Publications

evaluation of a rapid direct assay for identification of bacteria and the mec a and van genes from positive-testing blood cultures.	we performed the first evaluation of a dna strip assay (genotype blood culture; hain lifescience, nehren, germany) for the detection of the most relevant bacterial sepsis pathogens directly from positive bactec blood culture bottles (becton dickinson, heidelberg, germany). the test comprises two panels, one for the direct species identification of important gram-positive cocci and the other for gram-negative rods. additionally, detection of the mec a and the van genes are implemented. the genoty ...	2005	16207992
extended spectrum beta-lactamases among gram-negative bacteria of nosocomial origin from an intensive care unit of a tertiary health facility in tanzania.	resistance to third generation cephalosporins due to acquisition and expression of extended spectrum beta-lactamase (esbl) enzymes among gram-negative bacteria is on the increase. presence of esbl producing organisms has been reported to significantly affect the course and outcome of an infection. therefore infections due to esbl isolates continue to pose a challenge to infection management worldwide. the aim of this study was to determine the existence and to describe phenotypic and genotypic c ...	2005	16225701
surveillance of extended-spectrum beta-lactamases from clinical samples and faecal carriers in barcelona, spain.	the aim of the present study was to characterize and compare the extended-spectrum beta-lactamase (esbl)-producing organisms isolated from clinical samples and faecal carriers in 2001 and 2002.	2005	16244084
pseudomonas aeruginosa ampr is a global transcriptional factor that regulates expression of ampc and poxb beta-lactamases, proteases, quorum sensing, and other virulence factors.	in members of the family enterobacteriaceae, ampc, which encodes a beta-lactamase, is regulated by an upstream, divergently transcribed gene, ampr. however, in pseudomonas aeruginosa, the regulation of ampc is not understood. in this study, we compared the characteristics of a p. aeruginosa ampr mutant, paoampr, with that of an isogenic ampr+ parent. the ampr mutation greatly altered ampc production. in the absence of antibiotic, paoampr expressed increased basal beta-lactamase levels. however, ...	2005	16251297
molecular mechanisms of beta-lactam resistance mediated by ampc hyperproduction in pseudomonas aeruginosa clinical strains.	the molecular mechanisms of beta-lactam resistance mediated by ampc hyperproduction in natural strains of pseudomonas aeruginosa were investigated in a collection of 10 isogenic, ceftazidime-susceptible and -resistant pairs of isolates, each sequentially recovered from a different intensive care unit patient treated with beta-lactams. all 10 ceftazidime-resistant mutants hyper-produced ampc (beta-lactamase activities were 12- to 657-fold higher than those of the parent strains), but none of them ...	2005	16251318
recombination between the dfra12-orff-aada2 cassette array and an aada1 gene cassette creates a hybrid cassette, aada8b.	homologous recombination between closely related gene cassettes, such as aada1 and aada2, which are 89% identical, can create hybrid cassettes and hybrids of existing cassette arrays. a new cassette array, dfra12-orff-aada8b, which was created by such a recombination event occurring within the aada2 cassette in the dfra12-orff-aada2 array, has been identified.	2005	16251327
high prevalence of the plasmid-mediated quinolone resistance determinant qnra in multidrug-resistant enterobacteriaceae from blood cultures in liverpool, uk.	to determine the prevalence of the plasmid-mediated quinolone resistance qnra gene in a selected collection of blood culture isolates of enterobacteriaceae resistant to both ciprofloxacin and cefotaxime.	2005	16260446
identification of human and rat fad-amp lyase (cyclic fmn forming) as atp-dependent dihydroxyacetone kinases.	rat liver fad-amp lyase or fmn cyclase is the only known enzymatic source of the unusual flavin nucleotide riboflavin 4',5'-cyclic phosphate. to determine its molecular identity, a peptide-mass fingerprint of the purified rat enzyme was obtained. it pointed to highly related, mammalian hypothetical proteins putatively classified as dihydroxyacetone (dha) kinases due to weaker homologies to biochemically proven dha kinases of plants, yeasts, and bacteria. the human protein loc26007 cdna was used ...	2005	16289032
novel cyclic lipodepsipeptide from pseudomonas syringae pv. lachrymans strain 508 and syringopeptin antimicrobial activities.	the syringopeptins are a group of antimicrobial cyclic lipodepsipeptides produced by several plant-associated pseudomonads. a novel syringopeptin, sp508, was shown to be produced as two homologs (a and b) by pseudomonas syringae pv. lachrymans strain 508 from apple and to structurally resemble syringopeptin sp22. sp508 differed from sp22 and other syringopeptins by having three instead of four alpha,beta-unsaturated amino acids and a longer beta-hydroxy acyl chain. both sp508 and sp22 displayed ...	2005	16304170
vim-12, a novel plasmid-mediated metallo-beta-lactamase from klebsiella pneumoniae that resembles a vim-1/vim-2 hybrid.	a transferable plasmid from klebsiella pneumoniae carried a class 1 integron containing bla(vim-12), a novel bla(vim)-type gene, flanked by two copies of aaca7. bla(vim-12) was clustered between bla(vim-1) and bla(vim-2) and differed from bla(vim-1) by 18 nucleotides that were all located at the 3' end and matched the corresponding nucleotides in bla(vim-2). the bla(vim-12)-associated 59-base element was identical to that described in bla(vim-2) alleles.	2005	16304191
a view of consecutive binding events from structures of tetrameric endonuclease sfii bound to dna.	many reactions in cells proceed via the sequestration of two dna molecules in a synaptic complex. sfii is a member of a growing family of restriction enzymes that can bind and cleave two dna sites simultaneously. we present here the structures of tetrameric sfii in complex with cognate dna. the structures reveal two different binding states of sfii: one with both dna-binding sites fully occupied and the other with fully and partially occupied sites. these two states provide details on how sfii r ...	2005	16308566
f-like type iv secretion systems encode proteins with thioredoxin folds that are putative dsbc homologues.	f and r27 are conjugative plasmids of enteric bacteria belonging to the incf and inchi1 plasmid incompatibility groups, respectively. based on sequence analysis, two genes of the f transfer region, traf and trbb, and three genes of the r27 transfer region, trhf, dsbc, and htdt, are predicted to encode periplasmic proteins containing a c-terminal thioredoxin fold. the c-x-x-c active-site motif of thioredoxins is present in all of these proteins except traf(f). escherichia coli carrying a dsba mut ...	2005	16321931
comparison of the minimum inhibitory, mutant prevention and minimum bactericidal concentrations of ciprofloxacin, levofloxacin and garenoxacin against enteric gram-negative urinary tract infection pathogens.	acute, uncomplicated urinary tract infections (utis) are among the most commonly encountered bacterial infections and management has been made more complicated in the last decade due to the trend toward increasing antimicrobial resistance to ampicillin and trimethoprim/sulfamethoxazole (tmp/smx). fluoroquinolones are suggested as alternative antimicrobials for the treatment of utis in communities for which tmp/smx resistance is > or = 10%. the mutant-prevention concentration (mpc) is a novel sus ...	2005	16323436
legionella confirmation using real-time pcr and syto9 is an alternative to current methodology.	the currently accepted culture techniques for the detection of legionella spp. in water samples (as/nzs 3896:1998 and iso 11731 standard methods) are slow and laborious, requiring from 7 to 14 days for a result. we describe a fully validated rapid confirmation technique that uses real-time pcr incorporating the intercalating dye syto9 for the direct identification of primary cultures, significantly decreasing turnaround time and allowing faster remedial action to be taken by the industry.	2005	16332896
use of several inducer and substrate antibiotic combinations in a disk approximation assay format to screen for ampc induction in patient isolates of pseudomonas aeruginosa, enterobacter spp., citrobacter spp., and serratia spp.	two-hundred consecutive, single patient isolates of enterobacter spp., serratia spp., citrobacter spp., and pseudomonas aeruginosa were evaluated for ampc production using a variety of inducer-substrate antibiotic combinations in a disk approximation format. the combinations examined included cefoxitin-piperacillin, imipenem-cefotaxime, imipenem-ceftazidime, imipenem-piperacillin-tazobactam, and imipenem-cefoxitin. all isolates were also screened for the presence of extended-spectrum beta-lactam ...	2005	16333080
comparative genomic analysis of the ppt23a plasmid family of pseudomonas syringae.	members of the ppt23a plasmid family of pseudomonas syringae play an important role in the interaction of this bacterial pathogen with host plants. complete sequence analysis of several ppt23a family plasmids (pfps) has provided a glimpse of the gene content and virulence function of these plasmids. we constructed a macroarray containing 161 genes to estimate and compare the gene contents of 23 newly analyzed and eight known pfps from 12 pathovars of p. syringae, which belong to four genomospeci ...	2005	15743960
acquisition of resistance to extended-spectrum cephalosporins by salmonella enterica subsp. enterica serovar newport and escherichia coli in the turkey poult intestinal tract.	salmonella enterica subsp. enterica serovar newport resistant to the extended-spectrum cephalosporins (escs) and other antimicrobials causes septicemic salmonellosis in humans and animals and is increasingly isolated from humans, animals, foods, and environmental sources. mechanisms whereby serovar newport bacteria become resistant to escs and other classes of antimicrobials while inhabiting the intestinal tract are not well understood. the present study shows that 25.3% of serovar newport strai ...	2005	15746317
bioinformatics analysis of the locus for enterocyte effacement provides novel insights into type-iii secretion.	like many other pathogens, enterohaemorrhagic and enteropathogenic strains of escherichia coli employ a type-iii secretion system to translocate bacterial effector proteins into host cells, where they then disrupt a range of cellular functions. this system is encoded by the locus for enterocyte effacement. many of the genes within this locus have been assigned names and functions through homology with the better characterised ysc-yop system from yersinia spp. however, the functions and homologie ...	2005	15757514
mimivirus in pneumonia patients.	mimivirus, the largest virus known to date, is an amebal pathogen-like legionella sp. when mimivirus was used as an antigen in a microimmunofluorescense assay, seroconversion was found in patients with both community- and hospital-acquired pneumonia. mimivirus dna was found in respiratory samples of a patient with hospital-acquired pneumonia.	2005	15757563
prevalences of zoonotic bacteria among seabirds in rehabilitation centers along the pacific coast of california and washington, usa.	many seabirds are rehabilitated annually by wildlife rehabilitation centers along the pacific coast, usa. although various strains of zoonotic bacteria have been isolated from seabirds, risks to rehabilitators at these centers have not been well documented. from november 2001 through january 2003, we determined the prevalence of detectable enteric fauna by isolation and characterization of gram-negative bacteria from cloacal swabs taken from 26 common murres (uria aalge), 49 gulls (larus spp.), ...	2005	16456162
mechanical transmission of pathogenic organisms: the role of cockroaches.	cockroaches (diploptera punctata) are basically tropical insects and will do their best to find a home that is both warm and moist. their involvement in the transmission of tropical diseases is poorly investigated in africa.	2005	16457381
structure of citrobacter freundii l-methionine gamma-lyase.	l-methionine gamma-lyase (mgl) is a pyridoxal 5'-phosphate (plp) dependent enzyme that catalyzes gamma-elimination of l-methionine. the crystal structure of mgl from citrobacter freundii has been determined at 1.9 a resolution. the spatial fold of the protein is similar to those of mgls from pseudomonas putida and trichomonas vaginalis. the comparison of these structures revealed that there are differences in plp-binding residues and positioning of the surrounding flexible loops.	2005	16511092
crystallization and preliminary x-ray analysis of molecular chaperone-like diol dehydratase-reactivating factor in adp-bound and nucleotide-free forms.	adenosylcobalamin (coenzyme b12) dependent diol dehydratase (ec 4.2.1.28) catalyzes the conversion of 1,2-diols and glycerol to the corresponding aldehydes. it undergoes mechanism-based inactivation by glycerol. the diol dehydratase-reactivating factor (ddr) reactivates the inactivated holoenzymes in the presence of adenosylcobalamin, atp and mg2+ by mediating the release of a damaged cofactor. this molecular chaperone-like factor was overexpressed in escherichia coli, purified and crystallized ...	2005	16511107
prevalence of decreased susceptibility to carbapenems among serratia marcescens, enterobacter cloacae, and citrobacter freundii and investigation of carbapenemases.	between march and july 2002, total of 612 clinical isolates of serratia marcescens, enterobacter cloacae, and citrobacter freundii (201 s. marcescens, 228 e. cloacae, and 183 c. freundii) were collected from 13 clinical laboratories in a nationwide distribution. imipenem and meropenem minimum inhibitory concentrations (mics) were determined using the agar dilution method according to the national committee for clinical laboratory standards guidelines. for the isolates with a decreased susceptibi ...	2005	15994052
sulfolobus tengchongensis spindle-shaped virus stsv1: virus-host interactions and genomic features.	a virus infecting the hyperthermophilic archaeon sulfolobus tengchongensis has been isolated from a field sample from tengchong, china, and characterized. the virus, denoted stsv1 (sulfolobus tengchongensis spindle-shaped virus 1), has the morphology of a spindle (230 by 107 nm) with a tail of variable length (68 nm on average) at one end and is the largest of the known spindle-shaped viruses. after infecting its host, the virus multiplied rapidly to high titers (>10(10) pfu/ml). replication of ...	2005	15994761
ceftriaxone resistance of nontyphoidal salmonella enterica isolates in northern taiwan attributable to production of ctx-m-14 and cmy-2 beta-lactamases.	among 3,027 nontyphoidal salmonella enterica isolates identified between january 1999 and december 2002 in a medical center in northern taiwan, 31 were resistant to the extended-spectrum cephalosporin ceftriaxone (1.02% [31/3,027]), including 2 in 1999 (0.36% [2/549]), 13 in 2000 (1.49% [13/870]), 7 in 2001 (0.78% [7/893]), and 9 in 2002 (1.26% [9/715]). sixteen of these isolates belonged to salmonella serogroup b, nine belonged to serogroup c, four belonged to serogroup d, and two belonged to s ...	2005	16000441
comparative recovery of microorganisms from bact/alert plastic and glass fa and fn blood culture bottles.	biomerieux, inc., has recently introduced plastic bottles to replace glass bottles for use in the bact/alert blood culture system. we compared the performance of the plastic to the glass bottles in a large clinical evaluation. two blood cultures were collected from each patient, one using glass fa (aerobic) and fn (anaerobic) bottles and one using plastic fa and fn bottles. of the 4,040 sets of four bottles collected, 3,110 contained the recommended 8 to 12 ml of blood, yielding 524 microorganis ...	2005	16000442
extended-spectrum-beta-lactamase-producing enterobacteriaceae in yaounde, cameroon.	organisms producing extended-spectrum beta-lactamases (esbls) have been reported in many countries, but there is no information on the prevalence of esbl-producing members of the family enterobacteriaceae in cameroon. a total of 259 enterobacteriaceae strains were isolated between 1995 and 1998 from patients at the yaounde central hospital in cameroon. enterobacterial isolates resistant to extended-spectrum cephalosporin and monobactam were screened for esbl production by the double-disk (dd) sy ...	2005	16000447
countrywide spread of community- and hospital-acquired extended-spectrum beta-lactamase (ctx-m-15)-producing enterobacteriaceae in lebanon.	a prospective study was carried out to assess the extent of carriage of extended-spectrum beta-lactamase (esbl)-producing enterobacteriaceae at both hospital and community levels in lebanon. a total of 1,442 fecal samples were collected from hospital-based patients and 58 from health care workers of six lebanese tertiary care general hospitals located in different areas of lebanon between january and march 2003. a total of 382 fecal samples were also collected from healthy subjects between april ...	2005	16000453
repeated occurrence of diverse extended-spectrum beta-lactamases in minor serotypes of food-borne salmonella enterica subsp. enterica.	screening of greek nontyphoid salmonellae from 2000 to 2002 yielded three extended-spectrum beta-lactamase (esbl)-producing human isolates. salmonella enterica serotype brandenburg harbored a multiresistant shv-5 gene-carrying plasmid. s. enterica serotype blockley and s. enterica serotype hadar harbored a tem-52 gene-carrying plasmid. an s. enterica serotype virchow strain producing plasmid-mediated ctx-m-32 was isolated twice from poultry end products. all esbl plasmids were self-transferable ...	2005	16000476
rapid method for enumeration of viable legionella pneumophila and other legionella spp. in water.	a sensitive and specific method has been developed to enumerate viable l. pneumophila and other legionella spp. in water by epifluorescence microscopy in a short period of time (a few hours). this method allows the quantification of l. pneumophila or other legionella spp. as well as the discrimination between viable and nonviable legionella. it simultaneously combines the specific detection of legionella cells using antibodies and a bacterial viability marker (chemchrome v6), the enumeration bei ...	2005	16000824
retrievable günther tulip filter complicated by sepsis and retroperitoneal hemorrhage: successful management by filter retrieval.	we encountered complications of septic shock and retroperitoneal hemorrhage which occurred after implantation of a retrievable günther tulip filter. a 79-year-old woman was diagnosed as right femoral vein thrombosis, and a retrievable günther tulip filter was deployed prior to a total knee replacement surgery. however, the patient developed septicemia due to citrobacter freundii, followed by thrombocytopenia and retroperitoneal hemorrhage. a large hematoma was formed along the lateral side of th ...	2005	16020886
genetic basis for dissemination of arma.	arma is a novel plasmid-borne 16s rrna methyltransferase that confers high-level resistance to 4,6-disubstituted deoxystreptamines. recently, we have isolated from a high-level broad-spectrum aminoglycoside-resistant escherichia coli animal isolate a plasmid, pmur050, that bore the arma gene. in order to elucidate the genetic basis for the spread of arma, we have determined the complete nucleotide sequence of pmur050.	2005	16027145
quantification of escherichia coli by kinetic 5'-nuclease polymerase chain reaction (real-time pcr) oriented to sfmd gene.	a kinetic 5'-nuclease polymerase chain reaction (real-time pcr) for the quantification of escherichia coli was developed.	2005	16033509
characterization of pseudomonas aeruginosa isolated from chronically infected children with cystic fibrosis in india.	pseudomonas aeruginosa is the leading cause of morbidity and mortality in patients with cystic fibrosis (cf). with chronicity of infection, the organism resides as a biofilm, shows multi-drug resistance, diversifies its colony morphology and becomes auxotrophic. the patients have been found to be colonized with multiple genotypes. the present work was carried out to characterize p. aeruginosa isolated from children with cystic fibrosis using phenotypic and genotypic methods.	2005	16033658
in vitro and in vivo antibacterial activities of cs-023 (ro4908463), a novel parenteral carbapenem.	cs-023 (ro4908463, formerly r-115685) is a novel 1beta-methylcarbapenem with 5-substituted pyrrolidin-3-ylthio groups, including an amidine moiety at the c-2 position. its antibacterial activity was tested against 1,214 clinical isolates of 32 species and was compared with those of imipenem, meropenem, ceftazidime, ceftriaxone, ampicillin, amikacin, and levofloxacin. cs-023 exhibited a broad spectrum of activity against gram-positive and -negative aerobes and anaerobes, including methicillin-res ...	2005	16048932
efficacy of cefepime and imipenem in experimental murine pneumonia caused by porin-deficient klebsiella pneumoniae producing cmy-2 beta-lactamase.	previous studies have shown decreased in vitro activity of zwitterionic cephalosporins and carbapenems against porin-deficient klebsiella pneumoniae expressing a plasmid-mediated ampc-type beta-lactamase (pacbl). the in vitro and in vivo activities of cefepime and imipenem were evaluated against the porin-deficient strain k. pneumoniae c2 and its cmy-2-producing derivative [k. pneumoniae c2(pmg248)]. the mics (in micrograms/milliliter) of cefepime and imipenem against k. pneumoniae c2 were 0.125 ...	2005	16048941
origin of plasmid-mediated quinolone resistance determinant qnra.	plasmid-mediated resistance to quinolones is increasingly reported in studies of enterobacteriaceae. using a pcr-based strategy, a series of gram-negative species were screened for qnra-like genes. shewanella algae, an environmental species from marine and fresh water, was identified as its reservoir. this is a one of the very few examples of progenitor identification of an acquired antibiotic resistance gene.	2005	16048974
in vivo transfer of plasmid-encoded acc-1 ampc from klebsiella pneumoniae to escherichia coli in an infant and selection of impermeability to imipenem in k. pneumoniae.	we describe in vivo selection of a klebsiella pneumoniae strain with diminished imipenem susceptibility attributable to plasmid-encoded acc-1 beta-lactamase production and loss of a 36-kda major outer membrane protein, together with transfer of this plasmid from k. pneumoniae to escherichia coli in a tunisian infant.	2005	16048985
use of the roche lightcycler strep b assay for detection of group b streptococcus from vaginal and rectal swabs.	the results for a real-time pcr assay, using the lightcycler strep b analyte-specific reagents (roche diagnostics corporation, indianapolis, ind.), were compared to a direct plate method combined with a broth enrichment culture method for detection of group b streptococcus colonization in pregnant women. two separate evaluations were conducted using two different automated nucleic extraction instruments, the magna pure lc instrument (roche diagnostics corporation) and the lower-capacity magna pu ...	2005	16081949
development of pcr assays targeting genes in o-antigen gene clusters for detection and identification of escherichia coli o45 and o55 serogroups.	the escherichia coli o45 o-antigen gene cluster of strain o45:h2 96-3285 was sequenced, and conventional (singleplex), multiplex, and real-time pcr assays were designed to amplify regions in the wzx (o-antigen flippase) and wzy (o-antigen polymerase) genes. in addition, pcr assays targeting the e. coli o55 wzx and wzy genes were designed based on previously published sequences. pcr assays targeting e. coli o45 showed 100% specificity for this serogroup, whereas by pcr assays specific for e. coli ...	2005	16085897
the assessment of biological activities associated with the major constituents of the methanol extract of 'wild carrot' (daucus carota l) seeds.	daucus carota l. (family: apiaceae alt. umbelliferae), commonly known as 'wild carrot' or 'queen anne's-lace,' is an ecologically invasive erect biennial naturalized to scotland. the ethnobotanical uses of this species include applications in the treatment of cough, diarrhea, dysentery, cancer, malaria and tumors, and as an antiseptic, abortifacient, aphrodisiac, carminative, stimulant, stomachic and tonic. the major constituents isolated from the methanol extract of d. carota seeds by reversed- ...	2005	16093236
detection and identification of bacterial dna in serum from patients with acute pancreatitis.	bacterial infections are common complications in patients with acute pancreatitis, and translocation of bacteria from the intestinal lumen is probably the first step in the pathogenesis of these infections. as blood cultures in afebrile patients are usually negative, more sensitive methods to investigate this hypothesis in patients are needed. our group has recently developed a method to detect the presence of bacterial dna in biological fluids, and we aimed to detect bacterial dna in patients w ...	2005	16099797
multidrug-resistant pseudomonas aeruginosa strain that caused an outbreak in a neurosurgery ward and its aac(6')-iae gene cassette encoding a novel aminoglycoside acetyltransferase.	we characterized multidrug-resistant pseudomonas aeruginosa strains isolated from patients involved in an outbreak of catheter-associated urinary tract infections that occurred in a neurosurgery ward of a hospital in sendai, japan. pulsed-field gel electrophoresis of spei-, xbai-, or hpai-digested genomic dnas from the isolates revealed that clonal expansion of a p. aeruginosa strain designated imcj2.s1 had occurred in the ward. this strain possessed broad-spectrum resistance to aminoglycosides, ...	2005	16127047
detection of vi-negative salmonella enterica serovar typhi in the peripheral blood of patients with typhoid fever in the faisalabad region of pakistan.	the synthesis and transportation proteins of the vi capsular polysaccharide of salmonella enterica serovar typhi (serovar typhi) are encoded by the viab operon, which resides on a 134-kb pathogenicity island known as spi-7. in recent years, vi-negative strains of serovar typhi have been reported in regions where typhoid fever is endemic. however, because vi negativity can arise during in vitro passage, the clinical significance of vi-negative serovar typhi is not clear. to investigate the loss o ...	2005	16145086
widespread transfer of resistance genes between bacterial species in an intensive care unit: implications for hospital epidemiology.	a transferable plasmid encoding shv-12 extended-spectrum beta-lactamase, tem-116, and aminoglycoside resistance was responsible for two sequential clonal outbreaks of enterobacter cloacae and acinetobacter baumannii bacteria. a similar plasmid was present among isolates of four different bacterial species. recognition of plasmid transfer is crucial for control of outbreaks of multidrug-resistant nosocomial pathogens.	2005	16145160
isolation of a hop-sensitive variant of lactobacillus lindneri and identification of genetic markers for beer spoilage ability of lactic acid bacteria.	we have isolated a hop-sensitive variant of the beer spoilage bacterium lactobacillus lindneri dsm 20692. the variant lost a plasmid carrying two contiguous open reading frames (orf s) designated horb(l) and horc(l) that encode a putative regulator and multidrug transporter presumably belonging to the resistance-nodulation-cell division superfamily. the loss of hop resistance ability occurred with the loss of resistance to other drugs, including ethidium bromide, novobiocin, and cetyltrimethylam ...	2005	16151091
new gammaproteobacteria associated with blood-feeding leeches and a broad phylogenetic analysis of leech endosymbionts.	many monophagous animals have coevolutionary relationships with bacteria that provide unavailable nutrients to the host. frequently, these microbial partners are vertically inherited and reside in specialized structures or tissues. here we report three new lineages of bacterial symbionts of blood-feeding leeches, one from the giant amazonian leech, haementeria ghilianii, and two others from placobdelloides species. these hosts each possess a different mycetome or esophageal organ morphology wher ...	2005	16151107
the pcoo plasmid of enterotoxigenic escherichia coli is a mosaic cointegrate.	cs1 is the prototype of a class of pili of enterotoxigenic escherichia coli (etec) associated with diarrheal disease in humans. the genes encoding this pilus are carried on a large plasmid, pcoo. we report the sequence of the complete 98,396-bp plasmid. like many other virulence plasmids, pcoo is a mosaic consisting of regions derived from multiple sources. complete and fragmented insertion sequences (is) make up 24% of the total dna and are scattered throughout the plasmid. the pcoo dna between ...	2005	16159784
magnetic nanoparticle-antibody conjugates for the separation of escherichia coli o157:h7 in ground beef.	the immunomagnetic separation with magnetic nanoparticle-antibody conjugates (mncs) was investigated and evaluated for the detection of escherichia coli o157:h7 in ground beef samples. mncs were prepared by immobilizing biotin-labeled polyclonal goat anti-e. coli antibodies onto streptavidin-coated magnetic nanoparticles. for bacterial separation, mncs were mixed with inoculated ground beef samples, then nanoparticle-antibody-e. coli o157:h7 complexes were separated from food matrix with a magne ...	2005	16161677
detection and quantification of citrobacter freundii and c. braakii by 5'-nuclease polymerase chain reaction.	a new 5'-nuclease polymerase chain reaction (pcr) system for the detection and quantification of citrobacter freundii and c. braakii was developed with primers and the probe oriented to a specific region of the cfa gene encoding a cyclopropane fatty acid synthase. the qualitative variant of the method consisted of a conventional pcr with end-point fluorimetry or agarose gel electrophoresis, and the quantitative variant used kinetic real-time pcr measurement. the pcr system was specific for c. fr ...	2005	16163457
ceftiofur-resistant salmonella strains isolated from dairy farms represent multiple widely distributed subtypes that evolved by independent horizontal gene transfer.	salmonella is the leading cause of known food-borne bacterial infections in the united states, with an incidence rate of approximately 15 cases per 100,000 people. the rise of antimicrobial-resistant salmonella subtypes, including the appearance of subtypes resistant to ceftriaxone, represents a particular concern. ceftriaxone is used to treat invasive cases of salmonella in children and is closely related to ceftiofur, an antibiotic commonly used to treat diseases of cattle. in order to develop ...	2005	16189081
in vitro and in vivo antibacterial activities of sm-216601, a new broad-spectrum parenteral carbapenem.	sm-216601 is a novel parenteral 1beta-methylcarbapenem. in agar dilution susceptibility testing, the mic of sm-216601 for 90% of the methicillin-resistant staphylococcus aureus (mrsa) strains tested (mic(90)) was 2 microg/ml, which was comparable to those of vancomycin and linezolid. sm-216601 was also very potent against enterococcus faecium, including vancomycin-resistant strains (mic(90) = 8 microg/ml). sm-216601 exhibited potent activity against penicillin-resistant streptococcus pneumoniae, ...	2005	16189097
kinetic properties of four plasmid-mediated ampc beta-lactamases.	the heterologous production in escherichia coli, the purification, and the kinetic characterization of four plasmid-encoded class c beta-lactamases (act-1, mir-1, cmy-2, and cmy-1) were performed. except for their instability, these enzymes are very similar to the known chromosomally encoded ampc beta-lactamases. their kinetic parameters did not show major differences from those obtained for the corresponding chromosomal enzymes. however, the k(m) values of cmy-2 for cefuroxime, cefotaxime, and ...	2005	16189104
covert operations of uropathogenic escherichia coli within the urinary tract.	entry into host cells is required for many bacterial pathogens to effectively disseminate within a host, avoid immune detection and cause disease. in recent years, many ostensibly extracellular bacteria have been shown to act as opportunistic intracellular pathogens. among these are strains of uropathogenic escherichia coli (upec), the primary causative agents of urinary tract infections (utis). upec are able to transiently invade, survive and multiply within the host cells and tissues constitut ...	2005	15569242
efficacy and safety of pharmacokinetically enhanced amoxicillin-clavulanate at 2,000/125 milligrams twice daily for 5 days versus amoxicillin-clavulanate at 875/125 milligrams twice daily for 7 days in the treatment of acute exacerbations of chronic bronchitis.	this randomized, controlled trial was designed to show that a short, 5-day course of pharmacokinetically enhanced amoxicillin-clavulanate at 2,000/125 mg (augmentin xr) is as effective clinically as a longer, 7-day course of conventional amoxicillin-clavulanate at 875/125 mg (both given twice daily) in the treatment of acute exacerbations of chronic bronchitis (aecb). amoxicillin-clavulanate at 2,000/125 mg was designed to extend the therapeutic levels of amoxicillin in serum over the 12-h dosin ...	2005	15616290
monitoring of antibiotic-induced alterations in the human intestinal microflora and detection of probiotic strains by use of terminal restriction fragment length polymorphism.	terminal restriction fragment length polymorphism (t-rflp) was investigated as a tool for monitoring the human intestinal microflora during antibiotic treatment and during ingestion of a probiotic product. fecal samples from eight healthy volunteers were taken before, during, and after administration of clindamycin. during treatment, four subjects were given a probiotic, and four subjects were given a placebo. changes in the microbial intestinal community composition and relative abundance of sp ...	2005	15640226
manual and automated instrumentation for identification of enterobacteriaceae and other aerobic gram-negative bacilli.	identification of gram-negative bacilli, both enteric and nonenteric, by conventional methods is not realistic for clinical microbiology laboratories performing routine cultures in today's world. the use of commercial kits, either manual or automated, to identify these organisms is a common practice. the advent of rapid or "spot" testing has eliminated the need for some commonly isolated organisms to be identified with the systems approach. commercially available systems provide more in-depth id ...	2005	15653824
a homology model of restriction endonuclease sfii in complex with dna.	restriction enzymes (reases) are commercial reagents commonly used in recombinant dna technologies. they are attractive models for studying protein-dna interactions and valuable targets for protein engineering. they are, however, extremely divergent: the amino acid sequence of a typical rease usually shows no detectable similarities to any other proteins, with rare exceptions of other reases that recognize identical or very similar sequences. from structural analyses and bioinformatics studies i ...	2005	15667656
16s rdna sequencing revealed citrobacter freundii as the cause of liver abcess after banding of rectal haemorrhoids.		2005	15667920
plasmid-mediated quinolone resistance in isolates obtained in german intensive care units.	screening of 703 isolates of enterobacteriaceae, obtained from 34 german intensive care units (icus), revealed qnr-positive, integron-containing isolates of enterobacter sp. and citrobacter freundii from four patients in 2 german icus. this is one of the first reports of qnr-positive strains obtained from patients in europe.	2005	15673764
escherichia coli producing an acc-1 class c beta-lactamase isolated in barcelona, spain.		2005	15673793
detection and characterization of beta-lactamase genes in subgingival bacteria from patients with refractory periodontitis.	fifty-three beta-lactamase-producing strains of oral bacteria isolated from patients with refractory periodontitis in norway and usa were screened for the presence of the bla(tem), bla(shv), bla(oxa), bla(ampc), bla(cfxa), and bla(cepa/cbla) genes by the polymerase chain reaction (pcr). the pcr products were characterized by direct sequencing of the amplified dna. thirty-four of the 53 enzyme-producing strains (64%) were positive in one of the pcr assays. all beta-lactamase-producing prevotella ...	2005	15621454
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
the tyra family of aromatic-pathway dehydrogenases in phylogenetic context.	the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size.	2005	15888209
performances of vitek 2 colorimetric cards for identification of gram-positive and gram-negative bacteria.	the purpose of this study was to evaluate the new vitek 2 identification cards that use colorimetric reading to identify gram-positive and gram-negative bacteria (gp and gn cards, respectively) in comparison to fluorimetric cards (id-gpc and id-gnb, respectively). a total of 580 clinical isolates and stock collection strains belonging to 116 taxa were included in the study. of the 249 gram-positive strains tested with both the id-gpc and gp cards, 218 (87.5%) and 235 (94.4%) strains were correct ...	2005	16145083
structure of hinp1i endonuclease reveals a striking similarity to the monomeric restriction enzyme mspi.	hinp1i, a type ii restriction endonuclease, recognizes and cleaves a palindromic tetranucleotide sequence (g/cgc) in double-stranded dna, producing 2 nt 5' overhanging ends. here, we report the structure of hinp1i crystallized as one protein monomer in the crystallographic asymmetric unit. hinp1i displays an elongated shape, with a conserved catalytic core domain containing an active-site motif of sdx18qxk and a putative dna-binding domain. without significant sequence homology, hinp1i displays ...	2005	15805123
controlled alteration of the shape and conformational stability of alpha-helical cell-lytic peptides: effect on mode of action and cell specificity.	a novel method, based on the rational and systematic modulation of macroscopic structural characteristics on a template originating from a large number of natural, cell-lytic, amphipathic alpha-helical peptides, was used to probe how the depths and shapes of hydrophobic and polar faces and the conformational stability affect antimicrobial activity and selectivity with respect to eukaryotic cells. a plausible mode of action explaining the peptides' behaviour in model membranes, bacteria and host ...	2005	15836439
evaluating antibiograms to monitor drug resistance.	we used hospital antibiograms to assess predominant pathogens and their patterns of in vitro antimicrobial resistance in central illinois, usa. we found a lack of information about national guidelines for in vitro antimicrobial susceptibility testing and differences in interpretation among laboratories in the region.	2005	16102325
is26-associated in4-type integrons forming multiresistance loci in enterobacterial plasmids.	three distinct multiresistant loci from enterobacterial plasmids each comprised an integron and an is26-associated sequence. sequence comparison suggested a common ancestral structure that derived from an is26 insertion into the 5' conserved segment of an in4-type integron and evolved through acquisition of gene cassettes and is26-mediated recruitment of additional resistance genes of diverse origin.	2005	16048979
survey of enterobacteriaceae producing extended-spectrum beta-lactamases in a slovak hospital: dominance of shv-2a and characterization of tem-132.	eighty-five extended-spectrum beta-lactamase-producing enterobacteriaceae from a slovak hospital have been studied. shv-2a was predominant, but other variants have been detected, namely, shv-5, shv-12, tem-12, tem-15, and tem-132, which differed from tem-1 by amino acid substitutions r164h, e240k, and i173v and had kinetic properties similar to those of tem-28.	2005	15980402
global spread of multiple aminoglycoside resistance genes.	emergence of the newly identified 16s rrna methylases rmta, rmtb, and arma in pathogenic gram-negative bacilli has been a growing concern. arma, which had been identified exclusively in europe, was also found in several gram-negative pathogenic bacilli isolated in japan, suggesting global dissemination of hazardous multiple aminoglycoside resistance genes.	2005	15963295
validation of performance of plastic versus glass bottles for culturing anaerobes from blood in bact/alert sn medium.	to validate performance, we compared the new plastic bact/alert (biomérieux, durham, nc) sn bottle to the current glass sn bottle with samples of blood obtained for culture from adults and found them comparable for both recovery and speed of detection of microorganisms. we conclude that the safety advantage of plastic bottles can be achieved without compromising performance.	2005	16333117
wide dissemination of a carbapenemase plasmid among gram-negative bacteria: implications of the variable phenotype.		2005	16145178
antimicrobial activity and spectrum of ppi-0903m (t-91825), a novel cephalosporin, tested against a worldwide collection of clinical strains.	ppi-0903m is a novel n-phosphono-type cephalosporin active against oxacillin-resistant staphylococci and many other gram-positive organisms. this study evaluated the in vitro activity and spectrum of ppi-0903m against 1,478 recent clinical isolates collected from 80 medical centers (22 countries). ppi-0903m demonstrated broader in vitro activity against gram-positive bacteria, particularly against multidrug-resistant staphylococci and streptococci of current clinical concern, than currently avai ...	2005	16048970
effect of medium age and supplementation with the biocatalytic oxygen-reducing reagent oxyrase on in vitro activities of tigecycline against recent clinical isolates.	in determining the quality control limits for the clinical laboratory standards institute-recommended quality control organisms with tigecycline, a number of inconsistencies in the results were encountered that appeared to be related to the age of the mueller-hinton broth ii. this study was performed to examine the effect of medium age and supplementation with oxyrase on the activity of tigecycline using a large number of clinical isolates.	2005	16127070
controlled clinical comparison of plastic and glass bottles of bact/alert fa medium for culturing organisms from blood of adult patients.	a new, clear-plastic nonvented aerobic fa bottle, designed to prevent breakage, has been developed for the bact/alert blood culture system. we assessed the new plastic fa bottle by comparing its performance with that of the current glass fa bottle for recovery of microorganisms and time to detection of growth in blood samples obtained for culture from adult patients with suspected bloodstream infections. we conclude that the bact/alert plastic and glass fa bottles are comparable for recovery of ...	2005	15815032
contamination of multiple-dose vials in a veterinary hospital.	bacterial contamination of multiple-dose saline bottles and medication vials in a veterinary teaching hospital was evaluated. bacterial contamination was identified in 16/88 (18%) containers, with no difference in contamination between the large animal clinic, small animal clinic, and ruminant ambulatory clinic. contamination of multiple-dose containers containing substances for injection was common, and potential pathogens were present in many situations. while the clinical significance is not ...	2006	16933556
tigecycline (tygacil): the first in the glycylcycline class of antibiotics.		2006	16609746
messing with bacterial quorum sensing.	quorum sensing is widely recognized as an efficient mechanism to regulate expression of specific genes responsible for communal behavior in bacteria. several bacterial phenotypes essential for the successful establishment of symbiotic, pathogenic, or commensal relationships with eukaryotic hosts, including motility, exopolysaccharide production, biofilm formation, and toxin production, are often regulated by quorum sensing. interestingly, eukaryotes produce quorum-sensing-interfering (qsi) compo ...	2006	17158701
controlled clinical comparison of versatrek and bact/alert blood culture systems.	to assess the relative yields in automated microbial detection systems of bacteria and yeasts isolated from the blood of adult patients with suspected sepsis, we compared the new versatrek system (vti) (trek diagnostic systems, cleveland, oh) to the bact/alert 3d system (3d) (biomérieux, inc., durham, nc). identical protocols were followed for the two systems. paired aerobic (redox 1) and anaerobic (redox 2) vti media were compared with standard aerobic (sa) and anaerobic (sn) 3d media; each of ...	2006	17122016
controlled clinical comparison of versatrek and bact/alert blood culture systems.	to assess the relative yields in automated microbial detection systems of bacteria and yeasts isolated from the blood of adult patients with suspected sepsis, we compared the new versatrek system (vti) (trek diagnostic systems, cleveland, oh) to the bact/alert 3d system (3d) (biomérieux, inc., durham, nc). identical protocols were followed for the two systems. paired aerobic (redox 1) and anaerobic (redox 2) vti media were compared with standard aerobic (sa) and anaerobic (sn) 3d media; each of ...	2006	17122016
effectiveness of cephalosporins in the sputum of patients with nosocomial bronchopneumonia.	nosocomial bronchopneumonia is a frequent complication in patients with chronic intratracheal intubation. despite targeted antibiotic treatment, production of abundant bronchial secretion containing pathogen bacteria often tends to be chronic, and so mortality drastically increases. this problem led to an investigation of the penetration of five cephalosporin antibiotics into the sputum. serum and sputum were collected from 24 chronically intubated patients having purulent nosocomial bronchopneu ...	2006	16954290
in vitro and in vivo antibacterial activities of dw-224a, a new fluoronaphthyridone.	dw-224a showed the most potent in vitro activity among the quinolone compounds tested against clinical isolates of gram-positive bacteria. against gram-negative bacteria, dw-224a was slightly less active than the other fluoroquinolones. the in vivo activities of dw-224a against gram-positive bacteria were more potent than those of other quinolones.	2006	16723601
antibiotic resistance as a global threat: evidence from china, kuwait and the united states.	antimicrobial resistance is an under-appreciated threat to public health in nations around the globe. with globalization booming, it is important to understand international patterns of resistance. if countries already experience similar patterns of resistance, it may be too late to worry about international spread. if large countries or groups of countries that are likely to leap ahead in their integration with the rest of the world--china being the standout case--have high and distinctive patt ...	2006	16603071
tigecycline: an evidence-based review of its antibacterial activity and effectiveness in complicated skin and soft tissue and intraabdominal infections.	there is an urgent need for novel agents to manage serious bacterial infections, particularly those contracted in healthcare facilities. tigecycline is a novel broad-spectrum glycylcycline with good activity against gram-positive, many gram-negative, anaerobic, and some atypical pathogens that has been developed to address this need.	2006	22500153
surveillance bronchoscopy in children during the first year after lung transplantation: is it worth it?	since january 2002, routine surveillance bronchoscopy with bronchoalveolar lavage (bal) and transbronchial biopsy has been performed in all paediatric recipients of lung and heart-lung transplants at the great ormond street hospital for children, london, uk, using a newly revised treatment protocol.	2006	16928706
surveillance bronchoscopy in children during the first year after lung transplantation: is it worth it?	since january 2002, routine surveillance bronchoscopy with bronchoalveolar lavage (bal) and transbronchial biopsy has been performed in all paediatric recipients of lung and heart-lung transplants at the great ormond street hospital for children, london, uk, using a newly revised treatment protocol.	2006	16928706
new antimicrobial agents approved by the u.s. food and drug administration in 2005 and new indications for previously approved agents.		2006	16641478
prevalence and genetic analysis of plasmid-mediated quinolone resistance determinants qnra and qnrs in enterobacteriaceae isolates from a french university hospital.	the spread of plasmid-mediated quinolone resistance determinants qnra and qnrs was evaluated in a collection of 186 extended-spectrum beta-lactamase (esbl)-positive enterobacterial isolates from 2002 to 2005 and 185 nalidixic acid-resistant strains isolated during the first 6 months of 2005 at the bicêtre hospital, france. out of these 186 esbl-positive isolates, 2.2 and 1.6% carried a qnra1 and a qnrs1 determinant, respectively. the esbls associated with qnra1 were veb-1, shv-12, and ctx-m-1, w ...	2006	16982792
evaluation of the new vitek 2 extended-spectrum beta-lactamase (esbl) test for rapid detection of esbl production in enterobacteriaceae isolates.	extended-spectrum beta-lactamases (esbls) are a large, rapidly evolving group of enzymes that confer resistance to oxyimino cephalosporins and monobactams and are inhibited by clavulanate. rapid reliable detection of esbl production is a prerequisite for successful infection management and for monitoring resistance trends and implementation of intervention strategies. we evaluated the performance of the new vitek 2 esbl test system (biomérieux, inc, hazelwood, mo.) in the identification of esbl- ...	2006	16954257
widely distributed and predominant ctx-m extended-spectrum beta-lactamases in amsterdam, the netherlands.	three hundred sixty enterobacteriaceae and nonfermenting gram-negative bacilli, isolated during one week in may 2004 at five hospitals in amsterdam, the netherlands, were evaluated for the presence of extended-spectrum beta-lactamases (esbls). a prevalence of 7.8% was found, in contrast to the 1% observed in 1997. ctx-m esbls dominated, and four types were identified in 18 isolates.	2006	16891530
enumeration of bacterial cell numbers and detection of significant bacteriuria by use of a new flow cytometry-based device.	a new, automated flow cytometry-based urine bacterium analyzer (uba) was developed. we assessed the uba for linearity of measurement, reproducibility of results, carryover rate, and correlation of measured results with those determined by urine culture. we also evaluated its ability to screen urine samples for significant bacteriuria. the uba showed excellent linearity and a minor carryover rate. results from the uba were highly reproducible, and in between-run precision assays, the coefficients ...	2006	17021088
prospective evaluation of the risk of serious bacterial infection in children who present to the emergency department with hyperpyrexia (temperature of 106 degrees f or higher).	previous studies of children with temperatures > or = 106 degrees f (hyperpyrexia) disagree as to whether hyperpyrexia confers a high risk of serious bacterial infection.	2006	16818546
dna looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force.	proteins interacting at multiple sites on dna via looping play an important role in many fundamental biochemical processes. restriction endonucleases that must bind at two recognition sites for efficient activity are a useful model system for studying such interactions. here we used single dna manipulation to study sixteen known or suspected two-site endonucleases. in eleven cases (bpmi, bsgi, bspmi, cfr10i, eco57i, ecorii, foki, hpaii, nari, sau3ai and sgrai) we found that substitution of ca2+ ...	2006	16723432
nucleotide flips determine the specificity of the ecl18ki restriction endonuclease.	restricion endonuclease ecl18ki is specific for the sequence /ccngg and cleaves it before the outer c to generate 5 nt 5'-overhangs. it has been suggested that ecl18ki is evolutionarily related to ngomiv, a 6-bp cutter that cleaves the sequence g/ccggc and leaves 4 nt 5'-overhangs. here, we report the crystal structure of the ecl18ki-dna complex at 1.7 a resolution and compare it with the known structure of the ngomiv-dna complex. we find that ecl18ki flips both central nucleotides within the cc ...	2006	16628220
the deacylation mechanism of ampc beta-lactamase at ultrahigh resolution.	beta-lactamases confer bacterial resistance to beta-lactam antibiotics, such as penicillins. the characteristic class c beta-lactamase ampc catalyzes the reaction with several key residues including ser64, tyr150, and lys67. here, we describe a 1.07 a x-ray crystallographic structure of ampc beta-lactamase in complex with a boronic acid deacylation transition-state analogue. the high quality of the electron density map allows the determination of many proton positions. the proton on the tyr150 h ...	2006	16506777
how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.	the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ...	2006	17158705
evaluation of antimicrobial activity of the stem bark of cylicodiscus gabunensis (mimosaceae).	ethyl acetate (ea) extract of the stem bark of cylicodiscus gabunensis (cg) was analysed phytochemically and evaluated for its antimicrobial activity against 17 pathogenic species isolated from patient: escherichia coli, klebsiella pneumoniae, shigella dysenteriae, shigella flexneri, morganella morganii, proteus vulgaris, proteus mirabilis, salmonella typhi, citrobacter freundii, enterobacter cloacae, enterobacter agglomerans, staphylococcus aureus, streptococcus feacalis, pseudomonas aeruginosa ...	2006	20162076
production and characterisation of monoclonal antibodies specific for escherichia coli o157:h7.	seven monoclonal antibodies (mabs) specific for escherichia coli o157:h7, one of the major causes of haemorrhagic colitis in humans, were produced by immunising balb/c mice with the strain e. coli o157:h7. these monoclonal antibodies do not cross-react with other bacteria such as salmonella enterica serovar typhimurium, e. coli o14, e. coli jm109, s. enterica serovar enteritidis, s. panama, s. saintpaul, s. derby, s. muenchen, s. bredeney, s. hadar, yersinia enterocolitica, proteus vulgaris, shi ...	2006	20429059