Publications

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functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter.targeting sequencing to genes involved in key environmental processes, i.e., ecofunctional genes, provides an opportunity to sample nature's gene guilds to greater depth and help link community structure to process-level outcomes. vastly different approaches have been implemented for sequence processing and, ultimately, for taxonomic placement of these gene reads. the overall quality of next generation sequence analysis of functional genes is dependent on multiple steps and assumptions of unknow ...201324062736
complement-mediated opsonization of invasive group a streptococcus pyogenes strain ap53 is regulated by the bacterial two-component cluster of virulence responder/sensor (covrs) system.group a streptococcus pyogenes (gas) strain ap53 is a primary isolate from a patient with necrotizing fasciitis. these ap53 cells contain an inactivating mutation in the sensor component of the cluster of virulence (cov) responder (r)/sensor (s) two-component gene regulatory system (covrs), which enhances the virulence of the primary strain, ap53/covr(+)s(-). however, specific mechanisms by which the covrs system regulates the survival of gas in humans are incomplete. here, we show a key role fo ...201323928307
accurate identification of fastidious gram-negative rods: integration of both conventional phenotypic methods and 16s rrna gene analysis.accurate identification of fastidious gram-negative rods (gnr) by conventional phenotypic characteristics is a challenge for diagnostic microbiology. the aim of this study was to evaluate the use of molecular methods, e.g., 16s rrna gene sequence analysis for identification of fastidious gnr in the clinical microbiology laboratory.201323855986
rapid 16s rrna next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. we therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. we have combined a semiconductor deep sequencing protocol that produces reads spanning 16s ribosomal rna gene variable regions ...201323734239
where does neisseria acquire foreign dna from: an examination of the source of genomic and pathogenic islands and the evolution of the neisseria genus.pathogenicity islands (pais) or genomic islands (geis) are considered to be the result of a recent horizontal transfer. detecting pais/geis as well as their putative source can provide insight into the organism's pathogenicity within its host. previously we introduced a tool called s-plot which provides a visual representation of the variation in compositional properties across and between genomic sequences. utilizing s-plot and new functionality developed here, we examined 18 publicly available ...201324007216
a critical role for the ccca gene product, cytochrome c2, in diverting electrons from aerobic respiration to denitrification in neisseria gonorrhoeae.neisseria gonorrhoeae is a microaerophile that, when oxygen availability is limited, supplements aerobic respiration with a truncated denitrification pathway, nitrite reduction to nitrous oxide. we demonstrate that the ccca gene of neisseria gonorrhoeae strain f62 (accession number ng0292) is expressed, but the product, cytochrome c2, accumulates to only low levels. nevertheless, a ccca mutant reduced nitrite at about half the rate of the parent strain. we previously reported that cytochromes c4 ...201323543713
potential use of atlantic cod trypsin in biomedicine.surface proteins of viruses and bacteria used for cell attachment and invasion are candidates for degradation by proteases. trypsin from atlantic cod (gadus morhua) was previously demonstrated to have efficacy against influenza viruses in vitro and on skin. in this paper, cod trypsin is shown to be 3-12 times more effective in degrading large native proteins than its mesophilic analogue, bovine trypsin. this is in agreement with previous findings where cod trypsin was found to be the most active ...201323555095
pipeline of known chemical classes of antibiotics.many approaches are used to discover new antibiotic compounds, one of the most widespread being the chemical modification of known antibiotics. this type of discovery has been so important in the development of new antibiotics that most antibiotics used today belong to the same chemical classes as antibiotics discovered in the 1950s and 1960s. even though the discovery of new classes of antibiotics is urgently needed, the chemical modification of antibiotics in known classes is still widely used ...201327029317
inhaled colistin for treatment of pneumonia due to colistin-only-susceptible acinetobacter baumannii.colistin is used for the treatment of pneumonia associated with multidrug- resistant acinetobacter baumannii and pseudomonas aeruginosa. however, the best route of administration and dosage is not known. we report our experience with aerosolized colistin in twelve patients with pneumonia caused by colistin-only-susceptible (cos) a. baumannii.201324339296
inhaled colistin for treatment of pneumonia due to colistin-only-susceptible acinetobacter baumannii.colistin is used for the treatment of pneumonia associated with multidrug- resistant acinetobacter baumannii and pseudomonas aeruginosa. however, the best route of administration and dosage is not known. we report our experience with aerosolized colistin in twelve patients with pneumonia caused by colistin-only-susceptible (cos) a. baumannii.201324339296
proteinaceous determinants of surface colonization in bacteria: bacterial adhesion and biofilm formation from a protein secretion perspective.bacterial colonization of biotic or abiotic surfaces results from two quite distinct physiological processes, namely bacterial adhesion and biofilm formation. broadly speaking, a biofilm is defined as the sessile development of microbial cells. biofilm formation arises following bacterial adhesion but not all single bacterial cells adhering reversibly or irreversibly engage inexorably into a sessile mode of growth. among molecular determinants promoting bacterial colonization, surface proteins a ...201324133488
primary immunodeficiency diseases at reference and high-specialty hospitals in the state of guanajuato, mexico.in general, primary immunodeficiency diseases (pids) are underdiagnosed in most countries. the objective of this study was to describe the frequency and clinical spectrum of pid in the most important tertiary hospitals in our region.201324073395
new antibiotics for bad bugs: where are we?bacterial resistance to antibiotics is growing up day by day in both community and hospital setting, with a significant impact on the mortality and morbidity rates and the financial burden that is associated. in the last two decades multi drug resistant microorganisms (both hospital- and community-acquired) challenged the scientific groups into developing new antimicrobial compounds that can provide safety in use according to the new regulation, good efficacy patterns, and low resistance profile ...201323984642
prediction of methicillin-resistant staphylococcus aureus in patients with non-nosocomial pneumonia.methicillin-resistant staphylococcus aureus (mrsa) is recognized as an important cause of not only hospital acquired pneumonia, but also non-nosocomial pneumonia. however, the risk factors for non-nosocomial mrsa pneumonia are not clearly defined. our objective was to identify risk factors at admission that were associated with non-nosocomial mrsa pneumonia.201323937553
analysis of cftr gene variants in idiopathic bronchiectasis in serbian children.this study has investigated a potential role of common cystic fibrosis transmembrane conductance regulator (cftr) gene variants in the etiology of noncystic fibrosis bronchiectasis in serbian children. the study has encompassed 48 patients (19 male and 29 female, aged between 5 and 18 years, median age 10.6±3.3), diagnosed with idiopathic bronchiectasis based on high-resolution computed tomography of thorax and pathologic examination of lobectomy materials. the cftr gene analysis was performed o ...201323781395
significance of anaerobes and oral bacteria in community-acquired pneumonia.molecular biological modalities with better detection rates have been applied to identify the bacteria causing infectious diseases. approximately 10-48% of bacterial pathogens causing community-acquired pneumonia are not identified using conventional cultivation methods. this study evaluated the bacteriological causes of community-acquired pneumonia using a cultivation-independent clone library analysis of the 16s ribosomal rna gene of bronchoalveolar lavage specimens, and compared the results w ...201323671659
pcr-reverse blot hybridization assay for screening and identification of pathogens in sepsis.rapid and accurate identification of the pathogens involved in bloodstream infections is crucial for the prompt initiation of appropriate therapy, as this can decrease morbidity and mortality rates. a pcr-reverse blot hybridization assay for sepsis, the reverse blot hybridization assay (reba) sepsis-id test, was developed; it uses pan-probes to distinguish gram-positive and -negative bacteria and fungi. in addition, the assay was designed to identify bacteria and fungi using six genus-specific a ...201323447637
protein selection and export via outer membrane vesicles.outer membrane vesicles (omvs) are constitutively produced by all gram-negative bacteria. omvs form when buds from the outer membrane (om) of cells encapsulate periplasmic material and pinch off from the om to form spheroid particles approximately 10 to 300nm in diameter. omvs accomplish a diversity of functional roles yet the omv's utility is ultimately determined by its unique composition. inclusion into omvs may impart a variety of benefits to the protein cargo, including: protection from pro ...201324370777
protein selection and export via outer membrane vesicles.outer membrane vesicles (omvs) are constitutively produced by all gram-negative bacteria. omvs form when buds from the outer membrane (om) of cells encapsulate periplasmic material and pinch off from the om to form spheroid particles approximately 10 to 300nm in diameter. omvs accomplish a diversity of functional roles yet the omv's utility is ultimately determined by its unique composition. inclusion into omvs may impart a variety of benefits to the protein cargo, including: protection from pro ...201324370777
a guide to utilization of the microbiology laboratory for diagnosis of infectious diseases: 2013 recommendations by the infectious diseases society of america (idsa) and the american society for microbiology (asm)(a).the critical role of the microbiology laboratory in infectious disease diagnosis calls for a close, positive working relationship between the physician and the microbiologists who provide enormous value to the health care team. this document, developed by both laboratory and clinical experts, provides information on which tests are valuable and in which contexts, and on tests that add little or no value for diagnostic decisions. sections are divided into anatomic systems, including bloodstream i ...201323845951
binding properties of treponema denticola lipooligosaccharide.the cell-surface lipooligosaccharide (los) of treponema denticola possesses several biological properties. the aim of this study was to investigate the binding properties of t. denticola los to extracellular matrix (ecm) proteins, mucosal cells, and oral bacteria.201324049558
lessons learned and unlearned in periodontal microbiology.periodontal diseases are initiated by bacterial species living in polymicrobial biofilms at or below the gingival margin and progress largely as a result of the inflammation elicited by specific subgingival species. in the past few decades, efforts to understand the periodontal microbiota have led to an exponential increase in information about biofilms associated with periodontal health and disease. in fact, the oral microbiota is one of the best-characterized microbiomes that colonize the huma ...201323574465
from in vitro to in vivo models of bacterial biofilm-related infections.the influence of microorganisms growing as sessile communities in a large number of human infections has been extensively studied and recognized for 30-40 years, therefore warranting intense scientific and medical research. nonetheless, mimicking the biofilm-life style of bacteria and biofilm-related infections has been an arduous task. models used to study biofilms range from simple in vitro to complex in vivo models of tissues or device-related infections. these different models have progressi ...201325437038
plasmid diversity in arctic strains of psychrobacter spp.six strains of psychrobacter spp. isolated from guano of little auks collected on spitsbergen island (arctic) carried nine plasmids that were fully sequenced. these replicons (ranging in size from 2917 to 14924 bp) contained either repa (cole2-type) or repb (iteron-type) replication systems of a relatively narrow host range, limited to psychrobacter spp. all but one of the plasmids carried predicted mobilization for conjugal transfer systems, encoding relaxases of the mobq, mobv or mobp families ...201323479249
group a streptococci are protected from amoxicillin-mediated killing by vesicles containing β-lactamase derived from haemophilus influenzae.group a streptococci (gas) cause, among other infections, pharyngotonsillitis in children. the species is frequently localized with the gram-negative respiratory pathogens non-typeable haemophilus influenzae (nthi) and moraxella catarrhalis, which both produce outer membrane vesicles (omvs). the aim of this study was to investigate whether omvs isolated from nthi contain functional β-lactamase and whether the omvs hydrolyse amoxicillin and thus protect gas from killing by the antibiotic.201323912886
host antimicrobial peptides in bacterial homeostasis and pathogenesis of disease.innate immune responses function as a first line of host defense against the development of bacterial infection, and in some cases to preserve the sterility of privileged sites in the human host. bacteria that enter these sites must counter host responses for colonization. from the host's perspective, the innate immune system works expeditiously to minimize the bacterial threat before colonization and subsequent dysbiosis. the multifactorial nature of disease further challenges predictions of ho ...201426029470
polybacterial human disease: the ills of social networking.polybacterial diseases involve multiple organisms that act collectively to facilitate disease progression. although this phenomenon was highlighted early in the 20th century, recent technological advances in diagnostics have led to the appreciation that many infections are far more complex than originally believed. furthermore, it is apparent that although most treatments focus on the dominant bacterial species in an infection, other microbes, including commensals, can have a profound impact on ...201424938173
a quantitative prioritisation of human and domestic animal pathogens in europe.disease or pathogen risk prioritisations aid understanding of infectious agent impact within surveillance or mitigation and biosecurity work, but take significant development. previous work has shown the h-(hirsch-)index as an alternative proxy. we present a weighted risk analysis describing infectious pathogen impact for human health (human pathogens) and well-being (domestic animal pathogens) using an objective, evidence-based, repeatable approach; the h-index. this study established the highe ...201425136810
substrate binding protein sbp2 of a putative abc transporter as a novel vaccine antigen of moraxella catarrhalis.moraxella catarrhalis is a common respiratory tract pathogen that causes otitis media in children and infections in adults with chronic obstructive pulmonary disease. since the introduction of the pneumococcal conjugate vaccines with/without protein d of nontypeable haemophilus influenzae, m. catarrhalis has become a high-priority pathogen in otitis media. for the development of antibacterial vaccines and therapies, substrate binding proteins of atp-binding cassette transporters are important ta ...201424914218
ge23077 binds to the rna polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic ge23077 (ge) binds directly to the bacterial rna polymerase (rnap) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. the target-based resistance spectrum for ge is unusually small, reflecting the fact that the ge binding site on rnap includes residues of the rnap active center that ...201424755292
molecular basis of host specificity in human pathogenic bacteria.pathogenic bacteria display various levels of host specificity or tropism. while many bacteria can infect a wide range of hosts, certain bacteria have strict host selectivity for humans as obligate human pathogens. understanding the genetic and molecular basis of host specificity in pathogenic bacteria is important for understanding pathogenic mechanisms, developing better animal models and designing new strategies and therapeutics for the control of microbial diseases. the molecular mechanisms ...201426038515
persisters, persistent infections and the yin-yang model.persisters are a small fraction of quiescent bacterial cells that survive lethal antibiotics or stresses but can regrow under appropriate conditions. persisters underlie persistent and latent infections and post-treatment relapse, posing significant challenges for the treatment of many bacterial infections. the current definition of persisters has drawbacks, and a yin-yang model is proposed to describe the heterogeneous nature of persisters that have to be defined in highly specific conditions. ...201426038493
correlation between sputum and bronchoalveolar lavage fluid cultures.a correlation study of the cultured bacteria from paired sputum and bronchoalveolar lavage fluid samples was performed. the rates of concordant culture-positive paired specimens that were isolated within 1 or 7 days were 93.7% and 96.5%, respectively, suggesting that the culture of readily collectable sputum specimens may result in useful microbiologic diagnosis.201425540405
correlation between sputum and bronchoalveolar lavage fluid cultures.a correlation study of the cultured bacteria from paired sputum and bronchoalveolar lavage fluid samples was performed. the rates of concordant culture-positive paired specimens that were isolated within 1 or 7 days were 93.7% and 96.5%, respectively, suggesting that the culture of readily collectable sputum specimens may result in useful microbiologic diagnosis.201425540405
the microbial community of the cystic fibrosis airway is disrupted in early life.molecular techniques have uncovered vast numbers of organisms in the cystic fibrosis (cf) airways, the clinical significance of which is yet to be determined. the aim of this study was to describe and compare the microbial communities of the lower airway of clinically stable children with cf and children without cf.201425526264
ceftolozane/tazobactam: a new option in the treatment of complicated gram-negative infections.ceftolozane/tazobactam: a new option in the treatment of complicated gram-negative infections.201425516692
is there still room for novel viral pathogens in pediatric respiratory tract infections?viruses are the most frequent cause of respiratory disease in children. however, despite the advanced diagnostic methods currently in use, in 20 to 50% of respiratory samples a specific pathogen cannot be detected. in this work, we used a metagenomic approach and deep sequencing to examine respiratory samples from children with lower and upper respiratory tract infections that had been previously found negative for 6 bacteria and 15 respiratory viruses by pcr. nasal washings from 25 children (ou ...201425412469
the significance of mycobacterium abscessus subspecies abscessus isolation during mycobacterium avium complex lung disease therapy.isolation of mycobacterium abscessus subspecies abscessus (maa) is common during mycobacterium avium complex (mac) lung disease therapy, but there is limited information about the clinical significance of the maa isolates.201425357074
the significance of mycobacterium abscessus subspecies abscessus isolation during mycobacterium avium complex lung disease therapy.isolation of mycobacterium abscessus subspecies abscessus (maa) is common during mycobacterium avium complex (mac) lung disease therapy, but there is limited information about the clinical significance of the maa isolates.201425357074
genomic investigations unmask mycoplasma amphoriforme, a new respiratory pathogen.mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (pad). little is known about the natural history of infection with this organism and its ability to be transmitted in the community.201425344534
genomic investigations unmask mycoplasma amphoriforme, a new respiratory pathogen.mycoplasma amphoriforme has been associated with infection in patients with primary antibody deficiency (pad). little is known about the natural history of infection with this organism and its ability to be transmitted in the community.201425344534
sphingoid long chain bases prevent lung infection by pseudomonas aeruginosa.cystic fibrosis patients and patients with chronic obstructive pulmonary disease, trauma, burn wound, or patients requiring ventilation are susceptible to severe pulmonary infection by pseudomonas aeruginosa. physiological innate defense mechanisms against this pathogen, and their alterations in lung diseases, are for the most part unknown. we now demonstrate a role for the sphingoid long chain base, sphingosine, in determining susceptibility to lung infection by p. aeruginosa. tracheal and bron ...201425085879
treatment for infections with carbapenem-resistant enterobacteriaceae: what options do we still have?the global spread of carbapenem-resistant enterobacteriaceae (cre) is increasingly becoming a major challenge in clinical and public health settings. to date, the treatment for serious cre infections remains difficult. the intelligent use of antimicrobials and effective infection control strategies is crucial to prevent further cre spread. early consultation with experts in the treatment of infections with multidrug-resistant organisms is valuable in patient management. this brief review will fo ...201425041592
characterization of bcam0224, a multifunctional trimeric autotransporter from the human pathogen burkholderia cenocepacia.members of the trimeric autotransporter adhesin (taa) family play a crucial role in adhesion of gram-negative pathogens to host cells. moreover, these proteins are multifunctional virulence factors involved in several other biological traits, including invasion into host cells and evasion of the host immune system. in cystic fibrosis epidemic burkholderia cenocepacia strain j2315, we identified a unique taa (bcam0224)-encoding gene, previously described as being implicated in virulence. here, we ...201424659767
performance of mass spectrometric identification of bacteria and yeasts routinely isolated in a clinical microbiology laboratory using maldi-tof ms.matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) is an emerging technology newly applied to identifying bacterial and yeast strains. the aim of this study was to evaluate the clinical performance of the vitek(®) ms system in the identification of bacteria and yeast strains routinely isolated from clinical samples.201424822114
mechanism of escherichia coli resistance to pyrrhocoricin.due to their lack of toxicity to mammalian cells and good serum stability, proline-rich antimicrobial peptides (pr-amps) have been proposed as promising candidates for the treatment of infections caused by antimicrobial-resistant bacterial pathogens. it has been hypothesized that these peptides act on multiple targets within bacterial cells, and therefore the likelihood of the emergence of resistance was considered to be low. here, we show that spontaneous escherichia coli mutants resistant to p ...201424590485
rapid identification of stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization.the objective of this study was to develop a novel peptide nucleic acid (pna) probe for stenotrophomonas maltophilia identification by fluorescence in situ hybridization (fish). the probe was evaluated using 33 human and veterinary clinical s. maltophilia isolates and 45 reference strains representing common bacterial species in the respiratory tract. the probe displayed 100% sensitivity and 100% specificity on pure cultures and allowed detection in sputum from cystic fibrosis patients. the dete ...201425356348
antimicrobial peptides from fish.antimicrobial peptides (amps) are found widely distributed through nature, and participate in the innate host defense of each species. fish are a great source of these peptides, as they express all of the major classes of amps, including defensins, cathelicidins, hepcidins, histone-derived peptides, and a fish-specific class of the cecropin family, called piscidins. as with other species, the fish peptides exhibit broad-spectrum antimicrobial activity, killing both fish and human pathogens. they ...201424594555
inhaled antibiotics for lower airway infections.inhaled antibiotics have been used to treat chronic airway infections since the 1940s. the earliest experience with inhaled antibiotics involved aerosolizing antibiotics designed for parenteral administration. these formulations caused significant bronchial irritation due to added preservatives and nonphysiologic chemical composition. a major therapeutic advance took place in 1997, when tobramycin designed for inhalation was approved by the u.s. food and drug administration (fda) for use in pati ...201424673698
lung microbiome for clinicians. new discoveries about bugs in healthy and diseased lungs.microbes are readily cultured from epithelial surfaces of the skin, mouth, and colon. in the last 10 years, culture-independent dna-based techniques demonstrated that much more complex microbial communities reside on most epithelial surfaces; this includes the lower airways, where bacterial culture had failed to reliably demonstrate resident bacteria. exposure to a diverse bacterial environment is important for adequate immunological development. the most common microbes found in the lower airwa ...201424460444
rna-seq-based analysis of cold shock response in thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene.although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. thermoanaerobacter tengcongensis mb4, a thermophile harboring only one known cold shock protein gene (ttescpc), can survive from 50° to 80 °c, but has poor natural competence under cold shock at 50 °c. we therefore examined cold shock responses ...201424667527
challenges and future prospects of antibiotic therapy: from peptides to phages utilization.bacterial infections are raising serious concern across the globe. the effectiveness of conventional antibiotics is decreasing due to global emergence of multi-drug-resistant (mdr) bacterial pathogens. this process seems to be primarily caused by an indiscriminate and inappropriate use of antibiotics in non-infected patients and in the food industry. new classes of antibiotics with different actions against mdr pathogens need to be developed urgently. in this context, this review focuses on seve ...201424860506
oligotyping analysis of the human oral microbiome.the human microbiome project provided a census of bacterial populations in healthy individuals, but an understanding of the biomedical significance of this census has been hindered by limited taxonomic resolution. a high-resolution method termed oligotyping overcomes this limitation by evaluating individual nucleotide positions using shannon entropy to identify the most information-rich nucleotide positions, which then define oligotypes. we have applied this method to comprehensively analyze the ...201424965363
a brief review: the z-curve theory and its application in genome analysis.in theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. in the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. the z-curve theory is a geometrical approach to genome analysis. the z-curve is a three-dimensional curve that represents a given dna sequence in the sense that each can be uniquely reconst ...201424822026
clinical importance and epidemiology of quinolone resistance.the quinolone class of antimicrobial agents is one of most widely used classes of antimicrobial agents in outpatient and inpatient treatment. however, quinolone resistance in gram-positive and gram-negative bacteria has emerged and increased globally. this resistance limits the usefulness of quinolones in clinical practice. the review summarizes mechanisms of quinolone resistance and its epidemiology and implications in the most common clinical settings, urinary tract infections, respiratory tra ...201425566402
recognition of protein-coding genes based on z-curve algorithms.recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. the z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. two z-curve based ab initio gene-finding programs have been developed: zcurve (for bacteria and archaea) and zcurve_v (for viruses and phages). zcurve_c (for 57 ...201424822027
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 ...201425433488
antibacterial activity and mode of action of selected glucosinolate hydrolysis products against bacterial pathogens.plants contain numerous components that are important sources of new bioactive molecules with antimicrobial properties. isothiocyanates (itcs) are plant secondary metabolites found in cruciferous vegetables that are arising as promising antimicrobial agents in food industry. the aim of this study was to assess the antibacterial activity of two isothiocyanates (itcs), allylisothiocyanate (aitc) and 2-phenylethylisothiocyanate (peitc) against escherichia coli, pseudomonas aeruginosa, staphylococcu ...201426243895
antibacterial activity and mode of action of selected glucosinolate hydrolysis products against bacterial pathogens.plants contain numerous components that are important sources of new bioactive molecules with antimicrobial properties. isothiocyanates (itcs) are plant secondary metabolites found in cruciferous vegetables that are arising as promising antimicrobial agents in food industry. the aim of this study was to assess the antibacterial activity of two isothiocyanates (itcs), allylisothiocyanate (aitc) and 2-phenylethylisothiocyanate (peitc) against escherichia coli, pseudomonas aeruginosa, staphylococcu ...201426243895
the yersinia pestis siderophore, yersiniabactin, and the znuabc system both contribute to zinc acquisition and the development of lethal septicaemic plague in mice.bacterial pathogens must overcome host sequestration of zinc (zn(2+) ), an essential micronutrient, during the infectious disease process. while the mechanisms to acquire chelated zn(2+) by bacteria are largely undefined, many pathogens rely upon the znuabc family of abc transporters. here we show that in yersinia pestis, irp2, a gene encoding the synthetase (hmwp2) for the siderophore yersiniabactin (ybt) is required for growth under zn(2+) -deficient conditions in a strain lacking znuabc. more ...201424979062
3,4-dhpea-ea from olea europaea l. is effective against standard and clinical isolates of staphylococcus sp.the aim of the present work was to evaluate the antibacterial effect of 3,4-dhpea-ea (methyl-4-(2-(3,4-dihydroxyphenethoxy)-2-oxoethyl)-3-formyl-2-methyl-3,4-dihydro-2h-pyran-5-carboxylate), a derivate of oleuropein, against a range of gram-positive bacteria, including atcc strains, food and clinical isolates.201424986240
carbohydrate-mimetic peptides for pan anti-tumor responses.molecular mimicry is fundamental to biology and transcends to many disciplines ranging from immune pathology to drug design. structural characterization of molecular partners has provided insight into the origins and relative importance of complementarity in mimicry. chemical complementarity is easy to understand; amino acid sequence similarity between peptides, for example, can lead to cross-reactivity triggering similar reactivity from their cognate receptors. however, conformational complemen ...201425071769
high-throughput sequencing for the study of bacterial pathogen biology.a revolution in sequencing technologies in recent years has led to dramatically increased throughput and reduced cost of bacterial genome sequencing. an increasing number of applications of the new technologies are providing broad insights into bacterial evolution, epidemiology, and pathogenesis. for example, the capacity to sequence large numbers of bacterial isolates is enabling high resolution phylogenetic analyses of bacterial populations leading to greatly enhanced understanding of the emer ...201425033019
nitropropenyl benzodioxole, an anti-infective agent with action as a protein tyrosine phosphatase inhibitor.we report on the activities of a broad spectrum antimicrobial compound,nitropropenyl benzodioxole (npbd) which are of relevance to its potential as an anti-infective drug. these investigations support the proposal that a major mechanism of npbd is action as a tyrosine mimetic, competitively inhibiting bacterial and fungal protein tyrosine phosphatases (ptp). npbd did not affect major anti-bacterial drug targets, namely, atp production, cell wall or cell membrane integrity, or transcription and t ...201424976873
pandemic 2009 influenza a (h1n1) virus infection in cancer and hematopoietic stem cell transplant recipients; a multicenter observational study.during march 2009 a novel influenza a virus emerged in mexico. we describe the clinical picture of the pandemic influenza a (h1n1) influenza in cancer patients during the 2009 influenza season.201425469231
pandemic 2009 influenza a (h1n1) virus infection in cancer and hematopoietic stem cell transplant recipients; a multicenter observational study.during march 2009 a novel influenza a virus emerged in mexico. we describe the clinical picture of the pandemic influenza a (h1n1) influenza in cancer patients during the 2009 influenza season.201425469231
lung disease and hypertension.chronic obstructive pulmonary disease (copd) patients are at a high risk of developing cardiovascular diseases. airflow limitation is a predictor of future risks of hypertension and cardiovascular events. copd is now understood as a systemic inflammatory disease, with the focus on inflammation of the lungs. an association between inflammation and sympathetic overactivity has also been reported. in this article, we review the association between chronic lung disease and the risks of hypertension, ...201426587450
lung disease and hypertension.chronic obstructive pulmonary disease (copd) patients are at a high risk of developing cardiovascular diseases. airflow limitation is a predictor of future risks of hypertension and cardiovascular events. copd is now understood as a systemic inflammatory disease, with the focus on inflammation of the lungs. an association between inflammation and sympathetic overactivity has also been reported. in this article, we review the association between chronic lung disease and the risks of hypertension, ...201426587450
the host immune dynamics of pneumococcal colonization: implications for novel vaccine development.the human nasopharynx (np) microbiota is complex and diverse and streptococcus pneumoniae (pneumococcus) is a frequent member. in the first few years of life, children experience maturation of their immune system thereby conferring homeostatic balance in which pneumococci are typically rendered as harmless colonizers in the upper respiratory environment. pneumococcal carriage declines in many children before they acquire capsular-specific antibodies, suggesting a capsule antibody-independent mec ...201425668673
the host immune dynamics of pneumococcal colonization: implications for novel vaccine development.the human nasopharynx (np) microbiota is complex and diverse and streptococcus pneumoniae (pneumococcus) is a frequent member. in the first few years of life, children experience maturation of their immune system thereby conferring homeostatic balance in which pneumococci are typically rendered as harmless colonizers in the upper respiratory environment. pneumococcal carriage declines in many children before they acquire capsular-specific antibodies, suggesting a capsule antibody-independent mec ...201425668673
subclinical infection and dosing in primary immunodeficiencies. 201425546767
molecular characterization of fluoroquinolone resistance in nontypeable haemophilus influenzae clinical isolates.nontypeable haemophilus influenzae (nthi) is a common cause of respiratory infections in adults, who are frequently treated with fluoroquinolones. the aims of this study were to characterize the genotypes of fluoroquinolone-resistant nthi isolates and their mechanisms of resistance. among 7,267 h. influenzae isolates collected from adult patients from 2000 to 2013, 28 (0.39%) were ciprofloxacin resistant according to clinical and laboratory standards institute (clsi) criteria. in addition, a nal ...201425385097
molecular characterization of fluoroquinolone resistance in nontypeable haemophilus influenzae clinical isolates.nontypeable haemophilus influenzae (nthi) is a common cause of respiratory infections in adults, who are frequently treated with fluoroquinolones. the aims of this study were to characterize the genotypes of fluoroquinolone-resistant nthi isolates and their mechanisms of resistance. among 7,267 h. influenzae isolates collected from adult patients from 2000 to 2013, 28 (0.39%) were ciprofloxacin resistant according to clinical and laboratory standards institute (clsi) criteria. in addition, a nal ...201425385097
seasonal variation in penicillin use in mexico and brazil: analysis of the impact of over-the-counter restrictions.during 2010, mexico and brazil implemented policies to enforce existing laws of restricting over-the-counter sales of antibiotics. we determined if the enforcement led to more appropriate antibiotic use by measuring changes in seasonal variation of penicillin use. we used retail quarterly sales data in defined daily doses per 1,000 inhabitant-days (ddd/tid) from ims health from the private sector in mexico and brazil from the first quarter of 2007 to the first quarter of 2013. this database cont ...201425313222
seasonal variation in penicillin use in mexico and brazil: analysis of the impact of over-the-counter restrictions.during 2010, mexico and brazil implemented policies to enforce existing laws of restricting over-the-counter sales of antibiotics. we determined if the enforcement led to more appropriate antibiotic use by measuring changes in seasonal variation of penicillin use. we used retail quarterly sales data in defined daily doses per 1,000 inhabitant-days (ddd/tid) from ims health from the private sector in mexico and brazil from the first quarter of 2007 to the first quarter of 2013. this database cont ...201425313222
predictors of viral pneumonia in patients with community-acquired pneumonia.viruses are increasingly recognized as major causes of community-acquired pneumonia (cap). few studies have investigated the clinical predictors of viral pneumonia, and the results have been inconsistent. in this study, the clinical predictors of viral pneumonia were investigated in terms of their utility as indicators for viral pneumonia in patients with cap.201425531901
the adult nasopharyngeal microbiome as a determinant of pneumococcal acquisition.several cohort studies have indicated associations between s. pneumoniae and other microbes in the nasopharynx. to study causal relationships between the nasopharyngeal microbiome and pneumococcal carriage, we employed an experimental human pneumococcal carriage model. healthy adult volunteers were assessed for pneumococcal carriage by culture of nasal wash samples (nws). those without natural pneumococcal carriage received an intranasal pneumococcal inoculation with serotype 6b or 23f. the comp ...201425671106
effect of a fever control protocol-based strategy on ventilator-associated pneumonia in severely brain-injured patients.fever is associated with a poor outcome in severely brain-injured patients, and its control is one of the therapies used in this condition. but, fever suppression may promote infection, and severely brain-injured patients are frequently exposed to infectious diseases, particularly ventilator-associated pneumonia (vap). therefore, we designed a study to explore the role of a fever control protocol in vap development during neuro-intensive care.201425498970
no direct association between asthma and the microbiome based on currently available techniques.current uses of culture-independent tools in previous studies have shown a significant relationship between microbiota and asthma. although these studies are relatively new, there is also evidence of the possibility of new therapeutic strategies for the treatment or prevention of asthma. this article retrospectively examines the possible association between microorganisms and asthma. data on all patients with different types of asthma were collected from hospital charts from the department of in ...201425501073
chemical composition and biological activity of rubus idaeus shoots--a traditional herbal remedy of eastern europe.the young shoots of rubus idaeus are traditionally used as a herbal remedy in common cold, fever and flu-like infections yet there is no research concerning this plant material. the aim of the study was to evaluate the chemical composition and biological properties of raspberry shoots from 11 cultivar varieties.201425496130
immunization with lipopolysaccharide-deficient whole cells provides protective immunity in an experimental mouse model of acinetobacter baumannii infection.the increasing clinical importance of infections caused by multidrug resistant acinetobacter baumannii warrants the development of novel approaches for prevention and treatment. in this context, vaccination of certain patient populations may contribute to reducing the morbidity and mortality caused by this pathogen. vaccines against gram-negative bacteria based on inactivated bacterial cells are highly immunogenic and have been shown to produce protective immunity against a number of bacterial s ...201425485716
correlation of nasopharyngeal cultures prior to and at onset of acute otitis media with middle ear fluid cultures.we sought to determine if nasopharyngeal (np) cultures taken at times of healthy visits or at onset of acute otitis media (aom) could predict the otopathogen mix and antibiotic-susceptibility of middle ear isolates as determined by middle ear fluid (mef) cultures obtained by tympanocentesis.201425475135
host-to-host variation of ecological interactions in polymicrobial infections.host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. however, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. by assuming that observed variations are random and independent, these models overlook the role of diffe ...201425473880
irak-4 and myd88 deficiencies impair igm responses against t-independent bacterial antigens.irak-4 and myd88 deficiencies impair interleukin 1 receptor and toll-like receptor (tlr) signaling and lead to heightened susceptibility to invasive bacterial infections. individuals with these primary immunodeficiencies have fewer immunoglobulin m (igm)(+)igd(+)cd27(+) b cells, a population that resembles murine splenic marginal zone b cells that mount t-independent antibody responses against bacterial antigens. however, the significance of this b-cell subset in humans is poorly understood. usi ...201425320238
severity-related changes of bronchial microbiome in chronic obstructive pulmonary disease.bronchial colonization by potentially pathogenic microorganisms (ppms) is often demonstrated in chronic obstructive pulmonary disease (copd), but culture-based techniques identify only a portion of the bacteria in mucosal surfaces. the aim of the study was to determine changes in the bronchial microbiome of copd associated with the severity of the disease. the bronchial microbiome of copd patients was analyzed by 16s rrna gene amplification and pyrosequencing in sputum samples obtained during st ...201425253795
diseases of the middle ear in childhood.middle ear diseases in childhood play an important role in daily ent practice due to their high incidence. some of these like acute otitis media or otitis media with effusion have been studied extensively within the last decades. in this article, we present a selection of important childhood middle ear diseases and discuss the actual literature concerning their treatment, management of complications and outcome. another main topic of this paper deals with the possibilities of surgical hearing re ...201425587371
diseases of the nose and paranasal sinuses in child.diseases of the pediatric nose and nasal sinuses as well as neighboring anatomical structures encompass a variety of pathologies, especially of inflammatory nature. congenital disease, such as malformations and structural deviations of the nasal septum, as well as systemic metabolic pathologies affecting the nose and sinuses, rarely require medical therapy from an otolaryngologist. the immunological function of the mucosa and genetic factors play a role in the development of disease in the pedia ...201425587370
recognition of streptococcus pneumoniae and muramyl dipeptide by nod2 results in potent induction of mmp-9, which can be controlled by lipopolysaccharide stimulation.matrix metallopeptidase 9 (mmp-9) is a protease involved in the degradation of extracellular matrix collagen. evidence suggests that mmp-9 is involved in pathogenesis during streptococcus pneumoniae infection. however, not much is known about the induction of mmp-9 and the regulatory processes involved. we show here that the gram-positive bacteria used in this study induced large amounts of mmp-9, in contrast to the gram-negative bacteria that were used. an important pathogen-associated molecula ...201425183734
analysis of the bacterial flora in the nasal cavity and the sphenoid sinus mucosa in patients operated on with an endoscopic endonasal transsphenoidal approach.the aim of this study was to analyze the bacterial flora in the nasal cavity and sphenoid sinus and evaluate the sensitivity of these bacteria to antibiotics that can be used to prevent postoperative meningitis. bacteria of the preoperative nasal cavity and intraoperative sphenoid sinus mucosa were cultured and analyzed in 40 patients (20 men and 20 women; mean age, 52.2 years) who underwent endoscopic transsphenoidal surgery. the sensitivity of these bacteria to cephalosporin, a representative ...201425446386
cephalosporinases associated with outer membrane vesicles released by bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics.to identify β-lactamase genes in gut commensal bacteroides species and to assess the impact of these enzymes, when carried by outer membrane vesicles (omvs), in protecting enteric pathogens and commensals.201425433011
cephalosporinases associated with outer membrane vesicles released by bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics.to identify β-lactamase genes in gut commensal bacteroides species and to assess the impact of these enzymes, when carried by outer membrane vesicles (omvs), in protecting enteric pathogens and commensals.201425433011
analysis of the bacterial community in chronic obstructive pulmonary disease sputum samples by denaturing gradient gel electrophoresis and real-time pcr.the global initiative defines copd for chronic obstructive lung disease as an entirely preventable and treatable disease characterized by sputum production, bacterial colonisation, neutrophilic bronchial airway inflammation and poor health status. the world health organization (who) estimates that copd will become the fourth-most common cause of death worldwide, just behind ischemic heart disease, cerebrovascular disease and hiv/aids, by 2030. the aim of this study was to determine the main stru ...201425403149
qdnamod: a statistical model-based tool to reveal intercellular heterogeneity of dna modification from smrt sequencing data.in an isogenic cell population, phenotypic heterogeneity among individual cells is common and critical for survival of the population under different environment conditions. dna modification is an important epigenetic factor that can regulate phenotypic heterogeneity. the single molecule real-time (smrt) sequencing technology provides a unique platform for detecting a wide range of dna modifications, including n6-methyladenine (6-ma), n4-methylcytosine (4-mc) and 5-methylcytosine (5-mc). here we ...201425404133
otitis media in sperm-associated antigen 6 (spag6)-deficient mice.mammalian spag6 protein is localized to the axoneme central apparatus, and it is required for normal flagella and cilia motility. recent studies demonstrated that the protein also regulates ciliogenesis and cilia polarity in the epithelial cells of brain ventricles and trachea. motile cilia are also present in the epithelial cells of the middle ear and eustachian tubes, where the ciliary system participates in the movement of serous fluid and mucus in the middle ear. cilia defects are associated ...201425393619
role of innate immunity in the pathogenesis of otitis media.otitis media (om) is a public health problem in both developed and developing countries. it is the leading cause of hearing loss and represents a significant healthcare burden. in some cases, acute om progresses to chronic suppurative om (csom), characterized by effusion and discharge, despite antimicrobial therapy. the emergence of antibiotic resistance and potential ototoxicity of antibiotics has created an urgent need to design non-conventional therapeutic strategies against om based on moder ...201425447732
from microbial gene essentiality to novel antimicrobial drug targets.bacterial respiratory tract infections, mainly caused by streptococcus pneumoniae, haemophilus influenzae and moraxella catarrhalis are among the leading causes of global mortality and morbidity. increased resistance of these pathogens to existing antibiotics necessitates the search for novel targets to develop potent antimicrobials.201425373505
ophthalmic infections in children presenting to angkor hospital for children, siem reap, cambodia.ophthalmic infections cause significant morbidity in cambodian children but aetiologic data are scarce. we investigated the causes of acute eye infections in 54 children presenting to the ophthalmology clinic at angkor hospital for children, siem reap between march and october 2012.201425369774
coagulase-negative staphylococcus culture in chronic rhinosinusitis.coagulase-negative staphylococcus (cons) is commonly isolated from patients with chronic rhinosinusitis (crs). however, the role of cons in crs remains controversial. we aimed to determine the association between positive cons culture at functional endoscopic sinus surgery (fess) and crs severity.201425367456
coagulase-negative staphylococcus culture in chronic rhinosinusitis.coagulase-negative staphylococcus (cons) is commonly isolated from patients with chronic rhinosinusitis (crs). however, the role of cons in crs remains controversial. we aimed to determine the association between positive cons culture at functional endoscopic sinus surgery (fess) and crs severity.201425367456
sterilizing immunity elicited by neisseria meningitidis carriage shows broader protection than predicted by serum antibody cross-reactivity in ceacam1-humanized mice.neisseria meningitidis asymptomatically colonizes the human upper respiratory tract but is also the cause of meningitis and severe septicemia. carriage or disease evokes an immune response against the infecting strain. hitherto, we have known little about the breadth of immunity induced by natural carriage of a single strain or its implications for subsequent infectious challenge. in this study, we establish that transgenic mice expressing human ceacam1 support nasal colonization by a variety of ...201425368118
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