| a longitudinal study on thermophilic campylobacter spp. in commercial turkey flocks in northern italy: occurrence and genetic diversity. | poultry are recognized as a main reservoir of thermophilic campylobacters, but few studies have been carried out on commercial meat turkeys. this study was aimed at assessing the occurrence of thermophilic campylobacter spp., their genetic diversity, and the trend of the infection during the whole production cycle of three turkey flocks from different farms in northern italy. flocks were monitored from the time of housing 1-day-old poults to slaughter time by collecting samples (meconium and clo ... | 2012 | 23397840 |
| actinobaculum suis detection using polymerase chain reaction. | actinobaculum suis is an important agent related to urinary infection in swine females. due to its fastidious growth characteristics, the isolation of this anaerobic bacterium is difficult, thus impairing the estimation of its prevalence. the purpose of this study was to develop and test a polymerase chain reaction (pcr) for the detection and identification of a. suis and then compare these results with traditional isolation methods. bacterial isolation and pcr were performed on one hundred and ... | 2012 | 23346017 |
| development of antimicrobial resistance in campylobacter jejuni and campylobacter coli adapted to biocides. | the potential for adaptive resistance of campylobacter jejuni and campylobacter coli after step-wise exposure to increasing sub-inhibitory concentrations of five biocides as triclosan, benzalkonium chloride, cetylpyridinium chloride, chlorhexidine diacetate and trisodium phosphate, was investigated, to identify the mechanisms underlying resistance. the biocide resistance and cross-resistance to the antimicrobials erythromycin and ciprofloxacin, and to sodium dodecyl sulphate, were examined accor ... | 2012 | 23290239 |
| comparative characterization of the virulence gene clusters (lipooligosaccharide [los] and capsular polysaccharide [cps]) for campylobacter coli, campylobacter jejuni subsp. jejuni and related campylobacter species. | campylobacter jejuni subsp. jejuni and campylobacter coli are leading causes of gastroenteritis, with virulence linked to cell surface carbohydrate diversity. although the associated gene clusters are well studied for c. jejuni subsp. jejuni, c. coli has been largely neglected. here we provide comparative analysis of the lipooligosaccharide (los) and capsular polysaccharide (cps) gene clusters, using genome and cluster sequence data for 36 c. coli strains, 67 c. jejuni subsp. jejuni strains and ... | 2012 | 23279811 |
| comparative characterization of the virulence gene clusters (lipooligosaccharide [los] and capsular polysaccharide [cps]) for campylobacter coli, campylobacter jejuni subsp. jejuni and related campylobacter species. | campylobacter jejuni subsp. jejuni and campylobacter coli are leading causes of gastroenteritis, with virulence linked to cell surface carbohydrate diversity. although the associated gene clusters are well studied for c. jejuni subsp. jejuni, c. coli has been largely neglected. here we provide comparative analysis of the lipooligosaccharide (los) and capsular polysaccharide (cps) gene clusters, using genome and cluster sequence data for 36 c. coli strains, 67 c. jejuni subsp. jejuni strains and ... | 2012 | 23279811 |
| identification and characterization of a periplasmic trilactone esterase, cee, revealed unique features of ferric enterobactin acquisition in campylobacter. | ferric enterobactin (feent) acquisition is a highly efficient and conserved iron scavenging system in gram-negative bacteria. recently, we have characterized two feent receptors (cfra and cfrb) in campylobacter jejuni and c. coli, the enteric human pathogens that do not produce any siderophores. in this study, whole-genome sequencing and comparative genomic analysis identified a unique ent trilactone esterase cee (cj1376) in c. jejuni. genomic analysis and biochemical assay strongly suggested th ... | 2012 | 23278903 |
| identification and characterization of a periplasmic trilactone esterase, cee, revealed unique features of ferric enterobactin acquisition in campylobacter. | ferric enterobactin (feent) acquisition is a highly efficient and conserved iron scavenging system in gram-negative bacteria. recently, we have characterized two feent receptors (cfra and cfrb) in campylobacter jejuni and c. coli, the enteric human pathogens that do not produce any siderophores. in this study, whole-genome sequencing and comparative genomic analysis identified a unique ent trilactone esterase cee (cj1376) in c. jejuni. genomic analysis and biochemical assay strongly suggested th ... | 2012 | 23278903 |
| mutational and transcriptomic changes involved in the development of macrolide resistance in campylobacter jejuni. | macrolide antibiotics are important for clinical treatment of infections caused by campylobacter jejuni. development of resistance to this class of antibiotics in campylobacter is a complex process, and the dynamic molecular changes involved in this process remain poorly defined. multiple lineages of macrolide-resistant mutants were selected by stepwise exposure of c. jejuni to escalating doses of erythromycin or tylosin. mutations in target genes were determined by dna sequencing, and the dynam ... | 2012 | 23274667 |
| evaluation of the immunogenicity of campylobacter jejuni cjaa protein delivered by salmonella enterica sv. typhimurium strain with regulated delayed attenuation in chickens. | campylobacter spp. are regarded as the most common bacterial cause of gastroenteritis worldwide, and consumption of chicken meat contaminated by campylobacter is considered to be one of the most frequent sources of human infection in developed countries. here we evaluated the immunogenicity and protective efficacy of salmonella typhimurium χ9718 producing the campylobacter jejuni cjaa protein as a chicken anti-campylobacter vaccine. in this study chickens were orally immunized with a new generat ... | 2013 | 23913025 |
| abc transporters involved in export of cell surface glycoconjugates. | complex glycoconjugates play critical roles in the biology of microorganisms. despite the remarkable diversity in glycan structures and the bacteria that produce them, conserved themes are evident in the biosynthesis-export pathways. one of the primary pathways involves representatives of the atp-binding cassette (abc) transporter superfamily. these proteins are responsible for the export of a wide variety of cell surface oligo- and polysaccharides in both gram-positive and gram-negative bacteri ... | 2010 | 20805402 |
| the zinc-ribbon domain of helicobacter pylori hp0958: requirement for rpon accumulation and possible roles of homologs in other bacteria. | helicobacter pylori hp0958 protein (flgz) prevents the rapid turnover of rpon (σ(54)), a transcription factor required for expression of several flagellar genes in h. pylori. flgz possesses a zinc-ribbon domain (duf164) that contains two conserved cxxc motifs which coordinate a zinc ion and is thought to interact with nucleic acids or proteins. two conserved cysteine residues in flgz (cys-202 and cys-223) were replaced with serine to assess their significance in flgz function. after confirming t ... | 2011 | 22408721 |
| welcome to microbial informatics and experimentation. | | 2011 | 22587655 |
| the molecular evolution of the qo motif. | quinol oxidation in the catalytic quinol oxidation site (q(o) site) of cytochrome (cyt) bc(1) complexes is the key step of the q cycle mechanism, which laid the ground for mitchell's chemiosmotic theory of energy conversion. bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels atp synthesis in cellular respiration and photosynthesis. the q(o) site architecture formed by cyt b and rieske iron- ... | 2014 | 25115012 |
| macrolide resistance conferred by base substitutions in 23s rrna. | | 2001 | 11120937 |
| traditional and molecular techniques for the study of emerging bacterial diseases: one laboratory's perspective. | identification of emerging bacterial pathogens generally results from a chain of events involving microscopy, serology, molecular tools, and culture. because of the spectacular molecular techniques developed in the last decades, some authors think that these techniques will shortly supplant culture. the key steps that led to the discovery of emerging bacteria have been reviewed to determine the real contribution of each technique. historically, microscopy has played a major role. serology provid ... | 2002 | 11897062 |
| phase and antigenic variation in bacteria. | phase and antigenic variation result in a heterogenic phenotype of a clonal bacterial population, in which individual cells either express the phase-variable protein(s) or not, or express one of multiple antigenic forms of the protein, respectively. this form of regulation has been identified mainly, but by no means exclusively, for a wide variety of surface structures in animal pathogens and is implicated as a virulence strategy. this review provides an overview of the many bacterial proteins a ... | 2004 | 15258095 |
| reproductive clonality of pathogens: a perspective on pathogenic viruses, bacteria, fungi, and parasitic protozoa. | we propose that clonal evolution in micropathogens be defined as restrained recombination on an evolutionary scale, with genetic exchange scarce enough to not break the prevalent pattern of clonal population structure, a definition already widely used for all kinds of pathogens, although not clearly formulated by many scientists and rejected by others. the two main manifestations of clonal evolution are strong linkage disequilibrium (ld) and widespread genetic clustering ("near-clading"). we hyp ... | 2012 | 22949662 |
| thermal control of virulence factors in bacteria: a hot topic. | pathogenic bacteria sense environmental cues, including the local temperature, to control the production of key virulence factors. thermal regulation can be achieved at the level of dna, rna or protein and although many virulence factors are subject to thermal regulation, the exact mechanisms of control are yet to be elucidated in many instances. understanding how virulence factors are regulated by temperature presents a significant challenge, as gene expression and protein production are often ... | 2014 | 25494856 |
| the sweet tooth of bacteria: common themes in bacterial glycoconjugates. | humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. however, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. glycoconjugates are an interesting class of molecules fo ... | 2014 | 25184559 |
| a quantitative prioritisation of human and domestic animal pathogens in europe. | disease or pathogen risk prioritisations aid understanding of infectious agent impact within surveillance or mitigation and biosecurity work, but take significant development. previous work has shown the h-(hirsch-)index as an alternative proxy. we present a weighted risk analysis describing infectious pathogen impact for human health (human pathogens) and well-being (domestic animal pathogens) using an objective, evidence-based, repeatable approach; the h-index. this study established the highe ... | 2014 | 25136810 |
| the challenge of efflux-mediated antibiotic resistance in gram-negative bacteria. | the global emergence of multidrug-resistant gram-negative bacteria is a growing threat to antibiotic therapy. the chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. multidrug pumps, particularly those represented by the clinically relevant acrab-tolc and mex pumps of the resistance-nodulation-division (rnd) superfamily, not only mediate intrinsic and acquired mult ... | 2015 | 25788514 |
| evaluation of a protective effect of in ovo delivered campylobacter jejuni omvs. | campylobacter jejuni is the most prevalent cause of a food-borne gastroenteritis in the developed world, with poultry being the main source of infection. campylobacter jejuni, like other gram-negative bacteria, constitutively releases outer membrane vesicles (omvs). omvs are highly immunogenic, can be taken up by mammalian cells, and are easily modifiable by recombinant engineering. we have tested their usefulness for an oral (in ovo) vaccination of chickens. four groups of 18-day-old chicken em ... | 2016 | 27383607 |
| what makes a bacterial species pathogenic?:comparative genomic analysis of the genus leptospira. | leptospirosis, caused by spirochetes of the genus leptospira, is a globally widespread, neglected and emerging zoonotic disease. while whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. in ... | 2016 | 26890609 |
| 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 |
| differential distribution of type ii crispr-cas systems in agricultural and nonagricultural campylobacter coli and campylobacter jejuni isolates correlates with lack of shared environments. | crispr (clustered regularly interspaced palindromic repeats)-cas (crispr-associated) systems are sequence-specific adaptive defenses against phages and plasmids which are widespread in prokaryotes. here we have studied whether phylogenetic relatedness or sharing of environmental niches affects the distribution and dissemination of type ii crispr-cas systems, first in 132 bacterial genomes from 15 phylogenetic classes, ranging from proteobacteria to actinobacteria. there was clustering of distinc ... | 2015 | 26338188 |
| accuracy of commercial kits and published primer pairs for the detection of periodontopathogens. | despite the input of microbiome research, a group of 20 bacteria continues to be the focus of periodontal diagnostics and therapy. the aim of this study was to compare three commercial kits and laboratory-developed primer pairs for effectiveness in detecting such periodontopathogens. | 2016 | 27020914 |
| 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 |
| multiplex pcr: optimization and application in diagnostic virology. | pcr has revolutionized the field of infectious disease diagnosis. to overcome the inherent disadvantage of cost and to improve the diagnostic capacity of the test, multiplex pcr, a variant of the test in which more than one target sequence is amplified using more than one pair of primers, has been developed. multiplex pcrs to detect viral, bacterial, and/or other infectious agents in one reaction tube have been described. early studies highlighted the obstacles that can jeopardize the production ... | 2000 | 11023957 |
| the era of molecular and other non-culture-based methods in diagnosis of sepsis. | sepsis, a leading cause of morbidity and mortality throughout the world, is a clinical syndrome with signs and symptoms relating to an infectious event and the consequent important inflammatory response. from a clinical point of view, sepsis is a continuous process ranging from systemic inflammatory response syndrome (sirs) to multiple-organ-dysfunction syndrome (mods). blood cultures are the current "gold standard" for diagnosis, and they are based on the detection of viable microorganisms pres ... | 2010 | 20065332 |
| multidrug-resistant campylobacter coli in men who have sex with men, quebec, canada, 2015. | | 2016 | 27533504 |
| the flik protein and flagellar hook-length control. | the bacterial flagellum is a highly complex prokaryotic organelle. it is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two-component systems. part of the flagellum is a type iii secretion system, and it is via this structure that flagellar components are exported. the assem ... | 2007 | 17456739 |
| detection of zoonotic pathogens and characterization of novel viruses carried by commensal rattus norvegicus in new york city. | norway rats (rattus norvegicus) are globally distributed and concentrate in urban environments, where they live and feed in closer proximity to human populations than most other mammals. despite the potential role of rats as reservoirs of zoonotic diseases, the microbial diversity present in urban rat populations remains unexplored. in this study, we used targeted molecular assays to detect known bacterial, viral, and protozoan human pathogens and unbiased high-throughput sequencing to identify ... | 2014 | 25316698 |
| detection of mycobacteria, mycobacterium avium subspecies, and mycobacterium tuberculosis complex by a novel tetraplex real-time pcr assay. | mycobacterium tuberculosis complex, mycobacterium avium, and many other nontuberculous mycobacteria are worldwide distributed microorganisms of major medical and veterinary importance. considering the growing epidemiologic significance of wildlife-livestock-human interrelation, developing rapid detection tools of high specificity and sensitivity is vital to assess their presence and accelerate the process of diagnosing mycobacteriosis. here we describe the development and evaluation of a novel t ... | 2015 | 25588660 |
| functional metagenomics of spacecraft assembly cleanrooms: presence of virulence factors associated with human pathogens. | strict planetary protection practices are implemented during spacecraft assembly to prevent inadvertent transfer of earth microorganisms to other planetary bodies. therefore, spacecraft are assembled in cleanrooms, which undergo strict cleaning and decontamination procedures to reduce total microbial bioburden. we wanted to evaluate if these practices selectively favor survival and growth of hardy microorganisms, such as pathogens. three geographically distinct cleanrooms were sampled during the ... | 2016 | 27667984 |
| the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains. | ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ... | 2006 | 16859499 |
| gram-negative flagella glycosylation. | protein glycosylation had been considered as an eccentricity of a few bacteria. however, through advances in analytical methods and genome sequencing, it is now established that bacteria possess both n-linked and o-linked glycosylation pathways. both glycosylation pathways can modify multiple proteins, flagellins from archaea and eubacteria being one of these. flagella o-glycosylation has been demonstrated in many polar flagellins from gram-negative bacteria and in only the gram-positive genera ... | 2014 | 24557579 |
| the polar and lateral flagella from plesiomonas shigelloides are glycosylated with legionaminic acid. | plesiomonas shigelloides is the unique member of the enterobacteriaceae family able to produce polar flagella when grow in liquid medium and lateral flagella when grown in solid or semisolid media. in this study on p. shigelloides 302-73 strain, we found two different gene clusters, one exclusively for the lateral flagella biosynthesis and the other one containing the biosynthetic polar flagella genes with additional putative glycosylation genes. p. shigelloides is the first enterobacteriaceae w ... | 2015 | 26167161 |
| bacterial flagella: twist and stick, or dodge across the kingdoms. | the flagellum organelle is an intricate multiprotein assembly best known for its rotational propulsion of bacteria. however, recent studies have expanded our knowledge of other functions in pathogenic contexts, particularly adherence and immune modulation, e.g., for salmonella enterica, campylobacter jejuni, pseudomonas aeruginosa, and escherichia coli. flagella-mediated adherence is important in host colonisation for several plant and animal pathogens, but the specific interactions that promote ... | 2015 | 25590430 |
| short-sequence dna repeats in prokaryotic genomes. | short-sequence dna repeat (ssr) loci can be identified in all eukaryotic and many prokaryotic genomes. these loci harbor short or long stretches of repeated nucleotide sequence motifs. dna sequence motifs in a single locus can be identical and/or heterogeneous. ssrs are encountered in many different branches of the prokaryote kingdom. they are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors ... | 1998 | 9618442 |
| amplified-fragment length polymorphism analysis: the state of an art. | | 1999 | 10488158 |
| nomenclature for new tetracycline resistance determinants. | letters of the english alphabet have heretofore been used to name tetracycline resistance determinants. since all 26 letters have now been used, a nomenclature employing numerals is recommended for future determinants, and one laboratory has offered to coordinate the assignment of numerals. | 1999 | 10348788 |
| rapid detection of the chlamydiaceae and other families in the order chlamydiales: three pcr tests. | few identification methods will rapidly or specifically detect all bacteria in the order chlamydiales, family chlamydiaceae. in this study, three pcr tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. two tests exclusively recognized the chlamydiaceae: a multiplex test targeting the ompa gene and the rrna intergenic spacer and a taqman test targeting the 23s ribosomal dna. the multiplex test was able to detect as few as 200 inclusion ... | 1999 | 9986815 |
| antiseptics and disinfectants: activity, action, and resistance. | antiseptics and disinfectants are extensively used in hospitals and other health care settings for a variety of topical and hard-surface applications. a wide variety of active chemical agents (biocides) are found in these products, many of which have been used for hundreds of years, including alcohols, phenols, iodine, and chlorine. most of these active agents demonstrate broad-spectrum antimicrobial activity; however, little is known about the mode of action of these agents in comparison to ant ... | 1999 | 9880479 |
| web-based phylogenetic assignment tool for analysis of terminal restriction fragment length polymorphism profiles of microbial communities. | culture-independent dna fingerprints are commonly used to assess the diversity of a microbial community. however, relating species composition to community profiles produced by community fingerprint methods is not straightforward. terminal restriction fragment length polymorphism (t-rflp) is a community fingerprint method in which phylogenetic assignments may be inferred from the terminal restriction fragment (t-rf) sizes through the use of web-based resources that predict t-rf sizes for known b ... | 2003 | 14602639 |
| versatility of aminoglycosides and prospects for their future. | aminoglycoside antibiotics have had a major impact on our ability to treat bacterial infections for the past half century. whereas the interest in these versatile antibiotics continues to be high, their clinical utility has been compromised by widespread instances of resistance. the multitude of mechanisms of resistance is disconcerting but also illuminates how nature can manifest resistance when bacteria are confronted by antibiotics. this article reviews the most recent knowledge about the mec ... | 2003 | 12857776 |
| assessing sensitivity to antibacterial topoisomerase ii inhibitors. | both prokaryotes and eukaryotes have two major classes of topoisomerases that make transient single- or double-strand cuts in dna. while these enzymes play critical roles in cellular processes, they are also important targets of therapeutic agents. this unit describes assays to use in characterizing topoisomerase ii-targeting agents in vitro and in bacterial cells. it provides protocols for characterizing the action of small molecules against bacterial type ii topoisomerases in vitro and the in ... | 2007 | 21948169 |
| case-case analysis of enteric diseases with routine surveillance data: potential use and example results. | case-control studies and outbreak investigations are the major epidemiological tools for providing detailed information on enteric disease sources and risk factors, but these investigations can be constrained by cost and logistics. | 2008 | 18976484 |
| dna mimics for the rapid identification of microorganisms by fluorescence in situ hybridization (fish). | fluorescence in situ hybridization (fish) is a well-established technique that is used for a variety of purposes, ranging from pathogen detection in clinical diagnostics to the determination of chromosomal stability in stem cell research. the key step of fish involves the detection of a nucleic acid region and as such, dna molecules have typically been used to probe for the sequences of interest. however, since the turn of the century, an increasing number of laboratories have started to move on ... | 2008 | 19325728 |
| multiplex pcr to diagnose bloodstream infections in patients admitted from the emergency department with sepsis. | sepsis is caused by a heterogeneous group of infectious etiologies. early diagnosis and the provision of appropriate antimicrobial therapy correlate with positive clinical outcomes. current microbiological techniques are limited in their diagnostic capacities and timeliness. multiplex pcr has the potential to rapidly identify bloodstream infections and fill this diagnostic gap. we identified patients from two large academic hospital emergency departments with suspected sepsis. the results of a m ... | 2009 | 19846634 |
| multiplex pcr to diagnose bloodstream infections in patients admitted from the emergency department with sepsis. | sepsis is caused by a heterogeneous group of infectious etiologies. early diagnosis and the provision of appropriate antimicrobial therapy correlate with positive clinical outcomes. current microbiological techniques are limited in their diagnostic capacities and timeliness. multiplex pcr has the potential to rapidly identify bloodstream infections and fill this diagnostic gap. we identified patients from two large academic hospital emergency departments with suspected sepsis. the results of a m ... | 2009 | 19846634 |
| occurrence of campylobacter jejuni and campylobacter coli and their biotypes in beef and dairy cattle from the south of chile. | the prevalence of campylobacter jejuni and campylobacter coli and their biotypes in beef and dairy cattle from the south of chile was established. campylobacter were statistically more prevalent among beef cattle (35.9%) than among dairy cattle (21.3%), being c. jejuni the species most frequently isolated. | 2009 | 24031386 |
| rapid identification of bacterial pathogens using a pcr- and microarray-based assay. | during the course of a bacterial infection, the rapid identification of the causative agent(s) is necessary for the determination of effective treatment options. we have developed a method based on a modified broad-range pcr and an oligonucleotide microarray for the simultaneous detection and identification of 12 bacterial pathogens at the species level. the broad-range pcr primer mixture was designed using conserved regions of the bacterial topoisomerase genes gyrb and pare. the primer design a ... | 2009 | 19664269 |
| comprehensive and rapid real-time pcr analysis of 21 foodborne outbreaks. | a set of four duplex sybr green i pcr (sg-pcr) assay combined with dna extraction using qiaamp dna stool mini kit was evaluated for the detection of foodborne bacteria from 21 foodborne outbreaks. the causative pathogens were detected in almost all cases in 2 hours or less. the first run was for the detection of 8 main foodborne pathogens in 5 stool specimens within 2 hours and the second run was for the detection of other unusual suspect pathogens within a further 45 minutes. after 2 to 4 days, ... | 2009 | 20016673 |
| drug efflux pump deficiency and drug target resistance masking in growing bacteria. | recent experiments have shown that drug efflux pump deficiency not only increases the susceptibility of pathogens to antibiotics, but also seems to "mask" the effects of mutations, that decrease the affinities of drugs to their intracellular targets, on the growth rates of drug-exposed bacteria. that is, in the presence of drugs, the growth rates of drug-exposed wt and target mutated strains are the same in a drug efflux pump deficient background, but the mutants grow faster than wt in a drug ef ... | 2009 | 19416855 |
| risk assessment of growth hormones and antimicrobial residues in meat. | growth promoters including hormonal substances and antibiotics are used legally and illegally in food producing animals for the growth promotion of livestock animals. hormonal substances still under debate in terms of their human health impacts are estradiol-17β, progesterone, testosterone, zeranol, trenbolone, and melengestrol acetate (mga) . many of the risk assessment results of natural steroid hormones have presented negligible impacts when they are used under good veterinary practices. for ... | 2010 | 24278538 |
| molecular characterization of the 16s rrna gene of helicobacter fennelliae isolated from stools and blood cultures from paediatric patients in south africa. | forty strains of h. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in cape town, south africa, were amplified by pcr of the 16s rrna. two distinct genotypes of h. fennelliae were identified based on the phylogenetic analysis. this was confirmed by sequencing a portion of the beta subunit of the rna polymerase (rpob) gene. all isolates from south africa clustered with a proposed novel helicobacter strain (accession number af237612) iso ... | 2010 | 22567323 |
| molecular characterization of the 16s rrna gene of helicobacter fennelliae isolated from stools and blood cultures from paediatric patients in south africa. | forty strains of h. fennelliae collected from paediatric blood and stool samples over an 18 year period at a children's hospital in cape town, south africa, were amplified by pcr of the 16s rrna. two distinct genotypes of h. fennelliae were identified based on the phylogenetic analysis. this was confirmed by sequencing a portion of the beta subunit of the rna polymerase (rpob) gene. all isolates from south africa clustered with a proposed novel helicobacter strain (accession number af237612) iso ... | 2010 | 22567323 |
| tir domain-containing adaptor sarm is a late addition to the ongoing microbe-host dialog. | toll/interleukin-1 receptor (tir) domain-containing proteins play important roles in defense against pathogens in both animals and plants, connecting the immunity signaling pathways via a chain of specific protein-protein interactions. among them is sarm, the only tir domain-containing adaptor that can negatively regulate tlr signaling. by extensive phylogenetic analysis, we show here that sarm is closely related to bacterial proteins with tir domains, suggesting that this family has a different ... | 2010 | 21110998 |
| tir domain-containing adaptor sarm is a late addition to the ongoing microbe-host dialog. | toll/interleukin-1 receptor (tir) domain-containing proteins play important roles in defense against pathogens in both animals and plants, connecting the immunity signaling pathways via a chain of specific protein-protein interactions. among them is sarm, the only tir domain-containing adaptor that can negatively regulate tlr signaling. by extensive phylogenetic analysis, we show here that sarm is closely related to bacterial proteins with tir domains, suggesting that this family has a different ... | 2010 | 21110998 |
| flagellin as an adjuvant: cellular mechanisms and potential. | flagellin is a potent activator of a broad range of cell types involved in innate and adaptive immunity. an increasing number of studies have demonstrated the effectiveness of flagellin as an adjuvant, as well as its ability to promote cytokine production by a range of innate cell types, trigger a generalized recruitment of t and b lymphocytes to secondary lymphoid sites, and activate tlr5(+)cd11c(+) cells and t lymphocytes in a manner that is distinct from cognate ag recognition. the plasticity ... | 2010 | 21048152 |
| successful treatment of cryptosporidiosis in 2 common marmosets (callithrix jacchus) by using paromomycin. | two pair-housed, 1-y-old common marmosets (callithrix jacchus) had intermittent loose feces and weight loss for approximately 2 mo. cryptosporidum parvum was identified by elisa in the feces of both animals. cbc and blood chemistry values, including liver enzymes, were within normal range. both marmosets were treated with the antibiotic paromomycin (15 mg/kg po) twice daily for 28 d. resolution of clinical signs coincided with treatment. three follow-up samples, taken 2 wk apart after treatment ... | 2010 | 21205457 |
| simultaneous screening of 24 target genes of foodborne pathogens in 35 foodborne outbreaks using multiplex real-time sybr green pcr analysis. | a set of 8 multiplex real-time sybr green pcr (sg-pcr) assays including 3 target primers and an internal amplification control (iac) primer was simultaneously evaluated in 3 h or less with regard to detection of 24 target genes of 23 foodborne pathogens in 7 stool specimens of foodborne outbreak using a 96-well reaction plate. this assay, combined with dna extraction (qiaamp dna stool mini kit), offered detection of greater than 10(3)-10(4) foodborne pathogens per g in stool specimens. the produ ... | 2010 | 20936159 |
| solexaqa: at-a-glance quality assessment of illumina second-generation sequencing data. | illumina's second-generation sequencing platform is playing an increasingly prominent role in modern dna and rna sequencing efforts. however, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data. | 2010 | 20875133 |
| microbial diagnostic microarray for food- and water-borne pathogens. | a microbial diagnostic microarray for the detection of the most relevant bacterial food- and water-borne pathogens and indicator organisms was developed and thoroughly validated. the microarray platform based on sequence-specific end labelling of oligonucleotides and the pyhylogenetically robust gyrb marker gene allowed a highly specific (resolution on genus/species level) and sensitive (0.1% relative and 10(4) cfu absolute detection sensitivity) detection of the target pathogens. validation was ... | 2010 | 21255342 |
| methods for determining disease burden and calibrating national surveillance data in the united kingdom: the second study of infectious intestinal disease in the community (iid2 study). | infectious intestinal disease (iid), usually presenting as diarrhoea and vomiting, is frequently preventable. though often mild and self-limiting, its commonness makes iid an important public health problem. in the mid 1990s around 1 in 5 people in england suffered from iid a year, costing around pound0.75 billion. no routine information source describes the uk's current community burden of iid. we present here the methods for a study to determine rates and aetiology of iid in the community, pre ... | 2010 | 20444246 |
| human isolates of cronobacter sakazakii bind efficiently to intestinal epithelial cells in vitro to induce monolayer permeability and apoptosis. | cronobacter sakazakii (cs) is an emerging opportunistic pathogen that causes life-threatening infections in infants. this pathogen has been implicated in the outbreaks of necrotizing enterocolitis (nec) with associated rates of high mortality and morbidity. in this study, we compared the abilities of cs strains isolated from human and environmental sources to bind to intestinal epithelial cells and trigger apoptosis. | 2011 | 22221600 |
| human isolates of cronobacter sakazakii bind efficiently to intestinal epithelial cells in vitro to induce monolayer permeability and apoptosis. | cronobacter sakazakii (cs) is an emerging opportunistic pathogen that causes life-threatening infections in infants. this pathogen has been implicated in the outbreaks of necrotizing enterocolitis (nec) with associated rates of high mortality and morbidity. in this study, we compared the abilities of cs strains isolated from human and environmental sources to bind to intestinal epithelial cells and trigger apoptosis. | 2011 | 22221600 |
| identification of genes involved in the glycosylation of modified viosamine of flagellins in pseudomonas syringae by mass spectrometry. | previously we revealed that flagellin proteins in pseudomonas syringae pv. tabaci 6605 (pta 6605) were glycosylated with a trisaccharide, modified viosamine (mvio)-rhamnose-rhamnose and that glycosylation was required for virulence. we further identified some glycosylation-related genes, including vioa, viob, viot, fgt1, and fgt2. in this study, we newly identified vior and viom in a so-called viosamine island as biosynthetic genes for glycosylation of mvio in pta 6605 by the mass spectrometry ( ... | 2011 | 24710292 |
| defining the causes of diarrhea: novel approaches. | diarrheal disease causes substantial morbidity and mortality worldwide; however, defining the microbiologic causes are challenging due to the large number of potential enteropathogens that require testing, insensitivity of existing conventional methods, the frequent occurrence of mixed infections, and high rates of background carriage in many communities. | 2011 | 21844805 |
| inadequacies of minimum spanning trees in molecular epidemiology. | minimum spanning trees (msts) are frequently used in molecular epidemiology research to estimate relationships among individual strains or isolates. nevertheless, there are significant caveats to mst algorithms that have been largely ignored in molecular epidemiology studies and that have the potential to confound or alter the interpretation of the results of those analyses. specifically, (i) presenting a single, arbitrarily selected mst illustrates only one of potentially many equally optimal s ... | 2011 | 21849692 |
| cytolethal distending toxin: a conserved bacterial genotoxin that blocks cell cycle progression, leading to apoptosis of a broad range of mammalian cell lineages. | cytolethal distending toxin (cdt) is a heterotrimeric ab-type genotoxin produced by several clinically important gram-negative mucocutaneous bacterial pathogens. irrespective of the bacterial species of origin, cdt causes characteristic and irreversible cell cycle arrest and apoptosis in a broad range of cultured mammalian cell lineages. the active subunit cdtb has structural homology with the phosphodiesterase family of enzymes including mammalian dnase i, and alone is necessary and sufficient ... | 2011 | 21565933 |
| a comparison between hippurate hydrolysis and multiplex pcr for differentiating campylobacter coli and campylobacter jejuni. | species identification is important for epidemiological, clinical and treatment purposes. the aim of this study was to find out whether hippurate hydrolysis is a reliable test for differentiating between campylobacter coli and campylobacter jejuni. to achieve this, hippurate hydrolysis test was compared with multiplex polymerase chain reaction (mpcr) for their ability to speciate c. coli and c. jejuni. eighteen campylobacter strains from poultry samples were used for this study. the results from ... | 2011 | 24575212 |
| evolution of the oligopeptide transporter family. | the oligopeptide transporter (opt) family of peptide and iron-siderophore transporters includes members from both prokaryotes and eukaryotes but with restricted distribution in the latter domain. eukaryotic members were found only in fungi and plants with a single slime mold homologue clustering with the fungal proteins. all functionally characterized eukaryotic peptide transporters segregate from the known iron-siderophore transporters on a phylogenetic tree. prokaryotic members are widespread, ... | 2011 | 21347612 |
| microbial efflux pump inhibition: tactics and strategies. | traditional antimicrobials are increasingly suffering from the emergence of multidrug resistance among pathogenic microorganisms. to overcome these deficiencies, a range of novel approaches to control microbial infections are under investigation as potential alternative treatments. multidrug efflux is a key target of these efforts. efflux mechanisms are broadly recognized as major components of resistance to many classes of chemotherapeutic agents as well as antimicrobials. efflux occurs due to ... | 2011 | 21470111 |
| 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 |
| live virus-free or die: coupling of antivirus immunity and programmed suicide or dormancy in prokaryotes. | the virus-host arms race is a major theater for evolutionary innovation. archaea and bacteria have evolved diverse, elaborate antivirus defense systems that function on two general principles: i) immune systems that discriminate self dna from nonself dna and specifically destroy the foreign, in particular viral, genomes, whereas the host genome is protected, or ii) programmed cell suicide or dormancy induced by infection. | 2012 | 23151069 |
| immunogenomics for identification of disease resistance genes in pigs: a review focusing on gram-negative bacilli. | over the past years, infectious disease has caused enormous economic loss in pig industry. among the pathogens, gram negative bacteria not only cause inflammation, but also cause different diseases and make the pigs more susceptible to virus infection. vaccination, medication and elimination of sick pigs are major strategies of controlling disease. genetic methods, such as selection of disease resistance in the pig, have not been widely used. recently, the completion of the porcine whole genome ... | 2012 | 23137309 |
| 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 |
| regulation of energy metabolism by the extracytoplasmic function (ecf) σ factors of arcobacter butzleri. | the extracytoplasmic function (ecf) σ factors are fundamental for bacterial adaptation to distinct environments and for survival under different stress conditions. the emerging pathogen arcobacter butzleri possesses seven putative pairs of σ/anti-σ factors belonging to the ecf family. here, we report the identification of the genes regulated by five out of the seven a. butzleri ecf σ factors. three of the ecf σ factors play an apparent role in transport, energy generation and the maintenance of ... | 2012 | 23028624 |
| 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 |
| phylogenetic analysis reveals common antimicrobial resistant campylobacter coli population in antimicrobial-free (abf) and commercial swine systems. | the objective of this study was to compare the population biology of antimicrobial resistant (ar) campylobacter coli isolated from swine reared in the conventional and antimicrobial-free (abf) swine production systems at farm, slaughter and environment. a total of 200 c. coli isolates selected from fecal, environmental, and carcass samples of abf (n = 100) and conventional (n = 100) swine production systems were typed by multilocus sequence typing (mlst). sequence data from seven housekeeping ge ... | 2012 | 22984540 |
| 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 |
| detection of kudoa septempunctata 18s ribosomal dna in patient fecal samples from novel food-borne outbreaks caused by consumption of raw olive flounder (paralichthys olivaceus). | kudoa septempunctata is a newly identified myxosporean parasite of olive flounder (paralichthys olivaceus) and a suspected causative agent of several food-borne gastroenteritis outbreaks in japan. here, we report the detection of k. septempunctata 18s ribosomal dna in fecal samples of outbreak patients using an efficient method based on real-time pcr. we first performed a spiking experiment to assess whether our previously developed real-time pcr assay was applicable to detect k. septempunctata ... | 2012 | 22760033 |
| analysis of helicobacter pylori caga promoter elements required for salt-induced upregulation of caga expression. | helicobacter pylori infection and consumption of a high-salt diet are each associated with an increased risk for the development of gastric cancer. to investigate potential synergism between these factors, we used a global proteomic approach to analyze h. pylori strains cultured in media containing varying salt concentrations. among the differentially expressed proteins identified, caga exhibited the greatest increase in expression in response to high salt concentrations. analysis of 36 h. pylor ... | 2012 | 22710874 |
| 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 |