Publications

superiority of transcriptional profiling over procalcitonin for distinguishing bacterial from viral lower respiratory tract infections in hospitalized adults.	distinguishing between bacterial and viral lower respiratory tract infection (lrti) remains challenging. transcriptional profiling is a promising tool for improving diagnosis in lrti.	2015	25637350
microbiome changes in healthy volunteers treated with gsk1322322, a novel antibiotic targeting bacterial peptide deformylase.	gsk1322322 is a novel antibacterial agent under development, and it has known antibacterial activities against multidrug-resistant respiratory and skin pathogens through its inhibition of the bacterial peptide deformylase. here, we used next-generation sequencing (ngs) of the bacterial 16s rrna genes from stool samples collected from 61 healthy volunteers at the predosing and end-of-study time points to determine the effects of gsk1322322 on the gastrointestinal (gi) microbiota in a phase i, ran ...	2015	25487798
the relationship of c-reactive protein levels and positive culture with quality of life in acute rhinosinusitis.	acute rhinosinusitis (ars) has been shown to significantly reduce patient quality of life (qol). while the qol in patients with chronic rhinosinusitis has been the subject of intensive research over the last decade, studies measuring the impact of ars on patient qol have remained relatively scarce. the aim of this study was to determine the relationship between the qol and parameters suggestive of acute bacterial rhinosinusitis (c-reactive protein [crp] levels and positive culture) and to see if ...	2015	25670887
mortality in healthcare-associated pneumonia in a low resistance setting: a prospective observational study.	the classification of pneumonia as community-acquired pneumonia (cap) or healthcare-associated pneumonia (hcap) has implications for selection of initial antimicrobial therapy. hcap has been associated with an increased prevalence of multidrug-resistant (mdr) pathogens and with high mortality leading to recommendations for broad empiric therapy.	2015	25664503
aetiology of acute lower respiratory infections among children under five years in accra, ghana.	the study aimed to investigate the aetiological agents and clinical presentations associated with acute lower respiratory infections (alri) among children under five years old at the korle-bu teaching hospital in ghana. this was a cross-sectional study carried from february to december 2001. nasopharyngeal aspirates and venous blood specimens obtained from 108 children with features suggestive of alri, were cultured and the isolated bacterial organisms were identified biochemically. nasopharynge ...	2015	25629622
diagnosis and management of primary ciliary dyskinesia.	primary ciliary dyskinesia (pcd) is a rare autosomal recessive disorder with defective structure and/or function of motile cilia/flagella, causing chronic upper and lower respiratory tract infections, fertility problems, and disorders of organ laterality. diagnosing pcd requires a combined approach utilizing characteristic phenotypes and complementary methods for detection of defects of ciliary function and ultrastructure, measurement of nasal nitric oxide and genetic testing. currently, biallel ...	2015	25610612
the extracellular rna complement of escherichia coli.	the secretion of biomolecules into the extracellular milieu is a common and well-conserved phenomenon in biology. in bacteria, secreted biomolecules are not only involved in intra-species communication but they also play roles in inter-kingdom exchanges and pathogenicity. to date, released products, such as small molecules, dna, peptides, and proteins, have been well studied in bacteria. however, the bacterial extracellular rna complement has so far not been comprehensively characterized. here, ...	2015	25611733
oropharyngeal colonization with neisseria lactamica, other nonpathogenic neisseria species and moraxella catarrhalis among young healthy children in ahvaz, iran.	neisseria lactamica as one of the main commensal in oropharynx during the childhood is related to the induction of a natural immunity against meningococcal meningitis. also moraxella catarrhalis in oropharynx of children is a predisposing factor for otitis media infection.	2015	25964847
etiology and antimicrobial susceptibility of middle ear fluid pathogens in costa rican children with otitis media before and after the introduction of the 7-valent pneumococcal conjugate vaccine in the national immunization program: acute otitis media microbiology in costa rican children.	acute otitis media (aom) microbiology was evaluated in children after 7-valent pneumococcal conjugate vaccine (pcv7) introduction in costa rica (private sector, 2004; national immunization program, 2009). this was a combined prospective and retrospective study conducted in a routine clinical setting in san josé, costa rica. in the prospective part of the study, which was conducted post-pcv7 introduction (2010-2012), standard bacteriological procedures were used to evaluate the etiology and serot ...	2015	25590837
bilateral conjunctivitis in a returned traveller.		2015	25590460
culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age.	the upper respiratory tract (urt) is a crucial site for host defense, as it is home to bacterial communities that both modulate host immune defense and serve as a reservoir of potential pathogens. young children are at high risk of respiratory illness, yet the composition of their urt microbiota is not well understood. microbial profiling of the respiratory tract has traditionally focused on culturing common respiratory pathogens, whereas recent culture-independent microbiome profiling can only ...	2015	25575312
endophthalmitis: state of the art.	endophthalmitis is an uncommon diagnosis but can have devastating visual outcomes. endophthalmitis may be endogenous or exogenous. exogenous endophthalmitis is caused by introduction of pathogens through mechanisms such as ocular surgery, open-globe trauma, and intravitreal injections. endogenous endophthalmitis occurs as a result of hematogenous spread of bacteria or fungi into the eye. these categories of endophthalmitis have different risk factors and causative pathogens, and thus require dif ...	2015	25609911
validation of a new aspergillus real-time pcr assay for direct detection of aspergillus and azole resistance of aspergillus fumigatus on bronchoalveolar lavage fluid.	azole resistance in aspergillus fumigatus is increasingly reported. here, we describe the validation of the aspergenius, a new multiplex real-time pcr assay consisting of two multiplex real-time pcrs, one that identifies the clinically relevant aspergillus species, and one that detects the tr34, l98h, t289a, and y121f mutations in cyp51a and differentiates susceptible from resistant a. fumigatus strains. the diagnostic performance of the aspergenius assay was tested on 37 bronchoalveolar lavage ...	2015	25568431
chronic obstructive pulmonary disease and asthma-associated proteobacteria, but not commensal prevotella spp., promote toll-like receptor 2-independent lung inflammation and pathology.	recent studies of healthy human airways have revealed colonization by a distinct commensal bacterial microbiota containing gram-negative prevotella spp. however, the immunological properties of these bacteria in the respiratory system remain unknown. here we compare the innate respiratory immune response to three gram-negative commensal prevotella strains (prevotella melaninogenica, prevotella nanceiensis and prevotella salivae) and three gram-negative pathogenic proteobacteria known to colonize ...	2015	25179236
entericidin is required for a probiotic treatment (enterobacter sp. strain c6-6) to protect trout from cold-water disease challenge.	flavobacterium psychrophilum causes bacterial cold-water disease in multiple fish species, including salmonids. an autochthonous enterobacter strain (c6-6) inhibits the in vitro growth of f. psychrophilum, and when ingested as a putative probiotic, it provides protection against injection challenge with f. psychrophilum in rainbow trout. in this study, low-molecular-mass (≤3 kda) fractions from both enterobacter c6-6 and escherichia coli k-12 culture supernatants inhibited the growth of f. psych ...	2015	25381243
acute-phase protein α1-anti-trypsin: diverting injurious innate and adaptive immune responses from non-authentic threats.	one would assume that the anti-inflammatory activity of α1-anti-trypsin (aat) is the result of inhibiting neutrophil enzymes. however, aat exhibits tolerogenic activities that are difficult to explain by serine-protease inhibition or by reduced inflammatory parameters. targets outside the serine-protease family have been identified, supporting the notion that elastase inhibition, the only functional factory release criteria for clinical-grade aat, is over-emphasized. non-obvious developments in ...	2015	25351931
mechanisms of bacterial colonization of the respiratory tract.	respiratory tract infections are an important cause of morbidity and mortality worldwide. chief among these are infections involving the lower airways. the opportunistic bacterial pathogens responsible for most cases of pneumonia can cause a range of local and invasive infections. however, bacterial colonization (or carriage) in the upper airway is the prerequisite of all these infections. successful colonizers must attach to the epithelial lining, grow on the nutrient-limited mucosal surface, e ...	2015	26488280
compendium of pseudo conditions in sexually transmitted diseases.		2015	26392668
influence of pseudomonas aeruginosa on exacerbation in patients with bronchiectasis.	a majority of the studies done on the western population have shown that pseudomonas aeruginosa causes many severe infections in patients with bronchiectasis as compared to other pathogens. there is scarcity of similar data from the asian population.	2015	25722615
toward primary prevention of asthma. reviewing the evidence for early-life respiratory viral infections as modifiable risk factors to prevent childhood asthma.	a first step in primary disease prevention is identifying common, modifiable risk factors that contribute to a significant proportion of disease development. infant respiratory viral infection and childhood asthma are the most common acute and chronic diseases of childhood, respectively. common clinical features and links between these diseases have long been recognized, with early-life respiratory syncytial virus (rsv) and rhinovirus (rv) lower respiratory tract infections (lrtis) being strongl ...	2015	25369458
the microbiome in asthma.	the application of recently developed sensitive, specific, culture-independent tools for identification of microbes is transforming concepts of microbial ecology, including concepts of the relationships between the vast complex populations of microbes associated with ourselves and with states of health and disease. although most work initially focused on the community of microbes (microbiome) in the gastrointestinal tract and its relationship to gastrointestinal disease, interest has expanded to ...	2015	25567040
[analysis on clinical and epidemioloical characteristics of measles in hospitalized children in shanghai in 2012].	to investigate the main factors that influence measles morbidity and the genotype of measles virus, so as to provide evidence for scientific decision making to further control the prevalence of measles.	2015	26717659
the in vitro antimicrobial activity of cymbopogon essential oil (lemon grass) and its interaction with silver ions.	it is well known that cymbopogon (lemon grass) essential oil exhibits antimicrobial activity while the efficacy of silver ions as a disinfectant is equally well reported.	2015	26055131
pathogen transcriptional profile in nasopharyngeal aspirates of children with acute respiratory tract infection.	acute respiratory tract infections (ari) present a significant morbidity and pose a global health burden. patients are frequently treated with antibiotics although ari are most commonly caused by virus, strengthening the need for improved diagnostic methods.	2015	26209405
detection of chlamydophila pneumoniae and typical bacteria in patients with chronic cough.	the aim of research was to analyze the results of microbiological tests for typical and atypical bacteria in patients with symptoms of chronic cough. a total of 214 outpatients aged from 2 to 94 years (110 women, 64 men, and 40 children) with chronic cough were studied. four hundred twenty eight throat swabs were examined for atypical bacteria antigen (chlamydophila pneumoniae) (n=214) and typical pathogens (n=214). chl. pneumoniae detection was performed using indirect immunofluorescence test. ...	2015	25724797
the microbiome of otitis media with effusion in indigenous australian children.	indigenous australian children have a high prevalence of otitis media with effusion (ome) and associated conductive hearing loss. only three microbiological studies of middle ear fluid (mef) from indigenous australian children with ome have been reported. all of these were reliant on culture or species-specific pcr assays. the aim of this study was to characterise the middle ear fluid (mef), adenoid and nasopharyngeal (np) microbiomes of indigenous australian children, using culture-independent ...	2015	26228497
synthesis and structure-activity relationship of amidine derivatives of 3,4-ethylenedioxythiophene as novel antibacterial agents.	current antibacterial chemotherapeutics are facing an alarming increase in bacterial resistance pressuring the search for novel agents that would expand the available therapeutic arsenal against resistant bacterial pathogens. in line with these efforts, a series of 9 amidine derivatives of 3,4-ethylenedioxythiophene were synthesized and, together with 18 previously synthesized analogs, evaluated for their relative dna binding affinity, in vitro antibacterial activities and preliminary in vitro s ...	2015	25461312
distribution of pathogens causing nosocomial infection in patients with bronchial asthma.	this study aimed to analyze nosocomial respiratory infection (nri) in patients with bronchial asthma. among the clinical data of 575 asthmatic patients that was collected and analyzed, 52 were diagnosed with nri. the most common gram-positive bacterial species was streptococcus pneumoniae, which was detected in 8 patients, whereas the predominant gram-negative bacteria included haemophilus influenzae (11 patients), moraxella catarrhalis (8 patients), and escherichia coli (7 patients). the simult ...	2015	26662406
synthesis and structure-activity relationships of novel 9-oxime acylides with improved bactericidal activity.	9-oxime acylides have different sar and binding modes from 9-oxime ketolides. an aminopyridyl or carbamoylpyridyl group anchored at the end of the 9-oxime 2-propargyl group is beneficial for antimicrobial activity. both the 2-pyridyl and 3-pyridyl groups derived from 3-oh have stacking interactions with the base pair g2505/c2610 (escherichia coli numbering) of the bacterial rrna. compounds 3 presented characteristic features that belong to bactericidal agents when used against constitutive-erm r ...	2015	26349628
bacterial-resistance among outpatients of county hospitals in china: significant geographic distinctions and minor differences between central cities.	the purpose of this study was to survey antibacterial resistance in outpatients of chinese county hospitals. a total of 31 county hospitals were selected and samples continuously collected from august 2010 to august 2011. drug sensitivity testing was conducted in a central laboratory. a total of 2946 unique isolates were collected, including 634 strains of escherichia coli, 606 klebsiella pneumoniae, 476 staphylococcus aureus, 308 streptococcus pneumoniae, and 160 haemophilus influenzae. extende ...	2015	25708671
pharmacokinetic/pharmacodynamic analysis to evaluate ceftaroline fosamil dosing regimens for the treatment of community-acquired bacterial pneumonia and complicated skin and skin-structure infections in patients with normal and impaired renal function.	in this study, the probability of pharmacokinetic/pharmacodynamic target attainment (pta) of ceftaroline against clinical isolates causing community-acquired bacterial pneumonia (cabp) and complicated skin and skin-structure infection (csssi) in europe was evaluated. three dosing regimens were assessed: 600 mg every 12 h (q12 h) as a 1-h infusion (standard dose) or 600 mg every 8 h (q8 h) as a 2-h infusion in virtual patients with normal renal function; and 400 mg q12 h as a 1-h infusion in pati ...	2015	25700566
respiratory bacterial culture from two sequential bronchoalveolar lavages of the same lobe in children with chronic cough.	identification of bacteria causing lower-airway infections is important to determine appropriate antimicrobial therapy. flexible bronchoscopy with bronchoalveolar lavage (bal) is used to obtain lower-airway specimens in young children. the first lavage (lavage-1) is typically used for bacterial culture. however, no studies in children have compared the detection of cultivable bacteria from sequential lavages of the same lobe. bal fluid was collected from two sequential lavages of the same lobe i ...	2015	26399701
[a multicenter study of the antimicrobial susceptibility of streptococcus pneumoniae, streptococcus pyogenes, haemophilus influenzae, and moraxella catarrhalis from community acquired infections in saitama, japan].	we examined regional surveillance of antimicrobial susceptibility of community acquired bacterial pathogens from patients in saitama, japan. the fourth-year survey was conducted in three of the period 2007-2010 (period i, 2007-2008; period ii, 2008-2009; period iii, 2009-2010). antimicrobial susceptibility testing was conducted at the central reference laboratory according to the method recommended by japanese society of chemotherapy using maximum 13 antibacterial agents. susceptibility testing ...	2015	26742285
haemophilus influenzae isolates survive for up to 20 years at -70 °c in skim milk tryptone glucose glycerol broth (stggb) if thawing is avoided during re-culture.	haemophilus influenzae remains a major cause of disease worldwide requiring continued study. recently, isolates of streptococcus pneumoniae and moraxella catarrhalis, but not h. influenzae, were reported to survive long-term ultra-freeze storage in stggb. we show that nontypeable h. influenzae isolates survive for up to 20 years when thawing is avoided.	2015	26477641
vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry for identifying respiratory bacterial pathogens: a fast and efficient method.	mass spectrometry has become a reference resource for identifying microorganisms in clinical microbiology services. one hundred and fifty one clinical isolates were selected from respiratory specimens routinely identified as streptococcus pneumoniae (43), haemophilus influenzae (64) and moraxella catarrhalis (44). these identifications were compared with other phenotypical methods and mass spectrometry (maldi-tof-ms vitek). result discrepancies were assessed by 16s rrna sequencing. thirty-eight ...	2015	26437754
clinical characteristics of the patients with bacteremia due to moraxella catarrhalis in children: a case-control study.	invasive diseases due to moraxella catarrhalis are rare in children, even in immunocompromised hosts. therefore, data regarding clinical characteristics and risk factors of such patients are limited. the aim of this study is to compare the clinical characteristics of patients with bacteremia due to moraxella catarrhalis against those with bacteremia due to streptococcus pneumoniae and haemophilus influenzae.	2015	26861621
clinical characteristics of the patients with bacteremia due to moraxella catarrhalis in children: a case-control study.	invasive diseases due to moraxella catarrhalis are rare in children, even in immunocompromised hosts. therefore, data regarding clinical characteristics and risk factors of such patients are limited. the aim of this study is to compare the clinical characteristics of patients with bacteremia due to moraxella catarrhalis against those with bacteremia due to streptococcus pneumoniae and haemophilus influenzae.	2015	26861621
a phase 1 randomized, double-blind, placebo-controlled, crossover trial of das181 (fludase®) in adult subjects with well-controlled asthma.	influenza virus (ifv) infection is associated with increased morbidity and mortality in people with underlying lung disease. treatment options for ifv are currently limited and antiviral resistance is a growing concern. das181, an inhaled antiviral with a unique mechanism of action, has shown promise in early clinical trials involving generally healthy human subjects. this study was undertaken to assess the safety and tolerability of das181 in individuals with underlying reactive airway disease.	2015	26830468
a phase 1 randomized, double-blind, placebo-controlled, crossover trial of das181 (fludase®) in adult subjects with well-controlled asthma.	influenza virus (ifv) infection is associated with increased morbidity and mortality in people with underlying lung disease. treatment options for ifv are currently limited and antiviral resistance is a growing concern. das181, an inhaled antiviral with a unique mechanism of action, has shown promise in early clinical trials involving generally healthy human subjects. this study was undertaken to assess the safety and tolerability of das181 in individuals with underlying reactive airway disease.	2015	26830468
bacterial communities vary between sinuses in chronic rhinosinusitis patients.	chronic rhinosinusitis (crs) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in resu ...	2015	26834708
bacterial communities vary between sinuses in chronic rhinosinusitis patients.	chronic rhinosinusitis (crs) is a common and potentially debilitating disease characterized by inflammation of the sinus mucosa for longer than 12 weeks. bacterial colonization of the sinuses and its role in the pathogenesis of this disease is an ongoing area of research. recent advances in culture-independent molecular techniques for bacterial identification have the potential to provide a more accurate and complete assessment of the sinus microbiome, however there is little concordance in resu ...	2015	26834708
staphylococcus epidermidis and biofilm-associated neutrophils in chronic rhinosinusitis. a pilot study.	a key role of bacterial biofilm in the pathogenesis of chronic rhinosinusitis (crs) with (crswnp) and without nasal polyps (crssnp) is commonly accepted. however, the impact of some bacterial species isolated from inflamed sinus mucosa on biofilm formation is unclear. in particular, the role of staphylococcus epidermidis as aetiological agents of crs is controversial. moreover, the effect of biofilm formation on neutrophil infiltration and activity in crswnp calls for explanation. in this study, ...	2015	26765504
staphylococcus epidermidis and biofilm-associated neutrophils in chronic rhinosinusitis. a pilot study.	a key role of bacterial biofilm in the pathogenesis of chronic rhinosinusitis (crs) with (crswnp) and without nasal polyps (crssnp) is commonly accepted. however, the impact of some bacterial species isolated from inflamed sinus mucosa on biofilm formation is unclear. in particular, the role of staphylococcus epidermidis as aetiological agents of crs is controversial. moreover, the effect of biofilm formation on neutrophil infiltration and activity in crswnp calls for explanation. in this study, ...	2015	26765504
real-time detection of a virus using detection dogs.	viral infections are ubiquitous in humans, animals, and plants. real-time methods to identify viral infections are limited and do not exist for use in harsh or resource-constrained environments. previous research identified that tissues produce unique volatile organic compounds (voc) and demonstrated that voc concentrations change during pathologic states, including infection, neoplasia, or metabolic disease. patterns of voc expression may be pathogen specific and may be associated with an odor ...	2015	26779494
real-time detection of a virus using detection dogs.	viral infections are ubiquitous in humans, animals, and plants. real-time methods to identify viral infections are limited and do not exist for use in harsh or resource-constrained environments. previous research identified that tissues produce unique volatile organic compounds (voc) and demonstrated that voc concentrations change during pathologic states, including infection, neoplasia, or metabolic disease. patterns of voc expression may be pathogen specific and may be associated with an odor ...	2015	26779494
polymicrobial intensive care unit-acquired pneumonia: prevalence, microbiology and outcome.	microbial aetiology of intensive care unit (icu)-acquired pneumonia (icuap) determines antibiotic treatment and outcomes. the impact of polymicrobial icuap is not extensively known. we therefore investigated the characteristics and outcomes of polymicrobial aetiology of icuap.	2015	26703094
full genomic characterization of a saffold virus isolated in peru.	while studying respiratory infections of unknown etiology we detected saffold virus in an oropharyngeal swab collected from a two-year-old female suffering from diarrhea and respiratory illness. the full viral genome recovered by deep sequencing showed 98% identity to a previously described saffold strain isolated in japan. phylogenetic analysis confirmed the peruvian saffold strain belongs to genotype 3 and is most closely related to strains that have circulated in asia. this is the first docum ...	2015	26610576
spectrophotometric investigations of macrolide antibiotics: a brief review.	macrolides, one of the most commonly used class of antibiotics, are a group of drugs produced by streptomyces species. they belong to the polyketide class of natural products. their activity is due to the presence of a large macrolide lactone ring with deoxy sugar moieties. they are protein synthesis inhibitors and broad-spectrum antibiotics, active against both gram-positive and gram-negative bacteria. different analytical techniques have been reported for the determination of macrolides such a ...	2015	26609215
real life management of community-acquired pneumonia in adults in the gulf region and comparison with practice guidelines: a prospective study.	very few data exist on the management of community-acquired pneumonia (cap) in patients admitted to hospitals in the gulf region. the objectives of this study were to describe treatment patterns for cap in 38 hospitals in five gulf countries (united arab emirates, kuwait, bahrain, oman, and qatar) and to compare the findings to the most recent infectious diseases society of america (idsa)/american thoracic society (ats) guidelines.	2015	26424530
clinical characteristics of nursing home-acquired pneumonia in elderly patients admitted to a korean teaching hospital.	nursing home-acquired pneumonia (nhap) is included under healthcare-associated pneumonia. however, the optimal treatment strategy for nhap has been controversial in several studies. we evaluated the clinical features of nhap compared to community-acquired pneumonia (cap) in elderly patients admitted with pneumonia.	2015	26354058
differentiation of acute q fever from other infections in patients presenting to hospitals, the netherlands(1).	differentiating acute q fever from infections caused by other pathogens is essential. we conducted a retrospective case-control study to evaluate differences in clinical signs, symptoms, and outcomes for 82 patients with acute q fever and 52 control patients who had pneumonia, fever and lower respiratory tract symptoms, or fever and hepatitis, but had negative serologic results for q fever. patients with acute q fever were younger and had higher c-reactive protein levels but lower leukocyte coun ...	2015	26196955
profile of tedizolid phosphate and its potential in the treatment of acute bacterial skin and skin structure infections.	tedizolid phosphate is the first once-daily oxazolidinone approved by the united states food and drug administration for the treatment of acute bacterial skin and skin structure infections (absssi). it is more potent in vitro than linezolid against methicillin-resistant staphylococcus aureus (mrsa) and other gram-positive pathogens causing absssi, even retaining activity against some linezolid-resistant strains. tedizolid is approximately 90% protein bound, leading to lower free-drug concentrati ...	2015	25960671
bacteriological assessment of healthcare-associated pneumonia using a clone library analysis.	the causative pathogens of healthcare-associated pneumonia (hcap) remain controversial, and the use of conventional cultivation of sputum samples is occasionally inappropriate due to the potential for oral bacterial contamination. it is also sometimes difficult to determine whether methicillin-resistant staphylococcus aureus (mrsa) is a true causative pathogen of hcap.	2015	25874715
the burden and etiology of community-onset pneumonia in the aging japanese population: a multicenter prospective study.	the increasing burden of pneumonia in adults is an emerging health issue in the era of global population aging. this study was conducted to elucidate the burden of community-onset pneumonia (cop) and its etiologic fractions in japan, the world's most aged society.	2015	25822890
etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in norway.	despite recent advances in microbiological techniques, the etiology of community-acquired pneumonia (cap) is still not well described. we applied polymerase chain reaction (pcr) and conventional methods to describe etiology of cap in hospitalized adults and evaluated their respective diagnostic yields.	2015	25887603
colistin for lung infection: an update.	increasing incidence of resistance of gram-negative bacteria against even newer antibiotic including carbapenem has generated interest in the old antibiotic colistin, which are being used as salvage therapy in the treatment of multidrug resistant infection. colistin has excellent bactericidal activity against most gram-negative bacilli. it has shown persist level in the liver, kidney, heart, and muscle; while it is poorly distributed to the bones, cerebrospinal fluid, lung parenchyma, and pleura ...	2015	25705428
kingella kingae: carriage, transmission, and disease.	kingella kingae is a common etiology of pediatric bacteremia and the leading agent of osteomyelitis and septic arthritis in children aged 6 to 36 months. this gram-negative bacterium is carried asymptomatically in the oropharynx and disseminates by close interpersonal contact. the colonized epithelium is the source of bloodstream invasion and dissemination to distant sites, and certain clones show significant association with bacteremia, osteoarthritis, or endocarditis. kingella kingae produces ...	2015	25567222
procalcitonin levels in gram-positive, gram-negative, and fungal bloodstream infections.	procalcitonin (pct) can discriminate bacterial from viral systemic infections and true bacteremia from contaminated blood cultures. the aim of this study was to evaluate pct diagnostic accuracy in discriminating gram-positive, gram-negative, and fungal bloodstream infections. a total of 1,949 samples from patients with suspected bloodstream infections were included in the study. median pct value in gram-negative (13.8 ng/ml, interquartile range (iqr) 3.4-44.1) bacteremias was significantly highe ...	2015	25852221
abundant intergenic taactga direct repeats and putative alternate rna polymerase β' subunits in marine beggiatoaceae genomes: possible regulatory roles and origins.	the genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. the draft genome of a cand. "maribeggiatoa" filament from the guaymas basin (gulf of california, mexico) seafloor contains 169 sets of taactga direct repeats and one indirect repeat, with two to six copies per set. related heptamers are rarely or never found as direct repeat ...	2015	26733950
effects of vaccination with 10-valent pneumococcal non-typeable haemophilus influenza protein d conjugate vaccine (phid-cv) on the nasopharyngeal microbiome of kenyan toddlers.	pneumococcal conjugate vaccines reduce the prevalence of vaccine serotypes carried in the nasopharynx. because this could alter carriage of other potential pathogens, we assessed the nasopharyngeal microbiome of children who had been vaccinated with 10-valent pneumococcal non-typeable haemophilus influenzae protein-d conjugate vaccine (phid-cv).	2015	26083474
diagnostic value of bronchoalveolar lavage in leukemic and bone marrow transplant patients: the impact of antimicrobial therapy.	there is significant morbidity and mortality from pneumonia in leukemic and bone marrow transplant patients. we sought to explore the diagnostic yield of bronchoalveolar lavage (bal) in these patients with new pulmonary infiltrates. a retrospective chart review of approximately 200 non- human immunodeficiency virus (hiv) leukemic and hematopoietic stem cell transplantation (hsct) patients who underwent bronchoscopy at a single academic cancer center was performed. antimicrobial use for less than ...	2015	25574361
the impact of immunosenescence on pulmonary disease.	the global population is aging with significant gains in life expectancy particularly in the developed world. consequently, greater focus on understanding the processes that underlie physiological aging has occurred. key facets of advancing age include genomic instability, telomere shortening, epigenetic changes, and declines in immune function termed immunosenescence. immunosenescence and its associated chronic low grade systemic "inflamm-aging" contribute to the development and progression of ...	2015	26199462
pneumonia in the neutropenic cancer patient.	pneumonia is the leading cause of death among neutropenic cancer patients, particularly those with acute leukaemia. even with empiric therapy, case fatality rates of neutropenic pneumonias remain unacceptably high. however, recent advances in the management of neutropenic pneumonia offer hope for improved outcomes in the cancer setting. this review summarizes recent literature regarding the clinical presentation, microbiologic trends, diagnostic advances and therapeutic recommendations for cance ...	2015	25784246
performances and reliability of bruker microflex lt and vitek ms maldi-tof mass spectrometry systems for the identification of clinical microorganisms.	in clinical microbiology laboratories, routine microbial identification is mostly performed using culture based methodologies requiring 24 to 72 hours from culturing to identification. matrix assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) technology has been established as a cost effective, reliable, and faster alternative identification platform. in this study, we evaluated the reliability of the two available maldi-tof ms systems for their routine clinical ...	2015	26793718
metagenomic human repiratory air in a hospital environment.	hospital-acquired infection (hai) or nosocomial infection is an issue that frequent hospital environment. we believe conventional regulated petri dish method is insufficient to evaluate hai. to address this problem, metagenomic sequencing was applied to screen airborne microbes in four rooms of beijing hospital. with air-in amount of sampler being setup to one person's respiration quantity, metagenomic sequencing identified huge numbers of species in the rooms which had already qualified widely ...	2015	26431488
contact-dependent growth inhibition (cdi) and cdib/cdia two-partner secretion proteins.	bacteria have developed several strategies to communicate and compete with one another in complex environments. one important mechanism of inter-bacterial competition is contact-dependent growth inhibition (cdi), in which gram-negative bacteria use cdib/cdia two-partner secretion proteins to suppress the growth of neighboring target cells. cdib is an omp85 outer-membrane protein that exports and assembles cdia exoproteins onto the inhibitor cell surface. cdia binds to receptors on susceptible ba ...	2015	26388411
antibacterial effects of cinnamon: from farm to food, cosmetic and pharmaceutical industries.	herbs and spices have been used since ancient times, because of their antimicrobial properties increasing the safety and shelf life of food products by acting against foodborne pathogens and spoilage bacteria. plants have historically been used in traditional medicine as sources of natural antimicrobial substances for the treatment of infectious disease. therefore, much attention has been paid to medicinal plants as a source of alternative antimicrobial strategies. moreover, due to the growing d ...	2015	26378575
development of two real-time multiplex pcr assays for the detection and quantification of eight key bacterial pathogens in lower respiratory tract infections.	the frequent lack of a positive and timely microbiological diagnosis in patients with lower respiratory tract infection (lrti) is an important obstacle to antimicrobial stewardship. patients are typically prescribed broad-spectrum empirical antibiotics while microbiology results are awaited, but, because these are often slow, negative, or inconclusive, de-escalation to narrow-spectrum agents rarely occurs in clinical practice. the aim of this study was to develop and evaluate two multiplex real- ...	2015	25980353
impact of the cftr-potentiator ivacaftor on airway microbiota in cystic fibrosis patients carrying a g551d mutation.	airway microbiota composition has been clearly correlated with many pulmonary diseases, and notably with cystic fibrosis (cf), an autosomal genetic disorder caused by mutation in the cf transmembrane conductance regulator (cftr). recently, a new molecule, ivacaftor, has been shown to re-establish the functionality of the g551d-mutated cftr, allowing significant improvement in lung function.	2015	25853698
mannose-binding lectin protein and its association to clinical outcomes in copd: a longitudinal study.	functional deficiency of mannose-binding lectin (mbl) may contribute to the pathogenesis of chronic obstructive pulmonary disease. we hypothesized that specific mbl2 gene polymorphisms and circulating mbl protein levels are associated with clinically relevant outcomes in the predicting outcome using systemic markers in severe exacerbations of copd promise-copd cohort.	2015	26684757
comparison of serum procalcitonin in respiratory infections and bloodstream infections.	this study observed the relationship between procalcitonin (pct) and results of sputum culture, the relationship between pct and results of blood culture to evaluate and compare the value of pct in respiratory and bloodstream infections.	2015	26885109
multicenter evaluation of the bruker maldi biotyper ca system for the identification of clinical aerobic gram-negative bacterial isolates.	the prompt and accurate identification of bacterial pathogens is fundamental to patient health and outcome. recent advances in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (maldi-tof ms) have revolutionized bacterial identification in the clinical laboratory, but uniform incorporation of this technology in the u.s. market has been delayed by a lack of fda-cleared systems. in this study, we conducted a multicenter evaluation of the maldi biotyper ca (mbt-ca) system ...	2015	26529504
diagnosis, monitoring, and treatment of primary ciliary dyskinesia: pcd foundation consensus recommendations based on state of the art review.	primary ciliary dyskinesia (pcd) is a genetically heterogeneous, rare lung disease resulting in chronic oto-sino-pulmonary disease in both children and adults. many physicians incorrectly diagnose pcd or eliminate pcd from their differential diagnosis due to inexperience with diagnostic testing methods. thus far, all therapies used for pcd are unproven through large clinical trials. this review article outlines consensus recommendations from pcd physicians in north america who have been engaged ...	2015	26418604
diagnosis, monitoring, and treatment of primary ciliary dyskinesia: pcd foundation consensus recommendations based on state of the art review.	primary ciliary dyskinesia (pcd) is a genetically heterogeneous, rare lung disease resulting in chronic oto-sino-pulmonary disease in both children and adults. many physicians incorrectly diagnose pcd or eliminate pcd from their differential diagnosis due to inexperience with diagnostic testing methods. thus far, all therapies used for pcd are unproven through large clinical trials. this review article outlines consensus recommendations from pcd physicians in north america who have been engaged ...	2015	26418604
determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease.	changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ...	2015	26370552
determinants of bacteriological outcomes in exacerbations of chronic obstructive pulmonary disease.	changes in sputum microbiology following antibiotic treatment of acute exacerbations of chronic obstructive pulmonary disease (aecopd), including patterns of bacteriological relapse and superinfection are not well understood. sputum microbiology at exacerbation is not routinely performed, but pathogen presence and species are determinants of outcomes. therefore, we determined whether baseline clinical factors could predict the presence of bacterial pathogens at exacerbation. bacterial eradicatio ...	2015	26370552
meropenem population pharmacokinetics in critically ill patients with septic shock and continuous renal replacement therapy: influence of residual diuresis on dose requirements.	meropenem dosing in critically ill patients with septic shock and continuous renal replacement therapy (crrt) is complex, with the recommended maintenance doses being 500 mg to 1,000 mg every 8 h (q8h) to every 12 h. this multicenter study aimed to describe the pharmacokinetics (pks) of meropenem in this population to identify the sources of pk variability and to evaluate different dosing regimens to develop recommendations based on clinical parameters. thirty patients with septic shock and crrt ...	2015	26124172
infection control in the pulmonary function test laboratory.	pulmonary function testing plays a crucial role in the diagnostic evaluation of patients with lung diseases. cases of cross infection acquired from the pulmonary function laboratory, although rare, have been reported from various countries. it is therefore imperative to identify the risks and potential organisms implicated in cross infections in a pulmonary function test (pft) laboratory and implement better and more effective infection control procedures, which will help in preventing cross inf ...	2015	26180386
the microbiome of the human lower airways: a next generation sequencing perspective.	for a long time, the human lower airways were considered a sterile environment where the presence of microorganisms, typically revealed by culturing, was interpreted as an abnormal health state. more recently, high-throughput sequencing-based studies have led to a shift in this perception towards the notion that even in healthy conditions the lower airways show either transient presence or even permanent colonization by microorganisms. however, challenges related to low biomass and contamination ...	2015	26140078
aminomethyl spectinomycins as therapeutics for drug-resistant respiratory tract and sexually transmitted bacterial infections.	the antibiotic spectinomycin is a potent inhibitor of bacterial protein synthesis with a unique mechanism of action and an excellent safety index, but it lacks antibacterial activity against most clinically important pathogens. a series of n-benzyl-substituted 3'-(r)-3'-aminomethyl-3'-hydroxy spectinomycins was developed on the basis of a computational analysis of the aminomethyl spectinomycin binding site and structure-guided synthesis. these compounds had ribosomal inhibition values comparable ...	2015	25995221
bacterial adaptation during chronic respiratory infections.	chronic lung infections are associated with increased morbidity and mortality for individuals with underlying respiratory conditions such as cystic fibrosis (cf) and chronic obstructive pulmonary disease (copd). the process of chronic colonisation allows pathogens to adapt over time to cope with changing selection pressures, co-infecting species and antimicrobial therapies. these adaptations can occur due to environmental pressures in the lung such as inflammatory responses, hypoxia, nutrient de ...	2015	25738646
contribution of the bact/alert mb mycobacterium bottle to bloodstream infection surveillance in thailand: added yield for burkholderia pseudomallei.	community-acquired bloodstream infections cause substantial morbidity and mortality worldwide, but microbiology capacity and surveillance limitations have challenged good descriptions of pathogen distribution in many regions, including southeast asia. active surveillance for bloodstream infections has been conducted in two rural thailand provinces for >7 years. blood specimens were divided into two culture bottles, one optimized for aerobic growth (f bottle) and a second for enhanced growth of m ...	2015	25588650
whole-genome sequencing targets drug-resistant bacterial infections.	during the past two decades, the technological progress of whole-genome sequencing (wgs) had changed the fields of environmental microbiology and biotechnology, and, currently, is changing the underlying principles, approaches, and fundamentals of public health, epidemiology, health economics, and national productivity. today's wgs technologies are able to compete with conventional techniques in cost, speed, accuracy, and resolution for day-to-day control of infectious diseases and outbreaks in ...	2015	26243131
proteomics of aggregatibacter actinomycetemcomitans outer membrane vesicles.	aggregatibacter actinomycetemcomitans is an oral and systemic pathogen associated with aggressive forms of periodontitis and with endocarditis. outer membrane vesicles (omvs) released by this species have been demonstrated to deliver effector proteins such as cytolethal distending toxin (cdt) and leukotoxin (ltxa) into human host cells and to act as triggers of innate immunity upon carriage of nod1- and nod2-active pathogen-associated molecular patterns (pamps). to improve our understanding of t ...	2015	26381655
haemophilus influenzae: using comparative genomics to accurately identify a highly recombinogenic human pathogen.	haemophilus influenzae is an opportunistic bacterial pathogen that exclusively colonises humans and is associated with both acute and chronic disease. despite its clinical significance, accurate identification of h. influenzae is a non-trivial endeavour. h. haemolyticus can be misidentified as h. influenzae from clinical specimens using selective culturing methods, reflecting both the shared environmental niche and phenotypic similarities of these species. on the molecular level, frequent geneti ...	2015	26311542
aptamers against pathogenic microorganisms.	an important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. one of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. the present review summarizes va ...	2015	26258445
aptamers against pathogenic microorganisms.	an important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. one of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. the present review summarizes va ...	2015	26258445
development of a multilocus sequence typing scheme for molecular typing of mycoplasma pneumoniae.	mycoplasma pneumoniae is a major human respiratory pathogen causing both upper and lower respiratory disease in humans of all ages, and it can also result in other serious extrapulmonary sequelae. a multilocus sequence typing (mlst) scheme for m. pneumoniae was developed based on the sequences of eight housekeeping genes (ppa, pgm, gyrb, gmk, glya, atpa, arcc, and adk) and applied to 55 m. pneumoniae clinical isolates and the two type strains m129 and fh. a total of 12 sequence types (sts) resul ...	2015	26202118
structural basis of transcription inhibition by cbr hydroxamidines and cbr pyrazoles.	cbr hydroxamidines are small-molecule inhibitors of bacterial rna polymerase (rnap) discovered through high-throughput screening of synthetic-compound libraries. cbr pyrazoles are structurally related rnap inhibitors discovered through scaffold hopping from cbr hydroxamidines. cbr hydroxamidines and pyrazoles selectively inhibit gram-negative bacterial rnap and exhibit selective antibacterial activity against gram-negative bacteria. here, we report crystal structures of the prototype cbr hydroxa ...	2015	26190576
biological properties of extracellular vesicles and their physiological functions.	in the past decade, extracellular vesicles (evs) have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. this is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. while intensive investigation has targeted the role of evs in different pathological processes, for example, in cancer and autoimmune diseases, the ev-mediated ...	2015	25979354
moraxella catarrhalis acrab-oprm efflux pump contributes to antimicrobial resistance and is enhanced during cold shock response.	moraxella catarrhalis is a common pathogen of the human respiratory tract. multidrug efflux pumps play a major role in antibiotic resistance and virulence in many gram-negative organisms. in the present study, the role of the acrab-oprm efflux pump in antibiotic resistance was investigated by constructing mutants that lack the acra, acrb, and oprm genes in m. catarrhalis strain o35e. we observed a moderate (1.5-fold) decrease in the mics of amoxicillin and cefotaxime and a marked (4.7-fold) decr ...	2015	25583725
comparative evaluation of 2 g single dose versus conventional dose azithromycin in uncomplicated skin and skin structure infections.	uncomplicated skin and skin structure infections (usssis) are a common clinical problem. majority are caused by staphylococci and streptococci. different oral antibiotics are used for usssi, with comparable efficacy but varying treatment duration, cost, and adverse event profile. azithromycin is used in usssi in adults conventionally in a dose of 500 mg once for 5 days. the extensive tissue distribution of the drug and its long elimination half-life prompted us to explore whether a single 2 g do ...	2015	26288467
moraxella catarrhalis binds plasminogen to evade host innate immunity.	several bacterial species recruit the complement regulators c4b-binding protein, factor h, and vitronectin, resulting in resistance against the bactericidal activity of human serum. it was recently demonstrated that bacteria also bind plasminogen, which is converted to plasmin that degrades c3b and c5. in this study, we found that a series of clinical isolates (n = 58) of the respiratory pathogen moraxella catarrhalis, which is commonly isolated from preschool children and adults with chronic ob ...	2015	26099590
hepatocytes: a key cell type for innate immunity.	hepatocytes, the major parenchymal cells in the liver, play pivotal roles in metabolism, detoxification, and protein synthesis. hepatocytes also activate innate immunity against invading microorganisms by secreting innate immunity proteins. these proteins include bactericidal proteins that directly kill bacteria, opsonins that assist in the phagocytosis of foreign bacteria, iron-sequestering proteins that block iron uptake by bacteria, several soluble factors that regulate lipopolysaccharide sig ...	2015	26685902
hepatocytes: a key cell type for innate immunity.	hepatocytes, the major parenchymal cells in the liver, play pivotal roles in metabolism, detoxification, and protein synthesis. hepatocytes also activate innate immunity against invading microorganisms by secreting innate immunity proteins. these proteins include bactericidal proteins that directly kill bacteria, opsonins that assist in the phagocytosis of foreign bacteria, iron-sequestering proteins that block iron uptake by bacteria, several soluble factors that regulate lipopolysaccharide sig ...	2015	26685902
ccl20 and beta-defensin 2 production by human lung epithelial cells and macrophages in response to brucella abortus infection.	both ccl20 and human β-defensin 2 (hbd2) interact with the same membrane receptor and display chemotactic and antimicrobial activities. they are produced by airway epithelia in response to infectious agents and proinflammatory cytokines. whereas brucella spp. can infect humans through inhalation, their ability to induce ccl20 and hbd2 in lung cells is unknown. here we show that b. abortus induces ccl20 expression in human alveolar (a549) or bronchial (calu-6) epithelial cell lines, primary alveo ...	2015	26448160
moonlighting o-acetylserine sulfhydrylase: new functions for an old protein.	o-acetylserine sulfhydrylase a (cysk) is the pyridoxal 5'-phosphate-dependent enzyme that catalyzes the final reaction of cysteine biosynthesis in bacteria. cysk was initially identified in a complex with serine acetyltransferase (cyse), which catalyzes the penultimate reaction in the synthetic pathway. this "cysteine synthase" complex is stabilized by insertion of the cyse c-terminus into the active-site of cysk. remarkably, the cysk/cyse binding interaction is conserved in most bacterial and p ...	2015	25731080
empirical antibiotic therapy for pneumonia in intensive care units: a multicentre, retrospective analysis of potentially pathogenic microorganisms identified by endotracheal aspirates cultures.	the purpose of this investigation was to explore the presumed relationship between the days of hospitalisation and microorganisms identified by endotracheal aspirate cultures in relation to adequate empirical treatment strategies of pneumonia in the intensive care unit (icu). all potentially pathogenic microorganisms identified by (surveillance) cultures of endotracheal aspirates obtained in the icus of two dutch teaching hospitals in 2007 and 2012 were retrospectively collected and analysed. an ...	2015	26385348
discrepancy in maldi-tof ms identification of uncommon gram-negative bacteria from lower respiratory secretions in patients with cystic fibrosis.	early identification of microbial organisms from respiratory secretions of patients with cystic fibrosis (cf) is important to guide therapeutic decisions. the objective was to compare the accuracy of matrix-assisted laser desorption/ionization-time of flight mass spectrometry (maldi-tof ms) relative to the conventional phenotypic method in identifying common bacterial isolates, including nonfermenting gram-negative bacteria, in a cohort of patients with cf.	2015	25995646
pathogens protection against the action of disinfectants in multispecies biofilms.	biofilms constitute the prevalent way of life for microorganisms in both natural and man-made environments. biofilm-dwelling cells display greater tolerance to antimicrobial agents than those that are free-living, and the mechanisms by which this occurs have been investigated extensively using single-strain axenic models. however, there is growing evidence that interspecies interactions may profoundly alter the response of the community to such toxic exposure. in this paper, we propose an overvi ...	2015	26236291