| rapid identification of gram-negative bacteria with and without ctx-m extended-spectrum ß-lactamase from positive blood culture bottles by pcr followed by microchip gel electrophoresis. | we evaluated the usefulness of pcr analysis of the 16s-23s rrna gene internal transcribed spacer (its) and the ctx-m extended-spectrum ß-lactamase (esbl) followed by microchip gel electrophoresis (mge) for direct identification and ctx-m detection of gram-negative bacteria (gnb) from positive blood culture bottles. of 251 gnb isolated from blood cultures containing a single bacterium, 225 (90%) were correctly identified at the species level directly from positive blood culture bottles by compari ... | 2011 | 21289149 |
| a udp-hexnac:polyprenol-p galnac-1-p transferase (wecp) representing a new subgroup of the enzyme family. | the aeromonas hydrophila ah-3 wecp represents a new class of udp-hexnac:polyprenol-p hexnac-1-p transferases. these enzymes use a membrane-associated polyprenol phosphate acceptor (undecaprenyl phosphate [und-p]) and a cytoplasmic udp-d-n-acetylhexosamine sugar nucleotide as the donor substrate. until now, all the weca enzymes tested were able to transfer udp-glcnac to the und-p. in this study, we present in vitro and in vivo proofs that a. hydrophila ah-3 wecp transfers galnac to und-p and is u ... | 2011 | 21335454 |
| aminoglycoside resistance rates, phenotypes, and mechanisms of gram-negative bacteria from infected patients in upper egypt. | with the re-emergence of older antibiotics as valuable choices for treatment of serious infections, we studied the aminoglycoside resistance of gram-negative bacteria isolated from patients with ear, urinary tract, skin, and gastrointestinal tract infections at minia university hospital in egypt. escherichia coli (mainly from urinary tract and gastrointestinal tract infections) was the most prevalent isolate (28.57%), followed by pseudomonas aeruginosa (25.7%) (mainly from ear discharge and skin ... | 2011 | 21359143 |
| automated identification of medically important bacteria by 16s rrna gene sequencing using a novel comprehensive database, 16spathdb. | despite the increasing use of 16s rrna gene sequencing, interpretation of 16s rrna gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. to overcome the problems we encountered in the existing databases during 16s rrna gene sequence interpretation, we built a comprehensive database, 16spathdb (http://147.8.74.24/16spathdb) based on the 16s rrna gene sequences of all medically important bacteria listed in the manual of clinical microbiology ... | 2011 | 21389154 |
| characterization of the salmonella enterica serovar typhimurium ydci gene, which encodes a conserved dna binding protein required for full acid stress resistance. | salmonella enterica serovar typhimurium possesses a stimulon of genes that are differentially regulated in response to conditions of low fluid shear force that increase bacterial virulence and alter other phenotypes. in this study, we show that a previously uncharacterized member of this stimulon, ydci or stm1625, encodes a highly conserved dna binding protein with related homologs present in a range of gram-negative bacterial genera. gene expression analysis shows that ydci is expressed in diff ... | 2011 | 21398541 |
| highly specific and quick detection of mycobacterium avium subsp. paratuberculosis in feces and gut tissue of cattle and humans by multiple real-time pcr assays. | mycobacterium avium subsp. paratuberculosis is the causative agent of johne's disease (jd) in cattle and may be associated with crohn's disease (cd) in humans. it is the slowest growing of the cultivable mycobacteria, and culture from clinical, veterinary, food, or environmental specimens can take 4 months or even longer. currently, the insertion element is900 is used to detect m. avium subsp. paratuberculosis dna. however, closely related is900 elements are also present in other mycobacteria, t ... | 2011 | 21430100 |
| pyogenic liver abscess: an audit of 10 years' experience. | to describe our own experience with pyogenic liver abscesses over the past 10 years and investigate the risk factors associated with failure of initial percutaneous therapy. | 2011 | 21472130 |
| microbiology of animal bite wound infections. | the microbiology of animal bite wound infections in humans is often polymicrobial, with a broad mixture of aerobic and anaerobic microorganisms. bacteria recovered from infected bite wounds are most often reflective of the oral flora of the biting animal, which can also be influenced by the microbiome of their ingested prey and other foods. bacteria may also originate from the victim's own skin or the physical environment at the time of injury. our review has focused on bite wound infections in ... | 2011 | 21482724 |
| myd88 is pivotal for immune recognition of citrobacter koseri and astrocyte activation during cns infection†. | abstract: citrobacter koseri (c. koseri) is a gram-negative bacterium that can cause a highly aggressive form of neonatal meningitis, which often progresses to establish multi-focal brain abscesses. the roles of toll-like receptor 4 (tlr4) and its signaling adaptor myd88 during cns c. koseri infection have not yet been examined, which is important since recent evidence indicates that innate immune responses are tailored towards specific pathogen classes. here tlr4 wt (c3h/fej) and tlr4 mutant (c ... | 2011 | 21496301 |
| genetic regulation of the rama locus and its expression in clinical isolates of klebsiella pneumoniae. | tigecycline resistance has been attributed to rama overexpression and subsequent acra upregulation. the rama locus, originally identified in klebsiella pneumoniae, has homologues in enterobacter and salmonella spp. in this study, we identify in silico that the ramr binding site is also present in citrobacter spp. and that enterobacter, citrobacter and klebsiella spp. share key regulatory elements in the control of the roma-rama locus. race (rapid amplification of cdna ends) mapping indicated tha ... | 2011 | 21514798 |
| the novel gene ygaw (alae) encodes an inducible l-alanine exporter in escherichia coli. | we previously isolated a mutant hypersensitive to l-alanyl-l-alanine from an l-alanine non-metabolizing escherichia coli strain and found that it lacked an inducible l-alanine export system. consequently, this mutant showed a significant accumulation of intracellular l-alanine and a reduction in the l-alanine export rate compared to the parent strain. when the mutant was used as a host to clone a gene(s) that complements the dipeptide-hypersensitive phenotype, two uncharacterized genes, ygaw and ... | 2011 | 21531828 |
| antimicrobial resistance in urinary tract pathogens in canada from 2007 to 2009: canward surveillance study. | from january 2007 to december 2009 an annual canadian national surveillance study (canward) tested 2943 urinary culture pathogens for antimicrobial susceptibilities following clinical and laboratory standards institute (clsi) guidelines. the most frequently isolated urinary pathogens (n, % of all isolates) were escherichia coli (1581, 54%), enterococci (410, 14%), klebsiella pneumoniae (274, 9%), proteus mirabilis (122, 4%), pseudomonas aeruginosa (100, 3%), and staphylococcus aureus (80, 3%). r ... | 2011 | 21537027 |
| rapid detection of blakpc carbapenamase genes by internally controlled real-time pcr assay from bactec(r) blood culture bottles. | rapid detection of drug resistant bacteria in clinical samples plays an instrumental role in patients' infection management and in implementing effective infection control policies. in this report, we validated a multiplex taqman real-time pcr (q-pcr) assay for the detection of blakpc genes and the human gene rnase p, in bactec® blood culture bottles. the magna pure lc 2.0, was utilized to extract nucleic acids from the inoculated broth while bovine serum albumin (bsa) was utilized as pcr inhibi ... | 2011 | 21562110 |
| comparative genomic analysis of the hexuronate metabolism genes and their regulation in gamma-proteobacteria. | the hexuronate metabolism in escherichia coli is regulated by two related transcription factors from the fadr subfamily of the gntr family, uxur and exur. uxur controls the d-glucuronate metabolism, while exur represses genes involved in the metabolism of all hexuronates. here we use the comparative genomics approach to reconstruct the hexuronate metabolic pathways and transcriptional regulons in the gamma-proteobacteria. we demonstrate differences in the binding motifs of uxur and exur, identif ... | 2011 | 21622752 |
| the utility of matrix assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms) following introduction for routine laboratory bacterial identification. | maldi-tof ms was evaluated prospectively in a diagnostic laboratory. 927 organisms were tested in triplicate; 2351/2781 (85%) species and 2681/2781 (96%) genus identifications were correct. known issues such as the misidentification of α-haemolytic streptococci as streptococcus pneumonia were easily corrected. identifications cost $aud0.45 per isolate and were available in minutes. maldi-tof ms is rapid, accurate and inexpensive. | 2011 | 21632894 |
| the burden of invasive early-onset neonatal sepsis in the united states, 2005-2008. | background:: sepsis in the first 3 days of life is a leading cause of morbidity and mortality among infants. group b streptococcus (gbs), historically the primary cause of early-onset sepsis (eos), has declined through widespread use of intrapartum chemoprophylaxis. we estimated the national burden of invasive eos cases and deaths in the era of gbs prevention. methods:: population-based surveillance for invasive eos was conducted in 4 of the centers for disease control and prevention's active ba ... | 2011 | 21654548 |
| abscess caused by citrobacter koseri infection: three case reports and a literature review. | in this report, we present 3 cases of abscess caused by citrobacter koseri. all infected patients recovered after initial empirical antibiotic treatment and percutaneous drainage of the abscess. we reviewed the literature and found 9 adult cases of c. koseri abscess. most of these patients recovered after timely antibiotic treatment and drainage. | 2011 | 21673472 |
| rapid concentration and molecular enrichment approach for sensitive detection of escherichia coli/shigella in potable water samples. | in this work, we used a rapid, simple, and efficient concentration and recovery procedure combined with a dna enrichment method (dubbed crename), that we coupled to an escherichia coli/shigella-specific real-time pcr (rtpcr) assay targeting the tuf gene, to sensitively detect e. coli/shigella in water. this integrated method was compared to the usepa culture-based method 1604 on mi agar in terms of analytical specificity, ubiquity, detection limit, and rapidity. none of the 179 non-e. coli/shige ... | 2011 | 21764965 |
| high prevalence of extended-spectrum {beta}-lactamases and qnr determinants in citrobacter species from japan: dissemination of ctx-m-2. | objectives extended-spectrum +¦-lactamases (esbls) have become a problem among ampc-producing enterobacteriaceae and the emergence of concomitant quinolone resistance in +¦-lactamase-producing isolates poses a global threat. in this study we investigated the prevalence and regional variation of esbls in japanese clinical isolates of citrobacter spp. and analysed plasmid-mediated quinolone resistance (pmqr) determinants in esbl-producing citrobacter spp. methods a total of 348 clinical isolates o ... | 2011 | 21733965 |
| citrobacter spp. as a source of qnrb alleles. | qnrb is the most common of the five qnr families and has the greatest number of allelic variants. almost two thirds of the qnrb alleles have been reported in citrobacter spp., and several were shown to be located on the chromosome. in this study pcr was used to investigate the prevalence of plasmid-mediated quinolone resistance genes in 71 clinical isolates belonging to the citrobacter freundii complex. thirty-seven percent contained qnrb alleles, including 7 (qnrb32 to qnrb38) that were novel a ... | 2011 | 21844311 |
| structure and function of the d-galactose network in enterobacteria. | galactose is important for the survival and virulence of bacteria. in escherichia coli, galactose is utilized by the leloir pathway, which is controlled by a complex network. to shed light on the potential functions the galactose network could perform, we performed bioinformatical analysis of reference genome sequences belonging to the enterobacteriaceae family. we found that several genomes have reduced numbers of components compared to the e. coli galactose system, suggesting that the network ... | 2011 | 21712421 |
| Bacterial infection profiles in lung cancer patients with febrile neutropenia. | ABSTRACT: | 2011 | 21707992 |
| identification of bacteria from the oral cavity and cloaca of snakes imported from vietnam. | reptiles are used for various purposes these days, including public exhibits, medicinal applications, and as laboratory animals. as the international exchange of reptiles has gradually increased, more people have had the opportunity to come in contact with these animals. snakes typically live in the rhizosphere where various bacterial strains exist and as such they can lead to opportunistic human diseases. when snakes are encountered in veterinary medicine, it is necessary to monitor their micro ... | 2011 | 21998610 |
| toll-like receptor 2 (tlr2)-tlr9 crosstalk dictates il-12 family cytokine production in microglia. | microglia are the resident mononuclear phagocytes of the cns parenchyma and represent an initial line of defense against invading microorganisms. microglia utilize toll-like receptors (tlrs) for pathogen recognition and tlr2 specifically senses conserved motifs of gram-positive bacteria including lipoproteins, lipoteichoic acids, and peptidoglycan (pgn) leading to cytokine/chemokine production. interestingly, primary microglia derived from tlr2 knockout (ko) mice over-expressed numerous il-12 fa ... | 2012 | 21901759 |
| toll-like receptor 2 (tlr2)-tlr9 crosstalk dictates il-12 family cytokine production in microglia. | microglia are the resident mononuclear phagocytes of the cns parenchyma and represent an initial line of defense against invading microorganisms. microglia utilize toll-like receptors (tlrs) for pathogen recognition and tlr2 specifically senses conserved motifs of gram-positive bacteria including lipoproteins, lipoteichoic acids, and peptidoglycan (pgn) leading to cytokine/chemokine production. interestingly, primary microglia derived from tlr2 knockout (ko) mice over-expressed numerous il-12 fa ... | 2012 | 21901759 |
| identification of bacteria in blood culture broths using matrix-assisted laser desorption-ionization sepsityper™ and time of flight mass spectrometry. | matrix-assisted laser desorption ionization time of flight mass spectrometry (maldi-tof ms) is a novel method for the direct identification of bacteria from blood culture broths. we evaluate for the first time, the performance of the maldi sepsityper™ kit and ms for the identification of bacteria compared to standard phenotypic methods using the manufacturer's specified bacterial identification criteria (spectral scores ≥1.700-1.999 and ≥2.000 indicated identification to genus and species level, ... | 2011 | 21858058 |
| mrkh, a novel c-di-gmp-dependent transcriptional activator, controls klebsiella pneumoniae biofilm formation by regulating type 3 fimbriae expression. | klebsiella pneumoniae causes significant morbidity and mortality worldwide, particularly amongst hospitalized individuals. the principle mechanism for pathogenesis in hospital environments involves the formation of biofilms, primarily on implanted medical devices. in this study, we constructed a transposon mutant library in a clinical isolate, k. pneumoniae aj218, to identify the genes and pathways implicated in biofilm formation. three mutants severely defective in biofilm formation contained i ... | 2011 | 21901098 |
| Novel, improved sample preparation for rapid, direct identification from positive blood cultures using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. | Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) is widely used for rapid and reliable identification of bacteria and yeast grown on agar plates. Moreover, MALDI-TOF MS also holds promise for bacterial identification from blood culture (BC) broths in hospital laboratories. The most important technical step for the identification of bacteria from positive BCs by MALDI-TOF MS is sample preparation to remove blood cells and host proteins. We present a meth ... | 2011 | 21889611 |
| The effects of solid media type on routine identification of bacterial isolates using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. | Background: Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis is a rapid method for the identification of bacteria based upon the comparison of protein profiles. Factors that may alter profiles include culture conditions and presence of exogenous substances and could hinder identification. Methods: Bacterial isolates identified using conventional methods were cultured on various media and identified using the MALDI Biotyper system (Bruker Dalton ... | 2011 | 22162546 |
| cd4 count is associated with postoperative infection in patients with orthopaedic trauma who are hiv positive. | background: since the advent of effective antiretroviral therapy, the number of people with aids has increased and a certain percentage of these patients will require emergent orthopaedic surgery. little is known regarding orthopaedic infections and the association of cd4 counts with postoperative infection in patients with hiv infection who experience orthopaedic trauma. questions/purposes: we questioned whether ... | 2011 | 22207561 |
| cd4 count is associated with postoperative infection in patients with orthopaedic trauma who are hiv positive. | background: since the advent of effective antiretroviral therapy, the number of people with aids has increased and a certain percentage of these patients will require emergent orthopaedic surgery. little is known regarding orthopaedic infections and the association of cd4 counts with postoperative infection in patients with hiv infection who experience orthopaedic trauma. questions/purposes: we questioned whether ... | 2011 | 22207561 |
| complete genome sequence of "enterobacter lignolyticus" scf1. | in an effort to discover anaerobic bacteria capable of lignin degradation, we isolated "enterobacter lignolyticus" scf1 on minimal media with alkali lignin as the sole source of carbon. this organism was isolated anaerobically from tropical forest soils collected from the short cloud forest site in the el yunque national forest in puerto rico, usa, part of the luquillo long-term ecological research station. at this site, the soils experience strong fluctuations in redox potential and are net met ... | 2011 | 22180812 |
| a conserved rpos-dependent small rna controls the synthesis of major porin ompd. | a remarkable feature of many small non-coding rnas (srnas) of escherichia coli and salmonella is their accumulation in the stationary phase of bacterial growth. several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific srnas, but a widely conserved srna gene that is controlled by the major stationary phase and stress sigma factor, σ(s) (rpos), has remained elusive. we have studied in salmonella the conserved sdsr srna, previo ... | 2011 | 22180532 |
| a conserved rpos-dependent small rna controls the synthesis of major porin ompd. | a remarkable feature of many small non-coding rnas (srnas) of escherichia coli and salmonella is their accumulation in the stationary phase of bacterial growth. several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific srnas, but a widely conserved srna gene that is controlled by the major stationary phase and stress sigma factor, σ(s) (rpos), has remained elusive. we have studied in salmonella the conserved sdsr srna, previo ... | 2011 | 22180532 |
| diversity of extended-spectrum ?-lactamase-producing enterobacteriaceae on hospital admission. | abstract extended-spectrum ?-lactamase (esbl)-producing enterobacteriaceae have become prevalent in both the hospital and the community. we describe the epidemiology of esbl-producing isolates and patient characteristics at hospital admission. data on clinical properties, medical history, previous hospitalizations, and previous antibiotic treatments were collected. esbl genes (bla(ctx-m), bla(tem), and bla(shv)) were identified by polymerase chain reaction. one hundred and sixteen patients car ... | 2011 | 22066775 |
| the escherichia coli mntr miniregulon includes genes encoding a small protein and an efflux pump required for manganese homeostasis. | manganese is a critical micronutrient for cells, serving as an enzyme cofactor and protecting against oxidative stress. yet, manganese is toxic in excess and little is known about its distribution in cells. bacteria control intracellular manganese levels by the transcription regulator mntr. when this work began, the only escherichia coli k-12 gene known to respond to manganese via mntr repression was mnth, which encodes a manganese importer. we show that mnts (formerly the small rna gene ryba) i ... | 2011 | 21908668 |
| the metj regulon in gammaproteobacteria determined by comparative genomics methods. | whole-genome sequencing of bacteria has proceeded at an exponential pace but annotation validation has lagged behind. for instance, the metj regulon, which controls methionine biosynthesis and transport, has been studied almost exclusively in e. coli and salmonella, but homologs of metj exist in a variety of other species. these include some that are pathogenic (e.g. yersinia) and some that are important for environmental remediation (e.g. shewanella) but many of which have not been extensively ... | 2011 | 22082356 |
| The Repeat-In-Toxin (RTX) Family Member TosA Mediates Adherence of Uropathogenic Escherichia coli and Survival during Bacteremia. | Uropathogenic Escherichia coli (UPEC) are responsible for the majority of uncomplicated urinary tract infections (UTI) and represent the most common bacterial infection in adults. UPEC utilize a wide range of virulence factors to colonize the host, including the novel repeat-in-toxin (RTX) protein TosA, which is specifically expressed in the host urinary tract and contributes significantly to the virulence and survival of UPEC. tosA, found in strains within the B2 phylogenetic subgroup of E. col ... | 2011 | 22083710 |
| Detection of Citrobacter koseri carrying beta-lactamase KPC-2 in a hospitalised patient, Greece, July 2011. | This report describes the detection of Citrobacter koseri carrying K. pneumoniae carbapenemase (KPC-2) isolated in July 2011 from a Greek patient, who was also colonised by a Klebsiella pneumoniae strain coproducing KPC-2 and Verona integron-encoded metallo-beta-lactamase (VIM)-1. | 2011 | 22008199 |
| recombination in is26 and tn2 in the evolution of multiresistance regions carrying blactx-m-15 on conjugative incf plasmids from escherichia coli. | ctx-m-15 now appears to be the dominant extended-spectrum β-lactamase worldwide, and a number of different factors may contribute to this success. these include associations between bla(ctx-m-15) and particular plasmids (incf) and/or strains, such as escherichia coli st131, as well as the genetic contexts in which this gene is found. we previously identified bla(ctx-m-15) as the dominant esbl gene in the western sydney area, australia, and found that it was carried mainly on incf or inci1 plasmi ... | 2011 | 21859935 |
| late-onset citrobacter koseri endophthalmitis with suture exposure after secondary intraocular lens implantation. | a 54-year-old male patient was seen in clinic for ocular pain and decreased vision in the right eye with duration of two days. he underwent a cataract operation for his right eye 12 years ago, then a sclera-fixated secondary intraocular implantation and pars plana vitrectomy three years ago due to intraocular lens dislocation. at the initial visit, his visual acuity was restricted to the perception of hand motion. an edematous cornea, cells, flare with hypopyon, and exposed suture material at we ... | 2011 | 21860579 |
| Antibacterial activity of selected medicinal plants against multiple antibiotic resistant uropathogens: a study from Kolli Hills, Tamil Nadu, India. | The increasing incidence of antibiotic resistance among bacterial pathogens necessitates medicinal plants as an alternate therapy in restricting the resistant infectious organisms. In this primitive study, the antibiotic resistance of organisms isolated from urinary tract infected patients was evaluated using the National Committee for Clinical Laboratory Standards (NCCLS) method and Multiple Antibiotic Resistance (MAR) index values, and the MAR values was also calculated for plant extracts. The ... | 2011 | 21986363 |
| integrated analysis of three bacterial conjunctivitis trials of besifloxacin ophthalmic suspension, 0.6%: etiology of bacterial conjunctivitis and antibacterial susceptibility profile. | the purpose of this paper is to report on the bacterial species isolated from patients with bacterial conjunctivitis participating in three clinical trials of besifloxacin ophthalmic suspension, 0.6%, and their in vitro antibacterial susceptibility profiles. | 2011 | 22034556 |
| prevalence of bacterial pathogens in aseer region, kingdom of saudi arabia: emphasis on antimicrobial susceptibility of staphylococcus aureus. | this short study aims to determine the prevalence of various bacterial pathogens causing infections in the aseer regions, and to also assess the distribution of staphylococcus aureus in relation to different body sites as well as their in vitro antimicrobial susceptibility profile. | 2011 | 22216389 |
| first comprehensive evaluation of the m.i.c. evaluator device for aerobic gram-positive and gram-negative bacterial species compared to etest and clsi broth micro-dilution. | the m.i.c.evaluator™ strip (thermo fisher scientific, basingstoke, uk) uses similar methodology to etest. in this first assessment of the m.i.c.evaluator device, 409 strains of aerobic gram-positive bacteria (staphylococci, streptococci and enterococci) and 325 strains of enterobacteriaceae, pseudomonas species and acinetobacter species, were tested by m.i.c.evaluator strip, etest and by broth micro-dilution as a reference standard. the gram-positives included staphylococci (mrsa, mssa and cns), ... | 2012 | 22238441 |
| pcr detection and identification of histamine-forming bacteria in filleted tuna fish samples. | total of 14 filleted yellowfin tuna fish (thunnus albacares) sold in wholesale fish market and supermarkets in milan, italy, were purchased and tested to determine microbial count, histamine level, histamine-forming bacteria, and their ability to produce histamine in culture broth. although histamine level was less than 10 ppm, many samples showed high total viable bacterial and enterobacterial counts that reached dangerous levels after temperature abuse for short periods of time. a pcr assay ta ... | 2012 | 22251187 |
| bugs on film: the presence of bacterial rods (citrobacter koseri) on a routine blood film in a septic immunocompromised patient with a femoral vein line. | | 2011 | 22234128 |
| characterization and purification of a bacteriocin from lactobacillus paracasei subsp. paracasei bmk2005, an intestinal isolate active against multidrug-resistant pathogens. | a strain of lactobacillus paracasei subsp. paracasei bmk2005 isolated from healthy infant faeces has shown a remarkable antibacterial activity against 32 bacterial pathogenic strains of human clinical isolates. among them, 13 strains belonging to species of escherichia coli, citrobacter freundii, citrobacter diversus, klebsiella oxytoca, enterobacter cloacae and pseudomonas aeruginosa were resistant to cefotaxime (ctx) and ceftazidime (caz), and 4 strains of staphylococcus aureus were resistant ... | 2011 | 22805936 |
| modified hodge test: a simple and effective test for detection of carbapenemase production. | resistance among bacterial isolates is the leading cause of increased mortality and morbidity worldwide. carbapenems once thought to be effective are becoming ineffective mostly due to the emergence of carbapenemase. this study was designed to determine in vitro efficacy of modified hodge test for detection of carbapenemase production in gram negative rods. | 2011 | 22530087 |
| staphylococcus aureus- the predominant pathogen in the neonatal icu of a tertiary care hospital in amritsar, india. | background: an early treatment and the appropriate and the rational use of antibiotics would minimize the risk of severe morbidity and mortality in neonatal sepsis, and reduce the emergence of multi-drug resistant organisms in intensive care units. for the success of an early empiric treatment, a periodic review of the cases to assess any changing trends in the infecting organisms and their antimicrobial susceptibility is important. | 2012 | 23450439 |
| staphylococcus aureus- the predominant pathogen in the neonatal icu of a tertiary care hospital in amritsar, india. | background: an early treatment and the appropriate and the rational use of antibiotics would minimize the risk of severe morbidity and mortality in neonatal sepsis, and reduce the emergence of multi-drug resistant organisms in intensive care units. for the success of an early empiric treatment, a periodic review of the cases to assess any changing trends in the infecting organisms and their antimicrobial susceptibility is important. | 2012 | 23450439 |
| a universal method for the identification of bacteria based on general pcr primers. | the universal method (um) described here will allow the detection of any bacterial rdna leading to the identification of that bacterium. the method should allow prompt and accurate identification of bacteria. the principle of the method is simple; when a pure pcr product of the 16s gene is obtained, sequenced, and aligned against bacterial dna data base, then the bacterium can be identified. confirmation of identity may follow. in this work, several general 16s primers were designed, mixed and a ... | 2011 | 23024404 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes. | for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ... | 2016 | 26511485 |
| annotation of protein domains reveals remarkable conservation in the functional make up of proteomes across superkingdoms. | the functional repertoire of a cell is largely embodied in its proteome, the collection of proteins encoded in the genome of an organism. the molecular functions of proteins are the direct consequence of their structure and structure can be inferred from sequence using hidden markov models of structural recognition. here we analyze the functional annotation of protein domain structures in almost a thousand sequenced genomes, exploring the functional and structural diversity of proteomes. we find ... | 2011 | 24710297 |
| three decades of beta-lactamase inhibitors. | since the introduction of penicillin, beta-lactam antibiotics have been the antimicrobial agents of choice. unfortunately, the efficacy of these life-saving antibiotics is significantly threatened by bacterial beta-lactamases. beta-lactamases are now responsible for resistance to penicillins, extended-spectrum cephalosporins, monobactams, and carbapenems. in order to overcome beta-lactamase-mediated resistance, beta-lactamase inhibitors (clavulanate, sulbactam, and tazobactam) were introduced in ... | 2010 | 20065329 |
| 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 |
| experimental and natural infections in myd88- and irak-4-deficient mice and humans. | most toll-like-receptors (tlrs) and interleukin-1 receptors (il-1rs) signal via myeloid differentiation primary response 88 (myd88) and interleukin-1 receptor-associated kinase 4 (irak-4). the combined roles of these two receptor families in the course of experimental infections have been assessed in myd88- and irak-4-deficient mice for almost fifteen years. these animals have been shown to be susceptible to 46 pathogens: 27 bacteria, eight viruses, seven parasites, and four fungi. humans with i ... | 2012 | 23255009 |
| abstracts from the 37th annual meeting of the society of general internal medicine, 2014, san diego, ca, usa. | | 2014 | 24737224 |
| nitrate and periplasmic nitrate reductases. | the nitrate anion is a simple, abundant and relatively stable species, yet plays a significant role in global cycling of nitrogen, global climate change, and human health. although it has been known for quite some time that nitrate is an important species environmentally, recent studies have identified potential medical applications. in this respect the nitrate anion remains an enigmatic species that promises to offer exciting science in years to come. many bacteria readily reduce nitrate to nit ... | 2014 | 24141308 |
| individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology. | for bacteria, replication mainly involves growth by binary fission. however, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. they thereby evade detection by conventional culture-based methods. such dormant cells may also be observed in laboratory cultures and in clinical microbiology. they are usually more tolerant to s ... | 2015 | 26629334 |
| comparison of pcr/electron spray ionization-time-of-flight-mass spectrometry versus traditional clinical microbiology for active surveillance of organisms contaminating high-use surfaces in a burn intensive care unit, an orthopedic ward and healthcare workers. | understanding nosocomial pathogen transmission is restricted by culture limitations. novel platforms, such as pcr-based electron spray ionization-time-of-flight-mass spectrometry (esi-tof-ms), may be useful as investigational tools. | 2012 | 23050585 |
| prevalence of porphyromonas gingivalis four rag locus genotypes in patients of orthodontic gingivitis and periodontitis. | porphyromonas gingivalis is considered as a major etiological agent in periodontal diseases and implied to result in gingival inflammation under orthodontic appliance. rag locus is a pathogenicity island found in porphyromonas gingivalis. four rag locus variants are different in pathogenicity of porphyromonas gingivalis. moreover, there are different racial and geographic differences in distribution of rag locus genotypes. in this study, we assessed the prevalence of porphyromonas gingivalis and ... | 2013 | 23593379 |
| bacterial syntenies: an exact approach with gene quorum. | the automatic identification of syntenies across multiple species is a key step in comparative genomics that helps biologists shed light both on evolutionary and functional problems. | 2011 | 21605461 |
| unexploited opportunities for phage therapy. | | 2015 | 26441644 |
| directed networks reveal genomic barriers and dna repair bypasses to lateral gene transfer among prokaryotes. | lateral gene transfer (lgt) plays a major role in prokaryote evolution with only a few genes that are resistant to it; yet the nature and magnitude of barriers to lateral transfer are still debated. here, we implement directed networks to investigate donor-recipient events of recent lateral gene transfer among 657 sequenced prokaryote genomes. for 2,129,548 genes investigated, we detected 446,854 recent lateral gene transfer events through nucleotide pattern analysis. among these, donor-recipien ... | 2011 | 21270172 |
| 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 |
| comparison of the microflex lt and vitek ms systems for routine identification of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry. | this study compared the performance of three matrix-assisted laser desorption ionization-time of flight mass spectrometry systems: microflex lt (bruker daltonics, bremen, germany), vitek ms ruo (axima assurance-saramis database; biomérieux, marcy l'etoile, france), and vitek ms ivd (biomérieux). a total of 1,129 isolates, including 1,003 routine isolates, 73 anaerobes, and 53 bacterial enteropathogens, were tested on the microflex lt and axima assurance devices. the spectra were analyzed using t ... | 2012 | 22322345 |
| detection of campylobacter species and arcobacter butzleri in stool samples by use of real-time multiplex pcr. | the presence of campylobacter (or campylobacter-like) species in stools from patients suspected of infectious gastroenteritis (n = 493) was investigated using real-time pcr for detection of arcobacter butzleri (hsp60 gene), campylobacter coli (ceue gene), campylobacter jejuni (mapa), five acknowledged pathogenic campylobacter spp. (c16s_lund assay), and the campylobacter genus (c16s_lvi assay). in total, 71.4% of the samples were positive for campylobacter dna (n = 352) by a campylobacter genus- ... | 2013 | 23152553 |
| aminoglycoside modifying enzymes. | aminoglycosides have been an essential component of the armamentarium in the treatment of life-threatening infections. unfortunately, their efficacy has been reduced by the surge and dissemination of resistance. in some cases the levels of resistance reached the point that rendered them virtually useless. among many known mechanisms of resistance to aminoglycosides, enzymatic modification is the most prevalent in the clinical setting. aminoglycoside modifying enzymes catalyze the modification at ... | 2010 | 20833577 |
| performances of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology. | rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms)-based systems will replace conventional phenotypic methods for routine identification of bacteria. we report here the first evaluation of the new maldi-tof ms-based vitek ms system in a large clinical microbiology laboratory. this system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. we have te ... | 2012 | 22593596 |
| rectal swabs are suitable for quantifying the carriage load of kpc-producing carbapenem-resistant enterobacteriaceae. | it is more convenient and practical to collect rectal swabs than stool specimens to study carriage of colon pathogens. in this study, we examined the ability to use rectal swabs rather than stool specimens to quantify klebsiella pneumoniae carbapenemase (kpc)-producing carbapenem-resistant enterobacteriaceae (cre). we used a quantitative real-time pcr (qpcr) assay to determine the concentration of the bla(kpc) gene relative to the concentration of 16s rrna genes and a quantitative culture-based ... | 2013 | 23295937 |
| some bacteria degrade explosives, others prefer boiling methanol. | | 2007 | 17991022 |
| mechanism of action of and resistance to quinolones. | fluoroquinolones are an important class of wide-spectrum antibacterial agents. the first quinolone described was nalidixic acid, which showed a narrow spectrum of activity. the evolution of quinolones to more potent molecules was based on changes at positions 1, 6, 7 and 8 of the chemical structure of nalidixic acid. quinolones inhibit dna gyrase and topoisomerase iv activities, two enzymes essential for bacteria viability. the acquisition of quinolone resistance is frequently related to (i) chr ... | 2008 | 21261881 |
| mechanism of action of and resistance to quinolones. | fluoroquinolones are an important class of wide-spectrum antibacterial agents. the first quinolone described was nalidixic acid, which showed a narrow spectrum of activity. the evolution of quinolones to more potent molecules was based on changes at positions 1, 6, 7 and 8 of the chemical structure of nalidixic acid. quinolones inhibit dna gyrase and topoisomerase iv activities, two enzymes essential for bacteria viability. the acquisition of quinolone resistance is frequently related to (i) chr ... | 2008 | 21261881 |
| comparison of bruker biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometer to bd phoenix automated microbiology system for identification of gram-negative bacilli. | we compared the bd phoenix automated microbiology system to the bruker biotyper (version 2.0) matrix-assisted laser desorption ionization-time of flight (maldi-tof) mass spectrometry (ms) system for identification of gram-negative bacilli, using biochemical testing and/or genetic sequencing to resolve discordant results. the bd phoenix correctly identified 363 (83%) and 330 (75%) isolates to the genus and species level, respectively. the bruker biotyper correctly identified 408 (93%) and 360 (82 ... | 2011 | 21209160 |
| prospective evaluation of a matrix-assisted laser desorption ionization-time of flight mass spectrometry system in a hospital clinical microbiology laboratory for identification of bacteria and yeasts: a bench-by-bench study for assessing the impact on time to identification and cost-effectiveness. | matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) has been found to be an accurate, rapid, and inexpensive method for the identification of bacteria and yeasts. previous evaluations have compared the accuracy, time to identification, and costs of the maldi-tof ms method against standard identification systems or commercial panels. in this prospective study, we compared a protocol incorporating maldi-tof ms (maldi protocol) with the current standard ident ... | 2012 | 22855510 |
| production of organic acids by probiotic lactobacilli can be used to reduce pathogen load in poultry. | probiotic lactobacillus can be used to reduce the colonization of pathogenic bacteria in food animals, and therefore reduce the risk of foodborne illness to consumers. as a model system, we examined the mechanism of protection conferred by lactobacillus species to inhibit c. jejuni growth in vitro and reduce colonization in broiler chickens. possible mechanisms for the reduction of pathogens by lactobacilli include: 1) stimulation of adaptive immunity; 2) alteration of the cecal microbiome; and, ... | 2012 | 22962594 |
| development of a broad-range 23s rdna real-time pcr assay for the detection and quantification of pathogenic bacteria in human whole blood and plasma specimens. | molecular methods are important tools in the diagnosis of bloodstream bacterial infections, in particular in patients treated with antimicrobial therapy, due to their quick turn-around time. here we describe a new broad-range real-time pcr targeting the 23s rdna gene and capable to detect as low as 10 plasmid copies per reaction of targeted bacterial 23s rdna gene. two commercially available dna extraction kits were evaluated to assess their efficiency for the extraction of plasma and whole bloo ... | 2013 | 23586027 |
| host-specific induction of escherichia coli fitness genes during human urinary tract infection. | uropathogenic escherichia coli (upec) is the predominant etiological agent of uncomplicated urinary tract infection (uti), manifested by inflammation of the urinary bladder, in humans and is a major global public health concern. molecular pathogenesis of upec has been primarily examined using murine models of uti. translational research to develop novel therapeutics against this major pathogen, which is becoming increasingly antibiotic resistant, requires a thorough understanding of mechanisms i ... | 2014 | 25489107 |
| real-time comparative evaluation of biomerieux vitek ms versus bruker microflex ms, two matrix-assisted laser desorption-ionization time-of-flight mass spectrometry systems, for identification of clinically significant bacteria. | matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (maldi-tof ms) recently became available for the identification of bacteria in routine diagnostic laboratories. it is rapid and cost-effective and likely to replace phenotypic identification. this study was undertaken to compare two maldi-tof ms-based, bruker microflex ms (bms) and vitek ms (vms) systems, for identification (id) of clinically significant bacterial isolates. clinically relevant broad diversity of bacteri ... | 2014 | 25433488 |
| evaluation of three rapid diagnostic methods for direct identification of microorganisms in positive blood cultures. | the identification of organisms from positive blood cultures generally takes several days. however, recently developed rapid diagnostic methods offer the potential for organism identification within only a few hours of blood culture positivity. in this study, we evaluated the performance of three commercial methods to rapidly identify organisms directly from positive blood cultures: quickfish (advandx, wolburn, ma), verigene gram-positive blood culture (bc-gp; nanosphere, northbrook, il), and ma ... | 2014 | 24808235 |
| a qpcr assay to detect and quantify shiga toxin-producing e. coli (stec) in cattle and on farms: a potential predictive tool for stec culture-positive farms. | shiga toxin-producing e. coli (stec), of various serogroups harboring the intimin gene, form a serious threat to human health. they are asymptomatically carried by cattle. in this study, a quantitative real-time pcr (qpcr) method was developed as a molecular method to detect and quantify shiga toxin genes stx1 and stx2 and the intimin gene eae. subsequently, 59 fecal samples from six farms were tested using qpcr and a culture method as a reference. three farms had contaminated animals as demonst ... | 2014 | 24681714 |
| the arable ecosystem as battleground for emergence of new human pathogens. | disease incidences related to escherichia coli and salmonella enterica infections by consumption of (fresh) vegetables, sprouts, and occasionally fruits made clear that these pathogens are not only transmitted to humans via the "classical" routes of meat, eggs, and dairy products, but also can be transmitted to humans via plants or products derived from plants. nowadays, it is of major concern that these human pathogens, especially the ones belonging to the taxonomical family of enterobacteriace ... | 2014 | 24688484 |
| dysbiosis of the gut microbiota in disease. | there is growing evidence that dysbiosis of the gut microbiota is associated with the pathogenesis of both intestinal and extra-intestinal disorders. intestinal disorders include inflammatory bowel disease, irritable bowel syndrome (ibs), and coeliac disease, while extra-intestinal disorders include allergy, asthma, metabolic syndrome, cardiovascular disease, and obesity. | 2015 | 25651997 |
| recent advances in screening of anti-campylobacter activity in probiotics for use in poultry. | campylobacteriosis is the most common cause of bacterial gastroenteritis worldwide. campylobacter species involved in this infection usually include the thermotolerant species campylobacter jejuni. the major reservoir for c. jejuni leading to human infections is commercial broiler chickens. poultry flocks are frequently colonized by c. jejuni without any apparent symptoms. risk assessment analyses have identified the handling and consumption of poultry meat as one of the most important sources o ... | 2016 | 27303366 |
| optimized use of the maldi biotyper system and the filmarray bcid panel for direct identification of microbial pathogens from positive blood cultures. | despite the current reliance on blood cultures (bcs), the diagnosis of bloodstream infections (bsis) can be sped up using new technologies performed directly on positive bc bottles. two methods (the maldi biotyper system and filmarray blood culture identification [bcid] panel) are potentially applicable. in this study, we performed a large-scale clinical evaluation (1,585 microorganisms from 1,394 bsi episodes) on the combined use of the maldi biotyper and filmarray bcid panel compared to a refe ... | 2016 | 26677254 |
| principles and applications of methods for dna-based typing of microbial organisms. | | 1999 | 10325304 |
| adhesins involved in attachment to abiotic surfaces by gram-negative bacteria. | during the first step of biofilm formation, initial attachment is dictated by physicochemical and electrostatic interactions between the surface and the bacterial envelope. depending on the nature of these interactions, attachment can be transient or permanent. to achieve irreversible attachment, bacterial cells have developed a series of surface adhesins promoting specific or nonspecific adhesion under various environmental conditions. this article reviews the recent advances in our understandi ... | 2015 | 26350310 |
| microbial source tracking in adjacent karst springs. | modern man-made environments, including urban, agricultural, and industrial environments, have complex ecological interactions among themselves and with the natural surroundings. microbial source tracking (mst) offers advanced tools to resolve the host source of fecal contamination beyond indicator monitoring. this study was intended to assess karst spring susceptibilities to different fecal sources using mst quantitative pcr (qpcr) assays targeting human, bovine, and swine markers. it involved ... | 2015 | 26002893 |
| ethanolamine utilization in vibrio alginolyticus. | ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ... | 2012 | 23234435 |
| biofilm formation protects escherichia coli against killing by caenorhabditis elegans and myxococcus xanthus. | enteric bacteria, such as escherichia coli, are exposed to a variety of stresses in the nonhost environment. the development of biofilms provides e. coli with resistance to environmental insults, such as desiccation and bleach. we found that biofilm formation, specifically production of the matrix components curli and cellulose, protected e. coli against killing by the soil-dwelling nematode caenorhabditis elegans and the predatory bacterium myxococcus xanthus. additionally, matrix-encased bacte ... | 2014 | 25192998 |
| the phosphopantetheinyl transferases: catalysis of a post-translational modification crucial for life. | covering: up to 2013. although holo-acyl carrier protein synthase, acps, a phosphopantetheinyl transferase (pptase), was characterized in the 1960s, it was not until the publication of the landmark paper by lambalot et al. in 1996 that pptases garnered wide-spread attention being classified as a distinct enzyme superfamily. in the past two decades an increasing number of papers have been published on pptases ranging from identification, characterization, structure determination, mutagenesis, inh ... | 2014 | 24292120 |
| characterization of a novel chaperone/usher fimbrial operon present on kpgi-5, a methionine trna gene-associated genomic island in klebsiella pneumoniae. | several strain-specific klebsiella pneumoniae virulence determinants have been described, though these have almost exclusively been linked with hypervirulent liver abscess-associated strains. through pcr interrogation of integration hotspots, chromosome walking, island-tagging and fosmid-based marker rescue we captured and sequenced kpgi-5, a novel genomic island integrated into the met56 trna gene of k. pneumoniae kr116, a bloodstream isolate from a patient with pneumonia and neutropenic sepsis ... | 2012 | 22520965 |
| natural products genomics. | | 2008 | 21261848 |
| describing the structural robustness landscape of bacterial small rnas. | the potential role of rna molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes. | 2012 | 22500888 |
| seasonally variable intestinal metagenomes of the red palm weevil (rhynchophorus ferrugineus). | the intestinal microbes residing in the red palm weevil (rpw, rhynchophorus ferrugineus) larva consume tender interior fibrous tissues of date palm trunks. the understanding of such microbiota at molecular level provides vital clues for the biological control of this devastating pest. using pyrosequencing and shotgun strategy, we first study taxonomic profiles of the microbiota sampled at different months (march, july and november), and then confirm the impact of high-temperature stress on the m ... | 2013 | 24102776 |
| parallel histories of horizontal gene transfer facilitated extreme reduction of endosymbiont genomes in sap-feeding insects. | bacteria confined to intracellular environments experience extensive genome reduction. in extreme cases, insect endosymbionts have evolved genomes that are so gene-poor that they blur the distinction between bacteria and endosymbiotically derived organelles such as mitochondria and plastids. to understand the host's role in this extreme gene loss, we analyzed gene content and expression in the nuclear genome of the psyllid pachypsylla venusta, a sap-feeding insect that harbors an ancient endosym ... | 2014 | 24398322 |
| control of the escherichia coli sialoregulon by transcriptional repressor nanr. | nanr, one of >8,500 gntr superfamily helix-turn-helix transcriptional regulators, controls expression of the genes required for catabolism of sialic acids in escherichia coli. it is predicted to do the same in related bacteria harboring orthologs of nanr. the sialic acids are a family of over 40 naturally occurring nine-carbon keto-sugar acids found mainly in the animal lineage, which includes starfish to humans in the deuterostome lineage. sialic acids function in development, immunity, protein ... | 2013 | 23935044 |
| strategies used by bacteria to grow in macrophages. | intracellular bacteria are often clinically relevant pathogens that infect virtually every cell type found in host organisms. however, myeloid cells, especially macrophages, constitute the primary cells targeted by most species of intracellular bacteria. paradoxically, macrophages possess an extensive antimicrobial arsenal and are efficient at killing microbes. in addition to their ability to detect and signal the presence of pathogens, macrophages sequester and digest microorganisms using the p ... | 2016 | 27337444 |