Publications

aetiology of diarrhoeal disease and evaluation of viral-bacterial coinfection in children under 5 years old in china: a matched case-control study.	globally, diarrhoeal diseases are the second leading cause of death among children under 5 years old. few case-control studies on the aetiology of diarrhoea have been conducted in china. a case-control study on 922 children under 5 years old who presented with diarrhoea and individually matched controls was conducted in china between may 2011 and january 2013. quantitative pcr was used to analyze stool samples for 10 diarrhoeal pathogens. potential enteric pathogens were detected in 377 (81.8%) ...	2016	26724990
gastrointestinal disorders associated with common variable immune deficiency (cvid) and chronic granulomatous disease (cgd).	common variable immune deficiency (cvid) and chronic granulomatous disease (cgd) are two of the well-characterized primary immune deficiencies with distinct pathologic defects. while cvid is predominantly a disorder of the adaptive immune system, in cgd, innate immunity is impaired. in both syndromes, the clinical manifestations include an increased susceptibility to infections and a number of non-infectious, inflammatory conditions including systemic autoimmunity, as well as organ-specific path ...	2016	26951230
vaxar: a web-based database of laboratory animal responses to vaccinations and its application in the meta-analysis of different animal responses to tuberculosis vaccinations.	animal models are indispensable for vaccine research and development. however, choosing which species to use and designing a vaccine study that is optimized for that species is often challenging. vaxar (http://www.violinet.org/vaxar/) is a web-based database and analysis system that stores manually curated data regarding vaccine-induced responses in animals. to date, vaxar encompasses models from 35 animal species including rodents, rabbits, ferrets, primates, and birds. these 35 species have be ...	2016	27053566
proteomics as a tool for studying bacterial virulence and antimicrobial resistance.	proteomic studies have improved our understanding of the microbial world. the most recent advances in this field have helped us to explore aspects beyond genomics. for example, by studying proteins and their regulation, researchers now understand how some pathogenic bacteria have adapted to the lethal actions of antibiotics. proteomics has also advanced our knowledge of mechanisms of bacterial virulence and some important aspects of how bacteria interact with human cells and, thus, of the pathog ...	2016	27065974
copper-containing anti-biofilm nanofiber scaffolds as a wound dressing material.	copper particles were incorporated into nanofibers during the electrospinning of poly-d,l-lactide (pdlla) and poly(ethylene oxide) (peo). the ability of the nanofibers to prevent pseudomonas aeruginosa pa01 and staphylococcus aureus (strain xen 30) to form biofilms was tested. nanofibers containing copper particles (cu-f) were thinner (326 ± 149 nm in diameter), compared to nanofibers without copper (cf; 445 ± 93 nm in diameter). the crystalline structure of the copper particles in cu-f was conf ...	2016	27028292
growth phase, oxygen, temperature, and starvation affect the development of viable but non-culturable state of vibrio cholerae.	vibrio cholerae can enter into a viable but non-culturable (vbnc) state in order to survive in unfavorable environments. in this study, we studied the roles of five physicochemical and microbiological factors or states, namely, different strains, growth phases, oxygen, temperature, and starvation, on the development of vbnc of v. cholerae in artificial sea water (asw). different strains of the organism, the growth phase, and oxygen levels affected the progress of vbnc development. it was found t ...	2016	27065970
toll-like receptor-4 dependent intestinal gene expression during arcobacter butzleri infection of gnotobiotic il-10 deficient mice.	we have previously shown that arcobacter butzleri infection induces toll-like receptor (tlr) -4 dependent immune responses in perorally infected gnotobiotic il-10(-/-) mice. here, we analyzed tlr-4-dependent expression of genes encoding inflammatory mediators and matrix-degrading gelatinases mmp-2 and -9 in the small and large intestines of gnotobiotic tlr-4-deficient il-10(-/-) mice that were perorally infected with a. butzleri strains ccug 30485 or c1, of human and chicken origin, respectively ...	2016	27141316
intestinal expression of genes encoding inflammatory mediators and gelatinases during arcobacter butzleri infection of gnotobiotic il-10 deficient mice.	we have previously shown that arcobacter butzleri induces intestinal, extra-intestinal, and systemic immune responses in perorally infected gnotobiotic il-10(-/-) mice in a strain-dependent fashion. here, we present a comprehensive survey of small and large intestinal expression profiles of inflammatory and regulatory mediators as well as of the matrix-degrading gelatinases mmp-2 and mmp-9 following murine a. butzleri infection. gnotobiotic il-10(-/-) mice were infected with a. butzleri strains ...	2016	27141315
anti-ganglioside antibodies are removed from circulation in mice by neuronal endocytosis.	see van doorn and jacobs doi101093/brain/aww078 for a scientific commentary on this article : in axonal forms of guillain-barré syndrome, anti-ganglioside antibodies bind gangliosides on nerve surfaces, thereby causing injury through complement activation and immune cell recruitment. why some nerve regions are more vulnerable than others is unknown. one reason may be that neuronal membranes with high endocytic activity, including nerve terminals involved in neurotransmitter recycling, are able ...	2016	27017187
automated broad-range molecular detection of bacteria in clinical samples.	molecular detection methods, such as quantitative pcr (qpcr), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. most routinely used methods, however, are directed at specific species. thus, anything that is not explicitly searched for will be missed. this greatly limits the flexibility and universal application of these techniques. we investigated the application of a rapid universal bacterial molecular identification method, is-pro, to rout ...	2016	26763956
pneumococcus with the "6e" cps locus produces serotype 6b capsular polysaccharide.	genetic studies of serogroup 6 isolates ofstreptococcus pneumoniaeidentified putative serotype 6e. although its capsular polysaccharide structure has not been elucidated, putative serotype 6e is described in an increasing number of studies as a potentially new serotype. we show here that spec6b, which is widely used as a target strain for serotype 6b opsonophagocytosis assays, has the genetic features of the putative serotype 6e but produces capsular polysaccharide identical to 6b capsular polys ...	2016	26818670
a highly macrolide-resistant campylobacter jejuni strain with rare a2074t mutations in 23s rrna genes.		2016	26810658
nitazoxanide inhibits pilus biogenesis by interfering with folding of the usher protein in the outer membrane.	many bacterial pathogens assemble surface fibers termed pili or fimbriae that facilitate attachment to host cells and colonization of host tissues. the chaperone/usher (cu) pathway is a conserved secretion system that is responsible for the assembly of virulence-associated pili by many different gram-negative bacteria. pilus biogenesis by the cu pathway requires a dedicated periplasmic chaperone and an integral outer membrane (om) assembly and secretion platform termed the usher. nitazoxanide (n ...	2016	26824945
unusual non-fluorescent broad spectrum siderophore activity (sid egyii) by pseudomonas aeruginosa strain egyii dsm 101801 and a new insight towards simple siderophore bioassay.	present study highlights an unusual non-fluorescent hydroxamate broad spectrum siderophore (sid egyii) activity from pseudomonas aeruginosa strain egyii dsm 101801, a soil bacterial isolate, along with simple low cost effective siderophore bioassay. detection of sid egyii activity qualitatively was proved by masking this activity against erwinia amylovora strain egy1 dsm 101800, an indicator strain, in well-cut diffusion assay containing 100 µm fecl3. sid egyii activity was expressed quantitativ ...	2016	27015845
acute tuberculous myopericarditis mimicking acute myocardial infarction: a case report and literature review.	a number of cases of acute myopericarditis mimicking acute myocardial infarction (ami) have previously been reported in the literature. however, to the best of our knowledge, such a case resulting from mycobacterium tuberculosis infection has not previously been described. the present study reports the case of a 21-year-old male patient presenting with acute chest pain, in whom focal st-segment elevation and elevated cardiac enzymes mimicked a diagnosis of ami. however, acute tuberculous myoperi ...	2016	27284323
crystal structure of cota laccase complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) at a novel binding site.	the cota laccase from bacillus subtilis is an abundant component of the spore outer coat and has been characterized as a typical laccase. the crystal structure of cota complexed with 2,2-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in a hole motif has been solved. the novel binding site was about 26 å away from the t1 binding pocket. comparison with known structures of other laccases revealed that the hole is a specific feature of cota. the key residues arg476 and ser360 were directly bo ...	2016	27050268
escherichia coli o104 in feedlot cattle feces: prevalence, isolation and characterization.	escherichia coli o104:h4, an hybrid pathotype of shiga toxigenic and enteroaggregative e. coli, involved in a major foodborne outbreak in germany in 2011, has not been detected in cattle feces. serogroup o104 with h type other than h4 has been reported to cause human illnesses, but their prevalence and characteristics in cattle have not been reported. our objectives were to determine the prevalence of e. coli o104 in feces of feedlot cattle, by culture and pcr detection methods, and characterize ...	2016	27010226
survival capacity of arcobacter butzleri inoculated in poultry meat at two different refrigeration temperatures.	arcobacter spp. are emerging enteropathogens and potential zoonotic agents that can be transmitted by food and water, being considered a public health risk. the high isolation rate of these bacteria from poultry products suggests that it may be a major source of human infections. one hallmark for differentiating the genus arcobacter from campylobacter includes their growing capacity at low temperatures (15-30 °c) under aerobic conditions. however, little is known about the population density var ...	2016	27007565
molecular markers for tracking the origin and worldwide distribution of invasive strains of puccinia striiformis.	investigating the origin and dispersal pathways is instrumental to mitigate threats and economic and environmental consequences of invasive crop pathogens. in the case of puccinia striiformis causing yellow rust on wheat, a number of economically important invasions have been reported, e.g., the spreading of two aggressive and high temperature adapted strains to three continents since 2000. the combination of sequence-characterized amplified region (scar) markers, which were developed from two s ...	2016	27066253
the sos response master regulator lexa regulates the gene transfer agent of rhodobacter capsulatus and represses transcription of the signal transduction protein ccka.	the gene transfer agent of rhodobacter capsulatus (rcgta) is a genetic exchange element that combines central aspects of bacteriophage-mediated transduction and natural transformation. rcgta particles resemble a small double-stranded dna bacteriophage, package random ∼4-kb fragments of the producing cell genome, and are released from a subpopulation (<1%) of cells in a stationary-phase culture. rcgta particles deliver this dna to surrounding r. capsulatus cells, and the dna is integrated into th ...	2016	26833411
identification of e-cadherin signature motifs functioning as cleavage sites for helicobacter pylori htra.	the cell adhesion protein and tumour suppressor e-cadherin exhibits important functions in the prevention of gastric cancer. as a class-i carcinogen, helicobacter pylori (h. pylori) has developed a unique strategy to interfere with e-cadherin functions. in previous studies, we have demonstrated that h. pylori secretes the protease high temperature requirement a (htra) which cleaves off the e-cadherin ectodomain (ntf) on epithelial cells. this opens cell-to-cell junctions, allowing bacterial tran ...	2016	26983597
gut microbiota: the brain peacekeeper.	gut microbiota regulates intestinal and extraintestinal homeostasis. accumulating evidence suggests that the gut microbiota may also regulate brain function and behavior. results from animal models indicate that disturbances in the composition and functionality of some microbiota members are associated with neurophysiological disorders, strengthening the idea of a microbiota-gut-brain axis and the role of microbiota as a "peacekeeper" in the brain health. here, we review recent discoveries on th ...	2016	27014255
cytokine responses in birds challenged with the human food-borne pathogen campylobacter jejuni implies a th17 response.	development of process orientated understanding of cytokine interactions within the gastrointestinal tract during an immune response to pathogens requires experimentation and statistical modelling. the immune response against pathogen challenge depends on the specific threat to the host. here, we show that broiler chickens mount a breed-dependent immune response to campylobacter jejuni infection in the caeca by analysing experimental data using frequentist and bayesian structural equation models ...	2016	27069644
biofilm morphotypes and population structure among staphylococcus epidermidis from commensal and clinical samples.	bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host's immune response and antibiotics. commensal s. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm acc ...	2016	26978068
diverse high-torque bacterial flagellar motors assemble wider stator rings using a conserved protein scaffold.	although it is known that diverse bacterial flagellar motors produce different torques, the mechanism underlying torque variation is unknown. to understand this difference better, we combined genetic analyses with electron cryo-tomography subtomogram averaging to determine in situ structures of flagellar motors that produce different torques, from campylobacter and vibrio species. for the first time, to our knowledge, our results unambiguously locate the torque-generating stator complexes and sh ...	2016	26976588
expanding the role of fura as essential global regulator in cyanobacteria.	in the nitrogen-fixing heterocyst-forming cyanobacterium anabaena sp. pcc 7120, the ferric uptake regulator fura plays a global regulatory role. failures to eliminate wild-type copies of fura gene from the polyploid genome suggest essential functions. in the present study, we developed a selectively regulated fura expression system by the replacement of fura promoter in the anabaena sp. chromosomes with the co2+/zn2+ inducible coat promoter from synechocystis sp. pcc 6803. by removing co2+ and z ...	2016	26967347
proton pump inhibitors and gastroenteritis.	an association between proton pump inhibitor (ppi) therapy and bacterial gastroenteritis has been suggested as well as contradicted. the aim of this study was to examine the association between the use of ppis and occurrence of bacterial gastroenteritis in the prospective rotterdam study. the rotterdam study is a population-based cohort study among 14,926 subjects aged 45 years and older with up to 24 years of follow-up. analyses were performed with a generalized estimating equations method in p ...	2016	26960438
atypical sensors for direct and rapid neuronal detection of bacterial pathogens.	bacterial infection can threaten the normal biological functions of a host, often leading to a disease. hosts have developed complex immune systems to cope with the danger. preceding the elimination of pathogens, selective recognition of the non-self invaders is necessary. at the forefront of the body's defenses are the innate immune cells, which are equipped with particular sensor molecules that can detect common exterior patterns of invading pathogens and their secreting toxins as well as with ...	2016	26960533
transcriptome landscape of lactococcus lactis reveals many novel rnas including a small regulatory rna involved in carbon uptake and metabolism.	rna sequencing has revolutionized genome-wide transcriptome analyses, and the identification of non-coding regulatory rnas in bacteria has thus increased concurrently. here we reveal the transcriptome map of the lactic acid bacterial paradigm lactococcus lactis mg1363 by employing differential rna sequencing (drna-seq) and a combination of manual and automated transcriptome mining. this resulted in a high-resolution genome annotation of l. lactis and the identification of 60 cis-encoded antisens ...	2016	26950529
discovery and dissection of metabolic oscillations in the microaerobic nitric oxide response network of escherichia coli.	the virulence of many pathogens depends upon their ability to cope with immune-generated nitric oxide (no·). in escherichia coli, the major no· detoxification systems are hmp, an no· dioxygenase (nod), and norv, an no· reductase (nor). it is well established that hmp is the dominant system under aerobic conditions, whereas norv dominates anaerobic conditions; however, the quantitative contributions of these systems under the physiologically relevant microaerobic regime remain ill defined. here, ...	2016	26951670
correction: updated campylobacter jejuni capsule pcr multiplex typing system and its application to clinical isolates from south and southeast asia.		2016	26950938
the efficacy of a commercial competitive exclusion product on campylobacter colonization in broiler chickens in a 5-week pilot-scale study.	the efficacy of the commercial competitive exclusion product broilact against campylobacter jejuni was evaluated in broiler chickens in a 5-week pilot-scale study. newly-hatched broiler chicks were brought from a commercial hatchery. after arrival 50 seeder chicks were challenged orally with approximately 10(3) cfu of c. jejuni, wing marked, and placed back in a delivery box and moved to a separate room. the rest of the chicks (contact chicks) were placed in floor pens, 100 chicks per pen. birds ...	2016	26944963
bacterial antisense rnas are mainly the product of transcriptional noise.	cis-encoded antisense rnas (asrnas) are widespread along bacterial transcriptomes. however, the role of most of these rnas remains unknown, and there is an ongoing discussion as to what extent these transcripts are the result of transcriptional noise. we show, by comparative transcriptomics of 20 bacterial species and one chloroplast, that the number of asrnas is exponentially dependent on the genomic at content and that expression of asrna at low levels exerts little impact in terms of energy c ...	2016	26973873
sialic acid-modified antigens impose tolerance via inhibition of t-cell proliferation and de novo induction of regulatory t cells.	sialic acids are negatively charged nine-carbon carboxylated monosaccharides that often cap glycans on glycosylated proteins and lipids. because of their strategic location at the cell surface, sialic acids contribute to interactions that are critical for immune homeostasis via interactions with sialic acid-binding ig-type lectins (siglecs). in particular, these interactions may be of importance in cases where sialic acids may be overexpressed, such as on certain pathogens and tumors. we now dem ...	2016	26941238
c1q-targeted inhibition of the classical complement pathway prevents injury in a novel mouse model of acute motor axonal neuropathy.	guillain-barré syndrome (gbs) is an autoimmune disease that results in acute paralysis through inflammatory attack on peripheral nerves, and currently has limited, non-specific treatment options. the pathogenesis of the acute motor axonal neuropathy (aman) variant is mediated by complement-fixing anti-ganglioside antibodies that directly bind and injure the axon at sites of vulnerability such as nodes of ranvier and nerve terminals. consequently, the complement cascade is an attractive target to ...	2016	26936605
horizontal dna transfer mechanisms of bacteria as weapons of intragenomic conflict.	horizontal dna transfer (hdt) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. much recent research has emphasised the adaptive benefit of acquiring novel dna, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of hdt. to test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing hdt through ...	2016	26934590
polynucleotide phosphorylase regulates multiple virulence factors and the stabilities of small rnas rsmy/z in pseudomonas aeruginosa.	post-transcriptional regulation enables bacteria to quickly response to environmental stresses. polynucleotide phosphorylase (pnpase), which contains an n-terminal catalytic core and c-terminal rna binding kh-s1 domains, is involved in rna processing. here we demonstrate that in pseudomonas aeruginosa the kh-s1 domains of pnpase are required for the type iii secretion system (t3ss) and bacterial virulence. transcriptome analysis revealed a pleiotropic role of pnpase in gene regulation. particula ...	2016	26973625
onset of ulcerative colitis after helicobacter pylori eradication therapy: a case report.	in japan, helicobacter pylori eradication has been approved since 2013 for treatment of h pylori-induced chronic gastritis, in an attempt to reduce the prevalence of gastric cancer, a leading cancer in japan. h pylori infection affects more than 50% of the world's population. h pylori eradication therapy is generally safe. to our knowledge, no case of newly diagnosed ulcerative colitis occurring immediately after h pylori eradication therapy has previously been reported.a 63-year-old man receive ...	2016	27043835
primary gastro intestinal lymphoma presenting as perforation peritonitis.	primary gastrointestinal lymphoma is very rare compared to gastrointestinal tract lymphoma arising secondary to primary nodal disease. extra nodal lymphoma can involve any part of the gastrointestinal tract, most commonly being the stomach followed by small intestine and ileocecal region. they are indistinguishable from other benign and malignant conditions and clinically non-specific. here, we have an interesting case where a patient presented with peritonitis and was found to have a perforated ...	2016	27134938
deletion of the entire interferon-γ receptor 1 gene causing complete deficiency in three related patients.	complete interferon-γ receptor 1 (ifn-γr1) deficiency is a primary immunodeficiency causing predisposition to severe infection due to intracellular pathogens. only 36 cases have been reported worldwide. the purpose of this article is to describe a large novel deletion found in 3 related cases, which resulted in the complete removal of the ifngr1 gene.	2016	26931784
assessment of yeast saccharomyces cerevisiae component binding to mycobacterium avium subspecies paratuberculosis using bovine epithelial cells.	since yeast saccharomyces cerevisiae and its components are being used for the prevention and treatment of enteric diseases in different species, they may also be useful for preventing johne's disease, a chronic inflammatory bowel disease of ruminants caused by mycobacterium avium spp. paratuberculosis (map). this study aimed to identify potential yeast derivatives that may be used to help prevent map infection. the adherence of mcherry-labeled map to bovine mammary epithelial cell line (mac-t c ...	2016	26932223
use of h-index and other bibliometric indicators to evaluate research productivity outcome on swine diseases.	h-index is the most commonly applied tool to evaluate scientific productivity. in this study, the use of the h-index to evaluate scientific production in swine veterinary medicine was explored. a database of 137 pig infectious agents was constructed, including its taxonomic division, zoonotic potential, status as emerging pathogen and whether it was oie-listed. the h-index and the total number of citations were calculated for those pathogens, the location of the affiliation of the first author o ...	2016	26930283
comparative genomic analysis of mannheimia haemolytica from bovine sources.	bovine respiratory disease is a common health problem in beef production. the primary bacterial agent involved, mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. the role of m. haemolytica in pathogenesis is linked to serotype with serotypes 1 (s1) and 6 (s6) isolated from pneumonic lesions and serotype 2 (s2) found in the upper respiratory tract of healthy animals. here, we sequenced the genomes of 11 strains of m. hae ...	2016	26926339
isothiocyanates as effective agents against enterohemorrhagic escherichia coli: insight to the mode of action.	production of shiga toxins by enterohemorrhagic escherichia coli (ehec) which is responsible for the pathogenicity of these strains, is strictly correlated with induction of lambdoid bacteriophages present in the host's genome, replication of phage dna and expression of stx genes. antibiotic treatment of ehec infection may lead to induction of prophage into a lytic development, thus increasing the risk of severe complications. this, together with the spread of multi-drug resistance, increases th ...	2016	26922906
optimized use of the maldi biotyper system and the filmarray bcid panel for direct identification of microbial pathogens from positive blood cultures.	despite the current reliance on blood cultures (bcs), the diagnosis of bloodstream infections (bsis) can be sped up using new technologies performed directly on positive bc bottles. two methods (the maldi biotyper system and filmarray blood culture identification [bcid] panel) are potentially applicable. in this study, we performed a large-scale clinical evaluation (1,585 microorganisms from 1,394 bsi episodes) on the combined use of the maldi biotyper and filmarray bcid panel compared to a refe ...	2016	26677254
cheese microbial risk assessments - a review.	cheese is generally considered a safe and nutritious food, but foodborne illnesses linked to cheese consumption have occurred in many countries. several microbial risk assessments related to listeria monocytogenes, staphylococcus aureus, and escherichia coli infections, causing cheese-related foodborne illnesses, have been conducted. although the assessments of microbial risk in soft and low moisture cheeses such as semi-hard and hard cheeses have been accomplished, it has been more focused on t ...	2016	26950859
program and abstracts from the canadian digestive diseases week™ 2016.		2016	27563641
maternal weaning modulates emotional behavior and regulates the gut-brain axis.	evidence shows that nutritional and environmental stress stimuli during postnatal period influence brain development and interactions between gut and brain. in this study we show that in rats, prevention of weaning from maternal milk results in depressive-like behavior, which is accompanied by changes in the gut bacteria and host metabolism. depressive-like behavior was studied using the forced-swim test on postnatal day (pnd) 25 in rats either weaned on pnd 21, or left with their mother until p ...	2016	26903212
reduced soluble rage is associated with disease severity of axonal guillain-barré syndrome.	soluble receptor for advanced glycation end products (srage) is an anti-inflammatory factor that mitigates the proinflammatory effects of high mobility group box 1 (hmgb1). the aim of this study was to investigate whether guillain-barré syndrome (gbs)-related inflammation are mediated by srage and hmgb1. we measured serum srage, hmgb1, il-6, and tnf-α levels in 86 patients with gbs and analysed associations between srage or hmgb1 and clinical variables in these subjects. in addition, we determin ...	2016	26902096
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 ...	2016	26925337
inflammation in irritable bowel syndrome: myth or new treatment target?	low-grade intestinal inflammation plays a key role in the pathophysiology of irritable bowel syndrome (ibs), and this role is likely to be multifactorial. the aim of this review was to summarize the evidence on the spectrum of mucosal inflammation in ibs, highlighting the relationship of this inflammation to the pathophysiology of ibs and its connection to clinical practice. we carried out a bibliographic search in medline and the cochrane library for the period of january 1966 to december 2014, ...	2016	26900287
cell wall anchoring of the campylobacter antigens to lactococcus lactis.	campylobacter jejuni is the most frequent cause of human food-borne gastroenteritis and chicken meat is the main source of infection. recent studies showed that broiler chicken immunization against campylobacter should be the most efficient way to lower the number of human infections by this pathogen. induction of the mucosal immune system after oral antigen administration should provide protective immunity to chickens. in this work we tested the usefulness of lactococcus lactis, the most extens ...	2016	26925040
distribution and genetic profiles of campylobacter in commercial broiler production from breeder to slaughter in thailand.	poultry and poultry products are commonly considered as the major vehicle of campylobacter infection in humans worldwide. to reduce the number of human cases, the epidemiology of campylobacter in poultry must be better understood. therefore, the objective of the present study was to determine the distribution and genetic relatedness of campylobacter in the thai chicken production industry. during june to october 2012, entire broiler production processes (i.e., breeder flock, hatchery, broiler fa ...	2016	26886590
spotyping: fast and accurate in silico mycobacterium spoligotyping from sequence reads.	spotyping is a fast and accurate program for in silico spoligotyping of mycobacterium tuberculosis isolates from next-generation sequencing reads. this novel method achieves high accuracy for reads of both uniform and varying lengths, and is about 20 to 40 times faster than spolpred. spotyping also integrates the function of producing a report summarizing associated epidemiological data from a global database of all isolates having the same spoligotype. spotyping is freely available at: https:// ...	2016	26883915
bacterial multidrug efflux pumps: much more than antibiotic resistance determinants.	bacterial multidrug efflux pumps are antibiotic resistance determinants present in all microorganisms. with few exceptions, they are chromosomally encoded and present a conserved organization both at the genetic and at the protein levels. in addition, most, if not all, strains of a given bacterial species present the same chromosomally-encoded efflux pumps. altogether this indicates that multidrug efflux pumps are ancient elements encoded in bacterial genomes long before the recent use of antibi ...	2016	27681908
utilization of carrageenan, citric acid and cinnamon oil as an edible coating of chicken fillets to prolong its shelf life under refrigeration conditions.	the present study was conducted to determine efficacy of edible coating of carrageenan and cinnamon oil to enhance the shelf life of chicken meat stored under refrigeration conditions.	2016	27051203
occurrence of campylobacter spp. in poultry meat at retail and processing plants' levels in central italy.	human campylobacteriosis remains the most commonly reported gastrointestinal disease in europe and campylobacter (c.) jejuni and c. coli are the two species most frequently involved in such foodborne disease. based on the sampling plan established in the region of lazio (central italy) the aim of our work was to investigate the occurrence of campylobacter spp. in poultry meat preparations collected by the local veterinary authority at retail shops and processing plants. we also observed whether ...	2016	27800429
development of a specific monoclonal antibody for the quantification of artemisinin in artemisia annua and rat serum.	artemisinin, extracted from artemisia annua, and its derivatives are important frontline antimalarials. to produce specific antibodies for the detection and quantification of artemisinin, artemisinin was transformed to 9-hydroxyartemisinin by microbial fermentation, which was used to prepare a 9-succinate artemisinin hapten for conjugation with ovalbumin. a monoclonal antibody (mab), designated as 3h7a10, was selected from hybridoma cell lines which showed high specificity to artemisinin. no com ...	2016	26822789
the epigenomic landscape of prokaryotes.	dna methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. here, we used single molecule, real-time sequencing to map dna modifications including m6a, m4c, and m5c across the genomes of 230 diverse bacterial and archaeal ...	2016	26870957
human campylobacteriosis in luxembourg, 2010-2013: a case-control study combined with multilocus sequence typing for source attribution and risk factor analysis.	campylobacteriosis has increased markedly in luxembourg during recent years. we sought to determine which campylobacter genotypes infect humans, where they may originate from, and how they may infect humans. multilocus sequence typing was performed on 1153 campylobacter jejuni and 136 c. coli human strains to be attributed to three putative animal reservoirs (poultry, ruminants, pigs) and to environmental water using the asymmetric island model. a nationwide case-control study (2010-2013) for do ...	2016	26860258
zika: the origin and spread of a mosquito-borne virus.	to describe the temporal and geographical distribution of zika virus infection and associated neurological disorders, from 1947 to 1 february 2016, when zika became a public health emergency of international concern (pheic).	2016	27708473
molecular mechanisms and potential clinical applications of campylobacter jejuni cytolethal distending toxin.	cytolethal distending toxin (cdt), a genotoxin produced by campylobacter jejuni, is composed of three subunits: cdta, cdtb, and cdtc. cdtb is a dnase that causes dna double-strand breaks (dsb) in the nucleus resulting in cell cycle arrest at the g2/m stage and apoptosis. cdta and cdtc bind to cholesterol-rich microdomains on the cytoplasmic membrane, a process required for the delivery of cdtb to cells. although a unique motif associated with cholesterol-binding activity has been identified in o ...	2016	26904508
tuning of hemes b equilibrium redox potential is not required for cross-membrane electron transfer.	in biological energy conversion, cross-membrane electron transfer often involves an assembly of two hemesb the hemes display a large difference in redox midpoint potentials (δem_b), which in several proteins is assumed to facilitate cross-membrane electron transfer and overcome a barrier of membrane potential. here we challenge this assumption reporting on hemebligand mutants of cytochromebc1in which, for the first time in transmembrane cytochrome, one natural histidine has been replaced by lysi ...	2016	26858251
genomic features of environmental and clinical vibrio parahaemolyticus isolates lacking recognized virulence factors are dissimilar.	vibrio parahaemolyticus is a bacterial pathogen that can cause illness after the consumption or handling of contaminated seafood. the primary virulence factors associated with v. parahaemolyticus illness are thermostable direct hemolysin (tdh) and tdh-related hemolysin (trh). however, clinical strains lacking tdh and trh have recently been isolated, and these clinical isolates are poorly understood. to help understand the emergence of clinical tdh- and trh-negative isolates, a genomic approach w ...	2016	26637607
immunomodulatory and anti-inflammatory activities of chicken cathelicidin-2 derived peptides.	host defence peptides and derived peptides are promising classes of antimicrobial and immunomodulatory lead compounds. for this purpose we examined whether chicken cathelicidin-2 (cath-2)-derived peptides modulate the function and inflammatory response of avian immune cells. using a chicken macrophage cell line (hd11) we found that full-length cath-2 dose-dependently induced transcription of chemokines cxcli2/il-8, mcp-3 and ccli4/rantes, but not of pro-inflammatory cytokine il-1β. in addition, ...	2016	26848845
the two-component system cpxra negatively regulates the locus of enterocyte effacement of enterohemorrhagic escherichia coli involving σ(32) and lon protease.	enterohemorrhagic escherichia coli (ehec) is a significant cause of serious human gastrointestinal disease worldwide. ehec strains contain a pathogenicity island called the locus of enterocyte effacement (lee), which encodes virulence factors responsible for damaging the gut mucosa. the cpx envelope stress response of e. coli is controlled by a two-component system (tcs) consisting of a sensor histidine kinase (cpxa) and a cytoplasmic response regulator (cpxr). in this study, we investigated the ...	2016	26904510
evolutionary genomics suggests that chev is an additional adaptor for accommodating specific chemoreceptors within the chemotaxis signaling complex.	escherichia coli and salmonella enterica are models for many experiments in molecular biology including chemotaxis, and most of the results obtained with one organism have been generalized to another. while most components of the chemotaxis pathway are strongly conserved between the two species, salmonella genomes contain some chemoreceptors and an additional protein, chev, that are not found in e. coli. the role of chev was examined in distantly related species bacillus subtilis and helicobacte ...	2016	26844549
multilocus sequence typing and antimicrobial resistance of campylobacter jejuni isolated from dairy calves in austria.	human campylobacteriosis is primarily associated with poultry but also cattle. in this study, 55 campylobacter jejuni strains isolated from 382 dairy calves' feces were differentiated by multilocus sequence typing and tested for antimicrobial resistance. the most prevalent sequence type (st) was st883 (20.0%), followed by st48 (14.5%), and st50 (9.1%). in contrast to st48 and st50, st883 has rarely been described in cattle previously. furthermore, risk factor analysis was performed for the prese ...	2016	26870027
recent development of mass spectrometry and proteomics applications in identification and typing of bacteria.	identification and typing of bacteria occupy a large fraction of time and work in clinical microbiology laboratories. with the certification of some ms platforms in recent years, more applications and tests of ms-based diagnosis methods for bacteria identification and typing have been created, not only on well-accepted maldi-tof-ms-based fingerprint matches, but also on solving the insufficiencies of maldi-tof-ms-based platforms and advancing the technology to areas such as targeted ms identific ...	2016	26751976
to what extent is faims beneficial in the analysis of proteins?	high field asymmetric waveform ion mobility spectrometry (faims), also known as differential ion mobility spectrometry, is emerging as a tool for biomolecular analysis. in this article, the benefits and limitations of faims for protein analysis are discussed. the principles and mechanisms of faims separation of ions are described, and the differences between faims and conventional ion mobility spectrometry are detailed. protein analysis is considered from both the top-down (intact proteins) and ...	2016	26843211
helicobacter pylori colonization in nepal; assessment of prevalence and potential risk factors in a hospital-based patient cohort.	helicobacter pylori, a gram-negative bacterium, can cause gastritis, peptic and duodenal ulcers. it is considered an important public health problem for both developed and developing world. this bacterium is classified as the class 1 carcinogen because it can cause cancer.	2016	26833400
cysteine mutational studies provide insight into a thiol-based redox switch mechanism of metal and dna binding in fura from anabaena sp. pcc 7120.	the ferric uptake regulator (fur) is the main transcriptional regulator of genes involved in iron homeostasis in most prokaryotes. fura from anabaena sp. pcc 7120 contains five cysteine residues, four of them arranged in two redox-active cxxc motifs. the protein needs not only metal but also reducing conditions to remain fully active in vitro. through a mutational study of the cysteine residues present in fura, we have investigated their involvement in metal and dna binding.	2016	26414804
magnetic resonance imaging differential diagnosis of brainstem lesions in children.	differential diagnosis of brainstem lesions, either isolated or in association with cerebellar and supra-tentorial lesions, can be challenging. knowledge of the structural organization is crucial for the differential diagnosis and establishment of prognosis of pathologies with involvement of the brainstem. familiarity with the location of the lesions in the brainstem is essential, especially in the pediatric population. magnetic resonance imaging (mri) is the most sensitive and specific imaging ...	2016	26834941
individual restriction of fine specificity variability in anti-gm1 igg antibodies associated with guillain-barré syndrome.	elevated titers of serum antibodies against gm1 ganglioside are associated with a variety of autoimmune neuropathies. much evidence indicates these autoantibodies play a primary role in the disease processes, but the mechanism for their appearance is unclear. we studied the fine specificity of anti-gm1 antibodies of the igg isotype present in sera from patients with guillain-barré syndrome (gbs), using thin-layer chromatogram-immunostaining of gm1, asialo-gm1 (ga1), gd1b and gm1-derivatives with ...	2016	26818965
diagnosing gastrointestinal illnesses using fecal headspace volatile organic compounds.	volatile organic compounds (vocs) emitted from stool are the components of the smell of stool representing the end products of microbial activity and metabolism that can be used to diagnose disease. despite the abundance of hydrogen, carbon dioxide, and methane that have already been identified in human flatus, the small portion of trace gases making up the vocs emitted from stool include organic acids, alcohols, esters, heterocyclic compounds, aldehydes, ketones, and alkanes, among others. thes ...	2016	26819529
an examination of co-infection in acute gastroenteritis and histo-blood group antigens leading to viral infection susceptibility.	the aim of the present study was to evaluate co-infection in the gastrointestinal tract in terms of viruses, bacteria and the abo blood group. we hypothesized that a combination of norovirus (nv) and bacteria in the gastrointestinal tract could affect the likelihood of an individual to contracting nv. histo-blood group antigens (hbgas) are considered to act as receptors that can lead to nv susceptibility. in addition to genetics, co-infection in the gastrointestinal tract may be associated with ...	2016	26998270
differential gene expression patterns in chicken cardiomyocytes during hydrogen peroxide-induced apoptosis.	hydrogen peroxide (h2o2) is both an exogenous and endogenous cytotoxic agent that can reliably induce apoptosis in numerous cell types for studies on apoptosis signaling pathways. however, little is known of these apoptotic processes in myocardial cells of chicken, a species prone to progressive heart failure. sequencing of mrna transcripts (rna-seq) allows for the identification of differentially expressed genes under various physiological and pathological conditions to elucidate the molecular ...	2016	26808997
novel α-l-fucosidases from a soil metagenome for production of fucosylated human milk oligosaccharides.	this paper describes the discovery of novel α-l-fucosidases and evaluation of their potential to catalyse the transglycosylation reaction leading to production of fucosylated human milk oligosaccharides. seven novel α-l-fucosidase-encoding genes were identified by functional screening of a soil-derived metagenome library and expressed in e. coli as recombinant 6xhis-tagged proteins. all seven fucosidases belong to glycosyl hydrolase family 29 (gh 29). six of the seven α-l-fucosidases were substr ...	2016	26800369
hib vaccines: past, present, and future perspectives.	haemophilus influenzae type b (hib) causes many severe diseases, including epiglottitis, pneumonia, sepsis, and meningitis. in developed countries, the annual incidence of meningitis caused by bacteria is approximately 5-10 cases per population of 100,000. the hib conjugate vaccine is considered protective and safe. adjuvants, molecules that can enhance and/or regulate the fundamental immunogenicity of an antigen, comprise a wide range of diverse compounds. while earlier developments of adjuvant ...	2016	26904695
evolutionary and functional relationships in the truncated hemoglobin family.	predicting function from sequence is an important goal in current biological research, and although, broad functional assignment is possible when a protein is assigned to a family, predicting functional specificity with accuracy is not straightforward. if function is provided by key structural properties and the relevant properties can be computed using the sequence as the starting point, it should in principle be possible to predict function in detail. the truncated hemoglobin family presents a ...	2016	26788940
within-host evolution of bacterial pathogens.	whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. the application of this technology to the longitudinal study of adaptation in an infected host--in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens--has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatability ...	2016	26806595
molecular characterization and subtyping of blastocystis species in irritable bowel syndrome patients from north india.	blastocystis species has been extensively studied in recent few years to establish its pathogenecity. present study was designed to identify and examine the association of blastocystis sp. and its subtypes with irritable bowel syndrome (ibs).blastocystis sp. detected using wet-mount microscopy, trichrome staining, in-vitro culture and polymerase chain reaction (pcr) assay in a cohort of ibs patients (n = 150) and healthy controls (n = 100). isolates of blastocystis sp.were subtyped using sequenc ...	2016	26784888
phase variation of a type iig restriction-modification enzyme alters site-specific methylation patterns and gene expression in campylobacter jejuni strain nctc11168.	phase-variable restriction-modification systems are a feature of a diverse range of bacterial species. stochastic, reversible switches in expression of the methyltransferase produces variation in methylation of specific sequences. phase-variable methylation by both type i and type iii methyltransferases is associated with altered gene expression and phenotypic variation. one phase-variable gene of campylobacter jejuni encodes a homologue of an unusual type iig restriction-modification system in ...	2016	26786317
the influence of efflux pump inhibitors on the activity of non-antibiotic nsaids against gram-negative rods.	most patients with bacterial infections suffer from fever and various pains that require complex treatments with antibiotics, antipyretics, and analgaesics. the most common drugs used to relieve these symptoms are non-steroidal anti-inflammatory drugs (nsaids), which are not typically considered antibiotics. here, we investigate the effects of nsaids on bacterial susceptibility to antibiotics and the modulation of bacterial efflux pumps.	2016	26771525
alterations of the volatile metabolome in mouse models of alzheimer's disease.	in the present study, we tested whether the volatile metabolome was altered by mutations of the alzheimer's disease (ad)-implicated amyloid precursor protein gene (app) and comprehensively examined urinary volatiles that may potentially serve as candidate biomarkers of ad. establishing additional biomarkers in screening populations for ad will provide enhanced diagnostic specificity and will be critical in evaluating disease-modifying therapies. having strong evidence of gross changes in the vol ...	2016	26762470
association of ulcerative colitis with fut2 and fut3 polymorphisms in patients from southeast china.	dysbiosis of intestinal microbiota has been implicated in ulcerative colitis (uc). fucosyltransferase (fut) 2 and fut3 determine expression of histo-blood group antigens in the gut and may affect the intestinal microbiota. we investigated the association between fut2 and fut3 polymorphisms and uc in chinese patients.	2016	26766790
resistant starch alters the microbiota-gut brain axis: implications for dietary modulation of behavior.	the increasing recognition that the gut microbiota plays a central role in behavior and cognition suggests that the manipulation of microbial taxa through diet may provide a means by which behavior may be altered in a reproducible and consistent manner in order to achieve a beneficial outcome for the host. resistant starch continues to receive attention as a dietary intervention that can benefit the host through mechanisms that include altering the intestinal microbiota. given the interest in di ...	2016	26745269
rehabilitation of a patient with overlap of acute transverse myelitis and bickerstaff's brainstem encephalitis: a case report.	we report on one patient with bickerstaff's brainstem encephalitis (bbe) and associated flaccid weakness. counter to previous studies with bbe which indicate weakness due to guillain-barre syndrome, our patient's presentation of paraplegia following bbe is consistent with concomitant acute transverse myelitis. her findings of bbe largely resolved, although she remained with t6 american spinal injury association (asia) a paraplegia. motor functional impairment measure scores improved from 20 at a ...	2016	28053734
human milk components modulate toll-like receptor-mediated inflammation.	toll-like receptor (tlr) signaling is central to innate immunity. aberrant expression of tlrs is found in neonatal inflammatory diseases. several bioactive components of human milk modulate tlr expression and signaling pathways, including soluble toll-like receptors (stlrs), soluble cluster of differentiation (scd) 14, glycoproteins, small peptides, and oligosaccharides. some milk components, such as sialyl (α2,3) lactose and lacto-n-fucopentaose iii, are reported to increase tlr signaling; unde ...	2016	26773018
whole-genome sequencing analysis accurately predicts antimicrobial resistance phenotypes in campylobacter spp.	the objectives of this study were to identify antimicrobial resistance genotypes for campylobacter and to evaluate the correlation between resistance phenotypes and genotypes using in vitro antimicrobial susceptibility testing and whole-genome sequencing (wgs). a total of 114 campylobacter species isolates (82 c. coli and 32 c. jejuni) obtained from 2000 to 2013 from humans, retail meats, and cecal samples from food production animals in the united states as part of the national antimicrobial re ...	2016	26519386
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 ...	2016	26729150
acute motor axonal neuropathy (aman) with motor conduction blocks in childhood; case report.	objective acute motor axonal neuropathy (aman), characterized with decreased compound muscle action potentials (cmap) and absence of demyelinating findings in electrophysiological studies, is a subtype of guillain-barre syndrome (gbs). a 4 yr-old male patient presented with ascending weakness, dysarthria and dysphagia to istanbul dr. lütfi kırdar kartal training and research hospital neurology outpatient for three days to in 2012. dysphonia, restricted eye movements, flaccid tetraplegia and aref ...	2016	27057191
multidrug resistant shigella flexneri infection simulating intestinal intussusception.	shigella enteritis remains an important cause of mortality and morbidity in all age groups, in developing as well as developed countries. owing to the emerging resistance to multiple antibiotics among shigella spp., it has been recognized as a major global public health concern and warrants constant monitoring of its resistance pattern. we report a case of segmental ileitis caused by non.-esbl producing multidrug resistant shigella flexneri in an infant clinically mimicking intussusception, whic ...	2016	27013815
sialic acids and autoimmune disease.	an important underlying mechanism that contributes to autoimmunity is the loss of inhibitory signaling in the immune system. sialic acid-recognizing ig superfamily lectins or siglecs are a family of cell surface proteins largely expressed in hematopoietic cells. the majority of siglecs are inhibitory receptors expressed in immune cells that bind to sialic acid-containing ligands and recruit sh2-domain-containing tyrosine phosphatases to their cytoplasmic tails. they deliver inhibitory signals th ...	2016	26683151
onset of ulcerative colitis during a low-carbohydrate weight-loss diet and treatment with a plant-based diet: a case report.	overweight and obesity are global health concerns. various effective weight-loss diets have been developed, including the atkins diet. the atkins diet is known as an extreme low-carbohydrate diet. this diet reduces body weight and has gained widespread popularity. however, the metabolite profiles of such a diet have been shown to be detrimental to colonic health. therefore, a concern for the long-term health effects of this diet exists. we encountered a case in which ulcerative colitis developed ...	2016	26824967
a comparison between plasmapheresis and intravenous immunoglobulin in children with guillain-barré syndrome in upper egypt.	the aim of our study is to assess the clinico-electrophysiological proﬁle of children with guillain-barré syndrome (gbs) in upper egypt and to compare the efficacy of plasmapheresis versus other treatment modalities.	2016	26788127
a gastrointestinal anti-infectious biotherapeutic agent: the heat-treated lactobacillus lb.	experimental in vitro and in vivo studies support the hypothesis that heat-treated, lyophilized lactobacillus acidophilus lb cells and concentrated, neutralized spent culture medium conserve the variety of pharmacological, antimicrobial activities of the live probiotic strain against several infectious agents involved in well-established acute and persistent watery diarrhoea and gastritis. heat-treated cells and heat-stable secreted molecules trigger multiple strain-specific activities explainin ...	2016	26770268
prevalence and risk factors for campylobacter spp., salmonella spp., coxiella burnetii, and newcastle disease virus in feral pigeons (columba livia) in public areas of montreal, canada.	feral pigeons (columbia livia) can harbor a range of zoonotic pathogens. a transversal study was undertaken to estimate the prevalence of feral pigeons infected by various pathogens in public areas in montreal, quebec. cloacal swabs from captured birds were cultured for salmonella spp. and campylobacter spp. and tested by real-time polymerase chain reaction (rt-pcr) for the detection of coxiella burnetii. an oropharyngeal swab was also submitted to real-time reverse-transcription polymerase chai ...	2016	26733736
bacteriophage-based tools: recent advances and novel applications.	bacteriophages (phages) are viruses that infect bacterial hosts, and since their discovery over a century ago they have been primarily exploited to control bacterial populations and to serve as tools in molecular biology. in this commentary, we highlight recent diverse advances in the field of phage research, going beyond bacterial control using whole phage, to areas including biocontrol using phage-derived enzybiotics, diagnostics, drug discovery, novel drug delivery systems and bionanotechnolo ...	2016	27990274
bibliometric analysis of publications on campylobacter: (2000-2015).	campylobacter species are widespread zoonotic pathogens. campylobacter jejuni causes a form of gastroenteritis called campylobacteriosis. campylobacter drug resistance is considered a serious threat. in order to better understand national and international research output on campylobacter, we conducted this bibliometric overview of publications on campylobacter. this study can be used to assess extent of interaction and response of researchers, food regulators, and health policy makers to global ...	2016	27899145