Publications

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
development of real-time pcr assays for the detection of moraxella macacae associated with bloody nose syndrome in rhesus (macaca mulatta) and cynomolgus (macaca fascicularis) macaques.	moraxella macacae is a recently described bacterial pathogen that causes epistaxis or so-called bloody nose syndrome in captive macaques. the aim of this study was to develop specific molecular diagnostic assays for m. macacae and to determine their performance characteristics.	2015	26365904
individuality, phenotypic differentiation, dormancy and 'persistence' in culturable bacterial systems: commonalities shared by environmental, laboratory, and clinical microbiology.	for bacteria, replication mainly involves growth by binary fission. however, in a very great many natural environments there are examples of phenotypically dormant, non-growing cells that do not replicate immediately and that are phenotypically 'nonculturable' on media that normally admit their growth. they thereby evade detection by conventional culture-based methods. such dormant cells may also be observed in laboratory cultures and in clinical microbiology. they are usually more tolerant to s ...	2015	26629334
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
abstracts from the 38th annual meeting of the society of general internal medicine.		2015	25869016
biofilm models of polymicrobial infection.	interactions between microbes are complex and play an important role in the pathogenesis of infections. these interactions can range from fierce competition for nutrients and niches to highly evolved cooperative mechanisms between different species that support their mutual growth. an increasing appreciation for these interactions, and desire to uncover the mechanisms that govern them, has resulted in a shift from monomicrobial to polymicrobial biofilm studies in different disease models. here w ...	2015	26592098
the influence of smoking on the peri-implant microbiome.	smokers are at high risk for 2 bacterially driven oral diseases: peri-implant mucositis and peri-implantitis. therefore, the purpose of this investigation was to use a deep-sequencing approach to identify the effect of smoking on the peri-implant microbiome in states of health and disease. peri-implant biofilm samples were collected from 80 partially edentulous subjects with peri-implant health, peri-implant mucositis, and peri-implantitis. bacterial dna was isolated and 16s ribsomal rna gene li ...	2015	26124222
a modified shuttle plasmid facilitates expression of a flavin mononucleotide-based fluorescent protein in treponema denticola atcc 35405.	oral pathogens, including treponema denticola, initiate the dysregulation of tissue homeostasis that characterizes periodontitis. however, progress of research on the roles of t. denticola in microbe-host interactions and signaling, microbial communities, microbial physiology, and molecular evolution has been hampered by limitations in genetic methodologies. this is typified by an extremely low transformation efficiency and inability to transform the most widely studied t. denticola strain with ...	2015	26162875
the role of the local microbial ecosystem in respiratory health and disease.	respiratory tract infections are a major global health concern, accounting for high morbidity and mortality, especially in young children and elderly individuals. traditionally, highly common bacterial respiratory tract infections, including otitis media and pneumonia, were thought to be caused by a limited number of pathogens including streptococcus pneumoniae and haemophilus influenzae. however, these pathogens are also frequently observed commensal residents of the upper respiratory tract (ur ...	2015	26150660
outer membrane vesicles - offensive weapons or good samaritans?	outer membrane vesicles (omvs) from gram-negative bacteria were first considered as artifacts and were followed with disbelief and bad reputation. later, their existence was accepted and they became characterized as bacterial bombs, virulence bullets, and even decoys. today, we know that omvs also can be involved in cell-cell signaling/communication and be mediators of immune regulation and cause disease protection. furthermore, omvs represent a distinct bacterial secretion pathway selecting and ...	2015	25840612
enzymatic synthesis using glycoside phosphorylases.	carbohydrate phosphorylases are readily accessible but under-explored catalysts for glycoside synthesis. their use of accessible and relatively stable sugar phosphates as donor substrates underlies their potential. a wide range of these enzymes has been reported of late, displaying a range of preferences for sugar donors, acceptors and glycosidic linkages. this has allowed this class of enzymes to be used in the synthesis of diverse carbohydrate structures, including at the industrial scale. as ...	2015	25060838
comparative genomic and phylogenetic analyses of gammaproteobacterial glg genes traced the origin of the escherichia coli glycogen glgbxcap operon to the last common ancestor of the sister orders enterobacteriales and pasteurellales.	production of branched α-glucan, glycogen-like polymers is widely spread in the bacteria domain. the glycogen pathway of synthesis and degradation has been fairly well characterized in the model enterobacterial species escherichia coli (order enterobacteriales, class gammaproteobacteria), in which the cognate genes (branching enzyme glgb, debranching enzyme glgx, adp-glucose pyrophosphorylase glgc, glycogen synthase glga, and glycogen phosphorylase glgp) are clustered in a glgbxcap operon arrang ...	2015	25607991
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
genome-wide gene order distances support clustering the gram-positive bacteria.	initially using 143 genomes, we developed a method for calculating the pair-wise distance between prokaryotic genomes using a monte carlo method to estimate the conservation of gene order. the method was based on repeatedly selecting five or six non-adjacent random orthologs from each of two genomes and determining if the chosen orthologs were in the same order. the raw distances were then corrected for gene order convergence using an adaptation of the jukes-cantor model, as well as using the co ...	2015	25653643
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.	for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...	2016	26511485
a structure-based classification of class a β-lactamases, a broadly diverse family of enzymes.	for medical biologists, sequencing has become a commonplace technique to support diagnosis. rapid changes in this field have led to the generation of large amounts of data, which are not always correctly listed in databases. this is particularly true for data concerning class a β-lactamases, a group of key antibiotic resistance enzymes produced by bacteria. many genomes have been reported to contain putative β-lactamase genes, which can be compared with representative types. we analyzed several ...	2016	26511485
the use of pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) to detect bacterial and fungal colonization in healthy military service members.	the role of microbial colonization in disease is complex. novel molecular tools to detect colonization offer theoretical improvements over traditional methods. we evaluated pcr/electrospray ionization-time-of-flight-mass spectrometry (pcr/esi-tof-ms) as a screening tool to study colonization of healthy military service members.	2016	27448413
multifunctional and redundant roles of borrelia burgdorferi outer surface proteins in tissue adhesion, colonization, and complement evasion.	borrelia burgdorferi is the causative agent of lyme disease in the u.s., with at least 25,000 cases reported to the cdc each year. b. burgdorferi is thought to enter and exit the bloodstream to achieve rapid dissemination to distal tissue sites during infection. travel through the bloodstream requires evasion of immune surveillance and pathogen clearance in the host, a process at which b. burgdorferi is adept. b. burgdorferi encodes greater than 19 adhesive outer surface proteins many of which h ...	2016	27818662
transition metals and virulence in bacteria.	transition metals are required trace elements for all forms of life. due to their unique inorganic and redox properties, transition metals serve as cofactors for enzymes and other proteins. in bacterial pathogenesis, the vertebrate host represents a rich source of nutrient metals, and bacteria have evolved diverse metal acquisition strategies. host metal homeostasis changes dramatically in response to bacterial infections, including production of metal sequestering proteins and the bombardment o ...	2016	27617971
potential use of antimicrobial peptides as vaginal spermicides/microbicides.	the concurrent increases in global population and sexually transmitted infection (sti) demand a search for agents with dual spermicidal and microbicidal properties for topical vaginal application. previous attempts to develop the surfactant spermicide, nonoxynol-9 (n-9), into a vaginal microbicide were unsuccessful largely due to its inefficiency to kill microbes. furthermore, n-9 causes damage to the vaginal epithelium, thus accelerating microbes to enter the women's body. for this reason, anti ...	2016	26978373
bronchiectasis in the last five years: new developments.	bronchiectasis, a chronic lung disease characterised by cough and purulent sputum, recurrent infections, and airway damage, is associated with considerable morbidity and mortality. to date, treatment options have been limited to physiotherapy to clear sputum and antibiotics to treat acute infections. over the last decade, there has been significant progress in understanding the epidemiology, pathophysiology, and microbiology of this disorder. over the last five years, methods of assessing severi ...	2016	27941638
cftr founder mutation causes protein trafficking defects in chinese patients with cystic fibrosis.	cystic fibrosis (cf) is a rare condition in asians. since 1985, only about 30 chinese patients have been reported with molecular confirmation.	2016	28116329
cftr founder mutation causes protein trafficking defects in chinese patients with cystic fibrosis.	cystic fibrosis (cf) is a rare condition in asians. since 1985, only about 30 chinese patients have been reported with molecular confirmation.	2016	28116329
respiratory infection rates differ between geographically distant paediatric cystic fibrosis cohorts.	respiratory infections are a major cause of pulmonary decline in children with cystic fibrosis (cf). we compared the prevalence of infection in early life at geographically distant cf treatment centres participating in the same surveillance programme in australia. lower airway microbiology, inflammation and structural lung disease at annual review were evaluated for 260 children 0-8 years old with cf at 1032 visits to cf treatment centres in melbourne or perth. melbourne patients were more likel ...	2016	27957481
high leptospira diversity in animals and humans complicates the search for common reservoirs of human disease in rural ecuador.	leptospirosis is a zoonotic disease responsible for high morbidity around the world, especially in tropical and low income countries. rats are thought to be the main vector of human leptospirosis in urban settings. however, differences between urban and low-income rural communities provide additional insights into the epidemiology of the disease.	2016	27622673
conserved patterns of microbial immune escape: pathogenic microbes of diverse origin target the human terminal complement inhibitor vitronectin via a single common motif.	pathogenicity of many microbes relies on their capacity to resist innate immunity, and to survive and persist in an immunocompetent human host microbes have developed highly efficient and sophisticated complement evasion strategies. here we show that different human pathogens including gram-negative and gram-positive bacteria, as well as the fungal pathogen candida albicans, acquire the human terminal complement regulator vitronectin to their surface. by using truncated vitronectin fragments we ...	2016	26808444
extraction of total nucleic acids from bacterial isolates using the biomérieux nuclisens easymag total nucleic acid extractor.	the biomerieux nuclisens easymag total nucleic acid extractor was evaluated for use on bacterial isolates in the clinical microbiology laboratory. forty eight isolates were extracted, yielding quantifiable amounts of dna for all isolates. the easymag is appropriate for dna extraction from bacterial isolates and will be incorporated in the clinical laboratory.	2016	27658494
the capricious nature of bacterial pathogens: phasevarions and vaccine development.	infectious diseases are a leading cause of morbidity and mortality worldwide, and vaccines are one of the most successful and cost-effective tools for disease prevention. one of the key considerations for rational vaccine development is the selection of appropriate antigens. antigens must induce a protective immune response, and this response should be directed to stably expressed antigens so the target microbe can always be recognized by the immune system. antigens with variable expression, due ...	2016	28018352
mechanisms of outer membrane vesicle entry into host cells.	bacterial outer membrane vesicles (omvs) are nano-sized compartments consisting of a lipid bilayer that encapsulates periplasm-derived, luminal content. omvs, which pinch off of gram-negative bacteria, are now recognized as a generalized secretion pathway which provides a means to transfer cargo to other bacterial cells as well as eukaryotic cells. compared with other secretion systems, omvs can transfer a chemically extremely diverse range of cargo, including small molecules, nucleic acids, pro ...	2016	27529760
development of a fast and low-cost qpcr assay for diagnosis of acute gas pharyngitis.	group a streptococci (gas) are the most common bacterial cause of acute pharyngitis and account for 15-30 % of cases of acute pharyngitis in children and 5-10 % of cases in adults. in this study, a real-time quantitative pcr (qpcr) based gas detection assay in pharyngeal swab specimens was developed.	2016	27501688
evaluation of an automated system for reading and interpreting disk diffusion antimicrobial susceptibility testing of fastidious bacteria.	results of disk diffusion antimicrobial susceptibility testing depend on individual visual reading of inhibition zone diameters. therefore, automated reading using camera systems might represent a useful tool for standardization. in this study, the adagio automated system (bio-rad) was evaluated for reading disk diffusion tests of fastidious bacteria. 144 clinical isolates (68 β-haemolytic streptococci, 28 streptococcus pneumoniae, 18 viridans group streptococci, 13 haemophilus influenzae, 7 mor ...	2016	27391898
comparative analysis of prophage-like elements in helicobacter sp. genomes.	prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. information on helicobacter sp. prophages remains scarce. in this study, sixteen prophages were identified and analyzed in detail. eight of them are described for the first time. based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. phylogenetic relationships of cluster a helicobacter ...	2016	27169002
the developing hypopharyngeal microbiota in early life.	the airways of healthy humans harbor a distinct microbial community. perturbations in the microbial community have been associated with disease, yet little is known about the formation and development of a healthy airway microbiota in early life. our goal was to understand the establishment of the airway microbiota within the first 3 months of life. we investigated the hypopharyngeal microbiota in the unselected copsac2010 cohort of 700 infants, using 16s rrna gene sequencing of hypopharyngeal a ...	2016	28038686
collective resistance in microbial communities by intracellular antibiotic deactivation.	the structure and composition of bacterial communities can compromise antibiotic efficacy. for example, the secretion of β-lactamase by individual bacteria provides passive resistance for all residents within a polymicrobial environment. here, we uncover that collective resistance can also develop via intracellular antibiotic deactivation. real-time luminescence measurements and single-cell analysis demonstrate that the opportunistic human pathogen streptococcus pneumoniae grows in medium supple ...	2016	28027306
repetitive elements in mycoplasma hyopneumoniae transcriptional regulation.	transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen mycoplasma hyopneumoniae. basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. dna repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. in this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all codin ...	2016	28005945
the evolution of human basophil biology from neglect towards understanding of their immune functions.	being discovered long ago basophils have been neglected for more than a century. during the past decade evidence emerged that basophils share features of innate and adaptive immunity. nowadays, basophils are best known for their striking effector role in the allergic reaction. they hence have been used for establishing new diagnostic tests and therapeutic approaches and for characterizing natural and recombinant allergens as well as hypoallergens, which display lower or diminished ige-binding ac ...	2016	28078302
evidence and evidence gaps in the treatment of eustachian tube dysfunction and otitis media.	evidence-based medicine is an approach to medical treatment intended to optimize patient-oriented decision-making on the basis of empirically proven effectiveness. for this purpose, a classification system has been established to categorize studies - and hence therapy options - in respect of associated evidence according to defined criteria. the eustachian tube connects the nasopharynx with the middle ear cavity. its key function is to ensure middle ear ventilation. compromised ventilation resul ...	2016	28025605
clinical features and outcomes of ipf patients hospitalized for pulmonary infection: a japanese cohort study.	many patients with idiopathic pulmonary fibrosis (ipf) undergo hospitalizations due to pulmonary infections. we retrospectively investigated the characteristics of hospitalizations due to pulmonary infection in patients with ipf to elucidate causative pathogens and mortality. we reviewed patients with ipf who were admitted between january 2008 and december 2014 for pulmonary infections including pneumonia and bronchitis. the causative pathogen, the relationship between the site of pneumonia and ...	2016	27959904
ecthyma associated with moraxella and staphylococcus epidermidis.		2016	27981222
'the microbiome and the pathophysiology of asthma'.	asthma is a chronic respiratory disease whose prevalence is increasing in the western world. recently research has begun to focus on the role the microbiome plays in asthma pathogenesis in the hope of further understanding this respiratory disorder. considered sterile until recently, the lungs have revealed themselves to contain a unique microbiota. a shift towards molecular methods for the quantification and sequencing of microbial dna has revealed that the airways harbour a unique microbiota w ...	2016	27919249
increased nasopharyngeal density and concurrent carriage of streptococcus pneumoniae, haemophilus influenzae, and moraxella catarrhalis are associated with pneumonia in febrile children.	we assessed nasopharyngeal (np) carriage of five pathogens in febrile children with and without acute respiratory infection (ari) of the upper (urti) or lower tract, attending health facilities in tanzania.	2016	27907156
oldenlandia diffusa extract inhibits biofilm formation by haemophilus influenzae clinical isolates.	oldenlandia diffusa has been empirically used as a therapeutic adjunct for the treatment of respiratory infections. to establish the basic evidence of its clinical usefulness, antimicrobial and biofilm inhibitory activities of an o. diffusa extract were examined against clinical isolates of haemophilus influenzae, a major causative pathogen of respiratory and sensory organ infections. no significant growth inhibitory activity was observed during incubation for more than 6 h after the extract add ...	2016	27902758
common lung microbiome identified among mechanically ventilated surgical patients.	the examination of the pulmonary microbiome in patients with non-chronic disease states has not been extensively examined. traditional culture based screening methods are often unable to identify bacteria from bronchoalveolar lavage samples. the advancement of next-generation sequencing technologies allows for a culture-independent molecular based analysis to determine the microbial composition in the lung of this patient population. for this study, the ion torrent pgm system was used to assess ...	2016	27898681
interactions of respiratory viruses and the nasal microbiota during the first year of life in healthy infants.	traditional culture techniques have shown that increased bacterial colonization is associated with viral colonization; however, the influence of viral colonization on the whole microbiota composition is less clear. we thus aimed to understand the interaction of viral infections and the nasal microbiota in early life to appraise their roles in disease development. thirty-two healthy, unselected infants were included in this prospective longitudinal cohort study within the first year of life. biwe ...	2016	27904883
positive clinical outcomes derived from using streptococcus salivarius k12 to prevent streptococcal pharyngotonsillitis in children: a pilot investigation.	streptococcus salivarius k12 (blis k12(®)) is a probiotic strain producing the bacteriocins salivaricin a2 and salivaricin b, both of which strongly antagonize the growth of streptococcus pyogenes, the most important bacterial cause of pharyngeal infections in humans. it successfully colonizes and exhibits persistence in the oral cavity and is endowed with an excellent safety profile. previous observations of a small group of children indicated that the use of blis k12 could also reduce the occu ...	2016	27920580
effect of high n-acetylcysteine concentrations on antibiotic activity against a large collection of respiratory pathogens.	the effect of high n-acetylcysteine (nac) concentrations (10 and 50 mm) on antibiotic activity against 40 strains of respiratory pathogens was investigated. nac compromised the activity of carbapenems (of mostly imipenem and, to lesser extents, meropenem and ertapenem) in a dose-dependent fashion. we demonstrated chemical instability of carbapenems in the presence of nac. with other antibiotics, 10 mm nac had no major effects, while 50 mm nac sporadically decreased (ceftriaxone and aminoglycosid ...	2016	27736757
coevolution of paired receptors in xenopus carcinoembryonic antigen-related cell adhesion molecule families suggests appropriation as pathogen receptors.	in mammals, ceacam1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. human ceacam1 and ceacam3 which have inhibitory itim/itsm and activating itam-like motifs, respectively, in their cytoplasmic regions are such paired receptors. various bacterial pathogens bind to ceacam1 on epithelial and immune cells facilitating both entry into the host and down-regulation of the immune response whereas i ...	2016	27852220
antimicrobial resistance and clinical outcomes in nursing home-acquired pneumonia, compared to community-acquired pneumonia.	patients with nursing home-acquired pneumonia (nhap) should be treated as hospital-acquired pneumonia (hap) according to guidelines published in 2005. however, controversy still exists on whether the high mortality of nhap results from multidrug resistant pathogens or underlying disease. we aimed to outline differences and factors contributing to mortality between nhap and community-acquired pneumonia (cap) patients.	2016	27873512
antimicrobial resistance and clinical outcomes in nursing home-acquired pneumonia, compared to community-acquired pneumonia.	patients with nursing home-acquired pneumonia (nhap) should be treated as hospital-acquired pneumonia (hap) according to guidelines published in 2005. however, controversy still exists on whether the high mortality of nhap results from multidrug resistant pathogens or underlying disease. we aimed to outline differences and factors contributing to mortality between nhap and community-acquired pneumonia (cap) patients.	2016	27873512
abstracts from the 16th international congress on circumpolar health.		2016	27829488
shifted focus of bronchoalveolar lavage in patients with suspected thoracic malignancy: an analysis of 224 patients.	bronchoscopies are extensively adopted for diagnosing and staging thoracic malignancies, but studies are missing as how to keep the process streamlined and more efficient. to evaluate current role of bronchoalveolar lavage (bal) for cancer and possible infection diagnosis when practicing comprehensive bronchoscopy for patients suspected with thoracic malignancy, and provide foundation for possible practice modification.	2016	28066604
microbiological features of upper respiratory tract infections in bulgarian children for the period 1998-2014.	across the globe, upper respiratory tract infections (urtis) are the most prevalent cause of morbidity in childhood.	2016	27994923
pharmacological management and prevention of exacerbations of chronic obstructive pulmonary disease in hospitalized patients.	rapid-acting bronchodilators, systemic corticosteroids, and antibiotics are among the keys to managing exacerbations of chronic obstructive pulmonary disease. preventing exacerbations should also be a component of therapy for the disease.	2016	27904303
use of next generation sequence to investigate potential novel macrolide resistance mechanisms in a population of moraxella catarrhalis isolates.	although previous studies have confirmed that 23s rrna gene mutation could be responsible for most of macrolide resistance in m. catarrhalis, a recent study suggested otherwise. next generation sequence based comparative genomics has revolutionized the mining of potential novel drug resistant mechanisms. in this study, two pairs of resistant and susceptible m. catarrhalis isolates with different multilocus sequence types, were investigated for potential differential genes or informative single n ...	2016	27774989
respiratory microbes present in the nasopharynx of children hospitalised with suspected pulmonary tuberculosis in cape town, south africa.	lower respiratory tract infection in children is increasingly thought to be polymicrobial in origin. children with symptoms suggestive of pulmonary tuberculosis (ptb) may have tuberculosis, other respiratory tract infections or co-infection with mycobacterium tuberculosis and other pathogens. we aimed to identify the presence of potential respiratory pathogens in nasopharyngeal (np) samples from children with suspected ptb.	2016	27776489
c-reactive protein in outpatients with acute exacerbation of copd: its relationship with microbial etiology and severity.	c-reactive protein (crp) measurement has proven valuable for detecting exacerbations, but its usefulness in predicting etiology remains controversial. likewise, its potential value as a marker of severity, which is well established in patients with pneumonia, remains unproven in chronic obstructive pulmonary disease (copd) exacerbations.	2016	27799762
throat swabs and sputum culture as predictors of p. aeruginosa or s. aureus lung colonization in adult cystic fibrosis patients.	due to frequent infections in cystic fibrosis (cf) patients, repeated respiratory cultures are obtained to inform treatment. when patients are unable to expectorate sputum, clinicians obtain throat swabs as a surrogate for lower respiratory cultures. there is no clear data in adult subjects demonstrating the adequacy of throat swabs as a surrogate for sputum or bal. our study was designed to determine the utility of throat swabs in identifying lung colonization with common organisms in adults wi ...	2016	27711152
nasal carriage of common bacterial pathogens among healthy kindergarten children in chaoshan region, southern china: a cross-sectional study.	nasal colonization with bacterial pathogens is associated with risk of invasive respiratory tract infections, but the related information for chinese healthy children is scarce.	2016	27741941
breathing better through bugs: asthma and the microbiome.	asthma is a highly heterogeneous disease characterized by inflammation of the airways, which invokes symptoms such as wheeze, dyspnea, and chest tightness. asthma is the product of multiple interconnected immunological processes and represents a constellation of related, but distinct, disease phenotypes. the prevalence of asthma has more than doubled since the 1980s, and efforts to understand this increase have inspired consideration of the microbiome as a key player in the pathophysiology and r ...	2016	27698615
bioelectromagnetics research within an australian context: the australian centre for electromagnetic bioeffects research (acebr).	mobile phone subscriptions continue to increase across the world, with the electromagnetic fields (emf) emitted by these devices, as well as by related technologies such as wi-fi and smart meters, now ubiquitous. this increase in use and consequent exposure to mobile communication (mc)-related emf has led to concern about possible health effects that could arise from this exposure. although much research has been conducted since the introduction of these technologies, uncertainty about the impac ...	2016	27690076
cytotoxicity of methanol extracts of annona muricata, passiflora edulis and nine other cameroonian medicinal plants towards multi-factorial drug-resistant cancer cell lines.	cancer cells rapidly acquire resistance leading to treatment failures. in the present study, we have evaluated the cytotoxicity of 17 methanol extracts from 11 cameroonian medicinal plants against the sensitive leukemia ccrf-cem cells and the best ones were further tested on a panel of 8 other human cancer cell lines, including various mdr phenotypes as well as against the normal aml12 hepatocytes.	2016	27730025
protective effect of xuebijing injection on d-galactosamine- and lipopolysaccharide-induced acute liver injury in rats through the regulation of p38 mapk, mmp-9 and ho-1 expression by increasing tipe2 expression.	xuebijing injection (xbj) has long been used to treat infectious diseases in china. the therapeutic effect of xbj is probably associated with anti-inflammatory effects. however, the precise mechanisms responsible for the effects of xbj remain unknown. the present study was conducted in order to evaluate the protective effects of xbj in a rat model of d-galactosamine (d-gal)- and lipopolysaccharide (lps)‑induced acute liver injury. in the present study, the rats were injected with d-gal and lps i ...	2016	27666960
the healthy infant nasal transcriptome: a benchmark study.	responses by resident cells are likely to play a key role in determining the severity of respiratory disease. however, sampling of the airways poses a significant challenge, particularly in infants and children. here, we report a reliable method for obtaining nasal epithelial cell rna from infants for genome-wide transcriptomic analysis, and describe baseline expression characteristics in an asymptomatic cohort. nasal epithelial cells were collected by brushing of the inferior turbinates, and ge ...	2016	27658638
neuroendocrine cell hyperplasia of infancy: an unusual cause of hypoxemia in children.	childhood interstitial lung disease (child) is a heterogeneous group of rare disorders characterized by abnormal imaging findings, impaired gas exchange; and is associated with substantial morbidity and mortality. neuroendocrine cell hyperplasia (nehi) is a unique sub-group, which is more prevalent in infants and children younger than 2 years of age, and typically manifests with chronic tachypnea, retractions, hypoxemia and failure to thrive. nehi insidiously appears in the first year of life, s ...	2016	27629751
the economic burden of otitis media in korea, 2012: a nationally representative cross-sectional study.	background. otitis media (om) is a common communicable disease that is associated with a substantial economic burden. however, no korean studies have evaluated om-related trends after the introduction of the pneumococcal conjugate vaccines. purpose. this study aimed to estimate the prevalence and economic burden of om in korea using nationally representative data. methods. the burden of om was estimated nationally representative data such as national health insurance claims data from 2012, based ...	2016	27703971
comprehensive approach for predicting toxicological effects of ionic liquids on several biological systems using unified descriptors.	the challenge and opportunity for design of environmentally-benign ionic liquids (ils) would start from prediction of their toxicological effects on several endpoints solely based on the structural formulas. especially, a comprehensive yet simple equation able to predict several biological responses to il toxicity is of much advantage. therefore, based on 50 toxicity testing systems on ils a comprehensively approachable prediction method was developed. for the modelling, approximately 1600 toxic ...	2016	27624396
ftsz-dependent elongation of a coccoid bacterium.	a mechanistic understanding of the determination and maintenance of the simplest bacterial cell shape, a sphere, remains elusive compared with that of more complex shapes. cocci seem to lack a dedicated elongation machinery, and a spherical shape has been considered an evolutionary dead-end morphology, as a transition from a spherical to a rod-like shape has never been observed in bacteria. here we show that a staphylococcus aureus mutant (m5) expressing the ftsz(g193d) allele exhibits elongated ...	2016	27601570
the effect of daily sedation interruption protocol on early incidence of ventilator-associated pneumonia among patients hospitalized in critical care units receiving mechanical ventilation.	ventilator-associated pneumonia (vap) is a common side effect in patients who receive intravenous sedation infusion. in routine care, after starting sedation infusion for patients who receive mechanical ventilation, interruption of sedation starts without protocol. this study aimed to evaluate the effect of daily sedation vacation protocol on the incidence of vap in mechanically ventilated patients.	2016	27904641
chronic suppurative lung disease in adults.	chronic suppurative lung disease (csld), characterized by a bronchiectasis-like syndrome in the absence of bronchial dilatation, is well described in the pediatric literature. in some patients, it may be a precursor of bronchiectasis. in adults, this syndrome has not been well described. we present four adult patients without obvious causative exposures who presented with prolonged cough and purulent sputum. sputum cultures revealed a variety of gram negative bacteria, fungi and mycobacteria. hi ...	2016	27747039
from erythromycin to azithromycin and new potential ribosome-binding antimicrobials.	macrolides, as a class of natural or semisynthetic products, express their antibacterial activity primarily by reversible binding to the bacterial 50s ribosomal subunits and by blocking nascent proteins' progression through their exit tunnel in bacterial protein biosynthesis. generally considered to be bacteriostatic, they may also be bactericidal at higher doses. the discovery of azithromycin from the class of macrolides, as one of the most important new drugs of the 20th century, is presented ...	2016	27598215
performance of an in-house real-time polymerase chain reaction for identification of mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting.	brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. in the present study, an in-house real-time polymerase chain reaction (pcr) assay targeting the mpt64 gene for identification of mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. from may 2011 to july 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or pra-hsp ...	2016	27598243
draft genome sequence of acinetobacter baumannii strain nctc 13423, a multidrug-resistant clinical isolate.	acinetobacter baumannii is a pathogen that is becoming increasingly important and causes serious hospital-acquired infections. we sequenced the genome of a. baumannii nctc 13423, a multidrug-resistant strain belonging to the international clone ii group, isolated from a human infection in the united kingdom in 2003. the 3,937,944 bp draft genome has a gc-content of 39.0 % and a total of 3672 predicted protein-coding sequences. the availability of genome sequences of multidrug-resistant a. bauman ...	2016	27594976
fast mechanically driven daughter cell separation is widespread in actinobacteria.	dividing cells of the coccoid gram-positive bacterium staphylococcus aureus undergo extremely rapid (millisecond) daughter cell separation (dcs) driven by mechanical crack propagation, a strategy that is very distinct from the gradual, enzymatically driven cell wall remodeling process that has been well described in several rod-shaped model bacteria. to determine if other bacteria, especially those in the same phylum (firmicutes) or with similar coccoid shapes as s. aureus, might use a similar m ...	2016	27578753
curative effects of suhuang zhike capsule on postinfectious cough: a meta-analysis of randomized trials.	objective. in this paper, we intended to systematically evaluate the efficacy of suhuang zhike capsule (szc) on postinfectious cough (pic) in adults (age > 18). methods. medline (pubmed), chinese national knowledge infrastructure (cnki), cqvip database (vip), and wanfang database were researched for the randomized controlled trials (rcts) of szc for pic. the search was limited to human studies, using the search keywords or free-text terms "cough," "post-infectious cough," "postinfectious cough," ...	2016	27648104
a method for assessing efficiency of bacterial cell disruption and dna release.	dna-based testing is becoming the preferred method both for identifying microorganisms and for characterizing microbial communities. however, no single dna extraction method exists that is suitable for all types of microorganisms because bacteria are variable in their susceptibility to lysis by available extraction procedures. to develop and test new dna extraction procedures, it would be helpful to determine their efficiencies. while the amount of extracted dna can readily be measured by differ ...	2016	27566276
changes in the prevalence and biofilm formation of haemophilus influenzae and haemophilus parainfluenzae from the respiratory microbiota of patients with sarcoidosis.	healthy condition and chronic diseases may be associated with microbiota composition and its properties. the prevalence of respiratory haemophili with respect to their phenotypes including the ability to biofilm formation in patients with sarcoidosis was assayed.	2016	27562460
ceacam1: expression and role in melanocyte transformation.	metastases represent the main cause of death in melanoma patients. despite the current optimized targeted therapy or immune checkpoint inhibitors the treatment of metastatic melanoma is unsatisfactory. because of the poor prognosis of advanced melanoma there is an urgent need to identify new biomarkers to differentiate melanoma cells from normal melanocytes, to stratify patients according to their risk, and to identify subgroups of patients that require close follow-up or more aggressive therapy ...	2016	27642217
bacterial findings in optimised sampling and characterisation of s. aureus in chronic rhinosinusitis.	the bacterial spectrum in chronic rhinosinusitis (crs) is clinically relevant. this study aimed to compare two sampling techniques and to characterise staphylococcus aureus isolated from crs patients. bacterial specimens were collected from the nares and maxillary sinus in 42 crs patients and from the nares in 57 healthy controls. maxillary sinus sampling was performed in two ways in each patient: with a cotton-tipped aluminium swab through the enlarged sinus ostium, and with a protected brush. ...	2016	27538736
bacterial findings in optimised sampling and characterisation of s. aureus in chronic rhinosinusitis.	the bacterial spectrum in chronic rhinosinusitis (crs) is clinically relevant. this study aimed to compare two sampling techniques and to characterise staphylococcus aureus isolated from crs patients. bacterial specimens were collected from the nares and maxillary sinus in 42 crs patients and from the nares in 57 healthy controls. maxillary sinus sampling was performed in two ways in each patient: with a cotton-tipped aluminium swab through the enlarged sinus ostium, and with a protected brush. ...	2016	27538736
toxic accumulation of lps pathway intermediates underlies the requirement of lpxh for growth of acinetobacter baumannii atcc 19606.	the lipid a moiety of lipopolysaccharide (lps) is the main constituent of the outer leaflet of the gram-negative bacterial outer membrane (om) and is essential in many gram-negative pathogens. an exception is acinetobacter baumannii atcc 19606, where mutants lacking enzymes occurring early in lipid a biosynthesis (lpxa, lpxc or lpxd), and correspondingly lacking lps, can grow. in contrast, we show here that lpxh, an enzyme that occurs downstream of lpxd in the lipid a biosynthetic pathway, is es ...	2016	27526195
tsr chemoreceptor interacts with il-8 provoking e. coli transmigration across human lung epithelial cells.	bacterial colonization of epithelial surfaces and subsequent transmigration across the mucosal barrier are essential for the development of infection. we hypothesized that the methyl-accepting proteins (mcps), known as chemoreceptors expressed on escherichia coli (e. coli) bacterial surface, play an important role in mediating bacterial transmigration. we demonstrated a direct interaction between human interleukin-8 (il-8) and tsr receptor, a major mcp chemoreceptor. stimulation of human lung ep ...	2016	27506372
retrospective review of factors associated with severe hospitalised community-acquired influenza in a tertiary paediatric hospital in south australia.	influenza infection can result in severe disease with debilitating complications. young children have the highest rate of influenza hospitalisations with various factors influencing influenza susceptibility and severity.	2016	27381474
high frequency and diversity of antimicrobial activities produced by nasal staphylococcus strains against bacterial competitors.	the human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as staphylococcus aureus. the potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied. of 89 nasal staphylococcus isolates, unexpectedly, the vast majority (84%) was found to produce antimicrobial substances in particular under habitat-specific stress conditions, such as iron limitation or exposure to hydrog ...	2016	27490492
neisserial opa protein-ceacam interactions: competition for receptors as a means of bacterial invasion and pathogenesis.	carcino-embryonic antigen-like cellular adhesion molecules (ceacams), members of the immunoglobulin superfamily, are responsible for cell-cell interactions and cellular signaling events. extracellular interactions with ceacams have the potential to induce phagocytosis, as is the case with pathogenic neisseria bacteria. pathogenic neisseria species express opacity-associated (opa) proteins, which interact with a subset of ceacams on human cells, and initiate the engulfment of the bacterium. we de ...	2016	27442026
serum albumin and ca2+ are natural competence inducers in the human pathogen acinetobacter baumannii.	the increasing frequency of bacteria showing antimicrobial resistance (amr) raises the menace of entering into a postantibiotic era. horizontal gene transfer (hgt) is one of the prime reasons for amr acquisition. acinetobacter baumannii is a nosocomial pathogen with outstanding abilities to survive in the hospital environment and to acquire resistance determinants. its capacity to incorporate exogenous dna is a major source of amr genes; however, few studies have addressed this subject. the tran ...	2016	27270286
in vitro and in vivo characterization of the novel oxabicyclooctane-linked bacterial topoisomerase inhibitor am-8722, a selective, potent inhibitor of bacterial dna gyrase.	oxabicyclooctane-linked novel bacterial topoisomerase inhibitors (nbtis) represent a new class of recently described antibacterial agents with broad-spectrum activity. nbtis dually inhibit the clinically validated bacterial targets dna gyrase and topoisomerase iv and have been shown to bind distinctly from known classes of antibacterial agents directed against these targets. herein we report the molecular, cellular, and in vivo characterization of am-8722 as a representative n-alkylated-1,5-naph ...	2016	27246784
discovery and analysis of natural-product compounds inhibiting protein synthesis in pseudomonas aeruginosa.	bacterial protein synthesis is the target for numerous natural and synthetic antibacterial agents. we have developed a poly(u) mrna-directed aminoacylation/translation (a/t) protein synthesis system composed of phenylalanyl-trna synthetases (phers), ribosomes, and ribosomal factors from pseudomonas aeruginosa this system has been used for high-throughput screening of a natural-compound library. assays were developed for each component of the system to ascertain the specific target of inhibitory ...	2016	27246774
comparison of the frequency of bacterial and viral infections among children with community-acquired pneumonia hospitalized across distinct severity categories: a prospective cross-sectional study.	the comparison of the frequencies of bacterial and viral infections among children with community-acquired pneumonia (cap) admitted in distinct severity categories, in an original study, is lacking in literature to-date. we aimed to achieve this goal.	2016	27449898
complete genome sequence of moraxella osloensis strain kmc41, a producer of 4-methyl-3-hexenoic acid, a major malodor compound in laundry.	we report the complete genome sequence of moraxella osloensis strain kmc41, isolated from laundry with malodor. the kmc41 genome comprises a 2,445,556-bp chromosome and three plasmids. a fatty acid desaturase and at least four β-oxidation-related genes putatively associated with 4-methyl-3-hexenoic acid generation were detected in the kmc41 chromosome.	2016	27445387
antibiotic utilization patterns in patients with ventilator-associated pneumonia: a canadian context.	this retrospective cohort study describes the patterns of antibiotic use for the treatment of ventilator-associated pneumonia (vap) in the calgary zone of alberta health services. timing, appropriateness, and duration of antibiotics were evaluated in two hundred consecutive cases of vap derived from 4 adult intensive care units (icu). antibiotic therapy was initiated in less than 24 hours from vap diagnosis in 83% of cases. although most patients (89%) received empiric therapy that demonstrated ...	2016	27525016
atp-binding cassette (abc) transporters of the human respiratory tract pathogen, moraxella catarrhalis: role in virulence.	moraxella catarrhalis is a human respiratory tract pathogen that causes otitis media (middle ear infections) in children and respiratory tract infections in adults with chronic obstructive pulmonary disease. in view of the huge global burden of disease caused by m. catarrhalis, the development of vaccines to prevent these infections and better approaches to treatment have become priorities. in previous work, we used a genome mining approach that identified three substrate binding proteins (sbps) ...	2016	27391026