Publications

zoo animals as reservoirs of gram-negative bacteria harboring integrons and antimicrobial resistance genes.	a total of 232 isolates of gram-negative bacteria were recovered from mammals, reptiles, and birds housed at asa zoological park, hiroshima prefecture, japan. forty-nine isolates (21.1%) showed multidrug resistance phenotypes and harbored at least one antimicrobial resistance gene. pcr and dna sequencing identified class 1 and class 2 integrons and many beta-lactamase-encoding genes, in addition to a novel ampc beta-lactamase gene, bla(cmy-26). furthermore, the plasmid-mediated quinolone resista ...	2007	17720829
maternal serum concentrations of the chemokine cxcl10/ip-10 are elevated in acute pyelonephritis during pregnancy.	acute pyelonephritis is one of the most frequent medical complications of pregnancy, as well as a common cause of antepartum hospitalization. interferon (ifn)-gamma inducible protein, cxcl10/ip-10, is a member of the cxc chemokine family with pro-inflammatory and anti-angiogenic properties. the purpose of this study was to determine whether maternal serum concentrations of cxcl10/ip-10 change in patients with acute pyelonephritis during pregnancy.	2007	17763275
maternal serum soluble cd30 is increased in pregnancies complicated with acute pyelonephritis.	normal pregnancy is characterized by activation of the innate immunity and suppression of the adaptive limb of the immune response. however, pregnant women are more susceptible to the effects of infection and microbial products than non-pregnant women. cd30 is a member of the tumor necrosis factor receptor superfamily and is preferentially expressed by activated t cells producing th2-type cytokines. its soluble form (scd30) is proposed to be an index of th2 immune response. high serum concentrat ...	2007	17853184
dry stress and survival time of enterobacter sakazakii and other enterobacteriaceae in dehydrated powdered infant formula.	powdered infant formula is not a sterile product, and opportunistic pathogens could multiply in the reconstituted product, resulting in neonatal infections. in this study, the generation of sublethally injured enterobacteriaceae during desiccation and their persistence in dehydrated powdered infant formula was assessed during a 2.5-year period. the study included 27 strains of enterobacter sakazakii, enterobacter cloacae, salmonella enteritidis, citrobacter koseri, citrobacter freundii, escheric ...	2007	17900090
some bacteria degrade explosives, others prefer boiling methanol.		2007	17991022
interrupted time series analysis of vancomycin compared to cefuroxime for surgical prophylaxis in patients undergoing cardiac surgery.	the increased incidence of methicillin-resistant staphylococcus aureus (mrsa), the emergence of community-acquired mrsa, and the continued high incidence of methicillin-resistant staphylococcus epidermidis have required that certain institutions choose vancomycin for surgical prophylaxis. however, the data supporting the use of vancomycin for surgical prophylaxis are controversial. the purpose of this project was to assess the effect of the change from cefuroxime to vancomycin for surgical site ...	2008	18025116
interrupted time series analysis of vancomycin compared to cefuroxime for surgical prophylaxis in patients undergoing cardiac surgery.	the increased incidence of methicillin-resistant staphylococcus aureus (mrsa), the emergence of community-acquired mrsa, and the continued high incidence of methicillin-resistant staphylococcus epidermidis have required that certain institutions choose vancomycin for surgical prophylaxis. however, the data supporting the use of vancomycin for surgical prophylaxis are controversial. the purpose of this project was to assess the effect of the change from cefuroxime to vancomycin for surgical site ...	2008	18025116
a rare case of lethal retroperitoneal abscess caused by citrobacter koseri.	retroperitoneal abscesses are very uncommon clinical conditions. the characteristically vague symptomatology of retroperitoneal abscess and the inherent difficulty of identifying retroperitoneal disease by physical examination contributed to these dismal therapeutic outcomes. we present an unusual case of lethal retroperitoneal abscess, caused by citrobacter diversus(koseri), treated with surgical drainage. citrobacter species have rarely been involved in deep tissue infection and there is no re ...	2007	18025858
identification of type 3 fimbriae in uropathogenic escherichia coli reveals a role in biofilm formation.	catheter-associated urinary tract infection (cauti) is the most common nosocomial infection in the united states. uropathogenic escherichia coli (upec), the most common cause of cauti, can form biofilms on indwelling catheters. here, we identify and characterize novel factors that affect biofilm formation by upec strains that cause cauti. sixty-five cauti upec isolates were characterized for phenotypic markers of urovirulence, including agglutination and biofilm formation. one isolate, e. coli m ...	2008	18055599
detection of intracellular bacterial communities in human urinary tract infection.	urinary tract infections (utis) are one of the most common bacterial infections and are predominantly caused by uropathogenic escherichia coli (upec). while utis are typically considered extracellular infections, it has been recently demonstrated that upec bind to, invade, and replicate within the murine bladder urothelium to form intracellular bacterial communities (ibcs). these ibcs dissociate and bacteria flux out of bladder facet cells, some with filamentous morphology, and ultimately establ ...	2007	18092884
how novel methods can help discover more information about foodborne pathogens.	considerable emphasis is being placed on quantitative risk assessment modelling as a basis for regulation of trade in food products. however, for models to be accurate, information about the behaviour of potential pathogens in foods needs to be available. the question is how to obtain this knowledge in a simple and cost effective way. one technique that has great potential is the use of reporter bacteria which have been genetically modified to express a phenotype that can be easily monitored, su ...	2000	18159282
copeptin, a novel prognostic biomarker in ventilator-associated pneumonia.	the present study sought to investigate the correlation of copeptin with the severity of septic status in patients with ventilator-associated pneumonia (vap), and to analyze the usefulness of copeptin as a predictor of mortality in vap.	2008	18252006
rapid antimicrobial susceptibility determination of uropathogens in clinical urine specimens by use of atp bioluminescence.	we describe the first direct testing of the antimicrobial susceptibilities of bacterial pathogens in human clinical fluid samples by the use of atp bioluminescence. we developed an atp bioluminescence assay that eliminates somatic sources of atp to selectively quantify the bacterial load in clinical urine specimens with a sensitivity of <1,000 cfu per milliliter. there was a log-log relationship between light emission and the numbers of cfu in clinical urine specimens. a clinical study was perfo ...	2008	18272708
the gut-brain barrier in major depression: intestinal mucosal dysfunction with an increased translocation of lps from gram negative enterobacteria (leaky gut) plays a role in the inflammatory pathophysiology of depression.	there is now evidence that major depression (mdd) is accompanied by an activation of the inflammatory response system (irs) and that pro-inflammatory cytokines and lipopolysacharide (lps) may induce depressive symptoms. the aim of the present study was to examine whether an increased gastrointestinal permeability with an increased translocation of lps from gram negative bacteria may play a role in the pathophysiology of mdd. toward this end, the present study examines the serum concentrations of ...	2008	18283240
prosthetic vascular graft infection: a multi-center review of surgical management.	a multi-center retrospective review of major prosthetic graft infection outcomes was undertaken to determine graft preservation and limb salvage rates. the management of infected prosthetic vascular grafts continues to be controversial. the purpose of this study was to review the surgical management of major extracavitary prosthetic vascular graft infections and to correlate the outcomes on the basis of bacteriology and grade. the change in patient population seen by vascular surgeons and the re ...	2007	18299723
prosthetic vascular graft infection: a multi-center review of surgical management.	a multi-center retrospective review of major prosthetic graft infection outcomes was undertaken to determine graft preservation and limb salvage rates. the management of infected prosthetic vascular grafts continues to be controversial. the purpose of this study was to review the surgical management of major extracavitary prosthetic vascular graft infections and to correlate the outcomes on the basis of bacteriology and grade. the change in patient population seen by vascular surgeons and the re ...	2007	18299723
gram-negative bacteraemia in non-icu patients: factors associated with inadequate antibiotic therapy and impact on outcomes.	a considerable number of gram-negative bacteraemias occur outside intensive care units (icus). inadequate antibiotic therapy in icus has been associated with adverse outcomes; however, there are no prospective studies in non-icu patients.	2008	18344548
virulence studies of enterobacter sakazakii isolates associated with a neonatal intensive care unit outbreak.	in 1994, an outbreak of enterobacter sakazakii infections in france occurred in a neonatal intensive care unit during which 17 neonates were infected. more than half of the infected neonates had severe clinical symptoms; 7 cases of necrotising enterocolitis (one with abdominal perforation), one case of septicemia, and one case of meningitis. the other 8 neonates were shown to be colonized but remained asymptomatic. there were three deaths. four distinguishable pulsotypes of e. sakazakii were iso ...	2008	18423002
in vitro antibacterial activity of ce-156811, a novel analog derived from hygromycin a.	we evaluated a novel truncated hygromycin a analog in which the furanose ring was replaced with a 2-fluoro-2-cyclopropylethyl substituent for its activity against multidrug resistant gram-positive bacteria and compared its activity to the activities of linezolid, quinupristin-dalfopristin, and vancomycin. ce-156811 demonstrated robust in vitro activity against gram-positive bacteria that was comparable to that of linezolid.	2008	18426902
[nationwide surveillance of parenteral antibiotics containing meropenem activities against clinically isolated strains in 2006].	the antibacterial activity of meropenem (mepm) and other parenteral antibiotics against clinical isolates of 876 strains of gram-positive bacteria, 1764 strains of gram-negative bacteria, and 198 strains of anaerobic bacteria obtained from 30 medical institutions during 2006 was measured. the results were as follows; 1. mepm was more active than the other carbapenem antibiotics tested against gram-negative bacteria, especially against enterobacteriaceae and haemophilus influenzae. mepm was also ...	2007	18447206
mgta expression is induced by rob overexpression and mediates a salmonella enterica resistance phenotype.	rob is a member of the sox/mar subfamily of arac/xyls-type transcriptional regulators implicated in bacterial multidrug, heavy metal, superoxide, and organic solvent resistance phenotypes. we demonstrate that, in salmonella enterica, rob overexpression upregulates the transcription of mgta, which codes for the mgta mg2+ transporter. mgta was previously characterized as a member of the mg2+-modulated phopq regulon. here we demonstrate that rob (but not its paralog protein soxs or mara) is able to ...	2008	18487336
fluoroquinolone resistance during 2000-2005: an observational study.	moxifloxacin is a respiratory fluoroquinolone with a community acquired pneumonia indication. unlike other fluoroquinolones used in our healthcare system, moxifloxacin's urinary excretion is low and thus we hypothesized that increased use of moxifloxacin is associated with an increase in fluoroquinolone resistance amongst gram negative uropathogens.	2008	18501015
the escherichia coli rutr transcription factor binds at targets within genes as well as intergenic regions.	the escherichia coli rutr protein is the master regulator of genes involved in pyrimidine catabolism. here we have used chromatin immunoprecipitation in combination with dna microarrays to measure the binding of rutr across the chromosome of exponentially growing e. coli cells. twenty rutr-binding targets were identified and analysis of these targets generated a dna consensus logo for rutr binding. complementary in vitro binding assays showed high-affinity rutr binding to 16 of the 20 targets, w ...	2008	18515344
characterization of klebsiella pneumoniae type 1 fimbriae by detection of phase variation during colonization and infection and impact on virulence.	klebsiella pneumoniae is recognized as an important gram-negative opportunistic pathogen. the ability of bacteria to adhere to host structures is considered essential for the development of infections; however, few studies have examined the influence of adhesion factors on k. pneumoniae virulence. in this study, we cloned and characterized the type 1 fimbria gene cluster of a clinical k. pneumoniae isolate. although this cluster was not identical to the escherichia coli type 1 fimbria gene clust ...	2008	18559432
treatment of citrobacter koseri infection with ciprofloxacin and cefotaxime in a preterm infant.	to report a case of successful treatment of citrobacter koseri infection in a preterm infant as a means of challenging the current treatment recommendations on the basis of pharmacodynamic and pharmacokinetic considerations.	2008	18577764
antimicrobial activity and durability of a novel antimicrobial-impregnated bladder catheter.	the main objective of this study was to examine the antimicrobial activity and durability of a novel indwelling bladder catheter impregnated with minocycline and rifampin. thirty antimicrobial-impregnated bladder catheters were inserted transurethrally in spinal cord-injured patients and removed, in six groups of five catheters each, at 3, 7, 10, 14, 17 or 21 days. removed catheters had detectable zones of inhibition against two different clinical isolates of each of the 10 tested uropathogens ( ...	1997	18611809
rapid detection of blakpc carbapenemase genes by real-time pcr.	carbapenem resistance among enterobacteriaceae is an emerging problem worldwide. klebsiella pneumoniae carbapenemase (bla(kpc)) enzymes are among the most common beta-lactamases described. in this study, we report the development and validation of a real-time pcr (q-pcr) assay for the detection of bla(kpc) genes using taqman chemistry. the q-pcr amplification of bla(kpc) dna was linear over 7 log dilutions (r(2) = 0.999; slope, 3.54), and the amplification efficiency was 91.6%. the q-pcr detecti ...	2008	18614657
repression of small toxic protein synthesis by the sib and ohsc small rnas.	the sequences encoding the quad1 rnas were initially identified as four repeats in escherichia coli. these repeats, herein renamed sib, are conserved in closely related bacteria, although the number of repeats varies. all five sib rnas in e. coli mg1655 are expressed, and no phenotype was observed for a five-sib deletion strain. however, a phenotype reminiscent of plasmid addiction was observed for overexpression of the sib rnas, and further examination of the sib repeat sequences revealed conse ...	2008	18710431
in vitro antibacterial activity of vertilmicin and its susceptibility to modifications by the recombinant aac6'-aph2'' enzyme.	vertilmicin is a new semisynthetic aminoglycoside with a structure similar to that of netilmicin except for a methyl group at the c-6' position. in the present study, the in vitro antibacterial activity of vertilmicin was studied, and its susceptibility to modifications by the recombinant aminoglycoside bifunctional modifying enzyme aac(6')-aph(2'') was compared with those of verdamicin and netilmicin. a total of 1,185 clinical isolates collected from hospitals in beijing between 2000 and 2001 w ...	2008	18710917
urinary tract infections in a south american population: dynamic spread of class 1 integrons and multidrug resistance by homologous and site-specific recombination.	one hundred four bacterial strains mediating urinary tract infections in separate individuals from a uruguayan community were isolated. forty-six strains conferred a multidrug resistance phenotype. all 104 strains were examined for the presence of class 1, 2, and 3 integrons. class 1 integrons were found in 21 isolates across four distinct bacterial genera. a large class 1 integron in a klebsiella pneumoniae strain was fully sequenced and was 29,093 bp in length. this integron probably arose by ...	2008	18753343
analysis of the 16s-23s rrna gene internal transcribed spacer region in klebsiella species.	the 16s-23s rrna gene internal transcribed spacer (its) regions of klebsiella spp., including klebsiella pneumoniae subsp. pneumoniae, klebsiella pneumoniae subsp. ozaenae, klebsiella pneumoniae subsp. rhinoscleromatis, klebsiella oxytoca, klebsiella planticola, klebsiella terrigena, and klebsiella ornithinolytica, were characterized, and the feasibility of using its sequences to discriminate klebsiella species and subspecies was explored. a total of 336 its sequences from 21 representative stra ...	2008	18753345
characterization of endemic shigella boydii strains isolated in iran by serotyping, antimicrobial resistance, plasmid profile, ribotyping and pulsed-field gel electrophoresis.	shigellosis is one of the major causes of morbidity in children with diarrhea in iran. the present study was undertaken to characterize apparently sporadic shigella boydii strains isolated from pediatric patients in iran.	2008	18755045
aromatic amino acid-dependent expression of indole-3-pyruvate decarboxylase is regulated by tyrr in enterobacter cloacae uw5.	the plant growth-promoting rhizobacterium enterobacter cloacae uw5 synthesizes the plant growth hormone indole-3-acetic acid (iaa) via the indole-3-pyruvate pathway utilizing the enzyme indole-3-pyruvate decarboxylase that is encoded by ipdc. in this bacterium, ipdc expression and iaa production occur in stationary phase and are induced by an exogenous source of tryptophan, conditions that are present in the rhizosphere. the aim of this study was to identify the regulatory protein that controls ...	2008	18757531
[infectious complications of surgically treatment pelvic fractures].	based on case histories, the authors draw attention to important infectious complications in patients surgically treated for pelvic injuries. these complications were recorded in four out of 75 patients (5.3%) undergoing surgery for pelvic fracture in the period from 2001 to 2005. the chief risk factors for the development of infection included the poor state of health of a polytraumatized patient in combination with a long stay in an acute care unit, and severe trauma and bleeding of soft tissu ...	2008	18760086
extended-spectrum beta-lactamase detection with different panels for automated susceptibility testing and with a chromogenic medium.	infections caused by extended-spectrum beta-lactamase (esbl)- and ampc beta-lactamase-producing gram-negative bacteria complicate therapy and limit treatment options. several different panels for esbl detection with automated systems exist. in addition, a chromogenic agar medium is available for esbl screening. we compared two automated identification and susceptibility testing systems with regard to their effectiveness in detecting esbl production in enterobacteriaceae: the bd phoenix system (b ...	2008	18845821
characterization of puo-stvr2, a virulence-resistance plasmid evolved from the pslt virulence plasmid of salmonella enterica serovar typhimurium.	puo-stvr2 is a virulence-resistance plasmid which originated from pslt of salmonella enterica serovar typhimurium through acquisition of a complex resistance island, flanked by regions that provide a toxin-antitoxin system and an iron uptake system. the presence of resistance and virulence determinants on the same plasmid allows coselection of both properties, potentially increasing health risks.	2008	18852276
uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth.	intra-amniotic infection and inflammation are major causes of preterm birth (ptb). however, intra-amniotic inflammation is often detected in the absence of infection. this may partly be due to the culturing methods employed in hospital laboratories, which are unable to detect the uncultivated species. in this study, intra-amniotic microbial infections associated with ptb were examined by both culture and 16s rrna-based culture-independent methods and were corroborated by the presence of intra-am ...	2009	18971361
uncultivated bacteria as etiologic agents of intra-amniotic inflammation leading to preterm birth.	intra-amniotic infection and inflammation are major causes of preterm birth (ptb). however, intra-amniotic inflammation is often detected in the absence of infection. this may partly be due to the culturing methods employed in hospital laboratories, which are unable to detect the uncultivated species. in this study, intra-amniotic microbial infections associated with ptb were examined by both culture and 16s rrna-based culture-independent methods and were corroborated by the presence of intra-am ...	2009	18971361
de novo designed synthetic mimics of antimicrobial peptides.	antimicrobial peptides are small cationic amphiphiles that play an important role in the innate immune system. given their broad specificity, they appear to be ideal therapeutic agents. as a result, over the last decade, there has been considerable interest in developing them as intravenously administered antibiotics. however, it has proven difficult to accomplish this goal with peptide-based structures. although it has been possible to solve some relatively simple problems such as susceptibilit ...	2008	18996193
structure, membrane orientation, mechanism, and function of pexiganan--a highly potent antimicrobial peptide designed from magainin.	the growing problem of bacterial resistance to conventional antibiotic compounds and the need for new antibiotics have stimulated interest in the development of antimicrobial peptides (amps) as human therapeutics. development of topically applied agents, such as pexiganan (also known as msi-78, an analog of the naturally occurring magainin2, extracted from the skin of the african frog xenopus laevis) has been the focus of pharmaceutical development largely because of the relative safety of topic ...	2009	19010301
structure, membrane orientation, mechanism, and function of pexiganan--a highly potent antimicrobial peptide designed from magainin.	the growing problem of bacterial resistance to conventional antibiotic compounds and the need for new antibiotics have stimulated interest in the development of antimicrobial peptides (amps) as human therapeutics. development of topically applied agents, such as pexiganan (also known as msi-78, an analog of the naturally occurring magainin2, extracted from the skin of the african frog xenopus laevis) has been the focus of pharmaceutical development largely because of the relative safety of topic ...	2009	19010301
characterization of the myo-inositol utilization island of salmonella enterica serovar typhimurium.	knockout mutation of stm4432 resulted in a growth-deficient phenotype of salmonella enterica serovar typhimurium in the presence of myo-inositol (mi) as the sole carbon source. stm4432 is part of a 22.6-kb genomic island which spans stm4417 to stm4436 (genomic island 4417/4436) and is responsible for mi degradation. genome comparison revealed the presence of this island in only six salmonella strains and a high variability of the iol gene organization in gram-negative bacteria. upon nonpolar del ...	2009	19011032
characterization of the myo-inositol utilization island of salmonella enterica serovar typhimurium.	knockout mutation of stm4432 resulted in a growth-deficient phenotype of salmonella enterica serovar typhimurium in the presence of myo-inositol (mi) as the sole carbon source. stm4432 is part of a 22.6-kb genomic island which spans stm4417 to stm4436 (genomic island 4417/4436) and is responsible for mi degradation. genome comparison revealed the presence of this island in only six salmonella strains and a high variability of the iol gene organization in gram-negative bacteria. upon nonpolar del ...	2009	19011032
haem acquisition is facilitated by a novel receptor hma and required by uropathogenic escherichia coli for kidney infection.	iron acquisition, mediated by specific outer membrane receptors, is critical for colonization of the urinary tract by uropathogenic escherichia coli (upec). the role of specific iron sources in vivo, however, remains largely unknown. in this study, we identified a 79 kda haem receptor, haemacquisition protein hma, and established that it functions independently of chua to mediate haemin uptake by upec strain cft073. we demonstrated that expression of hma promotes tonb-dependent haemin utilizatio ...	2009	19019144
haem acquisition is facilitated by a novel receptor hma and required by uropathogenic escherichia coli for kidney infection.	iron acquisition, mediated by specific outer membrane receptors, is critical for colonization of the urinary tract by uropathogenic escherichia coli (upec). the role of specific iron sources in vivo, however, remains largely unknown. in this study, we identified a 79 kda haem receptor, haemacquisition protein hma, and established that it functions independently of chua to mediate haemin uptake by upec strain cft073. we demonstrated that expression of hma promotes tonb-dependent haemin utilizatio ...	2009	19019144
increased isolation and characterization of shigella sonnei obtained from hospitalized children in tehran, iran.	shigella flexneri has been the most frequent cause of shigellosis in children in iran. to evaluate the changes in frequency of serogroups, 302 shigella species were isolated in 2003 from hospitalized children, aged less than 12 years, with acute diarrhoea in tehran, iran. the number of collected s. sonnei, s. flexneri, s. boydii, and s. dysenteriae isolates was 178 (58.9%), 110 (37.4%), 10 (3.3%), and 4 (1.3%) respectively. most (94%) s. sonnei isolates were resistant to co-trimoxazole. they wer ...	2008	19069621
naturally occurring class a ss-lactamases from the burkholderia cepacia complex.	chromosomally encoded ss-lactamases from the burkholderia cepacia complex species (formerly pseudomonas cepacia) were characterized. cloning and sequencing identified an ambler class a ss-lactamase (penb) from b. cenocepacia. it shares 82% amino acid identity with the pena ss-lactamases previously identified from b. multivorans 249. its expression was dependent upon a lysr-type regulatory protein. its narrow-spectrum hydrolysis activity mostly included penicillins but also included expanded-spec ...	2009	19075063
naturally occurring class a ss-lactamases from the burkholderia cepacia complex.	chromosomally encoded ss-lactamases from the burkholderia cepacia complex species (formerly pseudomonas cepacia) were characterized. cloning and sequencing identified an ambler class a ss-lactamase (penb) from b. cenocepacia. it shares 82% amino acid identity with the pena ss-lactamases previously identified from b. multivorans 249. its expression was dependent upon a lysr-type regulatory protein. its narrow-spectrum hydrolysis activity mostly included penicillins but also included expanded-spec ...	2009	19075063
utility of pyrosequencing in identifying bacteria directly from positive blood culture bottles.	growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. the gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. providing more detailed information than the gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. the s ...	2009	19091813
utility of pyrosequencing in identifying bacteria directly from positive blood culture bottles.	growth in liquid media is the gold standard for detecting microorganisms associated with bloodstream infections. the gram stain provides the first clue as to the etiology of infection, with phenotypic identification completed 1 or 2 days later. providing more detailed information than the gram stain can impart, and in less time than subculturing, would allow the use of more directed empirical therapy and, thus, reduce the patient's exposure to unnecessary or ineffective antibiotics sooner. the s ...	2009	19091813
evaluation and implementation of a chromogenic agar medium for salmonella detection in stool in routine laboratory diagnostics.	we evaluated which chromogenic agar medium for salmonella detection in stool would be most sensitive and specific in our culture protocol. the use of bbl chromagar salmonella chromogenic medium combined with xylose-lysine-deoxycholate agar yielded a sensitivity of 100% and also reduced workload and costs.	2009	19091816
evaluation and implementation of a chromogenic agar medium for salmonella detection in stool in routine laboratory diagnostics.	we evaluated which chromogenic agar medium for salmonella detection in stool would be most sensitive and specific in our culture protocol. the use of bbl chromagar salmonella chromogenic medium combined with xylose-lysine-deoxycholate agar yielded a sensitivity of 100% and also reduced workload and costs.	2009	19091816
normalization of leaky gut in chronic fatigue syndrome (cfs) is accompanied by a clinical improvement: effects of age, duration of illness and the translocation of lps from gram-negative bacteria.	there is now evidence that an increased translocation of lps from gram negative bacteria with subsequent gut-derived inflammation, i.e. induction of systemic inflammation and oxidative & nitrosative stress (io&ns), is a new pathway in chronic fatigue syndrome (cfs).	2008	19112401
ampc beta-lactamases.	summary: ampc beta-lactamases are clinically important cephalosporinases encoded on the chromosomes of many of the enterobacteriaceae and a few other organisms, where they mediate resistance to cephalothin, cefazolin, cefoxitin, most penicillins, and beta-lactamase inhibitor-beta-lactam combinations. in many bacteria, ampc enzymes are inducible and can be expressed at high levels by mutation. overexpression confers resistance to broad-spectrum cephalosporins including cefotaxime, ceftazidime, an ...	2009	19136439
molecular identification of ctx-m and blaoxy/k1 beta-lactamase genes in enterobacteriaceae by sequencing of universal m13-sequence tagged pcr-amplicons.	plasmid encoded blactx-m enzymes represent an important sub-group of class a beta-lactamases causing the esbl phenotype which is increasingly found in enterobacteriaceae including klebsiella spp. molecular typing of clinical esbl-isolates has become more and more important for prevention of the dissemination of esbl-producers among nosocomial environment.	2009	19161622
temporal appearance of plasmid-mediated quinolone resistance genes.	one hundred fifty aac(6')-ib-positive gram-negative isolates collected between 1981 and 1991 were examined by pcr for the presence of the aac(6')-ib-cr variant and other plasmid-mediated quinolone resistance (pmqr) genes. none had the aac(6')-ib-cr variant, qnra, qnrs, qnrc, or qepa, but two strains collected in 1988 had qnrb alleles, making these the earliest known pmqr genes.	2009	19164145
molecular analyses of vibrio cholerae o1 clinical strains, including new nontoxigenic variants isolated in mexico during the cholera epidemic years between 1991 and 2000.	we studied the evolution of vibrio cholerae o1 during the 1991 to 2000 cholera epidemic in mexico by biochemical, serological, and molecular characterization of strains collected during this period. strains were divided into toxigenic and nontoxigenic groups according to the presence or absence of genes encoding cholera toxin. as previously reported, we characterized two populations among toxigenic strains, which were present from the first year of the epidemic. bgli rrna analysis revealed that ...	2009	19213700
class 1 and class 2 integrons and plasmid-mediated antibiotic resistance in coliforms isolated from ten rivers in northern turkey.	we aimed to determine the molecular mechanisms of antibiotic resistance in coliforms isolated from ten rivers in northern region of turkey. a total of 183 isolates were tested for antimicrobial susceptibility by disk diffusion and agar dilution methods. resistance to ampicillin, streptomycin, trimethoprim, tetracycline, and chloramphenicol was detected in 58%, 51.9%, 24%, 28.4%, and 12.5%, respectively. twelve (6.5%) phylogenetically distant organisms were detected to harbor self-transmissible p ...	2009	19229487
characterization of a beta-glucoside operon (bgc) prevalent in septicemic and uropathogenic escherichia coli strains.	escherichia coli strains, in general, do not ferment cellobiose and aryl-beta-d-glucosidic sugars, although "cryptic" beta-d-glucoside systems have been characterized. here we describe an additional cryptic operon (bgc) for the utilization of cellobiose and the aryl-beta-d-glucosides arbutin and salicin at low temperature. the bgc operon was identified by the characterization of beta-glucoside-positive mutants of an e. coli septicemia strain (i484) in which the well-studied bgl (aryl-beta-d-gluc ...	2009	19233952
the bacterial virulence factor lymphostatin compromises intestinal epithelial barrier function by modulating rho gtpases.	lymphocyte inhibitory factor a (lifa) in citrobacter rodentium encodes the large toxin lymphostatin, which contains two enzymatic motifs associated with bacterial pathogenesis, a glucosyltransferase and a protease. our aim was to determine the effects of each lymphostatin motif on intestinal epithelial-barrier function. in-frame mutations of c. rodentium lifa glucosyltransferase (crglm21) and protease (crprm5) were generated by homologous recombination. infection of both model intestinal epithel ...	2009	19286565
emergence of a plasmid mediated bla (vim-1) in citrobacter koseri: report from the sentry antimicrobial surveillance program (italy).		2009	19297281
evolution of a bacterial regulon controlling virulence and mg(2+) homeostasis.	related organisms typically rely on orthologous regulatory proteins to respond to a given signal. however, the extent to which (or even if) the targets of shared regulatory proteins are maintained across species has remained largely unknown. this question is of particular significance in bacteria due to the widespread effects of horizontal gene transfer. here, we address this question by investigating the regulons controlled by the dna-binding phop protein, which governs virulence and mg(2+) hom ...	2009	19300486
bacteriological assessment of urban water sources in khamis mushait governorate, southwestern saudi arabia.	urban water sources of khamis mushait governorate, southwestern saudi arabia, were studied to assess their bacteriological characteristics and suitability for potable purposes. a cross-sectional epidemiological method was adopted to investigate the four main urban water sources (i.e. bottled, desalinated, surface, and well water). these were sampled and examined between february and june 2007.	2009	19302710
triggering of toll-like receptor 4 expressed on human head and neck squamous cell carcinoma promotes tumor development and protects the tumor from immune attack.	toll-like receptors (tlr) expressed on inflammatory cells play a key role in host defense against pathogens, benefiting the host. tlr are also expressed on tumor cells. to evaluate the role of tlr in tumor cells, we investigated tlr4 signaling effects on human head and neck squamous cell carcinoma (hnscc). tumor tissues were obtained from 27 patients with laryngeal and 12 with oral cavity cancers. normal mucosa was obtained from 10 patients with nonneoplastic disorders. smears for bacteria were ...	2009	19318560
dnddb: a database focused on phosphorothioation of the dna backbone.	the dnd dna degradation phenotype was first observed during electrophoresis of genomic dna from streptomyces lividans more than 20 years ago. it was subsequently shown to be governed by the five-gene dnd cluster. similar gene clusters have now been found to be widespread among many other distantly related bacteria. recently the dnd cluster was shown to mediate the incorporation of sulphur into the dna backbone via a sequence-selective, stereo-specific phosphorothioate modification in escherichia ...	2009	19357771
cardiac tamponade caused by polymicrobial gram-negative organisms.	polymicrobial gram-negative pericarditis is a rare entity. we describe the first case of suppurative pericarditis with citrobacter diversus and proteus mirabilis.	2009	19395299
linear alkylbenzene sulfonate tolerance in bacteria isolated from sediment of tropical water bodies polluted with detergents.	the discharge of untreated detergent-bearing waste introduces linear alklcylbenzene sulfonates (las) to the aquatic environment. the surfactant persists in some streams and rivers in nigeria, some is adsorbed to suspended materials and end in the sediment of the receiving water bodies. in this study, bacteria isolated from sediments of some tropical detergent-effluent-polluted streams were tested for tolerance to las using the media dilution technique. las-tolerance was indicated by growth of th ...	2008	19419067
a genetic approach for finding small rnas regulators of genes of interest identifies rybc as regulating the dpia/dpib two-component system.	in escherichia coli, the largest class of small regulatory rnas binds to the rna chaperone hfq and regulates the stability and/or translation of specific mrnas. while recent studies have shown that some mrnas could be subject to post-transcriptional regulation by srnas (e.g. mrnas found by co-immunoprecipitation with hfq), no method has yet been described to identify small rnas that regulate them. we developed a method to easily make translational fusions of genes of interest to the lacz reporte ...	2009	19426207
regulation of clpqy (hslvu) gene expression in escherichia coli.	the escherichia coli clpyq (hsluv) complex is an atp-dependent protease, and the clpq(+)y(+) (hslv(+)u(+)) operon encodes two heat shock proteins, clpq and clpy, respectively. the transcriptional (op) or translational (pr) clpq(+)::lacz fusion gene was constructed, with the clpq(+)y(+) promoter fused to a lacz reporter gene. the clpq(+)::lacz (op or pr) fusion gene was each crossed into lambda phage. the lambdaclpq(+)::lacz(+) (op), a transcriptional fusion gene, was used to form lysogens in the ...	2009	19440251
study of the patency of different peritoneal drains used prophylactically in bariatric surgery.	to compare the performance of different types of abdominal drains used in bariatric surgery.	2009	19452575
signals, regulatory networks, and materials that build and break bacterial biofilms.	biofilms are communities of microorganisms that live attached to surfaces. biofilm formation has received much attention in the last decade, as it has become clear that virtually all types of bacteria can form biofilms and that this may be the preferred mode of bacterial existence in nature. our current understanding of biofilm formation is based on numerous studies of myriad bacterial species. here, we review a portion of this large body of work including the environmental signals and signaling ...	2009	19487730
homologs of the small rna sgrs are broadly distributed in enteric bacteria but have diverged in size and sequence.	sugar phosphate stress in escherichia coli is sensed and managed by the transcriptional regulator sgrr and the small rna (srna) sgrs. sgrs is a dual function rna that performs base pairing-dependent regulation of mrna targets and encodes a small protein, sgrt. homologs of sgrr were analyzed for gene synteny and inter-homolog identity to identify those that are likely to be functionally analogous. these 22 sgrr homologs were used to manually locate adjacent srnas functionally analogous to sgrs. s ...	2009	19531735
detection of genomic islands via segmental genome heterogeneity.	while the recognition of genomic islands can be a powerful mechanism for identifying genes that distinguish related bacteria, few methods have been developed to identify them specifically. rather, identification of islands often begins with cataloging individual genes likely to have been recently introduced into the genome; regions with many putative alien genes are then examined for other features suggestive of recent acquisition of a large genomic region. when few phylogenetic relatives are av ...	2009	19589805
the role of th17 in neuroimmune disorders: target for cam therapy. part ii.	decades of research went into understanding the role that th1 autoreactive t-cells play in neuroinflammation. here we describe another effector population, the il-17-producing t-helper lineage (th17), which drives the inflammatory process. through the recruitment of inflammatory infiltration neutrophils and the activation of matrix metalloproteinases, il-17, a cytokine secreted by th17 cells, contributes to blood-brain barrier breakdown and the subsequent attraction of macrophages and monocytes ...	2011	19622601
detection of enterobacter sakazakii and other pathogens associated with infant formula powder by use of a dna microarray.	pathogen detection is critical to the process of generating and testing powdered infant formula (pif). an obstacle associated with pif microbial surveillance is that most current procedures are time-consuming and labor-intensive. we have developed a rapid, dna microarray-based detection technique to identify 10 different pathogenic bacteria associated with pif contamination based on the 16s-23s rrna gene internal transcribed spacer (its) sequences and wzy (o antigen polymerase) gene. using this ...	2009	19641057
rapid identification of bacterial pathogens using a pcr- and microarray-based assay.	during the course of a bacterial infection, the rapid identification of the causative agent(s) is necessary for the determination of effective treatment options. we have developed a method based on a modified broad-range pcr and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. the broad-range pcr primer mixture was designed using conserved regions of the bacterial topoisomerase genes gyrb and pare. the primer design a ...	2009	19664269
outcome of acute prosthetic joint infections due to gram-negative bacilli treated with open debridement and retention of the prosthesis.	the aim of our study was to evaluate the outcome of acute prosthetic joint infections (pjis) due to gram-negative bacilli (gnb) treated without implant removal. patients with an acute pji due to gnb diagnosed from 2000 to 2007 were prospectively registered. demographics, comorbidity, type of implant, microbiology data, surgical treatment, antimicrobial therapy, and outcome were recorded. classification and regression tree analysis, the kaplan-meier survival method, and the cox regression model w ...	2009	19687237
high prevalence of plasmid-mediated quinolone resistance determinants in commensal members of the enterobacteriaceae in ho chi minh city, vietnam.	antimicrobial-resistant pathogenic members of the enterobacteriaceae are a well-defined global problem. we hypothesized that one of the main reservoirs of dissemination of antimicrobial resistance genes in vietnam is non-pathogenic intestinal flora, and sought to isolate antimicrobial-resistant organisms from hospitalized patients and non-hospitalized healthy individuals in ho chi minh city. the results identified substantial faecal carriage of gentamicin-, ceftazidime- and nalidixic acid-resist ...	2009	19696153
organic acid production in vitro and plant growth promotion in maize under controlled environment by phosphate-solubilizing fluorescent pseudomonas.	phosphorus deficiency is a major constraint to crop production due to rapid binding of the applied phosphorus into fixed forms not available to the plants. microbial solubilization of inorganic phosphates has been attributed mainly to the production of organic acids. phosphate-solubilizing microorganisms enhance plant growth under conditions of poor phosphorus availability by solubilizing insoluble phosphates in the soil. this paper describes the production of organic acids during inorganic phos ...	2009	19698133
citrobacter koseri meningitis: a neurosurgical condition?	a 2-month-old girl developed meningitis, ventriculitis and brain abscess in the course of citrobacter koseri infection. she was successfully treated with the combined use of antibiotics, intra-cavitary urokinase and surgery, thus avoiding the development of hydrocephalus and of ventricular loculation. c. koseri is a gram-negative pathogen with a strong predilection for the neonatal brain. brain abscesses develop in roughly 77% of cases, causing severe neurological sequels in one-half and death i ...	2010	19717321
a novel glucosyltransferase involved in o-antigen modification of shigella flexneri serotype 1c.	the o antigen of serotype 1c differs from the unmodified o antigen of serotype y by the addition of a disaccharide (two glucosyl groups) to the tetrasaccharide repeating unit. it was shown here that addition of the first glucosyl group is mediated by the previously characterized gtri cluster, which is found within a cryptic prophage at the proa locus in the bacterial chromosome. transposon mutagenesis was performed to disrupt the gene responsible for addition of the second glucosyl group, causin ...	2009	19717593
genetic structure and distribution of the colibactin genomic island among members of the family enterobacteriaceae.	a genomic island encoding the biosynthesis and secretion pathway of putative hybrid nonribosomal peptide-polyketide colibactin has been recently described in escherichia coli. colibactin acts as a cyclomodulin and blocks the eukaryotic cell cycle. the origin and prevalence of the colibactin island among enterobacteria are unknown. we therefore screened 1,565 isolates of different genera and species related to the enterobacteriaceae by pcr for the presence of this dna element. the island was dete ...	2009	19720753
direct 16s rrna gene sequencing from clinical specimens, with special focus on polybacterial samples and interpretation of mixed dna chromatograms.	ripseq (isentio, bergen, norway) is a web-based application for the analysis of mixed dna chromatograms. it opens the possibility to analyze chromatograms obtained by direct 16s rrna gene sequencing from polybacterial human clinical samples. in this study, we used direct 16s rrna gene sequencing to investigate 264 samples from a wide range of suspected human bacterial infections. the sequence-based identification was compared with the results from routine culture-based identification. a total of ...	2009	19741089
prognostic serum tumor necrosis factor-alpha in paediatric patients with sepsis.	to study the association of tumor necrosis factor-alpha (tnf-alpha) in paediatric patients with different etiological agents and levels of sepsis.	2009	19762956
nosocomial transmission of highly resistant microorganisms on a spinal cord rehabilitation ward.	to study the mechanism of nosocomial transmission of highly resistant microorganisms (hrmos).	2009	19777864
comparative genomics of ethanolamine utilization.	ethanolamine can be used as a source of carbon and nitrogen by phylogenetically diverse bacteria. ethanolamine-ammonia lyase, the enzyme that breaks ethanolamine into acetaldehyde and ammonia, is encoded by the gene tandem eutbc. despite extensive studies of ethanolamine utilization in salmonella enterica serovar typhimurium, much remains to be learned about eutbc structure and catalytic mechanism, about the evolutionary origin of ethanolamine utilization, and about regulatory links between the ...	2009	19783625
moraxella lacunata septic arthritis in a patient with lupus nephritis.	moraxella lacunata is a rare, usually commensal gram-negative rod most commonly associated with eye infections. we report a unique case of noniatrogenic m. lacunata bacteremia and septic knee arthritis in a patient with class iii-iv lupus nephritis and speculate on the association between invasive moraxella infection and renal impairment.	2009	19794049
comparison of beta-lactamase genes in clinical and food bacterial isolates in india.	the present study aimed to determine the occurrence of human disease-causing enteric bacteria on raw vegetables, fruits, meats, and milk products sold in indian markets. the study further aimed to analyze antibiotic resistance rates and the presence of blactx-m, blatem, blashv, and blaampc.	2009	19801801
microglial activation by citrobacter koseri is mediated by tlr4- and myd88-dependent pathways.	citrobacter koseri is a gram-negative bacterium that can cause a highly aggressive form of neonatal meningitis, which often progresses to establish multifocal brain abscesses. despite its tropism for the brain parenchyma, microglial responses to c. koseri have not yet been examined. microglia use tlrs to recognize invading pathogens and elicit proinflammatory mediator expression important for infection containment. in this study, we investigated the importance of the lps receptor tlr4 and myd88, ...	2009	19812209
infective endocarditis due to citrobacter koseri in an immunocompetent adult.	citrobacter koseri (formerly citrobacter diversus) is a motile gram-negative bacillus usually arising from urinary and gastrointestinal tracts. c. koseri rarely causes infection in immunocompetent patients and, thus far, has been considered an opportunistic pathogen. we report on a 30-year-old man, with no medical past, hospitalized for infective aortic endocarditis due to c. koseri. four weeks of antibiotherapy led to a full recovery for this patient. however, this case is unusual, as previous ...	2009	19812281
diagnostic importance of pulmonary interleukin-1beta and interleukin-8 in ventilator-associated pneumonia.	ventilator-associated pneumonia (vap) is the most commonly fatal nosocomial infection. clinical diagnosis of vap remains notoriously inaccurate. the hypothesis was tested that significantly augmented inflammatory markers distinguish vap from conditions closely mimicking vap.	2010	19825784
endogenous endophthalmitis caused by citrobacter koseri.	endogenous endophthalmitis occurs when organisms are hematogenously disseminated in to the eye from a distant focus of infection. the most common isolated organisms that cause endogenous endophthalmitis are klebsiella pneumoniae and escherichia coli. previous reports on endophthalmitis caused by citrobacter species are limited. we present the first case of endogenous endophthalmitis caused by citrobacter koseri bacteremia and renal abscesses.	2009	19834321
plasma protein c levels in immunocompromised septic patients are significantly lower than immunocompetent septic patients: a prospective cohort study.	activated protein c [apc] improves outcome in immunocompetent patients with severe sepsis particularly in those who are perceived to have high mortality risk. before embarking on a trial of apc administration in immunocompromised septic patients, a preliminary study on plasma levels of protein c in this cohort is essential.	2009	19840396
multilocus sequence typing of cronobacter sakazakii and cronobacter malonaticus reveals stable clonal structures with clinical significance which do not correlate with biotypes.	the cronobacter genus (enterobacter sakazakii) has come to prominence due to its association with infant infections, and the ingestion of contaminated reconstituted infant formula. c. sakazakii and c. malonaticus are closely related, and are defined according their biotype. due to the ubiquitous nature of the organism, and the high severity of infection for the immunocompromised, a multilocus sequence typing (mlst) scheme has been developed for the fast and reliable identification and discrimina ...	2009	19852808
pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus.	pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ...	2010	19854913
pantothenate kinase from the thermoacidophilic archaeon picrophilus torridus.	pantothenate kinase (coaa) catalyzes the first step of the coenzyme a (coa) biosynthetic pathway and controls the intracellular concentrations of coa through feedback inhibition in bacteria. an alternative enzyme found in archaea, pantoate kinase, is missing in the order thermoplasmatales. the pto0232 gene from picrophilus torridus, a thermoacidophilic euryarchaeon, is shown to be a distant homologue of the prokaryotic type i coaa. the cloned gene clearly complements the poor growth of the tempe ...	2010	19854913
brain abscesses due to citrobacter koseri in a pair of twins.		2009	19859021
why hypothetical protein kpn00728 of klebsiella pneumoniae should be classified as chain c of succinate dehydrogenase?	twenty percent of genes that encode for hypothetical proteins from klebsiella pneumoniae mgh78578 were identified, leading to kpn00728 and kpn00729 after bioinformatics analysis. both open reading frames showed high sequence homology to succinate dehydrogenase chain c (sdhc) and d (sdhd) from escherichia coli. recently, kpn00729 was assigned as sdhd. kpn00728 thus remains of particular interest as no annotated genes from the complete genome sequence encode for sdhc. we discovered kpn00728 has a ...	2009	19859792
genome sequence of the versatile fish pathogen edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches.	edwardsiella tarda is the etiologic agent of edwardsiellosis, a devastating fish disease prevailing in worldwide aquaculture industries. here we describe the complete genome of e. tarda, eib202, a highly virulent and multi-drug resistant isolate in china.	2009	19865481
molecular and biochemical characterization of the natural chromosome-encoded class a beta-lactamase from pseudomonas luteola.	pseudomonas luteola (formerly classified as cdc group ve-1 and named chryseomonas luteola) is an unusual pathogen implicated in rare but serious infections in humans. a novel beta-lactamase gene, bla(lut-1), was cloned from the whole-cell dna of the p. luteola clinical isolate lam, which had a weak narrow-spectrum beta-lactam-resistant phenotype, and expressed in escherichia coli. this gene encoded lut-1, a 296-amino-acid ambler class a beta-lactamase with a pi of 6 and a theoretical molecular m ...	2010	19884377