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balance between coiled-coil stability and dynamics regulates activity of bvgs sensor kinase in bordetella.the two-component system bvgas controls the expression of the virulence regulon of bordetella pertussis. bvgs is a prototype of bacterial sensor kinases with extracytoplasmic venus flytrap perception domains. following its transmembrane segment, bvgs harbors a cytoplasmic per-arnt-sim (pas) domain and then a predicted 2-helix coiled coil that precede the dimerization-histidine-phosphotransfer domain of the kinase. bvgs homologs have a similar domain organization, or they harbor only a predicted ...201626933056
surface proteoglycans as mediators in bacterial pathogens infections.infectious diseases remain an important global health problem. the interaction of a wide range of pathogen bacteria with host cells from many different tissues is frequently mediated by proteoglycans. these compounds are ubiquitous complex molecules which are not only involved in adherence and colonization, but can also participate in other steps of pathogenesis. to overcome the problem of microbial resistance to antibiotics new therapeutic agents could be developed based on the characteristics ...201626941735
neisseria meningitidis translation elongation factor p and its active-site arginine residue are essential for cell viability.translation elongation factor p (ef-p), a ubiquitous protein over the entire range of bacterial species, rescues ribosomal stalling at consecutive prolines in proteins. in escherichia coli and salmonella enterica, the post-translational β-lysyl modification of lys34 of ef-p is important for the ef-p activity. the β-lysyl ef-p modification pathway is conserved among only 26-28% of bacteria. recently, it was found that the shewanella oneidensis and pseudomonas aeruginosa ef-p proteins, containing ...201626840407
epigenetic segregation of microbial genomes from complex samples using restriction endonucleases hpaii and mcrb.we describe continuing work to develop restriction endonucleases as tools to enrich targeted genomes of interest from diverse populations. two approaches were developed in parallel to segregate genomic dna based on cytosine methylation. first, the methyl-sensitive endonuclease hpaii was used to bind non-cg methylated dna. second, a truncated fragment of mcrb was used to bind cpg methylated dna. enrichment levels of microbial genomes can exceed 100-fold with hpaii allowing improved genomic detect ...201626727463
differential responses of pattern recognition receptors to outer membrane vesicles of three periodontal pathogens.highly purified outer membrane vesicles (omvs) of the periodontal pathogens, porphyromonas gingivalis, treponema denticola and tannerella forsythia were produced using tangential flow ultrafiltration, ultracentrifugation and optiprep density gradient separation. cryo-tem and light scattering showed omvs to be single lipid-bilayers with modal diameters of 75 to 158 nm. enumeration of omvs by nanoparticle flow-cytometry at the same stage of late exponential culture indicated that p. gingivalis was ...201627035339
phosphatidylserine is a global immunosuppressive signal in efferocytosis, infectious disease, and cancer.apoptosis is an evolutionarily conserved and tightly regulated cell death modality. it serves important roles in physiology by sculpting complex tissues during embryogenesis and by removing effete cells that have reached advanced age or whose genomes have been irreparably damaged. apoptosis culminates in the rapid and decisive removal of cell corpses by efferocytosis, a term used to distinguish the engulfment of apoptotic cells from other phagocytic processes. over the past decades, the molecula ...201626915293
whole genome sequencing revealed host adaptation-focused genomic plasticity of pathogenic leptospira.leptospirosis, caused by pathogenic leptospira spp., has recently been recognized as an emerging infectious disease worldwide. despite its severity and global importance, knowledge about the molecular pathogenesis and virulence evolution of leptospira spp. remains limited. here we sequenced and analyzed 102 isolates representing global sources. a high genomic variability were observed among different leptospira species, which was attributed to massive gene gain and loss events allowing for adapt ...201626833181
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 ...201626808444
genome-wide discovery of putative srnas in paracoccus denitrificans expressed under nitrous oxide emitting conditions.nitrous oxide (n2o) is a stable, ozone depleting greenhouse gas. emissions of n2o into the atmosphere continue to rise, primarily due to the use of nitrogen-containing fertilizers by soil denitrifying microbes. it is clear more effective mitigation strategies are required to reduce emissions. one way to help develop future mitigation strategies is to address the currently poor understanding of transcriptional regulation of the enzymes used to produce and consume n2o. with this ultimate aim in mi ...201627895629
comparative methylome analysis of the occasional ruminant respiratory pathogen bibersteinia trehalosi.we examined and compared both the methylomes and the modification-related gene content of four sequenced strains of bibersteinia trehalosi isolated from the nasopharyngeal tracts of nebraska cattle with symptoms of bovine respiratory disease complex. the methylation patterns and the encoded dna methyltransferase (mtase) gene sets were different between each strain, with the only common pattern being that of dam (gatc). among the observed patterns were three novel motifs attributable to type i re ...201627556252
salmonella typhimurium utilizes a t6ss-mediated antibacterial weapon to establish in the host gut.the mammalian gastrointestinal tract is colonized by a high-density polymicrobial community where bacteria compete for niches and resources. one key competition strategy includes cell contact-dependent mechanisms of interbacterial antagonism, such as the type vi secretion system (t6ss), a multiprotein needle-like apparatus that injects effector proteins into prokaryotic and/or eukaryotic target cells. however, the contribution of t6ss antibacterial activity during pathogen invasion of the gut ha ...201627503894
dynamic duo-the salmonella cytolethal distending toxin combines adp-ribosyltransferase and nuclease activities in a novel form of the cytolethal distending toxin.the cytolethal distending toxin (cdt) is a well characterized bacterial genotoxin encoded by several gram-negative bacteria, including salmonella enterica (s. enterica). the cdt produced by salmonella (s-cdt) differs from the cdt produced by other bacteria, as it utilizes subunits with homology to the pertussis and subtilase toxins, in place of the traditional cdta and cdtc subunits. previously, s-cdt was thought to be a unique virulence factor of s. enterica subspecies enterica serotype typhi, ...201627120620
virb8-like protein trah is crucial for dna transfer in enterococcus faecalis.untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. conjugative dna transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a protein complex, known as type iv secretion system (t4ss). the core of the t4ss is a multiprotein complex that spans the bacterial envelope as a channel for macromolecular secretion. ...201627103580
glycoengineered outer membrane vesicles: a novel platform for bacterial vaccines.the world health organization has indicated that we are entering into a post-antibiotic era in which infections that were routinely and successfully treated with antibiotics can now be lethal due to the global dissemination of multidrug resistant strains. conjugate vaccines are an effective way to create a long-lasting immune response against bacteria. however, these vaccines present many drawbacks such as slow development, high price, and batch-to-batch inconsistencies. alternate approaches for ...201627103188
structural modeling of the flagellum ms ring protein flif reveals similarities to the type iii secretion system and sporulation complex.the flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. it is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. the flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, t ...201626925337
removal of fecal indicators, pathogenic bacteria, adenovirus, cryptosporidium and giardia (oo)cysts in waste stabilization ponds in northern and eastern australia.maturation ponds are used in rural and regional areas in australia to remove the microbial loads of sewage wastewater, however, they have not been studied intensively until present. using a combination of culture-based methods and quantitative real-time pcr, we assessed microbial removal rates in maturation ponds at four waste stabilization ponds (wsp) with (n = 1) and without (n = 3) baffles in rural and remote communities in australia. concentrations of total coliforms, e. coli, enterococci, c ...201626729150
mglc, a paralog of myxococcus xanthus gtpase-activating protein mglb, plays a divergent role in motility regulation.in order to optimize interactions with their environment and one another, bacteria regulate their motility. in the case of the rod-shaped cells of myxococcus xanthus, regulated motility is essential for social behaviors. m. xanthus moves over surfaces using type iv pilus-dependent motility and gliding motility. these two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small g protein mgla, the cognate mgla gtp ...201626574508
nitrogen fixation and molecular oxygen: comparative genomic reconstruction of transcription regulation in alphaproteobacteria.biological nitrogen fixation plays a crucial role in the nitrogen cycle. an ability to fix atmospheric nitrogen, reducing it to ammonium, was described for multiple species of bacteria and archaea. the transcriptional regulatory network for nitrogen fixation was extensively studied in several representatives of the class alphaproteobacteria. this regulatory network includes the activator of nitrogen fixation nifa, working in tandem with the alternative sigma-factor rpon as well as oxygen-respons ...201627617010
a t4ss effector targets host cell alpha-enolase contributing to brucella abortus intracellular lifestyle.brucella abortus, the causative agent of bovine brucellosis, invades and replicates within cells inside a membrane-bound compartment known as the brucella containing vacuole (bcv). after trafficking along the endocytic and secretory pathways, bcvs mature into endoplasmic reticulum-derived compartments permissive for bacterial replication. brucella type iv secretion system (virb) is a major virulence factor essential for the biogenesis of the replicative organelle. upon infection, brucella uses t ...201627900285
mechanism and function of type iv secretion during infection of the human host.bacterial pathogens employ type iv secretion systems (t4sss) for various purposes to aid in survival and proliferation in eukaryotic hosts. one large t4ss subfamily, the conjugation systems, confers a selective advantage to the invading pathogen in clinical settings through dissemination of antibiotic resistance genes and virulence traits. besides their intrinsic importance as principle contributors to the emergence of multiply drug-resistant "superbugs," detailed studies of these highly tractab ...201627337453
phosphotransferase-dependent accumulation of (p)ppgpp in response to glutamine deprivation in caulobacter crescentus.the alarmone (p)ppgpp is commonly used by bacteria to quickly respond to nutrient starvation. although (p)ppgpp synthetases such as spot have been extensively studied, little is known about the molecular mechanisms stimulating alarmone synthesis upon starvation. here, we describe an essential role of the nitrogen-related phosphotransferase system (pts(ntr)) in controlling (p)ppgpp accumulation in caulobacter crescentus. we show that cells sense nitrogen starvation by way of detecting glutamine d ...201627109061
hijacking complement regulatory proteins for bacterial immune evasion.the human complement system plays an important role in the defense against invading pathogens, inflammation and homeostasis. invading microbes, such as bacteria, directly activate the complement system resulting in the formation of chemoattractants and in effective labeling of the bacteria for phagocytosis. in addition, formation of the membrane attack complex is responsible for direct killing of gram-negative bacteria. in turn, bacteria have evolved several ways to evade complement activation o ...201628066340
modulating endotoxin activity by combinatorial bioengineering of meningococcal lipopolysaccharide.neisseria meningitidis contains a very potent hexa-acylated lps that is too toxic for therapeutic applications. we used systematic molecular bioengineering of meningococcal lps through deletion of biosynthetic enzymes in combination with induction of lps modifying enzymes to yield a variety of novel lps mutants with changes in both lipid a acylation and phosphorylation. mass spectrometry was used for detailed compositional determination of the lps molecular species, and stimulation of immune cel ...201627841285
ifnγ is required for optimal antibody-mediated immunity against genital chlamydia infection.defining the mechanisms of immunity conferred by the combination of antibody and cd4(+) t cells is fundamental to designing an efficacious chlamydial vaccine. using the chlamydia muridarum genital infection model of mice, which replicates many features of human c. trachomatis infection and avoids the characteristic low virulence of c. trachomatis in the mouse, we previously demonstrated a significant role for antibody in immunity to chlamydial infection. we found that antibody alone was not prot ...201627600502
tularemia vaccine development: paralysis or progress?francisella tularensis (ft) is a gram-negative intercellular pathogen and category a biothreat agent. however, despite 15 years of strong government investment and intense research focused on the development of a us food and drug administration-approved vaccine against ft, the primary goal remains elusive. this article reviews research efforts focused on developing an ft vaccine, as well as a number of important factors, some only recently recognized as such, which can significantly impact the d ...201627200274
listeria monocytogenes and the inflammasome: from cytosolic bacteriolysis to tumor immunotherapy.inflammasomes are cytosolic innate immune surveillance systems that recognize a variety of danger signals, including those from pathogens. listeria monocytogenes is a gram-positive intracellular bacterium evolved to live within the harsh environment of the host cytosol. further, l. monocytogenes can activate a robust cell-mediated immune response that is being harnessed as an immunotherapeutic platform. access to the cytosol is critical for both causing disease and inducing a protective immune r ...201627460808
quantitative proteomic analysis of shigella flexneri and shigella sonnei generalized modules for membrane antigens (gmma) reveals highly pure preparations.outer membrane blebs are naturally shed by gram-negative bacteria and are candidates of interest for vaccines development. genetic modification of bacteria to induce hyperblebbing greatly increases the yield of blebs, called generalized modules for membrane antigens (gmma). the composition of the gmma from hyperblebbing mutants of shigella flexneri 2a and shigella sonnei were quantitatively analyzed using high-sensitivity mass spectrometry with the label-free ibaq procedure and compared to the c ...201626746581
identification of ybey-protein interactions involved in 16s rrna maturation and stress regulation in escherichia coli.ybey is part of a core set of rnases in escherichia coli and other bacteria. this highly conserved endoribonuclease has been implicated in several important processes such as 16s rrna 3' end maturation, 70s ribosome quality control, and regulation of mrnas and small noncoding rnas, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. thus, ybey likely interacts with numerous protein or rna partners that are involved in various aspects of cell ...201627834201
burkholderia contaminans biofilm regulating operon and its distribution in bacterial genomes.biofilm formation by burkholderia spp. is a principal cause of lung chronic infections in cystic fibrosis patients. a "lacking biofilm production" (lbp) strain b. contaminans gimc4587:bct370-19 has been obtained by insertion modification of clinical strain with plasposon mutagenesis. it has an interrupted transcriptional response regulator (rr) gene. the focus of our investigation was a two-component signal transduction system determination, including this rr. b. contaminans clinical and lbp str ...201628070515
linocin and ompw are involved in attachment of the cystic fibrosis-associated pathogen burkholderia cepacia complex to lung epithelial cells and protect mice against infection.members of the burkholderia cepacia complex (bcc) cause chronic opportunistic lung infections in people with cystic fibrosis (cf), resulting in a gradual lung function decline and, ultimately, patient death. the bcc is a complex of 20 species and is rarely eradicated once a patient is colonized; therefore, vaccination may represent a better therapeutic option. we developed a new proteomics approach to identify bacterial proteins that are involved in the attachment of bcc bacteria to lung epithel ...201626902727
application of omics technologies for evaluation of antibacterial mechanisms of action of plant-derived products.in the face of increasing bacterial resistance to antibiotics currently in use, the search for new antimicrobial agents has received a boost in recent years, with natural products playing an important role in this field. in fact, several methods have been proposed to investigate the antibacterial activities of natural products. however, given that the ultimate aim is future therapeutic use as novel drugs, it is extremely necessary to elucidate their modes of action, stating the molecular effects ...201627729901
sensitivity of pseudomonas syringae to bovine lactoferrin hydrolysates and identification of a novel inhibitory peptide.the antimicrobial activity of bovine lactoferrin hydrolysates (blfh) was measured against pseudomonas strains (p. syringae and p. fluorescens) in vitro. to compare susceptibility to blfh, minimal inhibitory concentration (mic) values were determined using chemiluminescence assays and paper disc plate assays. antimicrobial effect against p. fluorescens was not observed by either assay, suggesting that blfh did not exhibit antimicrobial activity against p. fluorescens. however, a significant inhib ...201627621689
pseudomonas fluorescens filamentous hemagglutinin, an iron-regulated protein, is an important virulence factor that modulates bacterial pathogenicity.pseudomonas fluorescens is a common bacterial pathogen to a wide range of aquaculture animals including various species of fish. in this study, we employed proteomic analysis and identified filamentous hemagglutinin (fha) as an iron-responsive protein secreted by tss, a pathogenic p. fluorescens isolate. in vitro study showed that compared to the wild type, the fha mutant tssfha (i) exhibited a largely similar vegetative growth profile but significantly retarded in the ability of biofilm growth ...201627602029
pcr-independent detection of bacterial species-specific 16s rrna at 10 fm by a pore-blockage sensor.a pcr-free, optics-free device is used for the detection of escherichia coli (e. coli) 16s rrna at 10 fm, which corresponds to ~100-1000 colony forming units/ml (cfu/ml) depending on cellular rrna levels. the development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. since 16s rrna sequences are species specific and are present at high copy number in viable cells, these nucleic acids off ...201627455337
the impact of selection, gene conversion, and biased sampling on the assessment of microbial demography.recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. we identified 26 studies using skyline plots and found that 21 inferred overall population expansion. this surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (sfs). forward simulations based on biologically relevant param ...201626931140
fine-tuning of amino sugar homeostasis by eiia(ntr) in salmonella typhimurium.the nitrogen-metabolic phosphotransferase system, pts(ntr), consists of the enzymes i(ntr), npr and iia(ntr) that are encoded by ptsp, ptso, and ptsn, respectively. due to the proximity of ptso and ptsn to rpon, the pts(ntr) system has been postulated to be closely related with nitrogen metabolism. to define the correlation between pts(ntr) and nitrogen metabolism, we performed ligand fishing with eiia(ntr) as a bait and revealed that d-glucosamine-6-phosphate synthase (glms) directly interacted ...201627628932
substrate and cofactor range differences of two cysteine dioxygenases from ralstonia eutropha h16.cysteine dioxygenases (cdos), which catalyze the sulfoxidation of cysteine to cysteine sulfinic acid (csa), have been extensively studied in eukaryotes because of their roles in several diseases. in contrast, only a few prokaryotic enzymes of this type have been investigated. in ralstonia eutropha h16, two cdo homologues (cdoa and cdob) have been identified previously. in vivo studies showed that escherichia coli cells expressing cdoa could convert 3-mercaptopropionate (3mp) to 3-sulfinopropiona ...201626590284
horizontal gene acquisitions, mobile element proliferation, and genome decay in the host-restricted plant pathogen erwinia tracheiphila.modern industrial agriculture depends on high-density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared with ecologically intact settings. here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen erwinia tracheiphila (enterobacteriaceae) isolated from infected squash plants in new york, pennsylvania, kentucky, and michigan. these genomes exhibit a high pr ...201626992913
co-regulation of iron metabolism and virulence associated functions by iron and xibr, a novel iron binding transcription factor, in the plant pathogen xanthomonas.abilities of bacterial pathogens to adapt to the iron limitation present in hosts is critical to their virulence. bacterial pathogens have evolved diverse strategies to coordinately regulate iron metabolism and virulence associated functions to maintain iron homeostasis in response to changing iron availability in the environment. in many bacteria the ferric uptake regulator (fur) functions as transcription factor that utilize ferrous form of iron as cofactor to regulate transcription of iron me ...201627902780
the mosaic type iv secretion systems.escherichia coli and other gram-negative and -positive bacteria employ type iv secretion systems (t4sss) to translocate dna and protein substrates, generally by contact-dependent mechanisms, to other cells. the t4sss functionally encompass two major subfamilies, the conjugation systems and the effector translocators. the conjugation systems are responsible for interbacterial transfer of antibiotic resistance genes, virulence determinants, and genes encoding other traits of potential benefit to t ...201627735785
crystal structure of bacterial haem importer complex in the inward-facing conformation.pathogenic bacteria remove iron from the haem of host tissues and use it as a catalytic center of many enzymes. haem uptake by pathogenic bacteria is facilitated by the membrane-integrated haem importer, which belongs to the type ii atp-binding cassette (abc) transporter. here we present crystal structures of burkholderia cenocepacia haem importer bhuuv complexed with the periplasmic haem-binding protein bhut and in the absence of bhut. the transmembrane helices of these structures show an inwar ...201627830695
interferon control of the sterol metabolic network: bidirectional molecular circuitry-mediating host protection.the sterol metabolic network is emerging center stage in inflammation and immunity. historically, observational clinical studies show that hypocholesterolemia is a common side effect of interferon (ifn) treatment. more recently, comprehensive systems-wide investigations of the macrophage ifn response reveal a direct molecular link between cholesterol metabolism and infection. upon infection, flux through the sterol metabolic network is acutely moderated by the ifn response at multiple regulatory ...201628066443
tolerogenic plasmacytoid dendritic cells control paracoccidioides brasiliensis infection by inducting regulatory t cells in an ido-dependent manner.plasmacytoid dendritic cells (pdcs), considered critical for immunity against viruses, were recently associated with defense mechanisms against fungal infections. however, the immunomodulatory function of pdcs in pulmonary paracoccidiodomycosis (pcm), an endemic fungal infection of latin america, has been poorly defined. here, we investigated the role of pdcs in the pathogenesis of pcm caused by the infection of 129sv mice with 1 x 106 p. brasiliensis-yeasts. in vitro experiments showed that p. ...201627992577
vaccination in hajj: an overview of the recent findings.about two million people annually travel to kingdom of saudi arabia to perform hajj. the pilgrims may be at risk of exposure to communicable diseases in this mass gathering and their vaccination against contagious diseases can prevent many morbidities and mortalities. the aim of our study was to review the papers which evaluated effectiveness and compliance of the vaccines applied in hajj.201628105294
otopathogenic pseudomonas aeruginosa enters and survives inside macrophages.otitis media (om) is a broad term describing a group of infectious and inflammatory disorders of the middle ear. despite antibiotic therapy, acute om can progress to chronic suppurative otitis media (csom) characterized by ear drum perforation and purulent discharge. pseudomonas aeruginosa is the most common pathogen associated with csom. although, macrophages play an important role in innate immune responses but their role in the pathogenesis of p. aeruginosa-induced csom is not known. the obje ...201627917157
microorganisms causing community-acquired acute bronchitis: the role of bacterial infection.although acute bronchitis is quite common, there is relatively limited information regarding the microorganisms that are involved in this illness.201627788254
non-culture methods for detecting infection. 201627789929
etiology of influenza-like illnesses from sentinel network practitioners in réunion island, 2011-2012.in réunion island, despite an influenza surveillance established since 1996 by the sentinel general practitioner's network, little is known about the etiology of influenza like-illness (ili) that differs from influenza viruses in a tropical area. we set up a retrospective study using nasal swabs collected by sentinel gps from ili patients in 2011 and 2012. a total of 250 swabs were randomly selected and analyzed by multiplex reverse transcriptase polymerase chain reaction (rt-pcr) including rese ...201627654509
prevalence and seasonal distribution of respiratory viruses during the 2014 - 2015 season in istanbul.acute respiratory tract infection (arti) is one of the most common infections worldwide, causing significant morbidity and mortality.201627800148
epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in mexico.respiratory syncytial virus (rsv) is a leading etiological agent of acute respiratory tract infections and hospitalizations in children. however, little information is available regarding rsv infections in latin american countries, particularly among adult patients.201627439650
epidemiology and clinical characteristics of respiratory syncytial virus infections among children and adults in mexico.respiratory syncytial virus (rsv) is a leading etiological agent of acute respiratory tract infections and hospitalizations in children. however, little information is available regarding rsv infections in latin american countries, particularly among adult patients.201627439650
clinical evaluation of the new high-throughput luminex nxtag respiratory pathogen panel assay for multiplex respiratory pathogen detection.a broad range of viral and bacterial pathogens can cause acute respiratory tract infection. for rapid detection of a broad respiratory pathogen spectrum, multiplex real-time pcr is ideal. this study evaluated the performance of the new luminex nxtag respiratory pathogen panel (nxtag-rpp) in comparison with the biofire filmarray respiratory panel (fa-rp) or singleplex real-time pcr as reference. a total of 284 clinical respiratory specimens and 3 influenza a/h7n9 viral culture samples were tested ...201627122380
derivation and multicenter validation of the drug resistance in pneumonia clinical prediction score.the health care-associated pneumonia (hcap) criteria have a limited ability to predict pneumonia caused by drug-resistant bacteria and favor the overutilization of broad-spectrum antibiotics. we aimed to derive and validate a clinical prediction score with an improved ability to predict the risk of pneumonia due to drug-resistant pathogens compared to that of hcap criteria. a derivation cohort of 200 microbiologically confirmed pneumonia cases in 2011 and 2012 was identified retrospectively. ris ...201626856838
the standard of care of patients with ards: ventilatory settings and rescue therapies for refractory hypoxemia.severe ards is often associated with refractory hypoxemia, and early identification and treatment of hypoxemia is mandatory. for the management of severe ards ventilator settings, positioning therapy, infection control, and supportive measures are essential to improve survival.201627040102
risk factors for long-term mortality after hospitalization for community-acquired pneumonia: a 5-year prospective follow-up study.contributors to long-term mortality in patients with community-acquired pneumonia (cap) remain unclear, with little attention paid to pneumonia etiology. we examined long-term survival, causes of death, and risk factors for long-term mortality in adult patients who had been hospitalized for cap, with emphasis on demographic, clinical, laboratory, and microbiological characteristics.201626849359
bacterial secretion systems: an overview.bacterial pathogens utilize a multitude of methods to invade mammalian hosts, damage tissue sites, and thwart the immune system from responding. one essential component of these strategies for many bacterial pathogens is the secretion of proteins across phospholipid membranes. secreted proteins can play many roles in promoting bacterial virulence, from enhancing attachment to eukaryotic cells, to scavenging resources in an environmental niche, to directly intoxicating target cells and disrupting ...201626999395
transcriptome-wide identification of hfq-associated rnas in brucella suis by deep sequencing.recent breakthroughs in next-generation sequencing technologies have led to the identification of small noncoding rnas (srnas) as a new important class of regulatory molecules. in prokaryotes, srnas are often bound to the chaperone protein hfq, which allows them to interact with their partner mrna(s). we screened the genome of the zoonotic and human pathogen brucella suis 1330 for the presence of this class of rnas. we designed a coimmunoprecipitation strategy that relies on the use of hfq as a ...201626553849
circlator: automated circularization of genome assemblies using long sequencing reads.the assembly of dna sequence data is undergoing a renaissance thanks to emerging technologies capable of producing reads tens of kilobases long. assembling complete bacterial and small eukaryotic genomes is now possible, but the final step of circularizing sequences remains unsolved. here we present circlator, the first tool to automate assembly circularization and produce accurate linear representations of circular sequences. using pacific biosciences and oxford nanopore data, circlator correct ...201526714481
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 ...201526610576
diagnostic accuracy of c-reactive protein and procalcitonin in suspected community-acquired pneumonia adults visiting emergency department and having a systematic thoracic ct scan.community-acquired pneumonia (cap) requires prompt treatment, but its diagnosis is complex. improvement of bacterial cap diagnosis by biomarkers has been evaluated using chest x-ray infiltrate as the cap gold standard, producing conflicting results. we analyzed the diagnostic accuracy of biomarkers in suspected cap adults visiting emergency departments for whom cap diagnosis was established by an adjudication committee which founded its judgment on a systematic multidetector thoracic ct scan.201526472401
viral and atypical bacterial aetiologies of infection in hospitalised patients admitted with clinical suspicion of influenza in thailand, vietnam and indonesia.influenza constitutes a leading cause of morbidity and mortality worldwide. there is limited information about the etiology of infection presenting clinically as influenza in hospitalized adults and children in southeast asia. such data are important for future management of respiratory infections.201525980749
ifn-γ priming effects on the maintenance of effector memory cd4(+) t cells and on phagocyte function: evidences from infectious diseases.although it has been established that effector memory cd4(+) t cells play an important role in the protective immunity against chronic infections, little is known about the exact mechanisms responsible for their functioning and maintenance, as well as their effects on innate immune cells. here we review recent data on the role of ifn-γ priming as a mechanism affecting both innate immune cells and effector memory cd4(+) t cells. suboptimal concentrations of ifn-γ are seemingly crucial for the opt ...201526509177
surfactant protein d binds to coxiella burnetii and results in a decrease in interactions with murine alveolar macrophages.coxiella burnetii is a gram-negative, obligate intracellular bacterium and the causative agent of q fever. infections are usually acquired after inhalation of contaminated particles, where c. burnetii infects its cellular target cells, alveolar macrophages. respiratory pathogens encounter the c-type lectin surfactant protein d (sp-d) during the course of natural infection. sp-d is a component of the innate immune response in the lungs and other mucosal surfaces. many gram-negative pulmonary path ...201526366725
role of atypical pathogens and the antibiotic prescription pattern in acute bronchitis: a multicenter study in korea.the role of atypical bacteria and the effect of antibiotic treatments in acute bronchitis are still not clear. this study was conducted at 22 hospitals (17 primary care clinics and 5 university hospitals) in korea. outpatients (aged ≥ 18 yr) who had an acute illness with a new cough and sputum (≤ 30 days) were enrolled in 2013. multiplex real-time polymerase chain reaction (rt-pcr) was used to detect five atypical bacteria. a total of 435 patients were diagnosed as having acute bronchitis (vs. p ...201526425041
ifn-γ induction by neutrophil-derived il-17a homodimer augments pulmonary antibacterial defense.the role of interleukin-17a (il-17a) in host defense against legionella pneumophila remains elusive. to address this issue, we used il17a(-/-), il17f(-/-), and il17a/il17f(-/-) mice on a c57bl/6 (non-permissive) background and il-17 neutralizing abs in mice on an a/j (permissive) background. higher bacterial (l. pneumophila) counts in the lung and blood along with reduced neutrophil recruitment were detected in il17a(-/-), but not il17f(-/-), mice. we found that neutrophils produce il-17a homodi ...201526349661
ifn-γ induction by neutrophil-derived il-17a homodimer augments pulmonary antibacterial defense.the role of interleukin-17a (il-17a) in host defense against legionella pneumophila remains elusive. to address this issue, we used il17a(-/-), il17f(-/-), and il17a/il17f(-/-) mice on a c57bl/6 (non-permissive) background and il-17 neutralizing abs in mice on an a/j (permissive) background. higher bacterial (l. pneumophila) counts in the lung and blood along with reduced neutrophil recruitment were detected in il17a(-/-), but not il17f(-/-), mice. we found that neutrophils produce il-17a homodi ...201526349661
a rare case of diffuse alveolar hemorrhage secondary to acute pulmonary histoplasmosis.diffuse alveolar hemorrhage (dah) is a rare presentation of acute pulmonary histoplasmosis. while histoplasmosis has been reported to cause hemoptysis and alveolar hemorrhage in children, the english language literature lacks any adult case reports documenting this association. we report a case of pulmonary histoplasmosis where the initial presentation was pneumonia with a subsequent diagnosis of dah.201526435863
whole-genome sequencing for tracing the transmission link between two ard outbreaks caused by a novel hadv serotype 7 variant, china.from december 2012 to february 2013, two outbreaks of acute respiratory disease caused by hadv-7 were reported in china. we investigated possible transmission links between these two seemingly unrelated outbreaks by integration of epidemiological and whole-genome sequencing (wgs) data. wgs analyses showed that the hadv-7 isolates from the two outbreaks were genetically indistinguishable; however, a 12 bp deletion in the virus-associated rna gene distinguished the outbreak isolates from other had ...201526338697
cross-reactions in igm elisa tests to legionella pneumophila sg1 and bordetella pertussis among children suspected of legionellosis; potential impact of vaccination against pertussis?the objective of this study was preliminary evaluation of igm cross-reaction in sera collected from children hospitalized because of suspected legionellosis. sera with positive igm results to l. pneumophila sgs1-7, b. pertussis or with simultaneous detection of igm antibodies to l. pneumophila sgs1-7 and b. pertussis, or igm to l. pneumophila sgs1-7 and m. pneumoniae in routine tests, were selected. in total, an adapted pre-absorption test was used for the serological confirmation of legionellos ...201526557032
problem of immunoglobulin m co-detection in serological response to bacterial and viral respiratory pathogens among children suspected of legionellosis.the objective of this research was an analysis of the serological response to respiratory bacterial and viral pathogens, in 156 children admitted to hospital in warsaw with a suspicion of legionellosis. levels of immunoglobulin (ig) m to bordetella pertussis, mycoplasma pneumoniae, respiratory syncytial virus (rsv), adenoviruses, human parainfluenza virus (hpiv) t. 1-4 and influenza t. a + b viruses were determined retrospectively by elisas. in the prospective examinations (only legionella pneum ...201526557031
mapping type iv secretion signals on the primase encoded by the broad-host-range plasmid r1162 (rsf1010).the plasmid r1162 (rsf1010) encodes a primase essential for its replication. this primase makes up the c-terminal part of moba, a multifunctional protein with the relaxase as a separate n-terminal domain. the primase is also translated separately as the protein repb'. here, we map two signals for type iv secretion onto the recently solved structure of repb'. one signal is located internally within repb' and consists of a long α-helix and an adjacent disordered region rich in arginines. the secon ...201526381189
clinical and molecular epidemiology of human rhinovirus infections in patients with hematologic malignancy.human rhinoviruses (hrvs) are common causes of upper respiratory tract infection (urti) in hematologic malignancy (hm) patients. predictors of lower respiratory tract infection (lrti) including the impact of hrv species and types are poorly understood.201526370315
isothermal detection of mycoplasma pneumoniae directly from respiratory clinical specimens.mycoplasma pneumoniae is a leading cause of community-acquired pneumonia (cap) across patient populations of all ages. we have developed a loop-mediated isothermal amplification (lamp) assay that enables rapid, low-cost detection of m. pneumoniae from nucleic acid extracts and directly from various respiratory specimen types. the assay implements calcein to facilitate simple visual readout of positive results in approximately 1 h, making it ideal for use in primary care facilities and resource-p ...201526179304
identification of divergent type vi secretion effectors using a conserved chaperone domain.the type vi secretion system (t6ss) is a lethal weapon used by many bacteria to kill eukaryotic predators or prokaryotic competitors. killing by the t6ss results from repetitive delivery of toxic effectors. despite their importance in dictating bacterial fitness, systematic prediction of t6ss effectors remains challenging due to high effector diversity and the absence of a conserved signature sequence. here, we report a class of t6ss effector chaperone (tec) proteins that are required for effect ...201526150500
pneumonia outbreak caused by chlamydophila pneumoniae among us air force academy cadets, colorado, usa.during october 2013-may 2014, there were 102 cases of pneumonia diagnosed in us air force academy cadets. a total of 73% of tested nasal washes contained chlamydophila pneumoniae. this agent can be considered to be present on campus settings during outbreaks with numerous, seemingly disconnected cases of relatively mild pneumonia.201525988545
vitamin d every day to keep the infection away?within the last decade, vitamin d has emerged as a central regulator of host defense against infections. in this regard, vitamin d triggers effective antimicrobial pathways against bacterial, fungal and viral pathogens in cells of the human innate immune system. however, vitamin d also mediates potent tolerogenic effects: it is generally believed that vitamin d attenuates inflammation and acquired immunity, and thus potentially limits collateral tissue damage. nevertheless, several studies indic ...201526035244
bacterial pathogens and community composition in advanced sewage treatment systems revealed by metagenomics analysis based on high-throughput sequencing.this study used 454 pyrosequencing, illumina high-throughput sequencing and metagenomic analysis to investigate bacterial pathogens and their potential virulence in a sewage treatment plant (stp) applying both conventional and advanced treatment processes. pyrosequencing and illumina sequencing consistently demonstrated that arcobacter genus occupied over 43.42% of total abundance of potential pathogens in the stp. at species level, potential pathogens arcobacter butzleri, aeromonas hydrophila a ...201525938416
secretion of flagellar proteins by the pseudomonas aeruginosa type iii secretion-injectisome system.the opportunistic pathogen pseudomonas aeruginosa utilizes an injectisome-type iii secretion system (injectisome-t3ss) to elicit cytotoxicity toward epithelial cells and macrophages. macrophage killing results from the cytotoxic properties of the translocated effector proteins (exos, exot, exou, and exoy) and inflammasome-mediated induction of pyroptosis. inflammasome activation can occur following nlrc4-mediated recognition of cytosolic translocated flagellin (flic). in the present study, we de ...201525845843
spatiotemporal regulation of a legionella pneumophila t4ss substrate by the metaeffector sidj.modulation of host cell function is vital for intracellular pathogens to survive and replicate within host cells. most commonly, these pathogens utilize specialized secretion systems to inject substrates (also called effector proteins) that function as toxins within host cells. since it would be detrimental for an intracellular pathogen to immediately kill its host cell, it is essential that secreted toxins be inactivated or degraded after they have served their purpose. the pathogen legionella ...201525774515
survey and rapid detection of bordetella pertussis in clinical samples targeting the bp485 in china.bordetella pertussis is an important human respiratory pathogen. here, we describe a loop-mediated isothermal amplification (lamp) method for the rapid detection of b. pertussis in clinical samples based on a visual test. the lamp assay detected the bp485 target sequence within 60 min with a detection limit of 1.3 pg/μl, a 10-fold increase in sensitivity compared with conventional pcr. all 31 non-pertussis respiratory pathogens tested were negative for lamp detection, indicating the high specifi ...201525798436
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.201525887603
chances and limitations of nanosized titanium dioxide practical application in view of its physicochemical properties.nanotechnology is a field of science that is nowadays developing in a dynamic way. it seems to offer almost endless opportunities of contribution to many areas of economy and human activity, in general. thanks to nanotechnology, the so-called nanomaterials can be designed. they present structurally altered materials, with their physical, chemical and biological properties entirely differing from properties of the same materials manufactured in microtechnology. nanotechnology creates a unique opp ...201525852354
association between helicobacter spp. infections and hepatobiliary malignancies: a review.hepatobiliary cancers are highly lethal cancers that comprise a spectrum of invasive carcinomas originating in the liver hepatocellular carcinoma, the bile ducts intrahepatic cholangiocarcinoma and extrahepatic cholangiocarcinoma, the gallbladder and the ampulla of vater (collectively known as biliary tract cancers). these tumors account for approximately 13% of all annual cancer-related deaths worldwide and for 10%-20% of deaths from hepatobiliary malignancies. cholangiocarcinoma (cca) is a dev ...201525663761
essential domains of anaplasma phagocytophilum invasins utilized to infect mammalian host cells.anaplasma phagocytophilum causes granulocytic anaplasmosis, an emerging disease of humans and domestic animals. the obligate intracellular bacterium uses its invasins ompa, asp14, and aipa to infect myeloid and non-phagocytic cells. identifying the domains of these proteins that mediate binding and entry, and determining the molecular basis of their interactions with host cell receptors would significantly advance understanding of a. phagocytophilum infection. here, we identified the ompa bindin ...201525658707
identification of a novel human rhinovirus c type by antibody capture vidisca-454.causative agents for more than 30 percent of respiratory infections remain unidentified, suggesting that unknown respiratory pathogens might be involved. in this study, antibody capture vidisca-454 (virus discovery cdna-aflp combined with roche 454 high-throughput sequencing) resulted in the discovery of a novel type of rhinovirus c (rv-c). the virus has an rna genome of at least 7054 nt and carries the characteristics of rhinovirus c species. the gene encoding viral protein 1, which is used for ...201525606972
abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.bathymodiolus mussels live in symbiosis with intracellular sulfur-oxidizing (sox) bacteria that provide them with nutrition. we sequenced the sox symbiont genomes from two bathymodiolus species. comparison of these symbiont genomes with those of their closest relatives revealed that the symbionts have undergone genome rearrangements, and up to 35% of their genes may have been acquired by horizontal gene transfer. many of the genes specific to the symbionts were homologs of virulence genes. we di ...201526371554
the sugar kinase that is necessary for the catabolism of rhamnose in rhizobium leguminosarum directly interacts with the abc transporter necessary for rhamnose transport.rhamnose catabolism in rhizobium leguminosarum was found to be necessary for the ability of the organism to compete for nodule occupancy. characterization of the locus necessary for the catabolism of rhamnose showed that the transport of rhamnose was dependent upon a carbohydrate uptake transporter 2 (cut2) abc transporter encoded by rhastpq and on the presence of rhak, a protein known to have sugar kinase activity. a linker-scanning mutagenesis analysis of rhak showed that the kinase and transp ...201526416834
nopc is a rhizobium-specific type 3 secretion system effector secreted by sinorhizobium (ensifer) fredii hh103.sinorhizobium (ensifer) fredii hh103 is a broad host-range nitrogen-fixing bacterium able to nodulate many legumes, including soybean. in several rhizobia, root nodulation is influenced by proteins secreted through the type 3 secretion system (t3ss). this specialized secretion apparatus is a common virulence mechanism of many plant and animal pathogenic bacteria that delivers proteins, called effectors, directly into the eukaryotic host cells where they interfere with signal transduction pathway ...201526569401
edwardsiella tarda esce (orf13 protein) is a type iii secretion system-secreted protein that is required for the injection of effectors, secretion of translocators, and pathogenesis in fish.the type iii secretion system (t3ss) of edwardsiella tarda is crucial for its intracellular survival and pathogenesis in fish. the orf13 gene (esce) of e. tarda is located 84 nucleotides (nt) upstream of esrc in the t3ss gene cluster. we found that esce is secreted and translocated in a t3ss-dependent manner and that amino acids 2 to 15 in the n terminus were required for a completely functional t3ss in e. tarda. deletion of esce abolished the secretion of t3ss translocators, as well as the secr ...201526459509
edwardsiella tarda esce (orf13 protein) is a type iii secretion system-secreted protein that is required for the injection of effectors, secretion of translocators, and pathogenesis in fish.the type iii secretion system (t3ss) of edwardsiella tarda is crucial for its intracellular survival and pathogenesis in fish. the orf13 gene (esce) of e. tarda is located 84 nucleotides (nt) upstream of esrc in the t3ss gene cluster. we found that esce is secreted and translocated in a t3ss-dependent manner and that amino acids 2 to 15 in the n terminus were required for a completely functional t3ss in e. tarda. deletion of esce abolished the secretion of t3ss translocators, as well as the secr ...201526459509
targeting virulence not viability in the search for future antibacterials.new antibacterials need new approaches to overcome the problem of rapid antibiotic resistance. here we review the development of potential new antibacterial drugs that do not kill bacteria or inhibit their growth, but combat disease instead by targeting bacterial virulence.201524552512
structural and functional studies of the pseudomonas aeruginosa minor pilin, pile.many bacterial pathogens, including pseudomonas aeruginosa, use type iva pili (t4ap) for attachment and twitching motility. t4ap are composed primarily of major pilin subunits, which are repeatedly assembled and disassembled to mediate function. a group of pilin-like proteins, the minor pilins fimu and pilvwxe, prime pilus assembly and are incorporated into the pilus. we showed previously that minor pilin pile depends on the putative priming subcomplex pilvwx and the non-pilin protein pily1 for ...201526359492
phylogenetic and amino acid conservation analyses of bacterial l-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain.all organisms must synthesize the enzymatic cofactor coenzyme a (coa) from the precursor pantothenate. most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. the synthesis of β-alanine is catalyzed by l-aspartate-α-decarboxylase (pand), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-pand). active pand is generated by self-cleavage of pro-pand at gly24-ser25 creating the active-site pyruvoyl moiety. in salmonella enterica, this cleavage ...201526276430
the bordetella secreted regulator bspr is translocated into the nucleus of host cells via its n-terminal moiety: evaluation of bacterial effector translocation by the escherichia coli type iii secretion system.bordetella bronchiseptica is genetically related to b. pertussis and b. parapertussis, which cause respiratory tract infections in humans. these pathogens possess a large number of virulence factors, including the type iii secretion system (t3ss), which is required for the delivery of effectors into the host cells. in a previous study, we identified a transcriptional regulator, bspr, that is involved in the regulation of the t3ss-related genes in response to iron-starved conditions. a unique fea ...201526247360
beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold.for the past 25 years, phage display technology has been an invaluable tool for studies of protein-protein interactions. however, the inherent biological, biochemical, and biophysical properties of filamentous bacteriophage, as well as the ease of its genetic manipulation, also make it an attractive platform outside the traditional phage display canon. this review will focus on the unique properties of the filamentous bacteriophage and highlight its diverse applications in current research. part ...201526300850
an sos regulon under control of a noncanonical lexa-binding motif in the betaproteobacteria.the sos response is a transcriptional regulatory network governed by the lexa repressor that activates in response to dna damage. in the betaproteobacteria, lexa is known to target a palindromic sequence with the consensus sequence ctgt-n8-acag. we report the characterization of a lexa regulon in the iron-oxidizing betaproteobacterium sideroxydans lithotrophicus. in silico and in vitro analyses show that lexa targets six genes by recognizing a binding motif with the consensus sequence gaacgaacgt ...201525986903
brkautodisplay: functional display of multiple exogenous proteins on the surface of escherichia coli by using brka autotransporter.bacterial surface display technique enables the exogenous proteins or polypeptides displayed on the bacterial surface, while maintaining their relatively independent spatial structures and biological activities. the technique makes recombinant bacteria possess the expectant functions, subsequently, directly used for many applications. many proteins could be used to achieve bacterial surface display, among them, autotransporter, a member of the type v secretion system of gram-negative bacteria, h ...201526337099
genomic insights into intrinsic and acquired drug resistance mechanisms in achromobacter xylosoxidans.achromobacter xylosoxidans is an opportunistic pathogen known to be resistant to a wide range of antibiotics; however, the knowledge about the drug resistance mechanisms is limited. we used a high-throughput sequencing approach to sequence the genomes of the a. xylosoxidans type strain atcc 27061 and a clinical isolate, a. xylosoxidans x02736, and then we used different bioinformatics tools to analyze the drug resistance genes in these bacteria. we obtained the complete genome sequence for a. xy ...201525487802
a single serine residue determines selectivity to monovalent metal ions in metalloregulators of the merr family.merr metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. the sensor protein binds the inducer metal ion by using two conserved cysteine residues at the c-terminal metal-binding loop (mbl). divalent metal ion sensors, such as merr and zntr, require a third cysteine residue, located at the beginning of the dimerization (α ...201525691529
the lipid-modifying multiple peptide resistance factor is an oligomer consisting of distinct interacting synthase and flippase subunits.phospholipids are synthesized at the inner leaflet of the bacterial cytoplasmic membrane but have to be translocated to the outer leaflet to maintain membrane lipid bilayer composition and structure. even though phospholipid flippases have been proposed to exist in bacteria, only one such protein, mprf, has been described. mprf is a large integral membrane protein found in several prokaryotic phyla, whose c terminus modifies phosphatidylglycerol (pg), the most common bacterial phospholipid, with ...201525626904
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