this study was undertaken to determine whether concentrations of procalcitonin in the blood of neonates with nosocomial infections depend on the type of pathogen. qualification for the study group was based on the clinical signs of infection. we found that infections with gram-positive (chiefly coagulase-negative staphylococci) and gram-negative bacteria are accompanied by elevated concentrations of procalcitonin. in the case of gram-positive bacteria, other laboratory signs of infection studied ...	2011	21274587
mouse models of escherichia coli o157:h7 infection and shiga toxin injection.	escherichia coli o157:h7 has been responsible for multiple food- and waterborne outbreaks of diarrhea and/or hemorrhagic colitis (hc) worldwide. more importantly, a portion of e. coli o157:h7-infected individuals, particularly young children, develop a life-threatening sequela of infection called hemolytic uremic syndrome (hus). shiga toxin (stx), a potent cytotoxin, is the major virulence factor linked to the presentation of both hc and hus. currently, treatment of e. coli o157:h7 and other stx ...	2011	21274267
salmonella enterica serotype gambia with ctx-m-3 and arma resistance markers: nosocomial infections with a fatal outcome.	we report two cases of bacteremia caused by the salmonella enterica serotype gambia in our children's hospital, with one fatal outcome. the isolates showed indistinguishable genotypes and infrequent resistance markers: ctx-m-3 extended-spectrum ß-lactamase and arma methyltransferase. this is the first report of s. gambia exhibiting ctx-m-3 and arma markers involved in serious infections.	2011	21270227
is selective digestive decontamination useful in controlling aerobic gram-negative bacilli producing extended spectrum beta-lactamases?	to identify outbreak episodes of either carriage or infection due to extended spectrum beta-lactamases producing aerobic gram-negative bacilli (agnb-esbl); to establish whether agnb-esbl, sensitive to tobramycin, become resistant over time; and to evaluate the impact of selective decontamination of the digestive tract (sdd) on abnormal carriage of agnb-esbl.	2011	21268690
decreasing enterobacter sakazakii (cronobacter spp.) food contamination level with bacteriophages: prospects and problems.	enterobacter sakazakii (cronobacter spp.) is an opportunistic pathogen, which can cause rare, but life-threatening infections in neonates and infants through feeding of a contaminated milk formula. we isolated 67 phages from environmental samples and tested their lytic host range on a representative collection of 40 e. sakazakii strains. a cocktail of five phages prevented the outgrowth of 35 out of 40 test strains in artificially contaminated infant formula. two e. sakazakii phages represented ...	2008	21261874
massively parallel pathogen identification using high-density microarrays.	identification of microbial pathogens in clinical specimens is still performed by phenotypic methods that are often slow and cumbersome, despite the availability of more comprehensive genotyping technologies. we present an approach based on whole-genome amplification and resequencing microarrays for unbiased pathogen detection. this 10 h process identifies a broad spectrum of bacterial and viral species and predicts antibiotic resistance and pathogenicity and virulence profiles. we successfully ...	2008	21261824
massively parallel pathogen identification using high-density microarrays.	identification of microbial pathogens in clinical specimens is still performed by phenotypic methods that are often slow and cumbersome, despite the availability of more comprehensive genotyping technologies. we present an approach based on whole-genome amplification and resequencing microarrays for unbiased pathogen detection. this 10 h process identifies a broad spectrum of bacterial and viral species and predicts antibiotic resistance and pathogenicity and virulence profiles. we successfully ...	2008	21261824
characterization of swarming motility in citrobacter freundii.	bacterial swarming motility is a flagella-dependent translocation on the surface environment. it has received extensive attention as a population behavior involving numerous genes. here, we report that citrobacter freundii, an opportunistic pathogen, exhibits swarming movement on a solid medium surface with appropriate agar concentration. the swarming behavior of c. freundii was described in detail. insertional mutagenesis with transposon mini-tn5 was carried out to discover genetic determinants ...	2011	21261700
class 1 integron in staphylococci.	as a major concern in public health, methicillin-resistant staphylococci (mrs) still remains one of the most prevalent pathogens that cause nosocomial infections throughout the world and has been recently labeled as a "super bug" in antibiotic resistance. thus, surveillance and investigation on antibiotic resistance mechanisms involved in clinical mrs strains may raise urgent necessity and utmost significance. as a novel antibiotic resistance mechanism, class 1 integron has been identified as a ...	2011	21258866
evaluation of the immunogenicity and biological activity of the citrobacter freundii vi-crm197 conjugate as a vaccine for salmonella enterica serovar typhi.	typhoid fever remains a major health problem in developing countries. young children are at high risk, and a vaccine effective for this age group is urgently needed. purified capsular polysaccharide from salmonella enterica serovar typhi (vi) is licensed as a vaccine, providing 50 to 70% protection in individuals older than 5 years. however, this vaccine is ineffective in infants. vi conjugated to a carrier protein (i.e., an exoprotein a mutant from pseudomonas aeruginosa [repa]) is highly immun ...	2011	21248155
comparison of nine phenotypic methods for detection of extended-spectrum beta-lactamase production by enterobacteriaceae.	the detection of extended-spectrum β-lactamase-producing (esbl) bacteria is of importance for infection control and epidemiological surveillance. we aimed to compare phenotypic methods available in the routine laboratory and to evaluate two-step strategies using these methods for the detection of esbl-positive enterobacteriaceae. two methods used for routine susceptibility testing (vitek2 and disk diffusion methods) and seven methods designed for the detection of esbl production (esbl etests, co ...	2011	21248086
structure of pdut, a trimeric bacterial microcompartment protein with a 4fe-4s cluster-binding site.	propanediol metabolism in citrobacter freundii occurs within a metabolosome, a subcellular proteinaceous bacterial microcompartment. the propanediol-utilization (pdu) microcompartment shell is constructed from thousands of hexagonal-shaped protein complexes made from seven different types of protein subunit. here, the structure of the bacterial microcompartment protein pdut, which has a tandem structural repeat within the subunit and forms trimers with pseudo-hexagonal symmetry, is reported. thi ...	2011	21245529
comparative in vitro activities of the novel antibacterial finafloxacin against selected gram-positive and gram-negative bacteria tested in mueller-hinton broth and synthetic urine.	kill kinetics and mics of finafloxacin and ciprofloxacin against 34 strains with defined resistance mechanisms grown in cation-adjusted mueller-hinton broth (camhb) at ph values of 7.2 and 5.8 and in synthetic urine at ph 5.8 were determined. in general, finafloxacin gained activity at low ph values in camhb and remained almost unchanged in artificial urine. ciprofloxacin mics increased and bactericidal activity decreased strain dependently in acidic camhb and particularly in artificial urine.	2011	21245444
in vitro and in vivo properties of bal30376, a β-lactam and dual beta-lactamase inhibitor combination with enhanced activity against gram-negative bacilli that express multiple β-lactamases.	bal30376 is a triple combination comprising a siderophore monobactam, bal19764; a novel bridged monobactam, bal29880, which specifically inhibits class c β-lactamases; and clavulanic acid, which inhibits many class a and some class d β-lactamases. the mic(90) was ≤ 4 μg/ml (expressed as the concentration of bal19764) for most species of the enterobacteriaceae family, including strains that produced metallo-β-lactamases and were resistant to all of the other β-lactams tested. the mic(90) for sten ...	2011	21245441
characterization of the enterobacteriaceae community that developed during storage of minced beef under aerobic or modified atmosphere packaging conditions.	the whole cell protein and macrorestriction analysis of dna of enterobacteriaceae isolates recovered from minced beef stored at 0, 5, 10 and 15 °c aerobically and under modified atmosphere packaging consisting of 40% co(2)-30% o(2)-30% n(2) in the presence (map+) and absence (map-) of oregano essential oil were studied. sodium dodecyl sulphate polyacrylamide gel electrophoresis (sds-page) profiles obtained from whole cell protein analysis of the enterobacteriaceae isolates revealed seven groups. ...	2010	21216482
structural and mechanistic insight into covalent substrate binding by escherichia coli dihydroxyacetone kinase.	the escherichia coli dihydroxyacetone (dha) kinase is an unusual kinase because (i) it uses the phosphoenolpyruvate carbohydrate: phosphotransferase system (pts) as the source of high-energy phosphate, (ii) the active site is formed by two subunits, and (iii) the substrate is covalently bound to his218(k)* of the dhak subunit. the pts transfers phosphate to dham, which in turn phosphorylates the permanently bound adp coenzyme of dhal. this phosphoryl group is subsequently transferred to the dha ...	2011	21209328
detection of klebsiella pneumoniae carbapenemase (kpc) production in non-klebsiella pneumoniae enterobacteriaceae isolates by use of the phoenix, vitek 2, and disk diffusion methods.	in this study, we tested the abilities of the vitek 2, bd phoenix, and kirby bauer disk diffusion tests to detect carbapenemase production in a collection of 14 klebsiella pneumoniae carbapenemase (kpc)-producing non-klebsiella pneumoniae isolates. in addition, we evaluated 13 kpc-positive k. pneumoniae isolates by using each of these methods and applied both 2009 and 2010 clsi carbapenem interpretive guidelines.	2011	21209164
comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to bd phoenix automated microbiology system for identification of gram-negative bacilli.	we compared the bd phoenix automated microbiology system to the bruker biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) system for identification of gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. the bd phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. the bruker biotyper correctly identified 408 (93%) and 360 (82 ...	2011	21209160
molecular epidemiological survey of citrobacter freundii misidentified as cronobacter spp. (enterobacter sakazakii) and enterobacter hormaechei isolated from powdered infant milk formula.	a total of 75 powdered infant milk formula (pif) samples collected from pharmacies and drugstores in western sicily, italy, and representative of 12 different brands were analyzed in this study to evaluate their microbiological quality. according to the u.s. food and drug administration protocol, 32 samples out of 75 were contaminated by enterobacteria. commercial biochemical api(r) 20e-system identification method indicated that six pif samples were presumptively contaminated by cronobacter spp ...	2011	21204699
cd4(+) lymphoid tissue-inducer cells promote innate immunity in the gut.	fetal cd4(+) lymphoid tissue inducer (lti) cells play a critical role in the development of lymphoid tissues. recent studies identified that lti cells persist in adults and are related to a heterogeneous population of innate lymphoid cells that have been implicated in inflammatory responses. however, whether lti cells contribute to protective immunity remains poorly defined. we demonstrate that after infection with citrobacter rodentium, cd4(+) lti cells were a dominant source of interleukin-22 ...	2010	21194981
cd4(+) lymphoid tissue-inducer cells promote innate immunity in the gut.	fetal cd4(+) lymphoid tissue inducer (lti) cells play a critical role in the development of lymphoid tissues. recent studies identified that lti cells persist in adults and are related to a heterogeneous population of innate lymphoid cells that have been implicated in inflammatory responses. however, whether lti cells contribute to protective immunity remains poorly defined. we demonstrate that after infection with citrobacter rodentium, cd4(+) lti cells were a dominant source of interleukin-22 ...	2010	21194981
carbapenemases in enterobacteria, hong kong, china, 2009.		2011	21192875
emergence of new delhi metallo-β-lactamase, austria.		2011	21192874
pseudomonas aeruginosa β-lactamase induction requires two permeases, ampg and ampp.	in enterobacteriaceae, β-lactam antibiotic resistance involves murein recycling intermediates. murein recycling is a complex process with discrete steps taking place in the periplasm and the cytoplasm. the ampg permease is critical to this process as it transports n-acetylglucosamine anhydrous n-acetylmuramyl peptides across the inner membrane. in pseudomonadaceae, this intrinsic mechanism remains to be elucidated. since the mechanism involves two cellular compartments, the characterization of t ...	2010	21192796
strain-resolved community genomic analysis of gut microbial colonization in a premature infant.	the intestinal microbiome is a critical determinant of human health. alterations in its composition have been correlated with chronic disorders, such as obesity and inflammatory bowel disease in adults, and may be associated with neonatal necrotizing enterocolitis in premature infants. increasing evidence suggests that strain-level genomic variation may underpin distinct ecological trajectories within mixed populations, yet there have been few strain-resolved analyses of genotype-phenotype conne ...	2010	21191099
strain-resolved community genomic analysis of gut microbial colonization in a premature infant.	the intestinal microbiome is a critical determinant of human health. alterations in its composition have been correlated with chronic disorders, such as obesity and inflammatory bowel disease in adults, and may be associated with neonatal necrotizing enterocolitis in premature infants. increasing evidence suggests that strain-level genomic variation may underpin distinct ecological trajectories within mixed populations, yet there have been few strain-resolved analyses of genotype-phenotype conne ...	2010	21191099
reconstructed ancestral sequences improve pathogen identification using resequencing dna microarrays.	we describe the benefit of using reconstructed ancestral sequences (ras) on resequencing microarrays for rapid pathogen identification, with enterobacteriaceae rpob sequences as a model. our results demonstrate a sharp improvement of call rate and accuracy when using rass as compared to extant sequences. this improvement was attributed to the lower sequence divergence of rass, which also expanded the sequence space covered by the microarray. extension of this novel microarray design strategy to ...	2010	21187950
bioremediation of phenol by alkaliphilic bacteria isolated from alkaline lake of lonar, india.	phenol is an industrially important compound which has a wide range of applications. being highly soluble in water, it appears as the major pollutant in waste waters arising from both phenol manufacturing and from industrial units that utilise phenol. because of its toxicity, bioremediation of phenol is necessary. since some of the phenol-bearing industrial waste waters are alkaline in nature, use of alkaliphilic bacteria for bioremediation of phenol was investigated. alkaliphilic bacteria were ...	1998	21182701
phlegmonous gastritis after endoscopic submucosal dissection for early gastric cancer.	a 74-year-old man with diabetic nephropathy developed epigastric pain and high fever after endoscopic submucosal dissection (esd) for early gastric cancer. gastroscopy, endoscopic ultrasonography and computed tomography showed ulceration with a purulent lake, thickened entire gastric mucosal layers suggesting focal abscess formation, leading to the diagnosis of phlegmonous gastritis. he underwent total gastrectomy as an emergency. histological findings of the resected specimen showed severe infl ...	2008	21180517
crystal structure of ehec intimin: insights into the complementarity between epec and ehec.	enterohaemorrhagic e. coli (ehec) o157:h7 is a primary food-borne bacterial pathogen capable of causing life-threatening human infections which poses a serious challenge to public health worldwide. intimin, the bacterial outer-membrane protein, plays a key role in the initiating process of ehec infection. this activity is dependent upon translocation of the intimin receptor (tir), the intimin binding partner of the bacteria-encoded host cell surface protein. intimin has attracted considerable at ...	2010	21179574
global regulation of the response to sulfur availability in the cheese-related bacterium brevibacterium aurantiacum.	in this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in brevibacterium aurantiacum. in agreement with the growth of b. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cyse and cysk) or homocysteine (metx and mety) ...	2010	21169450
global regulation of the response to sulfur availability in the cheese-related bacterium brevibacterium aurantiacum.	in this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in brevibacterium aurantiacum. in agreement with the growth of b. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cyse and cysk) or homocysteine (metx and mety) ...	2010	21169450