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epidemiology and resistance patterns of bacterial and fungal colonization of biliary plastic stents: a prospective cohort study.plastic stents used for the treatment of biliary obstruction will become occluded over time due to microbial colonization and formation of biofilms. treatment of stent-associated cholangitis is often not effective because of inappropriate use of antimicrobial agents or antimicrobial resistance. we aimed to assess the current bacterial and fungal etiology of stent-associated biofilms, with particular emphasis on antimicrobial resistance.201627171497
the novel kasugamycin 2'-n-acetyltransferase gene aac(2')-iia, carried by the incp island, confers kasugamycin resistance to rice-pathogenic bacteria.kasugamycin (ksm), a unique aminoglycoside antibiotic, has been used in agriculture for many years to control not only rice blast caused by the fungus magnaporthe grisea but also rice bacterial grain and seedling rot or rice bacterial brown stripe caused by burkholderia glumae or acidovorax avenae subsp. avenae, respectively. since both bacterial pathogens are seed-borne and cause serious injury to rice seedlings, the emergence of ksm-resistant b. glumae and a. avenae isolates highlights the urg ...201222660700
characterization of acrd, a resistance-nodulation-cell division-type multidrug efflux pump from the fire blight pathogen erwinia amylovora.multidrug efflux pumps are membrane translocases that have the ability to extrude a variety of structurally unrelated compounds from the cell. acrd, a resistance-nodulation-cell division (rnd) transporter, was shown to be involved in efflux of highly hydrophilic aminoglycosides and a limited number of amphiphilic compounds in e. coli. here, a homologue of acrd in the plant pathogen and causal agent of fire blight disease erwinia amylovora was identified.201424443882
direct capture technologies for genomics-guided discovery of natural products.microbes are important producers of natural products, which have played key roles in understanding biology and treating disease. however, the full potential of microbes to produce natural products has yet to be realized; the overwhelming majority of natural product gene clusters encoded in microbial genomes remain "cryptic", and have not been expressed or characterized. in contrast to the fast-growing number of genomic sequences and bioinformatic tools, methods to connect these genes to natural ...201626456469
the gut microbiota of larvae of rhynchophorus ferrugineus oliver (coleoptera: curculionidae).the red palm weevil (rpw) rhynchophorus ferrugineus olivier (coleoptera: curculionidae) is one of the major pests of palms. the larvae bore into the palm trunk and feed on the palm tender tissues and sap, leading the host tree to death. the gut microbiota of insects plays a remarkable role in the host life and understanding the relationship dynamics between insects and their microbiota may improve the biological control of insect pests. the purpose of this study was to analyse the diversity of t ...201424884866
aerobic bacterial microflora of broad-snouted caiman (caiman latirostris) oral cavity and cloaca, originating from parque zoológico arruda câmara, paraíba, brazil.the objective of this study was to isolate and identify the aerobic bacterial microflora from the oral cavity mucosa and cloaca's samples, collected from broad-snouted caiman (caiman latirostris), born and bred in captivity at parque zoológico arruda câmara, joão pessoa, paraíba, brazil. the most common bacteria were staphylococcus sp. (14.74%), corynebacterium sp. (13.68%), escherichia coli (13.68%) and shigella sp.(11.58%), and the less common were citrobacter sp. (1.05%), klebsiella pneumonia ...200924031343
human gut microbes use multiple transporters to distinguish vitamin b₁₂ analogs and compete in the gut.genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. whether these predictions reflect actual functional redundancies is unclear. we report that the prominent human gut symbiont bacteroides thetaiotaomicron employs three functional, homologous vitamin b₁₂ transporters that in at least two cases confer a competitive advantage in the presence of distinct b₁₂ analogs (corrinoids). ...201424439897
dissecting the metal selectivity of merr monovalent metal ion sensors in salmonella.two homologous transcription factors, cuer and gols, that belong to the merr metalloregulatory family are responsible for salmonella cu and au sensing and resistance, respectively. they share similarities not only in their sequences, but also in their target transcription binding sites. while cuer responds similarly to au, ag, or cu to induce the expression of its target genes, gols shows higher activation by au than by ag or cu. we showed that the ability of gols to distinguish au from cu resid ...201323645605
risk factors to predict drug-resistant pathogens in hemodialysis-associated pneumonia.after the concept of healthcare associated pneumonia (hcap) was introduced in 2005 by the american thoracic society/infectious disease society of america (ats/idsa), pneumonia in hemodialysis patients has been classified as hcap. even though there are several risk factors and scoring systems of drug-resistant pathogens (drps) in hcap, the risk factors for drps in hemodialysis-associated pneumonia are unclear.201627502599
evaluation of a plastic nonvented aerobic blood culture bottle for use with the bact/alert microbial detection system.the current bact/alert sa (bta sa) aerobic blood culture bottle is made from glass, does not require venting, and contains a liquid emulsion sensor (les). its performance has been shown to be equivalent to that of the vented standard aerobic culture bottle. a further-improved version of the bta sa bottle, designated the bact/alert plastic sa (bta psa) culture bottle, is made from clear plastic to prevent breakage, does not require venting, and contains a modified les (les 2) to reduce the possib ...200212454188
procalcitonin as a marker of bacterial infection in the emergency department: an observational study.procalcitonin (pct) has been proposed as a marker of infection in critically ill patients; its level is related to the severity of infection. we evaluated the value of pct as a marker of bacterial infection for emergency department patients.200314975050
procalcitonin as a marker of bacterial infection in the emergency department: an observational study.procalcitonin (pct) has been proposed as a marker of infection in critically ill patients; its level is related to the severity of infection. we evaluated the value of pct as a marker of bacterial infection for emergency department patients.200314975050
computer-assisted surveillance for detecting clonal outbreaks of nosocomial infection.whole-house surveillance for healthcare-associated infection is no longer the recommended practice because of the large personnel time investment required. we developed a computer-based tracking system using microbiologic data as an aid in detecting potential outbreaks of healthcare-associated infections on a hospital-wide basis. monthly total isolates of 25 clinically significant hospital pathogens were tallied from 1991 to 1998 to form a database for future comparison. two different algorithm ...200415004070
inferring ancient metabolism using ancestral core metabolic models of enterobacteria.enterobacteriaceae diversified from an ancestral lineage ~300-500 million years ago (mya) into a wide variety of free-living and host-associated lifestyles. nutrient availability varies across niches, and evolution of metabolic networks likely played a key role in adaptation.201323758866
genetic variation among endosymbionts of widely distributed vestimentiferan tubeworms.vestimentiferan tubeworms thriving in sulfidic deep-sea hydrothermal vents and cold seeps are constrained by their nutritional reliance on chemoautotrophic endosymbionts. in a recent phylogenetic study using 16s ribosomal dna, we found that endosymbionts from vent and seep habitats form two distinct clades with little variation within each clade. in the present study, we used two different approaches to assess the genetic variation among biogeographically distinct vestimentiferan symbionts. dna ...200010653731
flagella from five cronobacter species induce pro-inflammatory cytokines in macrophage derivatives from human monocytes.cronobacter spp. are opportunistic pathogens linked to lie-threatening infections in neonates and contaminated powdered infant formula that has been epidemiologically associated with these cases. clinical symptoms of cronobacter include necrotizing enterocolitis, bacteremia, and meningitis. flagella from c. sakazakii are involved in biofilm formation and its adhesion to epithelial cells. we investigated the role of flagella from c. sakazakii st1 and st4, c. malonaticus, c. muytjensii, c. turicen ...201223284883
expert systems in clinical microbiology.this review aims to discuss expert systems in general and how they may be used in medicine as a whole and clinical microbiology in particular (with the aid of interpretive reading). it considers rule-based systems, pattern-based systems, and data mining and introduces neural nets. a variety of noncommercial systems is described, and the central role played by the eucast is stressed. the need for expert rules in the environment of reset eucast breakpoints is also questioned. commercial automated ...201121734247
comparison of nine phenotypic methods for detection of extended-spectrum beta-lactamase production by enterobacteriaceae.the detection of extended-spectrum β-lactamase-producing (esbl) bacteria is of importance for infection control and epidemiological surveillance. we aimed to compare phenotypic methods available in the routine laboratory and to evaluate two-step strategies using these methods for the detection of esbl-positive enterobacteriaceae. two methods used for routine susceptibility testing (vitek2 and disk diffusion methods) and seven methods designed for the detection of esbl production (esbl etests, co ...201121248086
whole-genome sequencing and identification of morganella morganii kt pathogenicity-related genes.the opportunistic enterobacterium, morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at changhua christian hospital, taiwan. the kt strain of m. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. m. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of th ...201223282187
admission surveillance cultures among patients admitted to intensive care unit. 201223272308
evaluation of the merlin micronaut system for rapid direct susceptibility testing of gram-positive cocci and gram-negative bacilli from positive blood cultures.bloodstream infections are life-threatening conditions which require the timely initiation of appropriate antimicrobial therapy. we evaluated the automated merlin micronaut system for rapid direct microtiter broth antimicrobial susceptibility testing (ast) of gram-positive cocci and gram-negative bacilli from bactec 9240 bottles with positive blood cultures in comparison to the standard method for the merlin micronaut system. this prospective study was conducted under routine working conditions ...200717202283
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.201019825784
epidemiology and genetics of ctx-m extended-spectrum β-lactamases in gram-negative bacteria.ctx-m enzymes, the plasmid-mediated cefotaximases, constitute a rapidly growing family of extended-spectrum β-lactamases (esbls) with significant clinical impact. ctx-ms are found in at least 26 bacterial species, particularly in escherichia coli, klebsiella pneumoniae and proteus mirabilis. at least 109 members in ctx-m family are identified and can be divided into seven clusters based on their phylogeny. ctx-m-15 and ctx-m-14 are the most dominant variants. chromosome-encoded intrinsic cefotax ...201222697133
epidemiology and genetics of ctx-m extended-spectrum β-lactamases in gram-negative bacteria.ctx-m enzymes, the plasmid-mediated cefotaximases, constitute a rapidly growing family of extended-spectrum β-lactamases (esbls) with significant clinical impact. ctx-ms are found in at least 26 bacterial species, particularly in escherichia coli, klebsiella pneumoniae and proteus mirabilis. at least 109 members in ctx-m family are identified and can be divided into seven clusters based on their phylogeny. ctx-m-15 and ctx-m-14 are the most dominant variants. chromosome-encoded intrinsic cefotax ...201222697133
current trends in culture-based and molecular detection of extended-spectrum-β-lactamase-harboring and carbapenem-resistant enterobacteriaceae.the ever-expanding role of extended-spectrum-β-lactamase (esbl)-harboring and carbapenem-resistant enterobacteriaceae in causing serious infections poses a grave public health threat because these organisms also tend to be multidrug resistant, for which very few (if any) antibiotic options remain available. rapid detection of such panresistant organisms offers one of the best solutions to improve patient screening and hospital infection control practices as well as curb inappropriate antibiotic ...201222259207
controlling false-positive results obtained with the hodge and masuda assays for detection of class a carbapenemase in species of enterobacteriaceae by incorporating boronic acid.the modified hodge method (mht) has been recommended by the clsi for confirmation of suspected class a carbapenemase production in species of enterobacteriaceae. this test and the masuda method (mas) have advantages over traditional phenotypic methods in that they directly analyze carbapenemase activity. in order to identify the potential interferences of these tests, we designed a panel composed of diverse bacterial genera with distinct carbapenem susceptibility patterns (42 carbapenemase produ ...201020181912
detection of carbapenemase producers in enterobacteriaceae by use of a novel screening medium.a drigalski agar-based culture medium containing an ertapenem, cloxacillin, and zinc sulfate (supercarba medium) was tested for screening carbapenemase-producing members of the family enterobacteriaceae. oxa-48 (n = 44), ndm (n = 25), vim or imp (n = 27), and kpc producers (n = 18) were detected with a low detection limit. its overall sensitivity (95.6%) was higher than those of the currently available chromid esbl (biomérieux) and chromagar kpc (chromagar) screening media. the supercarba medium ...201222357501
aetiological agents of ventilator-associated pneumonia and its resistance pattern - a threat for treatment.ventilator-associated pneumonia (vap) is a common type of nosocomial pneumonia encountered in intensive care units. there are several aetiological agents which make treatment challenging. improper antibiotic treatment of ventilated patients may lead to the emergence of multidrug resistant (mdr) pathogens.201324133535
storage of bronchoalveolar lavage fluid and accuracy of microbiologic diagnostics in the icu: a prospective observational study.early initiation of appropriate antimicrobial treatment is a cornerstone in managing pneumonia. because microbiologic processing may not be available around the clock, optimal storage of specimens is essential for accurate microbiologic identification of pathogenetic bacteria. the aim of our study was to determine the accuracy of two commonly used storage approaches for delayed processing of bronchoalveolar lavage in critically ill patients with suspected pneumonia.201323844796
impact of inappropriate empiric antimicrobial therapy on mortality of septic patients with bacteremia: a retrospective study.background. inappropriate empiric antimicrobials could be a major cause of unfavorable mortality rates in co-morbid patients. this study aimed to assess the prevalence and impact of first-dose and 24-hour inappropriate antimicrobials on mortality rates of bacteremic septic patients. methods. a retrospective cohort study was employed. case record forms of patients diagnosed as sepsis, severe sepsis, or septic shock with positive hemoculture during 2009 were retrieved from the medical wards, sirir ...201222919379
use of a commercial pcr-based line blot method for identification of bacterial pathogens and the meca and van genes from bactalert blood culture bottles.in this study, the pcr-based dna strip assay genotype bc for the identification of bacteria and the resistance genes meca, vana, vanb, vanc1, and vanc2/3 directly from positive bactalert blood culture bottles was evaluated in a multicenter study. of a total of 511 positive blood cultures, correct identification percentages for gram-negative bacteria, gram-positive bacteria, and the meca gene were 96.1%, 89.9%, and 92.9%, respectively. results were available 4 h after growth detection.201222075585
diagnostic value of latex agglutination test in diagnosis of acute bacterial meningitis.to know the incidence of bacterial meningitis in children below five years of age. to compare conventional culture and antigen detection methods (latex agglutination test).201324339598
nosocomial infections after severe trauma are associated with lower apolipoproteins b and aii.infection after severe trauma is a significant cause of morbidity and mortality days to weeks after the initial injury. apolipoproteins play important roles in host defense and circulating concentrations are altered by the acute inflammatory response. the purpose of this study was to determine if patients who acquire infection after severe trauma have significantly lower apolipoprotein levels than trauma patients who do not become infected.201323511146
lower respiratory tract infections (ltris): an insight into the prevalence and the antibiogram of the gram negative, respiratory, bacterial agents.community acquired respiratory tract infections are one of the commonest health issues globally, which demand frequent visits to the family practitioners. the emergence of antibiotic resistance in the frequently isolated pathogens has complicated the use of the empiric therapy with traditional agents.201323543819
potential usefulness of fdg pet/ct in patients with sepsis of unknown origin.the role of fdg pet in the evaluation of patients with sepsis of unknown origin remains unclear. we sought to assess the value of fdg pet/ct in patients with sepsis of unknown cause and to define its priority in this group of subjects.201323776621
chicken cathelicidins display antimicrobial activity against multiresistant bacteria without inducing strong resistance.the increased prevalence of multidrug-resistant (mdr) bacteria in combination with the relatively limited development of new antibiotics presents a serious threat to public health. in chicken, especially extended-spectrum ß-lactamase (esbl) carrying enterobacteriaceae are often asymptomatically present but can infect humans. due to their broad range antimicrobial activity cathelicidins and other host defence peptides, are considered to be an attractive alternative to conventional antibiotics. in ...201323613986
risk factors for infection with multidrug-resistant bacteria in non-ventilated patients with hospital-acquired pneumonia.to identify risk factors for the development of hospital-acquired pneumonia (hap) caused by multidrug-resistant (mdr) bacteria in non-ventilated patients.201323857697
clinical evaluation of the role of ceftaroline in the management of community acquired bacterial pneumonia.ceftaroline fosamil (ceftaroline) was recently approved for the treatment of community- acquired pneumonia (cap) and complicated skin infections. this newly developed cephalosporin possesses a broad spectrum of activity against gram-positive and gram-negative bacteria. most importantly, ceftaroline demonstrates potent in vitro antimicrobial activity against multi-drug resistant streptococcus pneumoniae and methicillin-resistant strains of staphylococcus aureus. in two phase iii, double-blinded, ...201222355258
efficacy of a marine bacterial nuclease against biofilm forming microorganisms isolated from chronic rhinosinusitis.the persistent colonization of paranasal sinus mucosa by microbial biofilms is a major factor in the pathogenesis of chronic rhinosinusitis (crs). control of microorganisms within biofilms is hampered by the presence of viscous extracellular polymers of host or microbial origin, including nucleic acids. the aim of this study was to investigate the role of extracellular dna in biofilm formation by bacteria associated with crs.201323441151
diagnostic accuracy of pulmonary host inflammatory mediators in the exclusion of ventilator-acquired pneumonia.excessive use of empirical antibiotics is common in critically ill patients. rapid biomarker-based exclusion of infection may improve antibiotic stewardship in ventilator-acquired pneumonia (vap). however, successful validation of the usefulness of potential markers in this setting is exceptionally rare.201425298325
diagnostic accuracy of pulmonary host inflammatory mediators in the exclusion of ventilator-acquired pneumonia.excessive use of empirical antibiotics is common in critically ill patients. rapid biomarker-based exclusion of infection may improve antibiotic stewardship in ventilator-acquired pneumonia (vap). however, successful validation of the usefulness of potential markers in this setting is exceptionally rare.201425298325
antimicrobial activity of ceftaroline-avibactam tested against clinical isolates collected from u.s. medical centers in 2010-2011.ceftaroline-avibactam and comparator agents were tested by the broth microdilution method against 20,089 isolates consecutively collected in 2010 and 2011 from 75 u.s. medical centers. ceftaroline-avibactam was active against enterobacteriaceae (4,908 strains; mic90, 0.25 μg/ml; highest mic, 4 μg/ml), including meropenem-nonsusceptible klebsiella spp. and ceftazidime-nonsusceptible enterobacter cloacae strains (mic90, 1 μg/ml for both). ceftaroline-avibactam was also active against ceftriaxone-n ...201323380730
evidence that intraspecific trait variation among nasal bacteria shapes the distribution of staphylococcus aureus.nasal carriage of staphylococcus aureus is a risk factor for infection, yet the bacterial determinants required for carriage are poorly defined. interactions between s. aureus and other members of the bacterial flora may determine colonization and have been inferred in previous studies by using correlated species distributions. however, traits mediating species interactions are often polymorphic, suggesting that understanding how interactions structure communities requires a trait-based approach ...201424980973
population pharmacokinetics and pharmacodynamics of sitafloxacin in patients with community-acquired respiratory tract infections.an optimal dosage regimen of sitafloxacin was considered based on a pharmacokinetics and pharmacodynamics (pk-pd) analysis in patients with community-acquired respiratory tract infections (rti). a population pharmacokinetic analysis of sitafloxacin was conducted using clinical data of five clinical pharmacology studies and one clinical pk-pd study in patients with rtis. the pharmacokinetic parameters in individual patients were estimated by the bayesian method to examine any correlation between ...201323529500
point-of-care multiplex pcr promises short turnaround times for microbial testing in hospital-acquired pneumonia--an observational pilot study in critical ill patients.the early beginning of an adequate antibiotic therapy is crucial in hospital-acquired pneumonia (hap), but depends on the results of conventional microbiological diagnostics (cmd). it was the aim of this study to evaluate the performance and turnaround times of a new point-of-care multiplex polymerase chain reaction (mpcr) system for rapid identification of pathogens and antibiotic resistance markers. we assessed the applicability of the system under real-life conditions in critical ill patients ...201526071191
ceftaroline activity against bacterial pathogens frequently isolated in u.s. medical centers: results from five years of the aware surveillance program.a total of 84,704 isolates were collected from 191 medical centers in 2009 to 2013 and tested for susceptibility to ceftaroline and comparator agents by broth microdilution methods. ceftaroline inhibited all staphylococcus aureus isolates at ≤2 μg/ml and was very active against methicillin-resistant strains (mic at which 90% of the isolates tested are inhibited [mic90], 1 μg/ml; 97.6% susceptible). among streptococcus pneumoniae isolates, the highest ceftaroline mic was 0.5 μg/ml, and ceftarolin ...201525645844
gram-stain-based antimicrobial selection reduces cost and overuse compared with japanese guidelines.the gram stain has been used as an essential tool for antimicrobial stewardship in our hospital since the 1970s. the objective of this study was to clarify the difference in the targeted therapies selected based on the gram stain and simulated empirical therapies based on the antimicrobial guidelines used in japan.201526503359
real-time microbiology laboratory surveillance system to detect abnormal events and emerging infections, marseille, france.infectious diseases are a major threat to humanity, and accurate surveillance is essential. we describe how to implement a laboratory data-based surveillance system in a clinical microbiology laboratory. two historical microsoft excel databases were implemented. the data were then sorted and used to execute the following 2 surveillance systems in excel: the bacterial real-time laboratory-based surveillance system (balyses) for monitoring the number of patients infected with bacterial species iso ...201526196165
assessing compliance with established pneumonia core measures at a comprehensive cancer center.healthcare organizations use pneumonia core measures (pcms) to ensure delivery of high-quality care. in this study, a multidisciplinary team was organized to optimize care and enhance compliance in a comprehensive cancer emergency center. we performed a four-phase study, three of which were interventional: intense education regarding pcm; microbiologic analysis of the pathogens responsible for the pneumonias; development and implementation of an institutional pneumonia algorithm and order set. i ...201524629128
bacterial aetiological agents of intra-amniotic infections and preterm birth in pregnant women.infection-related preterm birth is a leading cause of infant mortality and morbidity; knowledge of bacterial populations invading the amniotic cavity and the routes of invasion is required to make progress in the prevention of preterm birth. significant advances have been made in understanding bacterial communities in the vagina, but much less studied are intra-uterine bacterial populations during pregnancy. a systematic review of data published on the intra-uterine microbiome was performed; mol ...201324137568
culturable bacterial microbiota of the stomach of helicobacter pylori positive and negative gastric disease patients.human stomach is the only known natural habitat of helicobacter pylori (hp), a major bacterial pathogen that causes different gastroduodenal diseases. despite this, the impact of hp on the diversity and the composition of the gastric microbiota has been poorly studied. in this study, we have analyzed the culturable gastric microbiota of 215 malaysian patients, including 131 hp positive and 84 hp negative individuals that were affected by different gastric diseases. non-hp bacteria isolated from ...201425105162
cefepime shows good efficacy and no antibiotic resistance in pneumonia caused by serratia marcescens and proteus mirabilis - an observational study.many antibiotics have no effect on gram-positive and gram-negative microbes, which necessitates the prescription of broad-spectrum antimicrobial agents that can lead to increased risk of antibiotic resistance. these pathogens constitute a further threat because they are also resistant to numerous beta-lactam antibiotics, as well as other antibiotic groups. this study retrospectively investigates antimicrobial resistance in hospitalized patients suffering from pneumonia triggered by gram-negative ...201627004519
microbial yield from physiotherapy assisted sputum production in respiratory outpatients.sputum is a key diagnostic sample for those with chronic chest conditions including chronic and allergic aspergillus-related disease, but often not obtained in clinic. the objective of this study was to evaluate physiotherapeutic interventions to obtain sputum from those not able to spontaneously produce and the subsequent microbiological result.201626831895
antibiotic utilization patterns in patients with ventilator-associated pneumonia: a canadian context.this retrospective cohort study describes the patterns of antibiotic use for the treatment of ventilator-associated pneumonia (vap) in the calgary zone of alberta health services. timing, appropriateness, and duration of antibiotics were evaluated in two hundred consecutive cases of vap derived from 4 adult intensive care units (icu). antibiotic therapy was initiated in less than 24 hours from vap diagnosis in 83% of cases. although most patients (89%) received empiric therapy that demonstrated ...201627525016
fluoroquinolone-macrolide combination therapy for chronic bacterial prostatitis: retrospective analysis of pathogen eradication rates, inflammatory findings and sexual dysfunction.we previously demonstrated the safety and efficacy of fluoroquinolone-macrolide combination therapy in category ii chronic bacterial prostatitis (cbp). the aim of this study is to retrospectively compare the microbiological and clinical findings of two treatment schemes for cbp based on the combination of azithromycin (500 mg, thrice-weekly) with a once-daily 500- or 750-mg dose of ciprofloxacin (cipro-500 or cipro-750 cohort, respectively). combined administration of azithromycin (1500 mg week( ...201121765442
antimicrobial heteroresistance: an emerging field in need of clarity."heteroresistance" describes a phenomenon where subpopulations of seemingly isogenic bacteria exhibit a range of susceptibilities to a particular antibiotic. unfortunately, a lack of standard methods to determine heteroresistance has led to inappropriate use of this term. heteroresistance has been recognized since at least 1947 and occurs in gram-positive and gram-negative bacteria. its clinical relevance may be considerable, since more resistant subpopulations may be selected during antimicrobi ...201525567227
musculoskeletal infections associated with citrobacter koseri.introduction citrobacter koseri is a well known cause of central nervous system infections in the paediatric setting. musculoskeletal infections caused by c koseri are rare, with only 14 previously reported cases. we present the first recorded case of c koseri induced septic arthritis of the knee along with a review of the literature. methods a search of the pubmed, embase(®) and google scholar™ databases was undertaken. only complete or near complete cases were reviewed. findings fourteen muscu ...201627412805
a review of global initiatives to fight antibiotic resistance and recent antibiotics׳ discovery.data from across the world have shown an overall decline in the antibiotic pipeline and continually rising resistance to all first-line and last-resort antibiotics. the gaps in our knowledge of existing prevalence and mechanisms of antibiotic resistance (abr) are all too well known. several decades of antibiotic abuse in humans, animals, and agricultural practices have created health emergency situations and huge socio-economic impact. this paper discusses key findings of the studies conducted b ...201627818921
epidemiological study of hospital-acquired bacterial conjunctivitis in a level iii neonatal unit.conjunctivitis is one of the most frequently occurring hospital-acquired infections among neonates, although it is less studied than potentially life-threatening infections, such as sepsis and pneumonia.201323766676
incidence, etiology and risk factors associated with neonatal healthcare-associated conjunctivitis: a prospective study from a tertiary care hospital in india.healthcare-associated conjunctivitis (hac) can lead to serious sequelae including blindness. we conducted a one-year prospective study to determine the epidemiology of neonatal hac at a tertiary-care hospital in india.201526428196
comparative sequence, structure and redox analyses of klebsiella pneumoniae dsba show that anti-virulence target dsba enzymes fall into distinct classes.bacterial dsba enzymes catalyze oxidative folding of virulence factors, and have been identified as targets for antivirulence drugs. however, dsba enzymes characterized to date exhibit a wide spectrum of redox properties and divergent structural features compared to the prototypical dsba enzyme of escherichia coli dsba (ecdsba). nonetheless, sequence analysis shows that dsbas are more highly conserved than their known substrate virulence factors, highlighting the potential to inhibit virulence a ...201324244651
sialic acid utilization by cronobacter sakazakii.the cronobacter genus is composed of seven species, and can cause infections in all age groups. of particular concern is c. sakazakii, as this species is strongly associated with severe and often fatal cases of necrotizing enterocolitis and meningitis in neonates and infants. whole genome sequencing has revealed that the nanakt gene cluster required for the utilisation of exogenous sialic acid is unique to the c. sakazakii species (esa_03609-13).sialic acid is found in breast milk, infant formul ...201323706082
cronobacter, the emergent bacterial pathogen enterobacter sakazakii comes of age; mlst and whole genome sequence analysis.following the association of cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the world health organization (who) in 2004 requested the establishment of a molecular typing scheme to enable the international control of the organism. this paper presents the application of next generation sequencing (ngs) to cronobacter which has led to the establishment of the cronobacter pubmlst genome and sequence definition data ...201425515150
incidence, etiology and risk factors associated with neonatal healthcare-associated conjunctivitis: a prospective study from a tertiary care hospital in india.healthcare-associated conjunctivitis (hac) can lead to serious sequelae including blindness. we conducted a one-year prospective study to determine the epidemiology of neonatal hac at a tertiary-care hospital in india.201526428196
insights into the emergent bacterial pathogen cronobacter spp., generated by multilocus sequence typing and analysis.cronobacter spp. (previously known as enterobacter sakazakii) is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. one recognized route of infection being the consumption of contaminated infant formula. as a recently recognized bacterial pathogen of considerable importance and regulatory control, appropriate detection, and identification schemes are required. the application of multilocus sequence typing (mlst) and analysis (m ...201223189075
toll-like receptors in health and disease in the brain: mechanisms and therapeutic potential.the discovery of mammalian tlrs (toll-like receptors), first identified in 1997 based on their homology with drosophila toll, greatly altered our understanding of how the innate immune system recognizes and responds to diverse microbial pathogens. tlrs are evolutionarily conserved type i transmembrane proteins expressed in both immune and non-immune cells, and are typified by n-terminal leucine-rich repeats and a highly conserved c-terminal domain termed the tir [toll/interleukin (il)-1 receptor ...201121745188
crispr is an optimal target for the design of specific pcr assays for salmonella enterica serotypes typhi and paratyphi a.serotype-specific pcr assays targeting salmonella enterica serotypes typhi and paratyphi a, the causal agents of typhoid and paratyphoid fevers, are required to accelerate formal diagnosis and to overcome the lack of typing sera and, in some situations, the need for culture. however, the sensitivity and specificity of such assays must be demonstrated on large collections of strains representative of the targeted serotypes and all other bacterial populations producing similar clinical symptoms.201424498453
identification of the serotypes of bacterial meningitis agents; implication for vaccine usage.bacterial meningitis is one of the most serious infections and should be treated as emergency. as it has significant morbidity and mortality throughout the world, every country should have precise information regarding the etiological agents of disease and populations at risk to design public health prevention strategy. in the present study in addition of evaluation of common etiological agents (haemophilus influenzae, neisseria meningitidis, and streptococcus pneumoniae) in bacterial meningitis ...201425802702
routine testing for anaerobic bacteria in cerebrospinal fluid cultures improves recovery of clinically significant pathogens.in north america, the widespread use of vaccines targeting haemophilus influenzae type b and streptococcus pneumoniae have dramatically altered the epidemiology of bacterial meningitis, while the methodology for culturing cerebrospinal fluid (csf) specimens has remained largely unchanged. the aims of this study were 2-fold: to document the current epidemiology of bacterial meningitis at a tertiary care medical center and to assess the clinical utility of routinely querying for anaerobes in csf c ...201424622102
noncanonical dna-binding mode of repressor and its disassembly by antirepressor.dna-binding repressors are involved in transcriptional repression in many organisms. disabling a repressor is a crucial step in activating expression of desired genes. thus, several mechanisms have been identified for the removal of a stably bound repressor (rep) from the operator. here, we describe an uncharacterized mechanism of noncanonical dna binding and induction by a rep from the temperate salmonella phage spc32h; this mechanism was revealed using the crystal structures of homotetrameric ...201627099293
genetic properties of blactx-m and blaper β-lactamase genes in clinical isolates of enterobacteriaceae by polymerase chain reaction.blactx-m and blaper are two genes that encode class a extended-spectrum β-lactamases (esbls) and can be responsible for therapeutic problems. this study was carried out to evaluate the molecular properties of these genes in clinical isolates of enterobacteriaceae by polymerase chain reaction (pcr), restriction digestion and sequencing.201424967067
epidemiology and characteristics of urinary tract infections in children and adolescents.urinary tract infections (utis) are among the most common infections in the pediatric population. over the last two decades, antibiotic resistance is increasing significantly as extended spectrum beta lactamase (esbl) producing organisms are emerging. the aim of this study is to provide a comprehensive view of the epidemiologic characteristics of utis in hospitalized children, examine the risk factors of utis caused by esbl-producing organisms, and determine the resistance patterns in the isolat ...201526075187
microbial inhibition of oral epithelial wound recovery: potential role for quorum sensing molecules?awareness of the impact of microbiota in both health and disease is growing. using a new in vitro oral mucosa co-culture model, we recently showed a clear inhibition of epithelial wound healing in the presence of an oral microbial community. in this paper, we have used the same model in combination with specific oral microbial species to obtain a better insight into the role of the oral microbiota in wound healing. monocultures of klebsiella oxytoca and lactobacillus salivarius significantly inh ...201525995981
positive predictive values of the international classification of diseases, 10th revision diagnoses of gram-negative septicemia/sepsis and urosepsis for presence of gram-negative bacteremia.health care databases are a valuable resource for infectious disease epidemiology if diagnoses are accurately coded. we examined the ability of diagnostic coding to accurately identify gram-negative bacteremia.201525709502
dual priming oligonucleotides for broad-range amplification of the bacterial 16s rrna gene directly from human clinical specimens.broad-range amplification and sequencing of the bacterial 16s rrna gene directly from clinical specimens are offered as a diagnostic service in many laboratories. one major pitfall is primer cross-reactivity with human dna which will result in mixed chromatograms. mixed chromatograms will complicate subsequent sequence analysis and impede identification. in sybr green real-time pcr assays, it can also affect crossing threshold values and consequently the status of a specimen as positive or negat ...201222278843
the promoter architectural landscape of the salmonella phop regulon.the dna-binding protein phop controls virulence and mg²⁺ homeostasis in the gram-negative pathogen salmonella enterica serovar typhimurium. phop regulates expression of a large number of genes that differ both in their ancestry and in the biochemical functions and physiological roles of the encoded products. this suggests that phop-regulated genes are differentially expressed. to understand how a bacterial activator might generate varied gene expression behaviour, we investigated the cis-acting ...201222435712
the outcome of non-carbapenem-based empirical antibacterial therapy and vre colonisation in patients with hematological malignancies.febrile neutropenia (fn) is generally a complication of cancer chemotherapy.201324235937
performance of four chromogenic urine culture media after one or two days of incubation compared with reference media.four chromogenic urine culture media were compared to culture on blood agar, macconkey agar, and cled (cysteine-, lactose-, and electrolyte-deficient) agar for detection of uropathogens in 1,200 urine specimens. after 2 nights of incubation, 96% of all isolates were recovered on blood agar, 96% were recovered on cled agar, 92% were recovered on cps id2, 96% were recovered on chromagar orientation from bbl, 95% were recovered on chromagar orientation from the chromagar company, and 95% were recov ...200211923381
growing group of extended-spectrum beta-lactamases: the ctx-m enzymes. 200414693512
single daily amikacin versus cefotaxime in the short-course treatment of spontaneous bacterial peritonitis in cirrhotics.to compare the efficacy and safety of single daily amikacin vs. cefotaxime in the 5-d treatment of spontaneous bacterial peritonitis (sbp).200516425390
increased concentration of the complement split product c5a in acute pyelonephritis during pregnancy.pregnant women with acute pyelonephritis develop acute respiratory distress syndrome (ards) more frequently than non-pregnant women. the reasons for this remain unknown. the complement system is a complex set of self-assembling proteins that have been implicated in the pathophysiology of ards and sepsis. the purpose of this study was to determine if activation of the complement system occurs in pregnant women with acute pyelonephritis.200516147833
risk factors for umbilical cord infection among newborns of southern nepal.although umbilical cord infection contributes to neonatal mortality and morbidity and risk can be reduced with topical chlorhexidine, behavioral or other factors associated with cord infection in low-resource settings have not been examined. data on potential risk factors for omphalitis were collected during a community-based, umbilical cord care trial in nepal during 2002-2005. newborns were evaluated in the home for signs of umbilical cord infection (pus, redness, and swelling). omphalitis was ...200617065275
risk factors for umbilical cord infection among newborns of southern nepal.although umbilical cord infection contributes to neonatal mortality and morbidity and risk can be reduced with topical chlorhexidine, behavioral or other factors associated with cord infection in low-resource settings have not been examined. data on potential risk factors for omphalitis were collected during a community-based, umbilical cord care trial in nepal during 2002-2005. newborns were evaluated in the home for signs of umbilical cord infection (pus, redness, and swelling). omphalitis was ...200617065275
prevalence and genetic analysis of plasmid-mediated quinolone resistance determinants qnra and qnrs in enterobacteriaceae isolates from a french university hospital.the spread of plasmid-mediated quinolone resistance determinants qnra and qnrs was evaluated in a collection of 186 extended-spectrum beta-lactamase (esbl)-positive enterobacterial isolates from 2002 to 2005 and 185 nalidixic acid-resistant strains isolated during the first 6 months of 2005 at the bicêtre hospital, france. out of these 186 esbl-positive isolates, 2.2 and 1.6% carried a qnra1 and a qnrs1 determinant, respectively. the esbls associated with qnra1 were veb-1, shv-12, and ctx-m-1, w ...200616982792
decreases in procalcitonin and c-reactive protein are strong predictors of survival in ventilator-associated pneumonia.this study sought to assess the prognostic value of the kinetics of procalcitonin (pct), c-reactive protein (crp) and clinical scores (clinical pulmonary infection score (cpis), sequential organ failure assessment (sofa)) in the outcome of ventilator-associated pneumonia (vap) at an early time point, when adequacy of antimicrobial treatment is evaluated.200616956405
evaluation of the new vitek 2 extended-spectrum beta-lactamase (esbl) test for rapid detection of esbl production in enterobacteriaceae isolates.extended-spectrum beta-lactamases (esbls) are a large, rapidly evolving group of enzymes that confer resistance to oxyimino cephalosporins and monobactams and are inhibited by clavulanate. rapid reliable detection of esbl production is a prerequisite for successful infection management and for monitoring resistance trends and implementation of intervention strategies. we evaluated the performance of the new vitek 2 esbl test system (biomérieux, inc, hazelwood, mo.) in the identification of esbl- ...200616954257
widely distributed and predominant ctx-m extended-spectrum beta-lactamases in amsterdam, the netherlands.three hundred sixty enterobacteriaceae and nonfermenting gram-negative bacilli, isolated during one week in may 2004 at five hospitals in amsterdam, the netherlands, were evaluated for the presence of extended-spectrum beta-lactamases (esbls). a prevalence of 7.8% was found, in contrast to the 1% observed in 1997. ctx-m esbls dominated, and four types were identified in 18 isolates.200616891530
role of staged endoprosthetic revision with flap cover for limb salvage in endoprosthetic failure.endoprosthetic replacement (epr) is commonly required for limb salvage in bone malignancies. endoprosthetic failure is a term used to denote mechanical failure or infection usually requiring removal of the prosthesis. treatment of infection consists of epr revision with or without placement of a temporary spacer. flap cover (either local or free) may be required if the overlying soft tissues are of concern. it is claimed that the investment of the endoprosthesis in well-vacularised soft tissue f ...200616607554
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 ...200718299723
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 ...200718299723
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.200717763275
sonographic findings in bacterial meningitis in neonates and young infants.cranial sonography plays an important role in the initial evaluation of infants with suspected bacterial meningitis and in monitoring for complications of the disease. echogenic widening of the brain sulci, meningeal thickening and hyperemia suggest the diagnosis in an at-risk population. sonography can identify the presence of extra-axial fluid collections, and color doppler sonography can be very helpful in differentiating benign enlargement of subarachnoid spaces from subdural effusions. intr ...200717611750
sonographic findings in bacterial meningitis in neonates and young infants.cranial sonography plays an important role in the initial evaluation of infants with suspected bacterial meningitis and in monitoring for complications of the disease. echogenic widening of the brain sulci, meningeal thickening and hyperemia suggest the diagnosis in an at-risk population. sonography can identify the presence of extra-axial fluid collections, and color doppler sonography can be very helpful in differentiating benign enlargement of subarachnoid spaces from subdural effusions. intr ...200717611750
reevaluation of clinical and laboratory standards institute disk diffusion breakpoints for tetracyclines for testing enterobacteriaceae.we reevaluated enterobacteriaceae disk diffusion breakpoints for the tetracyclines published in the clinical and laboratory standards institute (clsi) document m100-s16, which were (susceptible/resistant) >or=19 mm/<or=14 mm for tetracycline, >or=16 mm/<or=12 mm for doxycycline, and >or=19 mm/<or=14 mm for minocycline. a collection of 504 recent clinical isolates of enterobacteriaceae were tested against these tetracycline compounds by disk diffusion and broth microdilution methods according to ...200717360844
immunological system status and the appearance of respiratory system disturbances in thymectomized patients.adult-onset thymoma may be responsible for several diseases, such as pure red cell aplasia, myasthenia gravis, and immunodeficiency (good's syndrome). thymectomy does not always improve the patient's condition, and may even produce additional symptoms. its pathogenesis is still not entirely understood, but autoimmunological processes and bone marrow defect are the most frequently suggested.200717277895
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 ...200818996193
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 ...200818845821
microbiological and histopathological aspects of canine pyometra.as pyometra is recognized as one of the main causes of disease and death in the bitch the purposes of this study were to evaluate microbiological and histopathological aspects of canine pyometra and to research the virulence factors of the e. coli isolates identifying possible risks to human health. the microbiological isolation from the intrauterine contents of 100 dogs with pyometra was carried out and the virulence factors in the e. coli strains were identified using pcr method. this study al ...200824031249
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.200818252006
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 ...200919696153
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