Publications

investigating the responses of cronobacter sakazakii to garlic-drived organosulfur compounds: a systematic study of pathogenic-bacterium injury by use of high-throughput whole-transcriptome sequencing and confocal micro-raman spectroscopy.	we present the results of a study using high-throughput whole-transcriptome sequencing (rna-seq) and vibrational spectroscopy to characterize and fingerprint pathogenic-bacterium injury under conditions of unfavorable stress. two garlic-derived organosulfur compounds were found to be highly effective antimicrobial compounds against cronobacter sakazakii, a leading pathogen associated with invasive infection of infants and causing meningitis, necrotizing entercolitis, and bacteremia. rna-seq show ...	2014	24271174
evaluation of phytate-degrading lactobacillus culture administration to broiler chickens.	probiotics have been demonstrated to promote growth, stimulate immune responses, and improve food safety of poultry. while widely used, their effectiveness is mixed, and the mechanisms through which they contribute to poultry production are not well understood. microbial phytases are increasingly supplemented in feed to improve digestibility and reduce antinutritive effects of phytate. the microbial origin of these exogenous enzymes suggests a potentially important mechanism of probiotic functio ...	2014	24271165
response to metronidazole and oxidative stress is mediated through homeostatic regulator hsra (hp1043) in helicobacter pylori.	metronidazole (mtz) is often used in combination therapies to treat infections caused by the gastric pathogen helicobacter pylori. resistance to mtz results from loss-of-function mutations in genes encoding rdxa and frxa nitroreductases. mtz-resistant strains, when cultured at sub-mics of mtz (5 to 20 μg/ml), show dose-dependent defects in bacterial growth; depressed activities of many krebs cycle enzymes, including pyruvate:ferredoxin oxidoreductase (pfor); and low transcript levels of porgdab ...	2014	24296668
exposure of escherichia coli atcc 12806 to sublethal concentrations of food-grade biocides influences its ability to form biofilm, resistance to antimicrobials, and ultrastructure.	escherichia coli atcc 12806 was exposed to increasing subinhibitory concentrations of three biocides widely used in food industry facilities: trisodium phosphate (tsp), sodium nitrite (sni), and sodium hypochlorite (shy). the cultures exhibited an acquired tolerance to biocides (especially to sni and shy) after exposure to such compounds. e. coli produced biofilms (as observed by confocal laser scanning microscopy) on polystyrene microtiter plates. previous adaptation to sni or shy enhanced the ...	2014	24317080
association of clustered regularly interspaced short palindromic repeat (crispr) elements with specific serotypes and virulence potential of shiga toxin-producing escherichia coli.	shiga toxin-producing escherichia coli (stec) strains (n = 194) representing 43 serotypes and e. coli k-12 were examined for clustered regularly interspaced short palindromic repeat (crispr) arrays to study genetic relatedness among stec serotypes. a subset of the strains (n = 81) was further analyzed for subtype i-e cas and virulence genes to determine a possible association of crispr elements with potential virulence. four types of crispr arrays were identified. crispr1 and crispr2 were presen ...	2014	24334663
role of alkyl hydroperoxide reductase (ahpc) in the biofilm formation of campylobacter jejuni.	biofilm formation of campylobacter jejuni, a major cause of human gastroenteritis, contributes to the survival of this pathogenic bacterium in different environmental niches; however, molecular mechanisms for its biofilm formation have not been fully understood yet. in this study, the role of oxidative stress resistance in biofilm formation was investigated using mutants defective in catalase (kata), superoxide dismutase (sodb), and alkyl hydroperoxide reductase (ahpc). biofilm formation was sub ...	2014	24498070
identification and characterization of lactic acid bacteria in a commercial probiotic culture.	the aim of the present study was to describe the identification and characterization (physiological properties) of two strains of lactic acid bacteria (lab 18 and 48) present in a commercial probiotic culture, floramax(®)-b11. isolates were characterized morphologically, and identified biochemically. in addition, the midi system id, the biolog id system, and 16s rrna sequence analyses for identification of lab 18 and lab 48 strains were used to compare the identification results. tolerance and r ...	2014	24936379
first complete genome sequence of escherichia albertii strain kf1, a new potential human enteric pathogen.	escherichia albertii has been recently recognized as an emerging human and bird enteric pathogen. here, we report the first complete chromosome nucleotide sequence of a clinical isolate of e. albertii strain kf1, which may provide information about the pathogenic potential of this new species and the mechanisms of evolution of enteropathogenic escherichia spp.	2014	24482506
compositional and functional features of the gastrointestinal microbiome and their effects on human health.	the human gastrointestinal tract contains distinct microbial communities that differ in composition and function based on their location, as well as age, sex, race/ethnicity, and diet of their host. we describe the bacterial taxa present in different locations of the gi tract, and their specific metabolic features. the distinct features of these specific microbial communities might affect human health and disease. several bacterial taxa and metabolic modules (biochemical functions) have been ass ...	2014	24486050
radical s-adenosylmethionine enzymes.		2014	24476342
simultaneous production of biosurfactants and bacteriocins by probiotic lactobacillus casei mrtl3.	lactic acid bacteria (lab) are ubiquitous and well-known commensal bacteria in the human and animal microflora. lab are extensively studied and used in a variety of industrial and food fermentations. they are widely used for humans and animals as adjuvants, probiotic formulation, and dietary supplements and in other food fermentation applications. in the present investigation, lab were isolated from raw milk samples collected from local dairy farms of haryana, india. further, the isolates were s ...	2014	24669225
long-term alteration of intestinal microbiota in patients with ulcerative colitis by antibiotic combination therapy.	previous work has demonstrated that intestinal bacteria, such as fusobacterium varium (f. varium), contribute to the clinical activity in ulcerative colitis (uc); thus, an antibiotic combination therapy (amoxicillin, tetracycline, and metronidazole (atm)) against f. varium can induce and maintain uc remission. therefore, we investigated whether atm therapy induces a long-term alteration of intestinal microbiota in patients with uc. patients with uc were enrolled in a multicenter, randomized, dou ...	2014	24489770
antimicrobial proteins in intestine and inflammatory bowel diseases.	mucosal surface of the intestinal tract is continuously exposed to a large number of microorganisms. to manage the substantial microbial exposure, epithelial surfaces produce a diverse arsenal of antimicrobial proteins (amps) that directly kill or inhibit the growth of microorganisms. thus, amps are important components of innate immunity in the gut mucosa. they are frequently expressed in response to colonic inflammation and infection. expression of many amps, including human β-defensin 2-4 and ...	2014	25349560
effect of noradrenaline on the virulence properties of campylobacter species.	campylobacter species cause a spectrum of illnesses in humans. the type of illness and the outcome is dependent on the virulence of the infecting pathogen strain and host immune status. acute stress can seriously compromise host immunity and increase susceptibility to infection. noradrenaline (na) is a stress hormone. several studies have shown that it stimulated growth and increased the pathogenicity of organisms including e. coli and campylobacter jejuni. however, the effect of na on other cam ...	2014	24669220
inflammation and colorectal cancer, when microbiota-host mutualism breaks.	structural changes in the gut microbial community have been shown to accompany the progressive development of colorectal cancer. in this review we discuss recent hypotheses on the mechanisms involved in the bacteria-mediated carcinogenesis, as well as the triggering factors favoring the shift of the gut microbiota from a mutualistic to a pro-carcinogenic configuration. the possible role of inflammation, bacterial toxins and toxic microbiota metabolites in colorectal cancer onset is specifically ...	2014	24574765
rapid diagnosis of campylobacter jejuni by stool gram stain examination.		2014	24473432
masquerading microbial pathogens: capsular polysaccharides mimic host-tissue molecules.	the increasing prevalence of antibiotic-resistant bacteria portends an impending postantibiotic age, characterized by diminishing efficacy of common antibiotics and routine application of multifaceted, complementary therapeutic approaches to treat bacterial infections, particularly multidrug-resistant organisms. the first line of defense for most bacterial pathogens consists of a physical and immunologic barrier known as the capsule, commonly composed of a viscous layer of carbohydrates that are ...	2014	24372337
neurological aspects of human parvovirus b19 infection: a systematic review.	parvovirus b19 has been linked with various clinical syndromes including neurological manifestations. however, its role in the latter remains not completely understood. although the last 10 years witnessed a surge of case reports on b19-associated neurological aspects, the literature data remains scattered and heterogeneous, and epidemiological information on the incidence of b19-associated neurological aspects cannot be accurately extrapolated. the aim of this review is to identify the characte ...	2014	24459081
mucosa-associated bacterial microbiome of the gastrointestinal tract of weaned pigs and dynamics linked to dietary calcium-phosphorus.	dietary composition largely influences pig's gastrointestinal microbiota and represents a useful prophylactic tool against enteric disturbances in young pigs. despite the importance for host-microbe interactions and bacterial colonization, dietary responses of the mucosa-associated bacterial communities are less well investigated. in the present study, we characterized the mucosa-associated bacterial communities at the pars non-glandularis of the stomach, ileum and colon, and identified shifts i ...	2014	24466298
three-dimensional structure of a sugar n-formyltransferase from francisella tularensis.	n-formylated sugars have been observed on the o-antigens of such pathogenic gram-negative bacteria as campylobacter jejuni and francisella tularensis. until recently, however, little was known regarding the overall molecular architectures of the n-formyltransferases that are required for the biosynthesis of these unusual sugars. here we demonstrate that the protein encoded by the wbtj gene from f. tularensis is an n-formyltransferase that functions on dtdp-4-amino-4,6-dideoxy-d-glucose as its su ...	2014	24347283
applying the resfinder and virulencefinder web-services for easy identification of acquired antibiotic resistance and e. coli virulence genes in bacteriophage and prophage nucleotide sequences.	extensive research is currently being conducted on the use of bacteriophages for applications in human medicine, agriculture and food manufacturing. however, phages are important vehicles of horisontal gene transfer and play a significant role in bacterial evolution. as a result, concern has been raised that this increased use and dissemination of phages could result in spread of deleterious genes, e.g., antibiotic resistance and virulence genes. meanwhile, in the wake of the genomic era, severa ...	2014	24575358
a novel o-linked glycan modulates campylobacter jejuni major outer membrane protein-mediated adhesion to human histo-blood group antigens and chicken colonization.	campylobacter jejuni is an important cause of human foodborne gastroenteritis; strategies to prevent infection are hampered by a poor understanding of the complex interactions between host and pathogen. previous work showed that c. jejuni could bind human histo-blood group antigens (bgags) in vitro and that bgags could inhibit the binding of c. jejuni to human intestinal mucosa ex vivo. here, the major flagella subunit protein (flaa) and the major outer membrane protein (momp) were identified as ...	2014	24451549
pre- and neonatal exposure to lipopolysaccharide or the enteric metabolite, propionic acid, alters development and behavior in adolescent rats in a sexually dimorphic manner.	alterations in the composition of the gut microbiome and/or immune system function may have a role in the development of autism spectrum disorders (asd). the current study examined the effects of prenatal and early life administration of lipopolysaccharide (lps), a bacterial mimetic, and the short chain fatty acid, propionic acid (ppa), a metabolic fermentation product of enteric bacteria, on developmental milestones, locomotor activity, and anxiety-like behavior in adolescent male and female of ...	2014	24466331
live genomics for pathogen monitoring in public health.	whole genome analysis based on next generation sequencing (ngs) now represents an affordable framework in public health systems. robust analytical pipelines of genomic data provides in short laps of time (hours) information about taxonomy, comparative genomics (pan-genome) and single polymorphisms profiles. pathogenic organisms of interest can be tracked at the genomic level, allowing monitoring at one-time several variables including: epidemiology, pathogenicity, resistance to antibiotics, viru ...	2014	25437609
twin-arginine translocation system in helicobacter pylori: tatc, but not tatb, is essential for viability.	the twin-arginine translocation (tat) system, needed to transport folded proteins across biological membranes, has not been characterized in the gastric pathogen helicobacter pylori. analysis of all h. pylori genome sequences available thus far reveals the presence of single copies of tata, tatb, and tatc needed for the synthesis of a fully functional tat system. based on the presence of the twin-arginine hallmark in their signal sequence, only four h. pylori proteins appear to be tat dependent: ...	2014	24449753
potential of known and short prokaryotic protein motifs as a basis for novel peptide-based antibacterial therapeutics: a computational survey.	short linear motifs (slims) are functional stretches of protein sequence that are of crucial importance for numerous biological processes by mediating protein-protein interactions. these motifs often comprise peptides of less than 10 amino acids that modulate protein-protein interactions. while well-characterized in eukaryotic intracellular signaling, their role in prokaryotic signaling is less well-understood. we surveyed the distribution of known motifs in prokaryotic extracellular and virulen ...	2014	24478765
deep-sea hydrothermal vent epsilonproteobacteria encode a conserved and widespread nitrate reduction pathway (nap).	despite the frequent isolation of nitrate-respiring epsilonproteobacteria from deep-sea hydrothermal vents, the genes coding for the nitrate reduction pathway in these organisms have not been investigated in depth. in this study we have shown that the gene cluster coding for the periplasmic nitrate reductase complex (nap) is highly conserved in chemolithoautotrophic, nitrate-reducing epsilonproteobacteria from deep-sea hydrothermal vents. furthermore, we have shown that the napa gene is expresse ...	2014	24430487
cytolethal distending toxin b as a cell-killing component of tumor-targeted anthrax toxin fusion proteins.	cytolethal distending toxin (cdt) is produced by gram-negative bacteria of several species. it is composed of three subunits, cdta, cdtb, and cdtc, with cdtb being the catalytic subunit. we fused cdtb from haemophilus ducreyi to the n-terminal 255 amino acids of bacillus anthracis toxin lethal factor (lfn) to design a novel, potentially potent antitumor drug. as a result of this fusion, cdtb was transported into the cytosol of targeted cells via the efficient delivery mechanism of anthrax toxin. ...	2014	24434511
single cell stochastic regulation of pilus phase variation by an attenuation-like mechanism.	the molecular triggers leading to virulence of a number of human-adapted commensal bacteria such as streptococcus gallolyticus are largely unknown. this opportunistic pathogen is responsible for endocarditis in the elderly and associated with colorectal cancer. colonization of damaged host tissues with exposed collagen, such as cardiac valves and pre-cancerous polyps, is mediated by appendages referred to as pil1 pili. populations of s. gallolyticus are heterogeneous with the majority of cells w ...	2014	24453966
epidemiology of campylobacteriosis in germany - insights from 10 years of surveillance.	campylobacteriosis caused by campylobacter spp. is the most common notifiable bacterial gastrointestinal disease in germany and a major problem in many other european countries as well. in contrast to other infectious diseases, e.g., salmonellosis, the annual number of notified campylobacteriosis cases has increased in germany and other european countries from 2001-2010.	2014	24422983
a variable homopolymeric g-repeat defines small rna-mediated posttranscriptional regulation of a chemotaxis receptor in helicobacter pylori.	phase variation of hypermutable simple sequence repeats (ssrs) is a widespread and stochastic mechanism to generate phenotypic variation within a population and thereby contributes to host adaptation of bacterial pathogens. although several examples of ssrs that affect transcription or coding potential have been reported, we now show that a ssr also impacts small rna-mediated posttranscriptional regulation. based on in vitro and in vivo analyses, we demonstrate that a variable homopolymeric g-re ...	2014	24474799
clinical detection of human probiotics and human pathogenic bacteria by using a novel high-throughput platform based on next generation sequencing.	the human body plays host to a vast array of bacteria, found in oral cavities, skin, gastrointestinal tract and the vagina. some bacteria are harmful while others are beneficial to the host. despite the availability of many methods to identify bacteria, most of them are only applicable to specific and cultivable bacteria and are also tedious. based on high throughput sequencing technology, this work derives 16s rrna sequences of bacteria and analyzes probiotics and pathogens species.	2014	24418497
nitazoxanide: nematicidal mode of action and drug combination studies.	intestinal nematodes or roundworms (aka soil-transmitted helminths or sths) cause great disease. they infect upwards of two billion people, leading to high morbidity and a range of health problems, especially in infected children and pregnant women. development of resistance to the two main classes of drugs used to treat intestinal nematode infections of humans has been reported. to fight sth infections, we need new and more effective drugs and ways to improve the efficacy of the old drugs. one ...	2014	24412397
association between stool enteropathogen quantity and disease in tanzanian children using taqman array cards: a nested case-control study.	etiologic studies of diarrhea are limited by uneven diagnostic methods and frequent asymptomatic detection of enteropathogens. polymerase chain reaction-based stool pathogen quantification may help distinguish clinically significant infections. we performed a nested case-control study of diarrhea in infants from a community-based birth cohort in tanzania. we tested 71 diarrheal samples and pre-diarrheal matched controls with a laboratory-developed taqman array card for 19 enteropathogens. with q ...	2014	24189366
quorum sensing controls flagellar morphogenesis in burkholderia glumae.	burkholderia glumae is a motile plant pathogenic bacterium that has multiple polar flagella and one luxr/luxi-type quorum sensing (qs) system, tofr/tofi. a qs-dependent transcriptional regulator, qsmr, activates flagellar master regulator flhdc genes. flhdc subsequently activates flagellar gene expression in b. glumae at 37°c. here, we confirm that the interplay between qs and temperature is critical for normal polar flagellar morphogenesis in b. glumae. in the wild-type bacterium, flagellar gen ...	2014	24416296
a low complexity rapid molecular method for detection of clostridium difficile in stool.	here we describe a method for the detection of clostridium difficile from stool using a novel low-complexity and rapid extraction process called heat elution (he). the he method is two-step and takes just 10 minutes, no specialist instruments are required and there is minimal hands-on time. a test method using he was developed in conjunction with loop-mediated isothermal amplification (lamp) combined with the real-time bioluminescent reporter system known as bart targeting the toxin b gene (tcdb ...	2014	24416173
immunopathology of inflammatory bowel disease.	inflammatory bowel disease (ibd) results from a complex series of interactions between susceptibility genes, the environment, and the immune system. the host microbiome, as well as viruses and fungi, play important roles in the development of ibd either by causing inflammation directly or indirectly through an altered immune system. new technologies have allowed researchers to be able to quantify the various components of the microbiome, which will allow for future developments in the etiology o ...	2014	24415853
peptidoglycan ld-carboxypeptidase pgp2 influences campylobacter jejuni helical cell shape and pathogenic properties and provides the substrate for the dl-carboxypeptidase pgp1.	despite the importance of campylobacter jejuni as a pathogen, little is known about the fundamental aspects of its peptidoglycan (pg) structure and factors modulating its helical morphology. a pg dl-carboxypeptidase pgp1 essential for maintenance of c. jejuni helical shape was recently identified. bioinformatic analysis revealed the cjj81176_0915 gene product as co-occurring with pgp1 in several organisms. deletion of cjj81176_0915 (renamed pgp2) resulted in straight morphology, representing the ...	2014	24394413
an update in guillain-barré syndrome.	guillain-barré syndrome (gbs) was first described in 1916 (guillain g, 1916) and is approaching its 100th anniversary. our knowledge of the syndrome has hugely expanded since that time. once originally considered to be only demyelinating in pathology we now recognise both axonal and demyelinating subtypes. numerous triggering or antecedent events including infections are recognised and gbs is considered an immunological response to these. gbs is now considered to be a clinical syndrome of an acu ...	2014	24511391
themes and variations: regulation of rpon-dependent flagellar genes across diverse bacterial species.	flagellar biogenesis in bacteria is a complex process in which the transcription of dozens of structural and regulatory genes is coordinated with the assembly of the flagellum. although the overall process of flagellar biogenesis is conserved among bacteria, the mechanisms used to regulate flagellar gene expression vary greatly among different bacterial species. many bacteria use the alternative sigma factor σ (54) (also known as rpon) to transcribe specific sets of flagellar genes. these bacter ...	2014	24672734
characterisation of a multi-ligand binding chemoreceptor ccml (tlp3) of campylobacter jejuni.	campylobacter jejuni is the leading cause of human gastroenteritis worldwide with over 500 million cases annually. chemotaxis and motility have been identified as important virulence factors associated with c. jejuni colonisation. group a transducer-like proteins (tlps) are responsible for sensing the external environment for bacterial movement to or away from a chemical gradient or stimulus. in this study, we have demonstrated cj1564 (tlp3) to be a multi-ligand binding chemoreceptor and report ...	2014	24391495
acute hemiplegia as a rare presentation of infantile guillain-barre syndrome.		2014	25399226
alpha heavy chain disease: a rare lymphoma hard to diagnose.		2014	25125965
role of gut pathogens in development of irritable bowel syndrome.	acute infectious gastroenteritis is one of the most commonly identifiable risk factors for the development of irritable bowel syndrome (ibs). a number of bacterial, viral and parasitic pathogens have been found to be associated with the development of ibs and other functional gastrointestinal (gi) disorders. epidemiological studies have identified demographic and acute enteritis-related risk factors for the development of post-infectious-ibs (pi-ibs). immune dysregulation, alterations in barrier ...	2014	24604037
central and peripheral demyelination.	several conditions cause damage to the inherently normal myelin of central nervous system, perepheral nervous system or both central and perepheral nervous system and hence termed as central demyelinating diseases, perepheral demyelinating diseases and combined central and perepheral demyelinating diseases respectively. here we analysed and foccused on the etiology, prevalance, incidence and age of these demyelinating disorders. clinical attention and various diagnostic tests are needed to adequ ...	2014	24741263
correlations between cytomegalovirus, epstein-barr virus, anti-ganglioside antibodies, electrodiagnostic findings and functional status in guillain-barré syndrome.	due to underlying autoimmune background of guillain-barré syndrome (gbs), the possible role of infectious agents cytomegalovirus (cmv) and epstein-barr virus (ebv) and also due to association of anti-ganglioside antibodies with gbs, the present study aimed to investigate the associations between serum anti-ganglioside antibodies (aga) level, type of infection and electrodiagnostic (ed) findings with the severity and three-month functional outcome of patients with gbs.	2014	24800041
gastric malt lymphoma: old and new insights.	the stomach is the most frequent site of extranodal lymphoma. gastric lymphoma originating from mucosa-associated lymphoid tissue (malt) is typically a low-grade, b-cell neoplasia strongly associated with helicobacter pylori (h. pylori) infection. only certain h. pylori strains in some predisposed patients determine lymphoma development in the stomach, according to a strain-host-organ specific process. the clinical presentation is poorly specific, symptoms ranging from vague dyspepsia to alarm s ...	2014	24714739
antisecretory and antimotility activity of aconitum heterophyllum and its significance in treatment of diarrhea.	the roots of the plant aconitum heterophyllum (eah) are traditionally used for curing hysteria, throat infection, dyspepsia, abdominal pain, diabetes, and diarrhea. therefore, the present study was undertaken to determine the mechanism involved in the anti-diarrheal activity of roots of a. heterophyllum.	2014	24550590
exposure to mimivirus collagen promotes arthritis.	collagens, the most abundant proteins in animals, also occur in some recently described nucleocytoplasmic large dna viruses such as mimiviridae, which replicate in amoebae. to clarify the impact of viral collagens on the immune response of animals exposed to mimiviridae, we have investigated the localization of collagens in acanthamoeba polyphaga mimivirus particles and the response of mice to immunization with mimivirus particles. using protein biotinylation, we have first shown that viral coll ...	2014	24173233
environmental determinants of transformation efficiency in helicobacter pylori.	helicobacter pylori uses natural competence and homologous recombination to adapt to the dynamic environment of the stomach mucosa and maintain chronic colonization. although h. pylori competence is constitutive, its rate of transformation is variable, and little is known about factors that influence it. to examine this, we first determined the transformation efficiency of h. pylori strains under low o2 (5% o2, 7.6% co2, 7.6% h2) and high o2 (15% o2, 2.9% co2, 2.9% h2) conditions using dna conta ...	2014	24187089
comparative metabolic systems analysis of pathogenic burkholderia.	burkholderia cenocepacia and burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. while they share similar genetic compositions, b. cenocepacia and b. multivorans exhibit important differences in pathogenesis. we have developed reconciled genome-scale metabolic network reconstructions of b. cenocepacia j2315 and b. multivorans at ...	2014	24163337
metaproteomics analysis reveals the adaptation process for the chicken gut microbiota.	the animal gastrointestinal tract houses a large microbial community, the gut microbiota, that confers many benefits to its host, such as protection from pathogens and provision of essential metabolites. metagenomic approaches have defined the chicken fecal microbiota in other studies, but here, we wished to assess the correlation between the metagenome and the bacterial proteome in order to better understand the healthy chicken gut microbiota. here, we performed high-throughput sequencing of 16 ...	2014	24212578
crisprs: molecular signatures used for pathogen subtyping.	rapid and accurate strain identification is paramount in the battle against microbial outbreaks, and several subtyping approaches have been developed. one such method uses clustered regular interspaced short palindromic repeats (crisprs), dna repeat elements that are present in approximately half of all bacteria. though their signature function is as an adaptive immune system against invading dna such as bacteriophages and plasmids, crisprs also provide an excellent framework for pathogen tracki ...	2014	24162568
use of bacteroidales microbial source tracking to monitor fecal contamination in fresh produce production.	in recent decades, fresh and minimally processed produce items have been associated with an increasing proportion of food-borne illnesses. most pathogens associated with fresh produce are enteric (fecal) in origin, and contamination can occur anywhere along the farm-to-fork chain. microbial source tracking (mst) is a tool developed in the environmental microbiology field to identify and quantify the dominant source(s) of fecal contamination. this study investigated the utility of an mst method b ...	2014	24212583
specific discrimination of three pathogenic salmonella enterica subsp. enterica serotypes by carb-based oligonucleotide microarray.	it is important to rapidly and selectively detect and analyze pathogenic salmonella enterica subsp. enterica in contaminated food to reduce the morbidity and mortality of salmonella infection and to guarantee food safety. in the present work, we developed an oligonucleotide microarray containing duplicate specific capture probes based on the carb gene, which encodes the carbamoyl phosphate synthetase large subunit, as a competent biomarker evaluated by genetic analysis to selectively and efficie ...	2014	24185846
higher water temperature and incubation under aerobic and microaerobic conditions increase the recovery and diversity of arcobacter spp. from shellfish.	some arcobacter species are considered emerging food-borne and waterborne pathogens, and shellfish have been suggested as one of their reservoirs. however, only a few studies have investigated the presence of arcobacter in this kind of food. this study assesses the prevalence and diversity of arcobacter spp. in shellfish by multiplex pcr (m-pcr) and culturing methods (under different atmospheric conditions) and evaluates the possible influence of environmental parameters (temperature, salinity, ...	2014	24185851
microbials for the production of monoclonal antibodies and antibody fragments.	monoclonal antibodies (mabs) and antibody fragments represent the most important biopharmaceutical products today. because full length antibodies are glycosylated, mammalian cells, which allow human-like n-glycosylation, are currently used for their production. however, mammalian cells have several drawbacks when it comes to bioprocessing and scale-up, resulting in long processing times and elevated costs. by contrast, antibody fragments, that are not glycosylated but still exhibit antigen bindi ...	2014	24183828
raw milk consumption among patients with non-outbreak-related enteric infections, minnesota, usa, 2001-2010.	raw milk has frequently been identified as the source of foodborne illness outbreaks; however, the number of illnesses ascertained as part of documented outbreaks likely represents a small proportion of the actual number of illnesses associated with this food product. analysis of routine surveillance data involving illnesses caused by enteric pathogens that were reportable in minnesota during 2001-2010 revealed that 3.7% of patients with sporadic, domestically acquired enteric infections had rep ...	2014	24520559
emergence and evolution.	the aminoacyl-trna synthetases (aarss) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate trnas. the aarss are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. although the aarss have long been viewed as a highly conserved group of enzymes, findings within ...	2014	23478877
rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations.	the incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. the conventional methods used to detect foodborne pathogen are time consuming and laborious. hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food ana ...	2014	25628612
rapid methods for the detection of foodborne bacterial pathogens: principles, applications, advantages and limitations.	the incidence of foodborne diseases has increased over the years and resulted in major public health problem globally. foodborne pathogens can be found in various foods and it is important to detect foodborne pathogens to provide safe food supply and to prevent foodborne diseases. the conventional methods used to detect foodborne pathogen are time consuming and laborious. hence, a variety of methods have been developed for rapid detection of foodborne pathogens as it is required in many food ana ...	2014	25628612
cj1386, an atypical hemin-binding protein, mediates hemin trafficking to kata in campylobacter jejuni.	catalase enzymes detoxify h2o2 by the dismutation of h2o2 into o2 and h2o through the use of hemin cofactors. while the structure and biochemical properties of catalase enzymes have been well characterized over many decades of research, it remained unclear how catalases acquire hemin. we have previously reported that cj1386 is essential for ensuring proper hemin content in campylobacter jejuni catalase (kata) (a. flint, y. q. sun, and a. stintzi, j bacteriol 194: 334-345, 2012). in this report, ...	2014	25548249
cj1386, an atypical hemin-binding protein, mediates hemin trafficking to kata in campylobacter jejuni.	catalase enzymes detoxify h2o2 by the dismutation of h2o2 into o2 and h2o through the use of hemin cofactors. while the structure and biochemical properties of catalase enzymes have been well characterized over many decades of research, it remained unclear how catalases acquire hemin. we have previously reported that cj1386 is essential for ensuring proper hemin content in campylobacter jejuni catalase (kata) (a. flint, y. q. sun, and a. stintzi, j bacteriol 194: 334-345, 2012). in this report, ...	2014	25548249
clinical importance and epidemiology of quinolone resistance.	the quinolone class of antimicrobial agents is one of most widely used classes of antimicrobial agents in outpatient and inpatient treatment. however, quinolone resistance in gram-positive and gram-negative bacteria has emerged and increased globally. this resistance limits the usefulness of quinolones in clinical practice. the review summarizes mechanisms of quinolone resistance and its epidemiology and implications in the most common clinical settings, urinary tract infections, respiratory tra ...	2014	25566402
transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen campylobacter concisus.	pathogenic species within the genus campylobacter are responsible for a considerable burden on global health. campylobacter concisus is an emergent pathogen that plays a role in acute and chronic gastrointestinal disease. despite ongoing research on campylobacter virulence mechanisms, little is known regarding the immunological profile of the host response to campylobacter infection. in this study, we describe a comprehensive global profile of innate immune responses to c. concisus infection in ...	2014	25486993
transcriptomic and proteomic analyses reveal key innate immune signatures in the host response to the gastrointestinal pathogen campylobacter concisus.	pathogenic species within the genus campylobacter are responsible for a considerable burden on global health. campylobacter concisus is an emergent pathogen that plays a role in acute and chronic gastrointestinal disease. despite ongoing research on campylobacter virulence mechanisms, little is known regarding the immunological profile of the host response to campylobacter infection. in this study, we describe a comprehensive global profile of innate immune responses to c. concisus infection in ...	2014	25486993
effect of administration route and dose escalation on plasma and intestinal concentrations of enrofloxacin and ciprofloxacin in broiler chickens.	the (mis)use of fluoroquinolones in the fowl industry has led to an alarming incidence of fluoroquinolone resistance in pathogenic as well as commensal bacteria. next to simply reducing antimicrobial consumption, optimizing dosage regimens can be regarded as a suitable strategy to reduce antimicrobial resistance development without jeopardizing therapy efficacy and outcome. a first step in order to limit antimicrobial resistance is to assess the exposure of the intestinal microbiota to enrofloxa ...	2014	25440469
multilocus sequence typing (mlst) and whole-genome mlst of campylobacter jejuni isolates from human infections in three districts during a seasonal peak in finland.	a total of 95 human campylobacter jejuni isolates acquired from domestic infections and collected from three districts in finland during the seasonal peak (june to september) in 2012 were analyzed by pcr-based multilocus sequence typing (mlst) and by whole-genome sequencing (wgs). four predominant sequence types (sts) were detected among the isolates: st-45 (21%) and st-230 (14%, st-45 clonal complex [cc]), st-267 (21%, st-283 cc), and st-677 (19%, st-677 cc). in districts 1 and 3, most of the i ...	2014	25232158
antimicrobial susceptibility profiles and molecular typing of campylobacter jejuni and campylobacter coli isolates from ducks in south korea.	campylobacter is a food-borne zoonotic pathogen that causes human gastroenteritis worldwide. campylobacter bacteria are commensal in the intestines of many food production animals, including ducks and chickens. the objective of the study was to determine the prevalence of campylobacter species in domestic ducks, and the agar dilution method was used to determine resistance of the isolates to eight antibiotics. in addition, multilocus sequence typing (mlst) was performed to determine the sequence ...	2014	25261524
systematic review and meta-analysis of the proportion of campylobacter cases that develop chronic sequelae.	understanding of chronic sequelae development after campylobacter infection is limited. the objective of the study was to determine via systematic review and meta-analysis the proportion of campylobacter cases that develop chronic sequelae.	2014	25416162
first case report of fatal sepsis due to campylobacter upsaliensis.	we encountered a rare case of severe fatal infection in a 70-year-old woman due to campylobacter upsaliensis, identified by pcr amplification and sequencing analysis of the 16s rrna gene using dna extracted from the isolates. to our knowledge, fatal sepsis due to this organism has never been described to date.	2014	25411172
first case report of fatal sepsis due to campylobacter upsaliensis.	we encountered a rare case of severe fatal infection in a 70-year-old woman due to campylobacter upsaliensis, identified by pcr amplification and sequencing analysis of the 16s rrna gene using dna extracted from the isolates. to our knowledge, fatal sepsis due to this organism has never been described to date.	2014	25411172
intraspecies comparison of streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin.	streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. while interspecific genomic diversity has been investigated among streptomyces, information is lacking on intraspecific genomic diversity. streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized.	2014	25399205
comparative genomics of the campylobacter lari group.	the campylobacter lari group is a phylogenetic clade within the epsilon subdivision of the proteobacteria and is part of the thermotolerant campylobacter spp., a division within the genus that includes the human pathogen campylobacter jejuni. the c. lari group is currently composed of five species (c. lari, campylobacter insulaenigrae, campylobacter volucris, campylobacter subantarcticus, and campylobacter peloridis), as well as a group of strains termed the urease-positive thermophilic campylob ...	2014	25381664
phenotypic and genotypic diversity of thermophilic campylobacter spp. in commercial turkey flocks: a longitudinal study.	poultry are recognized as a main reservoir of campylobacter spp. however, longitudinal studies investigating the persistence of campylobacter on commercial meat turkeys are rare. the objectives of this study were to determine the prevalence, antimicrobial susceptibility, and persistence of genotypically related strains of campylobacter spp. recovered from three commercial turkey farms in ohio belonging to a single producer. eight hundred ten samples were collected from birds aged 1 week to slaug ...	2014	25184688
campylobacter colonization and proliferation in the broiler chicken upon natural field challenge is not affected by the bird growth rate or breed.	the zoonotic association between campylobacter bacteria in poultry and humans has been characterized by decades of research which has attempted to elucidate the epidemiology of this complex relationship and to reduce carriage within poultry. while much work has focused on the mechanisms facilitating its success in contaminating chicken flocks (and other animal hosts), it remains difficult to consistently exclude campylobacter under field conditions. within the united kingdom poultry industry, va ...	2014	25172857
prevalence and antimicrobial susceptibility of campylobacter spp. in oklahoma conventional and organic retail poultry.	campylobacter is one of the most important foodborne pathogens that cause bacterial gastroenteritis.this study was conducted to investigate the prevalence and antimicrobial resistance of campylobacter in conventional and organic retail poultry samples purchased from grocery stores in tulsa, oklahoma.one hundred and fifty six chilled retail chicken samples (85 conventional and 71 organic) and 65 chilled retail conventional turkey samples were collected in this study. the prevalence of campylobact ...	2014	25408778
differences in carbon source utilisation distinguish campylobacter jejuni from campylobacter coli.	campylobacter jejuni and c. coli are human intestinal pathogens that are the most frequent causes of bacterial foodborne gastroenteritis in humans in the uk. in this study, we aimed to characterise the metabolic diversity of both c. jejuni and c. coli using a diverse panel of clinical strains isolated from the uk, pakistan and thailand, thereby representing both the developed and developing world. our aim was to apply multi genome analysis and biolog phenotyping to determine differences in carbo ...	2014	25348335
exploring pfge for detecting large plasmids in campylobacter jejuni and campylobacter coli isolated from various retail meats.	campylobacter spp. is one of the most prevalent bacterial pathogens in retail meat, particularly poultry, and is a leading cause of diarrhea in humans. studies related to campylobacter large plasmids are limited in the literature possibly due to difficulty in isolating them using available alkaline lysis methods. the objectives of this study were to determine the prevalence of plasmids, particularly large ones, in campylobacter spp. isolated from various oklahoma retail meats, and to explore pfg ...	2014	25436507
incidence of and factors associated with false positives in laboratory diagnosis of norovirus infection by amplification of the rna-dependent rna polymerase gene.	conventional reverse transcription-polymerase chain reaction (rt-pcr) amplification of the rna-dependent rna polymerase (rdrp) gene remains a used method for the rapid detection of norovirus (nv) in clinical laboratories. the incidence of and factors associated with false positives in this assay have not been previously evaluated.	2014	25264621
emerging rapid resistance testing methods for clinical microbiology laboratories and their potential impact on patient management.	atypical and multidrug resistance, especially esbl and carbapenemase expressing enterobacteriaceae, is globally spreading. therefore, it becomes increasingly difficult to achieve therapeutic success by calculated antibiotic therapy. consequently, rapid antibiotic resistance testing is essential. various molecular and mass spectrometry-based approaches have been introduced in diagnostic microbiology to speed up the providing of reliable resistance data. pcr- and sequencing-based approaches are th ...	2014	25343142
susceptibility to campylobacter infection is associated with the species composition of the human fecal microbiota.	the gut microbiota is essential for human health, but very little is known about how the composition of this ecosystem can influence and respond to bacterial infections. here we address this by prospectively studying the gut microbiota composition before, during, and after natural campylobacter infection in exposed poultry abattoir workers. the gut microbiota composition was analyzed with 16s amplicon sequencing of fecal samples from poultry abattoir workers during the peak season of campylobact ...	2014	25227462
accurate detection of campylobacter spp. antigens by immunochromatography and enzyme immunoassay in routine microbiological laboratory.	campylobacter spp. are fastidious microorganisms, and their detection by culture depends on the freshness of the stool sample and the skills of the laboratory staff. to improve laboratory diagnosis, assays for the detection of specific antigens have been developed. here, we evaluated two assays for the detection of campylobacter spp.-specific antigens, i.e., one immunochromatographic test and one enzyme-linked immunosorbent assay (eia), in 38 frozen campylobacter spp.-positive specimens and pros ...	2014	25215191
genomic evidence for the emergence and evolution of pathogenicity and niche preferences in the genus campylobacter.	the genus campylobacter includes some of the most relevant pathogens for human and animal health; the continuous effort in their characterization has also revealed new species putatively involved in different kind of infections. nowadays, the available genomic data for the genus comprise a wide variety of species with different pathogenic potential and niche preferences. in this work, we contribute to enlarge this available information presenting the first genome for the species campylobacter sp ...	2014	25193310
evolution and comparative genomics of campylobacter jejuni st-677 clonal complex.	campylobacter is the most common bacterial cause of gastroenteritis in the european union with over 200,000 laboratory-confirmed cases reported annually. this is the first study to describe findings related to comparative genomics analyses of the sequence type (st)-677 clonal complex (cc), a campylobacter jejuni lineage associated with bacteremia cases in humans. we performed whole-genome sequencing, using illumina hiseq sequencing technology, on five related st-677 cc isolates from two chicken ...	2014	25193305
identifying etiological agents causing diarrhea in low income ecuadorian communities.	continued success in decreasing diarrheal disease burden requires targeted interventions. to develop such interventions, it is crucial to understand which pathogens cause diarrhea. using a case-control design we tested stool samples, collected in both rural and urban ecuador, for 15 pathogenic microorganisms. pathogens were present in 51% of case and 27% of control samples from the urban community, and 62% of case and 18% of control samples collected from the rural community. rotavirus and shige ...	2014	25048373
same-day subtyping of campylobacter jejuni and c. coli isolates by use of multiplex ligation-dependent probe amplification-binary typing.	campylobacteriosis is the most commonly reported form of human bacterial gastroenteritis in the world. sound identification of infectious sources requires subtyping, but the most widely used methods have turnaround times measured in days and require specialist equipment and skills. a multiplex ligation-dependent probe amplification-binary typing (mbit) assay was developed for subtyping campylobacter jejuni and campylobacter coli. it was tested on 245 isolates, including recent isolates from belg ...	2014	24989612
emergence of multidrug-resistant campylobacter species isolates with a horizontally acquired rrna methylase.	antibiotic-resistant campylobacter constitutes a serious threat to public health, and resistance to macrolides is of particular concern, as this class of antibiotics is the drug of choice for clinical therapy of campylobacteriosis. very recently, a horizontally transferrable macrolide resistance mediated by the rrna methylase gene erm(b) was reported in a campylobacter coli isolate, but little is known about the dissemination of erm(b) among campylobacter isolates and the association of erm(b)-c ...	2014	24982085
occurrence of thermotolerant campylobacter in raw poultry meat, environmental and pigeon stools collected in open-air markets.	campylobacteriosis was the most commonly reported zoonosis for confirmed human cases in european union during 2011. poultry meat was very often implicated in campylobacter infections in humans. in italy commerce of raw poultry meat is common in open-air markets: these areas can be considered at high risk of bacterial contamination due to the high presence birds like pigeons. the aim of this study was to collect data about the contamination by thermotolerant campylobacter of raw poultry meat comm ...	2014	27800355
investigating the host specificity of campylobacter jejuni and campylobacter coli by sequencing gyrase subunit a.	surveillance and field investigations of campylobacter infections require molecular tools with genetic markers appropriate for tracing purposes, i.e. based on the principle that some campylobacter lineages acquire a host signature under adaptive selection pressure. we developed a sequence-based method targeting the quinolone resistance determining region within the subunit a of dna gyrase (gyra). host specificity was evaluated by characterizing two collections of campylobacter jejuni (n = 430) a ...	2014	25163418
a current overview of commercially available nucleic acid diagnostics approaches to detect and identify human gastroenteritis pathogens.	gastroenteritis is caused by a wide range of viral, bacterial and parasitic pathogens and causes millions of deaths worldwide each year, particularly in infant populations in developing countries. traditional microbiological culture and immunological based tests are time consuming, laborious and often lack diagnostic specificity and sensitivity. as a result patients can receive suboptimal and/or inappropriate antimicrobial treatment. in recent years, rapid nucleic acid diagnostics (nad) technolo ...	2014	27920992
campylobacter infection in a cohort of rural children in moramanga, madagascar.	campylobacter infection is the most common cause of bacterial gastroenteritis in developing countries, including madagascar. reports of pathogenicity have not been consistent and repeated exposures over time seem to lead to the development of protective immunity in developing areas. we conducted this study to support evidence for these hypotheses by exploring the association between infection and age, the reoccurrence of infection and the pathogenicity of campylobacter.	2014	24996559
comparison of fecalswab and eswab devices for storage and transportation of diarrheagenic bacteria.	using a collection (n = 12) of atcc and known stock isolates, as well as 328 clinical stool specimens, we evaluated the eswab and the new fecalswab liquid-based microbiology (lbm) devices for storing and transporting diarrheagenic bacteria. the stock isolates were stored in these swab devices up to 48 h at refrigeration (4°c) or room (∼25°c) temperature and up to 3 months at -20°c or -70°c. with the clinical stool specimens, the performances of the eswab and fecalswab were compared to those of r ...	2014	24740083
antimicrobial susceptibility of campylobacter jejuni and campylobacter coli isolates obtained in montreal, quebec, canada, from 2002 to 2013.	from 2002 to 2013 in montreal, quebec, canada, 38 campylobacter coli isolates were more frequently erythromycin, tetracycline, and ciprofloxacin resistant than 440 campylobacter jejuni subsp. jejuni isolates (18.4% versus 1.8%; p = 0.00005), of which the 148 isolates acquired abroad were more frequently erythromycin, tetracycline, and ciprofloxacin resistant than the 292 isolates acquired locally (5.4% versus 0%; p = 0.0001).	2014	24759726
the importance of the viable but non-culturable state in human bacterial pathogens.	many bacterial species have been found to exist in a viable but non-culturable (vbnc) state since its discovery in 1982. vbnc cells are characterized by a loss of culturability on routine agar, which impairs their detection by conventional plate count techniques. this leads to an underestimation of total viable cells in environmental or clinical samples, and thus poses a risk to public health. in this review, we present recent findings on the vbnc state of human bacterial pathogens. the characte ...	2014	24917854
inhibition controls for qualitative real-time pcr assays: are they necessary for all specimen matrices?	a retrospective analysis of 386,706 specimens representing a variety of matrix types used in qualitative real-time pcr assays determined the overall inhibition rate to be 0.87% when the inhibition control was added preextraction to 5,613 specimens and 0.01% when the inhibition control was added postextraction but preamplification in 381,093 specimens. inhibition rates of ≤ 1% were found for all specimen matrix types except urine and formalin-fixed, paraffin-embedded tissue.	2014	24740078
human diarrhea infections associated with domestic animal husbandry: a systematic review and meta-analysis.	domestic animal husbandry, a common practice globally, can lead to zoonotic transmission of enteric pathogens. however, this risk has received little attention to date. this systematic review and meta-analysis examines the evidence for an association between domestic exposure to food-producing animals and cases of human diarrhea and specific enteric infections. we performed a systematic review of available literature to examine domestic livestock and poultry as risk factors for diarrhea and appl ...	2014	24812065
high-throughput sequencing of campylobacter jejuni insertion mutant libraries reveals mapa as a fitness factor for chicken colonization.	campylobacter jejuni is a leading cause of gastrointestinal infections worldwide, due primarily to its ability to asymptomatically colonize the gastrointestinal tracts of agriculturally relevant animals, including chickens. infection often occurs following consumption of meat that was contaminated by c. jejuni during harvest. because of this, much interest lies in understanding the mechanisms that allow c. jejuni to colonize the chicken gastrointestinal tract. to address this, we generated a c. ...	2014	24633877
detection, identification and quantification of campylobacter jejuni, coli and lari in food matrices all at once using multiplex qpcr.	thermotolerant campylobacter jejuni, coli and lari are recognized as leading food-borne pathogens causing an acute bacterial enteritis worldwide. due to narrow spectrum of their biochemical activity, it is very complicated to distinguish between individual species. for reliable risk assessment, proper incidence evaluation or swift sample analysis regarding individual species, a demand for simple and rapid method for their distinguishing is reasonable. in this study, we evaluated a reliable and s ...	2014	25057300
comparison of maldi-tof ms, gene sequencing and the vitek 2 for identification of seventy-three clinical isolates of enteropathogens.	this study was performed to evaluate the analytical and practical performance of the matrix-assisted laser desorption ionization-time of flight mass spectrometry (maldi-tof ms) compared to the sequencing method and the vitek 2 system for identiﬁcation of enteropathogens in the clinical microbiology laboratory.	2014	24822116