Publications

zinc sequestration by the neutrophil protein calprotectin enhances salmonella growth in the inflamed gut.	neutrophils are innate immune cells that counter pathogens by many mechanisms, including release of antimicrobial proteins such as calprotectin to inhibit bacterial growth. calprotectin sequesters essential micronutrient metals such as zinc, thereby limiting their availability to microbes, a process termed nutritional immunity. we find that while calprotectin is induced by neutrophils during infection with the gut pathogen salmonella typhimurium, calprotectin-mediated metal sequestration does no ...	2012	22423963
pathogenetic importance and therapeutic implications of nf-κb in lymphoid malignancies.	derangement of the nuclear factor κb (nf-κb) pathway initiates and/or sustains many types of human cancer. b-cell malignancies are particularly affected by oncogenic mutations, translocations, and copy number alterations affecting key components the nf-κb pathway, most likely owing to the pervasive role of this pathway in normal b cells. these genetic aberrations cause tumors to be 'addicted' to nf-κb, which can be exploited therapeutically. since each subtype of lymphoid cancer utilizes differe ...	2012	22435566
the ambiguity in immunology.	in the present article, we discuss the various ambiguous aspects of the immune system that render this complex biological network so highly flexible and able to defend the host from different external invaders. this ambiguity stems mainly from the property of the immune system to be both protective and harmful. immunity cannot be fully protective without producing a certain degree of damage (immunopathology) to the host. the balance between protection and tissue damage is, therefore, critical fo ...	2012	22566903
inherited variation in pattern recognition receptors and cancer: dangerous liaisons?	the group of pattern recognition receptors includes families of toll-like receptors, nod-like receptors, c-type lectin receptors, and rig-i-like receptors. they are key sensors for a number of infectious agents, some of which are carcinogenic, and they launch an immune response against them. inherited structural variation in genes encoding these receptors and proteins of their signaling pathways may affect their function, modulating cancer risk and features of cancer progression. relevant malign ...	2012	22427729
molecular mimicry as a mechanism of autoimmune disease.	a variety of mechanisms have been suggested as the means by which infections can initiate and/or exacerbate autoimmune diseases. one mechanism is molecular mimicry, where a foreign antigen shares sequence or structural similarities with self-antigens. molecular mimicry has typically been characterized on an antibody or t cell level. however, structural relatedness between pathogen and self does not account for t cell activation in a number of autoimmune diseases. a proposed mechanism that could ...	2012	22095454
elemental economy: microbial strategies for optimizing growth in the face of nutrient limitation.	microorganisms play a dominant role in the biogeochemical cycling of nutrients. they are rightly praised for their facility for fixing both carbon and nitrogen into organic matter, and microbial driven processes have tangibly altered the chemical composition of the biosphere and its surrounding atmosphere. despite their prodigious capacity for molecular transformations, microorganisms are powerless in the face of the immutability of the elements. limitations for specific elements, either fleetin ...	2012	22633059
genome signature difference between deinococcus radiodurans and thermus thermophilus.	the extremely radioresistant bacteria of the genus deinococcus and the extremely thermophilic bacteria of the genus thermus belong to a common taxonomic group. considering the distinct living environments of deinococcus and thermus, different genes would have been acquired through horizontal gene transfer after their divergence from a common ancestor. their guanine-cytosine (gc) contents are similar; however, we hypothesized that their genomic signatures would be different. our findings indicate ...	2012	22500246
Contribution of enteric infection, altered intestinal barrier function, and maternal malnutrition to infant malnutrition in bangladesh.	Background. Malnourished children are at increased risk for death due to diarrhea. Our goal was to determine the contribution of specific enteric infections to malnutrition-associated diarrhea and to determine the role of enteric infections in the development of malnutrition. Methods. Children from an urban slum in Bangladesh were followed for the first year of life by every-other-day home visits. Enteropathogens were identified in diarrheal and monthly surveillance stools; intestinal barrier fu ...	2012	22109945
Contribution of enteric infection, altered intestinal barrier function, and maternal malnutrition to infant malnutrition in bangladesh.	Background. Malnourished children are at increased risk for death due to diarrhea. Our goal was to determine the contribution of specific enteric infections to malnutrition-associated diarrhea and to determine the role of enteric infections in the development of malnutrition. Methods. Children from an urban slum in Bangladesh were followed for the first year of life by every-other-day home visits. Enteropathogens were identified in diarrheal and monthly surveillance stools; intestinal barrier fu ...	2012	22109945
Fisher syndrome: clinical features, immunopathogenesis and management.	Since Miller Fisher's first report in 1956, evidence has accumulated about clinical and laboratory features, immunopathogenesis and treatment of Fisher syndrome (FS). Our literature review revealed the nature of FS. It has relatively uniform clinical and laboratory features. Ophthalmoplegia, ataxia and areflexia are essential prerequisites for an FS diagnosis, but there are several clinical variants with isolated ophthalmoplegia or ataxia. The discovery of serum anti-GQ1b antibody in FS has led ...	2012	22149656
Simultaneous Detection of Six Diarrhea-Causing Bacterial Pathogens with an In-House PCR-Luminex Assay.	Diarrhea can be caused by a range of pathogens, including several bacteria. Conventional diagnostic methods, such as culture, biochemical tests, and enzyme-linked immunosorbent assay (ELISA), are laborious. We developed a 7-plex PCR-Luminex assay to simultaneously screen for several of the major diarrhea-causing bacteria directly in fecal specimens, including pathogenic Aeromonas, Campylobacter jejuni, Campylobacter coli, Salmonella, Shigella, enteroinvasive Escherichia coli (EIEC), Vibrio, and ...	2012	22075596
fecal indicators and zoonotic pathogens in household drinking water taps fed from rainwater tanks in southeast queensland, australia.	in this study, the microbiological quality of household tap water samples fed from rainwater tanks was assessed by monitoring the numbers of escherichia coli bacteria and enterococci from 24 households in southeast queensland (seq), australia. quantitative pcr (qpcr) was also used for the quantitative detection of zoonotic pathogens in water samples from rainwater tanks and connected household taps. the numbers of zoonotic pathogens were also estimated in fecal samples from possums and various s ...	2012	22020514
phenotypic and genotypic methods for typing campylobacter jejuni and campylobacter coli in poultry.	human campylobacteriosis, an infection caused by the bacterium campylobacter, is a major issue in the united states food system, especially for poultry products. according to the center for disease control, campylobacterosis is estimated to affect over 2.4 million people annually. campylobacter jejuni and campylobacter coli are 2 species responsible for the majority of campylobacterosis infections. phenotypic and genotypic typing methods are often used to discriminate between bacteria at the spe ...	2012	22184452
Thermofluor-based optimization strategy for the stabilization and crystallization of Campylobacter jejuni desulforubrerythrin.	Desulforubrerythrin from Campylobacter jejuni has recently been biochemical and spectroscopically characterized. It is a member of the rubrerythrin family, and it is composed of three structural domains: the N-terminal desulforedoxin domain with a non-heme iron center, followed by a four-helix bundle domain harboring a binuclear iron center and finally a C-terminal rubredoxin domain. To date, this is the first example of a protein presenting this kind of structural domain organization, and there ...	2012	22051151
Bacteriocin production: a probiotic trait?	Bacteriocins are an abundant and diverse group of ribosomally synthesized antimicrobial peptides produced by bacteria and archaea. Traditionally, bacteriocin production has been considered an important trait in the selection of probiotic strains, but until recently, few studies have definitively demonstrated the impact of bacteriocin production on the ability of a strain to compete within complex microbial communities and/or positively influence the health of the host. Although research in this ...	2012	22038602
network analysis and protein function prediction with the prodistin web site.	interactions between macromolecules are deciphered to gain information about biological processes and protein function. this information is hidden in large interaction networks, yet very complicated to dissect. in this context, the prodistin web site is dedicated to the clustering of network proteins according to the identity of their interaction partners, and to the subsequent functional annotation of these clusters. it allows analysing functionally networks and eventually leads to the predicti ...	2012	22144161
cj1386 is an ankyrin-containing protein involved in heme trafficking to catalase in campylobacter jejuni.	campylobacter jejuni, a microaerophilic bacterium, is the most frequent cause of human bacterial gastroenteritis. c. jejuni is exposed to harmful reactive oxygen species (ros) produced during its own normal metabolic processes and during infection from the host immune system and from host intestinal microbiota. these ros will damage dna and proteins and cause peroxidation of lipids. consequently, identifying ros defense mechanisms is important for understanding how campylobacter survives this en ...	2012	22081390
Inaccuracy of the Disk Diffusion Method Compared with the Agar Dilution Method for Susceptibility Testing of Campylobacter spp.	The agar dilution method has been standardized by the CLSI for the susceptibility testing of Campylobacter species, and according to these standards, the disk diffusion method should be used only in screening for macrolide and ciprofloxacin resistance. Nevertheless, the disk diffusion test is currently widely used, since it is easy to perform in clinical microbiology laboratories. In this study, the disk diffusion method was compared to the agar dilution method by analyzing the in vitro activiti ...	2012	22075583
performances of the vitek ms matrix-assisted laser desorption ionization-time of flight mass spectrometry system for rapid identification of bacteria in routine clinical microbiology.	rapid and cost-effective matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms)-based systems will replace conventional phenotypic methods for routine identification of bacteria. we report here the first evaluation of the new maldi-tof ms-based vitek ms system in a large clinical microbiology laboratory. this system uses an original spectrum classifier algorithm and a specific database designed for the identification of clinically relevant species. we have te ...	2012	22593596
dprb facilitates inter- and intragenomic recombination in helicobacter pylori.	for naturally competent microorganisms, such as helicobacter pylori, the steps that permit recombination of exogenous dna are not fully understood. immediately downstream of an h. pylori gene (dpra) that facilitates high-frequency natural transformation is hp0334 (dprb), annotated to be a putative holliday junction resolvase (hjr). we showed that the hp0334 (dprb) gene product facilitates high-frequency natural transformation. we determined the physiologic roles of dprb by genetic analyses. dprb ...	2012	22609923
toll-like receptor 4 mediates intrauterine growth restriction after systemic campylobacter rectus infection in mice.	campylobacter rectus is associated with fetal exposure and low birthweight in humans. c. rectus also invades placental tissues and induces fetal intrauterine growth restriction (iugr) in mice, along with overexpression of toll-like receptors (tlr4), suggesting that tlr4 may mediate placental immunity and iugr in mice. to test this hypothesis we examined the effect of in vitro tlr4 neutralization on trophoblastic proinflammatory activity and studied the iugr phenotype in a congenic tlr4-mutant mo ...	2012	22958386
investigation of the enteric pathogenic potential of oral campylobacter concisus strains isolated from patients with inflammatory bowel disease.	campylobacter concisus, a bacterium colonizing the human oral cavity, has been shown to be associated with inflammatory bowel disease (ibd). this study investigated if patients with ibd are colonized with specific oral c. concisus strains that have potential to cause enteric diseases.	2012	22666490
novel functions for glycosyltransferases jhp0562 and galt in lewis antigen synthesis and variation in helicobacter pylori.	lewis (le) antigens are fucosylated oligosaccharides present in the helicobacter pylori lipopolysaccharide. expression of these antigens is believed to be important for h. pylori colonization, since le antigens also are expressed on the gastric epithelia in humans. a galactosyltransferase encoded by β-(1,3)galt is essential for production of type 1 (le(a) and le(b)) antigens. the upstream gene jhp0562, which is present in many but not all h. pylori strains, is homologous to β-(1,3)galt but is of ...	2012	22290141
putative mechanisms and biological role of coccoid form formation in campylobacter jejuni.	in certain conditions campylobacter jejuni cells are capable of changing their cell shape from a typically spiral to a coccoid form (cf). by similarity to other bacteria, the latter was initially considered to be a viable but non-culturable form capable of survival in unfavourable conditions. however, subsequent studies with c. jejuni and closely related bacteria helicobacter pylori suggested that cf represents a non-viable, degenerative form. until now, the issue on whether the cf of c. jejuni ...	2012	24611120
complete 6-deoxy-d-altro-heptose biosynthesis pathway from campylobacter jejuni: more complex than anticipated.	the campylobacter jejuni capsule is important for colonization and virulence in various infection models. in most strains, the capsule includes a modified heptose whose biological role and biosynthetic pathway are unknown. to decipher the biosynthesis pathway for the 6-deoxy-d-altro-heptose of strain 81-176, we previously showed that the 4,6-dehydratase wcbk and the reductase wcag generated gdp-6-deoxy-d-manno-heptose, but the c3 epimerase necessary to form gdp-6-deoxy-d-altro-heptose was not id ...	2012	22787156
molecular mechanisms and biological role of campylobacter jejuni attachment to host cells.	adhesion to host cells is an important step in pathogenesis of campylobacter jejuni, which is the most prevalent bacterial cause of human gastroenteritis worldwide. in contrast to other bacteria such as e. coli and salmonella, adherence of c. jejuni is not mediated by fimbria or pili. a number of c. jejuni adhesion-related factors have been described. however, the results obtained by different researchers in different laboratories are often contradictory and inconclusive, with only some of the f ...	2012	24611119
rodents on pig and chicken farms - a potential threat to human and animal health.	rodents can cause major problems through spreading various diseases to animals and humans. the two main species of rodents most commonly found on farms around the world are the house mouse (mus musculus) and the brown rat (rattus norvegicus). both species are omnivorous and can breed year-round under favourable conditions. this review describes the occurrence of pathogens in rodents on specialist pig and chicken farms, which are usually closed units with a high level of bio-security. however, wi ...	2012	22957130
biophysical and bioinformatic analyses implicate the treponema pallidum tp34 lipoprotein (tp0971) in transition metal homeostasis.	metal ion homeostasis is a critical function of many integral and peripheral membrane proteins. the genome of the etiologic agent of syphilis, treponema pallidum, is compact and devoid of many metabolic enzyme genes. nevertheless, it harbors genes coding for homologs of several enzymes that typically require either iron or zinc. the product of the tp0971 gene of t. pallidum, designated tp34, is a periplasmic lipoprotein that is thought to be tethered to the inner membrane of this organism. previ ...	2012	23042995
analysis of the salivary microbiome using culture-independent techniques.	the salivary microbiota is a potential diagnostic indicator of several diseases. culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated.	2012	22300522
proteome-wide protein interaction measurements of bacterial proteins of unknown function.	despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. in a typical genome, roughly 30% of genes have no assigned function. many of these proteins are conserved across a large number of bacterial genomes. to assign a putative function to these conserved proteins of unknown function, we created a physical interaction map by measuring biophysical interaction of these proteins. binary protein--prote ...	2012	23267104
proteome-wide protein interaction measurements of bacterial proteins of unknown function.	despite the enormous proliferation of bacterial genome data, surprisingly persistent collections of bacterial proteins have resisted functional annotation. in a typical genome, roughly 30% of genes have no assigned function. many of these proteins are conserved across a large number of bacterial genomes. to assign a putative function to these conserved proteins of unknown function, we created a physical interaction map by measuring biophysical interaction of these proteins. binary protein--prote ...	2012	23267104
the protein interaction network of a taxis signal transduction system in a halophilic archaeon.	the taxis signaling system of the extreme halophilic archaeon halobacterium (hbt.) salinarum differs in several aspects from its model bacterial counterparts escherichia coli and bacillus subtilis. we studied the protein interactions in the hbt. salinarum taxis signaling system to gain an understanding of its structure, to gain knowledge about its known components and to search for new members.	2012	23171228
immune development and intestinal microbiota in celiac disease.	celiac disease (cd) is an immune-mediated enteropathy, triggered by dietary wheat gluten and similar proteins of barley and rye in genetically susceptible individuals. the etiology of this disorder is complex, involving both environmental and genetic factors. the major genetic risk factor for cd is represented by hla-dq genes, which account for approximately 40% of the genetic risk; however, only a small percentage of carriers develop the disease. gluten is the main environmental factor responsi ...	2012	23008734
lab-on-a-chip pathogen sensors for food safety.	there have been a number of cases of foodborne illness among humans that are caused by pathogens such as escherichia coli o157:h7, salmonella typhimurium, etc. the current practices to detect such pathogenic agents are cell culturing, immunoassays, or polymerase chain reactions (pcrs). these methods are essentially laboratory-based methods that are not at all real-time and thus unavailable for early-monitoring of such pathogens. they are also very difficult to implement in the field. lab-on-a-ch ...	2012	23112625
reduced set of virulence genes allows high accuracy prediction of bacterial pathogenicity in humans.	although there have been great advances in understanding bacterial pathogenesis, there is still a lack of integrative information about what makes a bacterium a human pathogen. the advent of high-throughput sequencing technologies has dramatically increased the amount of completed bacterial genomes, for both known human pathogenic and non-pathogenic strains; this information is now available to investigate genetic features that determine pathogenic phenotypes in bacteria. in this work we determi ...	2012	22916122
rsfa (ybeb) proteins are conserved ribosomal silencing factors.	the ybeb (duf143) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea. while they have been shown to be associated with ribosomes, their molecular function remains unclear. here we show that ybeb is a ribosomal silencing factor (rsfa) in the stationary growth phase and during the transition from rich to poor media. a knock-out of the rsfa gene shows two strong phenotypes: (i) the viability of the mutant cells are sharply impaired during st ...	2012	22829778
diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.	the yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. sensitivity and selectivity have improved because of various technical tricks and experimental designs. here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment comp ...	2012	22688816
inferring a protein interaction map of mycobacterium tuberculosis based on sequences and interologs.	mycobacterium tuberculosis is an infectious bacterium posing serious threats to human health. due to the difficulty in performing molecular biology experiments to detect protein interactions, reconstruction of a protein interaction map of m. tuberculosis by computational methods will provide crucial information to understand the biological processes in the pathogenic microorganism, as well as provide the framework upon which new therapeutic approaches can be developed.	2012	22595003
the iron-regulated staphylococcal lipoproteins.	lipoproteins fulfill diverse roles in antibiotic resistance, adhesion, protein secretion, signaling and sensing, and many also serve as the substrate binding protein (sbp) partner to abc transporters for the acquisition of a diverse array of nutrients including peptides, sugars, and scarcely abundant metals. in the staphylococci, the iron-regulated sbps are significantly upregulated during iron starvation and function to sequester and deliver iron into the bacterial cell, enabling staphylococci ...	2012	22919632
coevolution of aah: a dps-like gene with the host bacterium revealed by comparative genomic analysis.	a protein named aah was isolated from the bacterium microbacterium arborescens se14, a gut commensal of the lepidopteran larvae. it showed not only a high sequence similarity to dps-like proteins (dna-binding proteins from starved cell) but also reversible hydrolase activity. a comparative genomic analysis was performed to gain more insights into its evolution. the gc profile of the aah gene indicated that it was evolved from a low gc ancestor. its stop codon usage was also different from the ge ...	2012	22454608
whole genome sequences of three treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence.	the yaws treponemes, treponema pallidum ssp. pertenue (tpe) strains, are closely related to syphilis causing strains of treponema pallidum ssp. pallidum (tpa). both yaws and syphilis are distinguished on the basis of epidemiological characteristics, clinical symptoms, and several genetic signatures of the corresponding causative agents.	2012	22292095
structure determination of lpxa from the lipopolysaccharide-synthesis pathway of acinetobacter baumannii.	acinetobacter baumannii is a gram-negative pathogenic bacterium which is resistant to most currently available antibiotics and that poses a significant health threat to hospital patients. lpxa is a key enzyme in the biosynthetic pathway of the lipopolysaccharides that are components of the bacterial outer membrane. it is a potential target for antibacterial agents that might be used to fight a. baumannii infections. this paper describes the structure determination of the apo form of lpxa in spac ...	2012	23192027
quantification of bacterial indicators and zoonotic pathogens in dairy wastewater ponds.	zoonotic pathogens in land-applied dairy wastewaters are a potential health risk. the occurrence and abundance of 10 pathogens and 3 fecal indicators were determined by quantitative real-time pcr (qpcr) in samples from 30 dairy wastewaters from southern idaho. samples tested positive for campylobacter jejuni, stx(1)- and eaea-positive escherichia coli, listeria monocytogenes, mycobacterium avium subsp. paratuberculosis, and salmonella enterica, with mean recoveries of genomic dna corresponding t ...	2012	22983964
extreme water-related weather events and waterborne disease.	global climate change is expected to affect the frequency, intensity and duration of extreme water-related weather events such as excessive precipitation, floods, and drought. we conducted a systematic review to examine waterborne outbreaks following such events and explored their distribution between the different types of extreme water-related weather events. four medical and meteorological databases (medline, embase, georef, pubmed) and a global electronic reporting system (promed) were searc ...	2012	22877498
extreme water-related weather events and waterborne disease.	global climate change is expected to affect the frequency, intensity and duration of extreme water-related weather events such as excessive precipitation, floods, and drought. we conducted a systematic review to examine waterborne outbreaks following such events and explored their distribution between the different types of extreme water-related weather events. four medical and meteorological databases (medline, embase, georef, pubmed) and a global electronic reporting system (promed) were searc ...	2012	22877498
expression of sialic acids and other nonulosonic acids in leptospira.	sialic acids are negatively charged nine carbon backbone sugars expressed on mammalian cell surfaces. sialic acids are part of a larger family of nonulosonic acid (nulo) molecules that includes pseudaminic and legionaminic acids. microbial expression of sialic acids and other nonulosonic acids has been shown to contribute to host-microbe interactions in a variety of contexts, including participation in colonization, immune subversion, and behaviors such as biofilm formation, autoagglutination an ...	2012	22853805
improved adhesive properties of recombinant bifidobacteria expressing the bifidobacterium bifidum-specific lipoprotein bopa.	bifidobacteria belong to one of the predominant bacterial groups in the intestinal microbiota of infants and adults. several beneficial effects on the health status of their human hosts have been demonstrated making bifidobacteria interesting candidates for probiotic applications. adhesion of probiotics to the intestinal epithelium is discussed as a prerequisite for colonisation of and persistence in the gastrointestinal tract.	2012	22694891
evaluation and comparison of native and recombinant lipl21 protein-based elisas for diagnosis of bovine leptospirosis.	a 21-kda leptospiral lipoprotein (lipl21) was evaluated for its diagnostic potential to detect bovine leptospirosis by elisa. both native lipl21 (nlipl21) and recombinant lipl21 (rlipl21) proteins were tested and compared regarding diagnostic efficiency, and no statistically significant difference was observed. the sensitivity of rlipl21 elisa for 62 microscopic agglutination test (mat) positive sera was 100% and the specificity with 378 mat negative sera was 97.09%. thus, rlipl21 protein-based ...	2012	22437542
leptospiral outer membrane protein microarray, a novel approach to identification of host ligand-binding proteins.	leptospirosis is a zoonosis with worldwide distribution caused by pathogenic spirochetes belonging to the genus leptospira. the leptospiral life cycle involves transmission via freshwater and colonization of the renal tubules of their reservoir hosts. infection requires adherence to cell surfaces and extracellular matrix components of host tissues. these host-pathogen interactions involve outer membrane proteins (omps) expressed on the bacterial surface. in this study, we developed an leptospira ...	2012	22961849
automatic assignment of prokaryotic genes to functional categories using literature profiling.	in the last years, there was an exponential increase in the number of publicly available genomes. once finished, most genome projects lack financial support to review annotations. a few of these gene annotations are based on a combination of bioinformatics evidence, however, in most cases, annotations are based solely on sequence similarity to a previously known gene, which was most probably annotated in the same way. as a result, a large number of predicted genes remain unassigned to any functi ...	2012	23077617
mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes.	the sizes of proteins are relevant to their biochemical structure and for their biological function. the statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes.	2012	22296664
progressive genome-wide introgression in agricultural campylobacter coli.	hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. the zoonotic pathogens campylobacter coli and c. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. using whole genome sequencing, we show that a single c. coli lineage, which has successfully colonized an agric ...	2012	23279096
progressive genome-wide introgression in agricultural campylobacter coli.	hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. the zoonotic pathogens campylobacter coli and c. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. using whole genome sequencing, we show that a single c. coli lineage, which has successfully colonized an agric ...	2012	23279096
diagnostic microbiologic methods in the gems-1 case/control study.	to understand the etiology of moderate-to-severe diarrhea among children in high mortality areas of sub-saharan africa and south asia, we performed a comprehensive case/control study of children aged <5 years at 7 sites. each site employed an identical case/control study design and each utilized a uniform comprehensive set of microbiological assays to identify the likely bacterial, viral and protozoal etiologies. the selected assays effected a balanced consideration of cost, robustness and perfo ...	2012	23169941
investigation of motility and biofilm formation by intestinal campylobacter concisus strains.	motility helps many pathogens swim through the highly viscous intestinal mucus. given the differing outcomes of campylobacter concisus infection, the motility of eight c. concisus strains isolated from patients with crohn's disease (n=3), acute (n=3) and chronic (n=1) gastroenteritis and a healthy control (n=1) were compared. following growth on solid or liquid media the eight strains formed two groups; however, the type of growth medium did not affect motility. in contrast, following growth in ...	2012	23241133
evaluation of the positive predictive value of a rapid immunochromatographic test to detect campylobacter in stools.	the recently developed rapid immunochromatographic tests (ict) have the potential to provide a quick and easy diagnosis of campylobacter enteritis in comparison to culture. in a previous study we found them sensitive but lacking in specificity. the aim of the present study was to focus on the problem of specificity and determine the positive predictive value (ppv) of a positive result of the immunocard stat! campy (meridian bioscience, cincinnati, oh, usa). for this purpose, the stools positive ...	2012	23206554
bioluminescent enzyme immunoassay for the detection of norovirus capsid antigen.	an ultrasensitive and fully automated bioluminescent enzyme immunoassay (bleia) was developed for the detection of norovirus (nv) capsid antigen. in the evaluation tests with recombinant virus-like particles, the bleia demonstrated broad reactivity against several nv genotypes (genotypes 1, 3, 4, 7, 8, and 12 in genogroup i [gi] and genotypes 1, 2, 3, 4, 5, 6, 12, and 13 in gii), a wide dose-response range from 0.25 pg/ml to 10,000 pg/ml, and good reproducibility with low coefficients of variati ...	2012	23081816
chromosomal tet(o)-harboring regions in campylobacter coli isolates from turkeys and swine.	in turkey-derived campylobacter coli isolates of a unique lineage (cluster ii), the tetracycline resistance determinant tet(o) was chromosomal and was part of a gene cassette (transposon) interrupting a campylobacter jejuni-associated putative citrate transporter gene. in contrast, the swine-derived c. coli strain 6461 harbored a chromosomal tet(o) in a different genomic location.	2012	23023744
association of campylobacter upsaliensis with persistent bloody diarrhea.	campylobacter upsaliensis is a zoonotic, emerging pathogen that is not readily recovered in traditional stool culture. this case represents the first report of persistent bloody diarrhea with c. upsaliensis that was confirmed by filtration culture, pcr, and sequencing.	2012	22915607
identification of cj1051c as a major determinant for the restriction barrier of campylobacter jejuni strain nctc11168.	campylobacter jejuni is a leading cause of human diarrheal illness in the world, and research on it has benefitted greatly by the completion of several genome sequences and the development of molecular biology tools. however, many hurdles remain for a full understanding of this unique bacterial pathogen. one of the most commonly used strains for genetic work with c. jejuni is nctc11168. while this strain is readily transformable with dna for genomic recombination, transformation with plasmids is ...	2012	22923403
prevalence and antimicrobial resistance of thermophilic campylobacter isolated from chicken in côte d'ivoire.	thermophilic campylobacters are major causes of gastroenteritis in human. the main risk factor of infection is consumption of contaminated or by cross-contaminated poultry meat. in côte d'ivoire, gastroenteritis is usually observed but no case of human campylobacteriosis has been formally reported to date. the aims of this study were to determine prevalence and antimicrobial resistance of campylobacter jejuni and campylobacter coli isolated from chickens ceaca in commercial slaughter in abidjan. ...	2012	23133454
bacterial toxin modulation of the eukaryotic cell cycle: are all cytolethal distending toxins created equally?	the cytolethal distending toxins (cdts) comprise a family of intracellular-acting bacterial protein toxins whose actions upon eukaryotic cells result in several consequences, the most characteristic of which is the induction of g(2)/m cell cycle arrest. most cdts are hetero-tripartite assemblies of cdta, cdtb, and cdtc, with cdtb required for cdt-mediated cell cycle arrest. several lines of evidence indicate that cdta and cdtc are required for the optimal intracellular activity of cdtb, although ...	2012	23061054
a longitudinal 6-year study of the molecular epidemiology of clinical campylobacter isolates in oxfordshire, united kingdom.	temporal and seasonal trends in campylobacter genotypes causing human gastroenteritis were investigated in a 6-year study of 3,300 recent isolates from oxfordshire, united kingdom. genotypes (sequence types [st]) were defined using multilocus sequence typing and assigned to a clonal complex (a cluster of related strains that share four or more identical alleles with a previously defined central genotype). a previously undescribed clonal complex (st-464) was identified which, together with st-42, ...	2012	22814466
identification of a novel genomic island conferring resistance to multiple aminoglycoside antibiotics in campylobacter coli.	historically, the incidence of gentamicin resistance in campylobacter has been very low, but recent studies reported a high prevalence of gentamicin-resistant campylobacter isolated from food-producing animals in china. the reason for the high prevalence was unknown and was addressed in this study. pcr screening identified aminoglycoside resistance genes apha-3 and apha-7 and the aade-sat4-apha-3 cluster among 41 campylobacter isolates from broiler chickens. importantly, a novel genomic island c ...	2012	22869568
case-control study of the etiology of infant diarrheal disease in 14 districts in madagascar.	acute diarrhea is a major cause of childhood morbidity and mortality worldwide. its microbiological causes and clinico-epidemiological aspects were examined during the rainy seasons from 2008 to 2009 in 14 districts in madagascar.	2012	23028555
a convenient and robust in vivo reporter system to monitor gene expression in the human pathogen helicobacter pylori.	thirty years of intensive research have significantly contributed to our understanding of helicobacter pylori biology and pathogenesis. however, the lack of convenient genetic tools, in particular the limited effectiveness of available reporter systems, has notably limited the toolbox for fundamental and applied studies. here, we report the construction of a bioluminescent h. pylori reporter system based on the photorhabdus luminescens luxcdabe cassette. the system is constituted of a promoterle ...	2012	22773640
outcome of infection of c57bl/6 il-10(-/-) mice with campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo.	human campylobacter jejuni infection can result in an asymptomatic carrier state, watery or bloody diarrhea, bacteremia, meningitis, or autoimmune neurological sequelae. infection outcomes of c57bl/6 il-10(-/-) mice orally infected with twenty-two phylogenetically diverse c. jejuni strains were evaluated to correlate colonization and disease phenotypes with genetic composition of the strains. variation between strains was observed in colonization, timing of development of clinical signs, and occ ...	2012	22960579
outcome of infection of c57bl/6 il-10(-/-) mice with campylobacter jejuni strains is correlated with genome content of open reading frames up- and down-regulated in vivo.	human campylobacter jejuni infection can result in an asymptomatic carrier state, watery or bloody diarrhea, bacteremia, meningitis, or autoimmune neurological sequelae. infection outcomes of c57bl/6 il-10(-/-) mice orally infected with twenty-two phylogenetically diverse c. jejuni strains were evaluated to correlate colonization and disease phenotypes with genetic composition of the strains. variation between strains was observed in colonization, timing of development of clinical signs, and occ ...	2012	22960579
analysis of evolutionary patterns of genes in campylobacter jejuni and c. coli.		2012	22929701
campylobacter antimicrobial resistance in peru: a ten-year observational study.	campylobacter jejuni and campylobacter coli are food-borne pathogens of great importance and feature prominently in the etiology of developing world enteritis and travellers' diarrhoea. increasing antimicrobial resistant campylobacter prevalence has been described globally, yet data from peru is limited. our objective was to describe the prevalence trends of fluoroquinolone and macrolide-resistant c. jejuni and c. coli stool isolates from three regions in peru over a ten-year period.	2012	22898609
acid stress response and protein induction in campylobacter jejuni isolates with different acid tolerance.	during the transmission route from poultry to the human host, the major foodborne pathogen c. jejuni may experience many types of stresses, including low ph caused by different acids. however, not all strains are equally sensitive to the stresses. the aim of this study was to investigate the response to acid stress of three sequenced c. jejuni strains with different acid tolerances using hcl and acetic acid.	2012	22889088
the complete genome sequence of bacteriophage cp21 reveals modular shuffling in campylobacter group ii phages.	campylobacter group ii phages described so far share a high degree of sequence similarity. we report the 182,833-bp genomic sequence of the closely related group ii phage cp21 and show that it has a completely different genomic organization. as in other group ii phages, the cp21 genome is composed of large modules separated by long dna repeat regions which obviously trigger recombination and modular shuffling.	2012	22843857
ischaemic colitis associated with oral contraceptive and bisacodyl use.	a woman with a history of hip replacement presented 3 days prior to revision of the hip with abdominal pain, diarrhoea and haematochezia. these symptoms began 6 h after she began taking bisacodyl in preparation for her upcoming surgery. she was on low-dose estradiol for hormone replacement therapy (hrt). subsequent colonoscopy and biopsies were consistent with acute colonic ischaemia (ci). she was treated with intravenous fluids and antibiotics and discharged and told to stop hrt and bisacodyl. ...	2012	22843752
guillain-barré syndrome and anti-ganglioside antibodies: a clinician-scientist's journey.	guillain-barré syndrome (gbs) is the most frequent cause of acute flaccid paralysis. having seen my first gbs patient in 1989, i have since then dedicated my time in research towards understanding the pathogenesis of gbs. along with several colleagues, we identified igg autoantibodies against ganglioside gm1 in two patients with gbs subsequent to campylobacter jejuni enteritis. we proceeded to demonstrate molecular mimicry between gm1 and bacterial lipo-oligosaccharide of c. jejuni isolated from ...	2012	22850724
restricted gene flow among hospital subpopulations of enterococcus faecium.	enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. here, we probe the population structure of e. faecium using bayesian-based population genetic modeling implemented in bayesian analysis of population structure (baps) software. the anal ...	2012	22807567
campylobacter epidemiology: a descriptive study reviewing 1 million cases in england and wales between 1989 and 2011.	to review campylobacter cases in england and wales over 2 decades and examine the main factors/mechanisms driving the changing epidemiology.	2012	22798256
estimating the relative roles of recombination and point mutation in the generation of single locus variants in campylobacter jejuni and campylobacter coli.	single locus variants (slvs) are bacterial sequence types that differ at only one of the seven canonical multilocus sequence typing (mlst) loci. estimating the relative roles of recombination and point mutation in the generation of new alleles that lead to slvs is helpful in understanding how organisms evolve. the relative rates of recombination and mutation for campylobacter jejuni and campylobacter coli were estimated at seven different housekeeping loci from publically available mlst data. th ...	2012	22767048
nutraceutical values of natural honey and its contribution to human health and wealth.	the use of natural honey (nh) as a nutraceutical agent is associated with nutritional benefits and therapeutic promises. nh is widely accepted as food and medicine by all generations, traditions and civilizations, both ancient and modern. the nutritional profiles, including its use in infant and children feeding reported in different literatures as well as health indices and biomarkers observed by various researchers are illustrated in this manuscript. the review documents folk medicine, experim ...	2012	22716101
detection of shiga toxin-producing escherichia coli by sandwich enzyme-linked immunosorbent assay using chicken egg yolk igy antibodies.	enterohemorrhagic escherichia coli (ehec), a subset of shiga toxin producing e. coli (stec) is associated with a spectrum of diseases that includes diarrhea, hemorrhagic colitis and a life-threatening hemolytic-uremic syndrome (hus). regardless of serotype, shiga toxins (stx1 and/or stx2) are uniformly expressed by all ehec, and so exploitable targets for laboratory diagnosis of these pathogens. in this study, a sandwich elisa for determination of shiga toxin (stx) was developed using anti-stx2b ...	2012	22919675
development and evaluation of a genus-specific, probe-based, internal-process-controlled real-time pcr assay for sensitive and specific detection of blastocystis spp.	blastocystis is a common intestinal parasite of unsettled clinical significance, which is not easily detected by standard parasitological methods. the genus comprises at least 13 subtypes (sts) (which likely represent separate species), 9 of which have been found in humans. recent data indicate that at least one of the subtypes is associated with intestinal disease. a quantitative taqman 5' nuclease real-time pcr (taqman pcr) including an internal process control (ipc) was developed for the dete ...	2012	22422846
development of a novel genus-specific real-time pcr assay for detection and differentiation of bartonella species and genotypes.	the genus bartonella includes numerous species with varied host associations, including several that infect humans. development of a molecular diagnostic method capable of detecting the diverse repertoire of bartonella species while maintaining genus specificity has been a challenge. we developed a novel real-time pcr assay targeting a 301-bp region of the ssra gene of bartonella and demonstrated specific amplification in over 30 bartonella species, subspecies, and strains. subsequent analysis o ...	2012	22378904
characterization of the structurally diverse n-linked glycans of campylobacter species.	the gram-negative bacterium campylobacter jejuni encodes an extensively characterized n-linked protein glycosylation system that modifies many surface proteins with a heptasaccharide glycan. in c. jejuni, the genes that encode the enzymes required for glycan biosynthesis and transfer to protein are located at a single pgl gene locus. similar loci are also present in the genome sequences of all other campylobacter species, although variations in gene content and organization are evident. in this ...	2012	22389484
a gene-by-gene approach to bacterial population genomics: whole genome mlst of campylobacter.	campylobacteriosis remains a major human public health problem world-wide. genetic analyses of campylobacter isolates, and particularly molecular epidemiology, have been central to the study of this disease, particularly the characterization of campylobacter genotypes isolated from human infection, farm animals, and retail food. these studies have demonstrated that campylobacter populations are highly structured, with distinct genotypes associated with particular wild or domestic animal sources, ...	2012	24704917
xer recombinase and genome integrity in helicobacter pylori, a pathogen without topoisomerase iv.	in the model organism e. coli, recombination mediated by the related xerc and xerd recombinases complexed with the ftsk translocase at specialized dif sites, resolves dimeric chromosomes into free monomers to allow efficient chromosome segregation at cell division. computational genome analysis of helicobacter pylori, a slow growing gastric pathogen, identified just one chromosomal xer gene (xerh) and its cognate dif site (difh). here we show that recombination between directly repeated difh sit ...	2012	22511919
longitudinal study of the persistence of antimicrobial-resistant campylobacter strains in distinct swine production systems on farms, at slaughter, and in the environment.	the objectives of this study were to compare and characterize the prevalence of antimicrobial-resistant (ar) campylobacter in conventional and antimicrobial-free (abf) production systems on farms, at slaughter, and in the environment. fecal and environmental samples were collected from abf farms (pigs, 1,239; environment, 797) and conventional farms (pigs, 1,650; environment, 1,325). at slaughter, we collected samples from carcasses, including postevisceration swabs, postchill swabs, and mesente ...	2012	22307299
molecular detection of campylobacter jejuni as a cause of culture-negative spondylodiscitis.	spondylodiscitis caused by campylobacter species is a rare disease which is most often caused by campylobacter fetus. we report a case of culture-negative spondylodiscitis and a psoas abscess due to campylobacter jejuni in a 68-year-old woman, as revealed by 16s rrna gene and campylobacter-specific pcrs from biopsied tissue.	2012	22259199
comparison of the microflex lt and vitek ms systems for routine identification of bacteria by matrix-assisted laser desorption ionization-time of flight mass spectrometry.	this study compared the performance of three matrix-assisted laser desorption ionization-time of flight mass spectrometry systems: microflex lt (bruker daltonics, bremen, germany), vitek ms ruo (axima assurance-saramis database; biomérieux, marcy l'etoile, france), and vitek ms ivd (biomérieux). a total of 1,129 isolates, including 1,003 routine isolates, 73 anaerobes, and 53 bacterial enteropathogens, were tested on the microflex lt and axima assurance devices. the spectra were analyzed using t ...	2012	22322345
campylobacter bacteremia: a rare and under-reported event?	bacteria belonging to the species campylobacter are the most common cause of bacterial diarrhoea in humans. the clinical phenotype associated with campylobacter infections ranges from asymptomatic conditions to severe colitis and bacteremia. in susceptible patients, campylobacter infections are associated with significant morbidity and mortality, with both host factors and bacterial factors being involved in the pathogenesis of bacteremia. in the host, age, gender and immune-compromising conditi ...	2012	24611124
current concepts in laboratory testing to guide antimicrobial therapy.	antimicrobial susceptibility testing (ast) is indicated for pathogens contributing to an infectious process that warrants antimicrobial therapy if susceptibility to antimicrobials cannot be predicted reliably based on knowledge of their identity. such tests are most frequently used when the etiologic agents are members of species capable of demonstrating resistance to commonly prescribed antibiotics. some organisms have predictable susceptibility to antimicrobial agents (ie, streptococcus pyogen ...	2012	22386185
characterization of protein glycosylation in francisella tularensis subsp. holarctica: identification of a novel glycosylated lipoprotein required for virulence.	fth_0069 is a previously uncharacterized strongly immunoreactive protein that has been proposed to be a novel virulence factor in francisella tularensis. here, the glycan structure modifying two c-terminal peptides of fth_0069 was identified utilizing high resolution, high mass accuracy mass spectrometry, combined with in-source cid tandem ms experiments. the glycan observed at m/z 1156 was determined to be a hexasaccharide, consisting of two hexoses, three n-acetylhexosamines, and an unknown mo ...	2012	22361235
development and comparison of a real-time pcr assay for detection of dichelobacter nodosus with culturing and conventional pcr: harmonisation between three laboratories.	ovine footrot is a contagious disease with worldwide occurrence in sheep. the main causative agent is the fastidious bacterium dichelobacter nodosus. in scandinavia, footrot was first diagnosed in sweden in 2004 and later also in norway and denmark. clinical examination of sheep feet is fundamental to diagnosis of footrot, but d. nodosus should also be detected to confirm the diagnosis. pcr-based detection using conventional pcr has been used at our institutes, but the method was laborious and t ...	2012	22293440
the genome and proteome of a campylobacter coli bacteriophage vb_ccom-ibb_35 reveal unusual features.	campylobacter is the leading cause of foodborne diseases worldwide. bacteriophages (phages) are naturally occurring predators of bacteria, ubiquitous in the environment, with high host specificity and thus considered an appealing option to control bacterial pathogens. nevertheless for an effective use of phages as antimicrobial agents, it is important to understand phage biology which renders crucial the analysis of phage genomes and proteomes. the lack of sequence data from campylobacter phages ...	2012	22284308
deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics.	bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. this review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor ...	2012	23276734
deciphering the bacterial glycocode: recent advances in bacterial glycoproteomics.	bacterial glycoproteins represent an attractive target for new antibacterial treatments, as they are frequently linked to pathogenesis and contain distinctive glycans that are absent in humans. despite their potential therapeutic importance, many bacterial glycoproteins remain uncharacterized. this review focuses on recent advances in deciphering the bacterial glycocode, including metabolic glycan labeling to discover and characterize bacterial glycoproteins, lectin-based microarrays to monitor ...	2012	23276734
application of protein purification methods for the enrichment of a cytotoxin from campylobacter jejuni.	campylobater jejuni, a major foodborne diarrhoeal pathogen is reported to produce a number of cytotoxins of which only a cytolethal distending toxin (cdt) has been characterised so far. one or more additional cytotoxins other than cdt, including a chinese hamster ovary (cho) cell active, vero cell inactive cytotoxin, may mediate inflammatory diarrhoea. our objective was to develop a method to enrich and thus partially characterise this cytotoxin, as a pathway to the eventual identification and c ...	2012	23259594
population structure in nontypeable haemophilus influenzae.	nontypeable haemophilus influenzae (nthi) frequently colonize the human pharynx asymptomatically, and are an important cause of otitis media in children. past studies have identified typeable h. influenzae as being clonal, but the population structure of nthi has not been extensively characterized. the research presented here investigated the diversity and population structure in a well-characterized collection of nthi isolated from the middle ears of children with otitis media or the pharynges ...	2012	23266487
population structure in nontypeable haemophilus influenzae.	nontypeable haemophilus influenzae (nthi) frequently colonize the human pharynx asymptomatically, and are an important cause of otitis media in children. past studies have identified typeable h. influenzae as being clonal, but the population structure of nthi has not been extensively characterized. the research presented here investigated the diversity and population structure in a well-characterized collection of nthi isolated from the middle ears of children with otitis media or the pharynges ...	2012	23266487
microevolutionary analysis of clostridium difficile genomes to investigate transmission.	the control of clostridium difficile infection is a major international healthcare priority, hindered by a limited understanding of transmission epidemiology for these bacteria. however, transmission studies of bacterial pathogens are rapidly being transformed by the advent of next generation sequencing.	2012	23259504
chemical probing of glycans in cells and organisms.	among the four major building blocks of life, glycans play essential roles in numerous physiological and pathological processes. due to their non-templated biosynthesis, advances towards elucidating the molecular details of glycan functions are relatively slow compared with the pace of protein and nucleic acid research. over the past 30 years, chemical tools have emerged as powerful allies to genetics and molecular biology in the study of glycans in their native environment. this tutorial review ...	2012	23257905
chemical probing of glycans in cells and organisms.	among the four major building blocks of life, glycans play essential roles in numerous physiological and pathological processes. due to their non-templated biosynthesis, advances towards elucidating the molecular details of glycan functions are relatively slow compared with the pace of protein and nucleic acid research. over the past 30 years, chemical tools have emerged as powerful allies to genetics and molecular biology in the study of glycans in their native environment. this tutorial review ...	2012	23257905