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ochre bathing of the bearded vulture: a bio-mimetic model for early humans towards smell prevention and health.since primordial times, vultures have been competing with man for animal carcasses. one of these vultures, the once widespread bearded vulture ( gypaetus barbatus ), has the habit of bathing its polluted feathers and skin in red iron oxide - ochre - tainted water puddles. why? primitive man may have tried to find out and may have discovered its advantages. red ochre, which has accompanied human rituals and everyday life for more than 100,000 years, is not just a simple red paint for decoration o ...201626784238
comparative genomic analysis of the flagellin glycosylation island of the gram-positive thermophile geobacillus.protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many gram-negative bacteria and archaea. several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, ...201627842516
recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview.waterborne diseases have emerged as global health problems and their rapid and sensitive detection in environmental water samples is of great importance. bacterial identification and enumeration in water samples is significant as it helps to maintain safe drinking water for public consumption. culture-based methods are laborious, time-consuming, and yield false-positive results, whereas viable but nonculturable (vbncs) microorganisms cannot be recovered. hence, numerous methods have been develop ...201627397728
contig-layout-authenticator (cla): a combinatorial approach to ordering and scaffolding of bacterial contigs for comparative genomics and molecular epidemiology.a wide variety of genome sequencing platforms have emerged in the recent past. high-throughput platforms like illumina and 454 are essentially adaptations of the shotgun approach generating millions of fragmented single or paired sequencing reads. to reconstruct whole genomes, the reads have to be assembled into contigs, which often require further downstream processing. the contigs can be directly ordered according to a reference, scaffolded based on paired read information, or assembled using ...201627248146
bacteriophage-based tools: recent advances and novel applications.bacteriophages (phages) are viruses that infect bacterial hosts, and since their discovery over a century ago they have been primarily exploited to control bacterial populations and to serve as tools in molecular biology. in this commentary, we highlight recent diverse advances in the field of phage research, going beyond bacterial control using whole phage, to areas including biocontrol using phage-derived enzybiotics, diagnostics, drug discovery, novel drug delivery systems and bionanotechnolo ...201627990274
bibliometric analysis of publications on campylobacter: (2000-2015).campylobacter species are widespread zoonotic pathogens. campylobacter jejuni causes a form of gastroenteritis called campylobacteriosis. campylobacter drug resistance is considered a serious threat. in order to better understand national and international research output on campylobacter, we conducted this bibliometric overview of publications on campylobacter. this study can be used to assess extent of interaction and response of researchers, food regulators, and health policy makers to global ...201627899145
exploiting bacterial whole-genome sequencing data for evaluation of diagnostic assays: campylobacter species identification as a case study.the application of whole-genome sequencing (wgs) to problems in clinical microbiology has had a major impact on the field. clinical laboratories are now using wgs for pathogen identification, antimicrobial susceptibility testing, and epidemiological typing. wgs data also represent a valuable resource for the development and evaluation of molecular diagnostic assays, which continue to play an important role in clinical microbiology. to demonstrate this application of wgs, this study used publicly ...201627733632
glucose metabolism via the entner-doudoroff pathway in campylobacter: a rare trait that enhances survival and promotes biofilm formation in some isolates.isolates of the zoonotic pathogen campylobacter are generally considered to be unable to metabolize glucose due to lack of key glycolytic enzymes. however, the entner-doudoroff (ed) pathway has been identified in campylobacter jejuni subsp. doylei and a few c. coli isolates. a systematic search for ed pathway genes in a wide range of campylobacter isolates and in the c. jejuni/coli pubmlst database revealed that 1.7% of >6,000 genomes encoded a complete ed pathway, including both c. jejuni and c ...201627920773
advances and challenges in viability detection of foodborne pathogens.foodborne outbreaks are a serious public health and food safety concern worldwide. there is a great demand for rapid, sensitive, specific, and accurate methods to detect microbial pathogens in foods. conventional methods based on cultivation of pathogens have been the gold standard protocols; however, they take up to a week to complete. molecular assays such as polymerase chain reaction (pcr), sequencing, microarray technologies have been widely used in detection of foodborne pathogens. among mo ...201627920757
epidemiology and rapd-pcr typing of thermophilic campylobacters from children under five years and chickens in morogoro municipality, tanzania.campylobacter species are gram negative and flagellated bacteria under the genus campylobacter, family campylobacteriaceae. these pathogens cause zoonotic infections among human and animal populations. this study was undertaken between december 2006 and may 2007 to determine prevalence, risk factors and genetic diversity of thermophilic campylobacter isolates from children less than 5 years and chickens in morogoro municipality, tanzania.201627871251
prevalence of enteropathogens in dogs attending 3 regional dog parks in northern california.the prevalence and risk factors for infection with enteropathogens in dogs frequenting dog parks have been poorly documented, and infected dogs can pose a potential zoonotic risk for owners.201627859745
momp from campylobacter jejuni is a trimer of 18-stranded β-barrel monomers with a ca(2+) ion bound at the constriction zone.the gram-negative organism campylobacter jejuni is the major cause of food poisoning. unlike escherichia coli, which has two major porins, ompc and ompf, c. jejuni has one, termed major outer membrane protein (momp) through which nutrients and antibiotics transit. we report the 2.1-å crystal structure of c. jejuni momp expressed in e. coli and a lower resolution but otherwise identical structure purified directly from c. jejuni. the 2.1-å resolution structure of recombinant momp showed that alth ...201627693650
evaluation of a microfluidic chip system for preparation of bacterial dna from swabs, air, and surface water samples.the detection of bacterial pathogens from complex sample matrices by pcr requires efficient dna extraction. in this study, a protocol for extraction and purification of dna from swabs, air, and water samples using a microfluidic chip system was established. the optimized protocol includes a combination of thermal, chemical and enzymatic lysis followed by chip-based dna purification using magnetic particles. the procedure was tested using gram-positive bacillus thuringiensis berliner var. kurstak ...201627520284
development of a droplet digital polymerase chain reaction for rapid and simultaneous identification of common foodborne pathogens in soft cheese.dairy products can harbor various microorganisms (e.g., campylobacter spp., salmonella spp., listeria monocytogenes, verocytotoxin-producing escherichia coli) arising from animal reservoirs, and which can become important sources of foodborne illness. therefore, early detection of food pathogens is crucial to prevent diseases. we wished to develop an accurate quantitative protocol based on a droplet digital polymerase chain reaction (ddpcr) involving eight individual taqman™ reactions to detect ...201627840628
prevalence of campylobacter jejuni and campylobacter coli in raw milk and some dairy products.this study was accomplished to test raw milk and certain dairy products sold in local markets of qena, egypt, for the presence of campylobacter coli and campylobacter jejuni.201627847427
molecular epidemiology, virulence determinants and antimicrobial resistance of campylobacter spreading in retail chicken meat in central china.campylobacter species are the major food-borne pathogens which could cause bacterial gastroenteritis in humans. contaminated chicken products have been recognized as the primary vehicles of campylobacter transmission to human beings. in this study, the prevalence of campylobacter in retail chicken meat in central china was investigated, and the isolates were further characterized using molecular approaches and tested for antibiotic resistance.201627800028
a direct-sensing galactose chemoreceptor recently evolved in invasive strains of campylobacter jejuni.a rare chemotaxis receptor, tlp11, has been previously identified in invasive strains of campylobacter jejuni, the most prevalent cause of bacterial gastroenteritis worldwide. here we use glycan and small-molecule arrays, as well as surface plasmon resonance, to show that tlp11 specifically interacts with galactose. tlp11 is required for the chemotactic response of c. jejuni to galactose, as shown using wild type, allelic inactivation and addition mutants. the inactivated mutant displays reduced ...201627762269
complete genome sequences of multidrug-resistant campylobacter jejuni strain 14980a (turkey feces) and campylobacter coli strain 14983a (housefly from a turkey farm), harboring a novel gentamicin resistance mobile element.multidrug resistance (mdr) in foodborne pathogens is a major food safety and public health issue. here we describe whole-genome sequences of two mdr strains of campylobacter jejuni and campylobacter coli from turkey feces and a housefly from a turkey farm. both strains harbor a novel chromosomal gentamicin resistance mobile element.201627795285
the risk of some veterinary antimicrobial agents on public health associated with antimicrobial resistance and their molecular basis.the risk of antimicrobial agents used in food-producing animals on public health associated with antimicrobial resistance continues to be a current topic of discussion as related to animal and human public health. in the present review, resistance monitoring data, and risk assessment results of some important antimicrobial agents were cited to elucidate the possible association of antimicrobial use in food animals and antimicrobial resistance in humans. from the selected examples, it was apparen ...201627803693
new weapons to fight old enemies: novel strategies for the (bio)control of bacterial biofilms in the food industry.biofilms are microbial communities characterized by their adhesion to solid surfaces and the production of a matrix of exopolymeric substances, consisting of polysaccharides, proteins, dna and lipids, which surround the microorganisms lending structural integrity and a unique biochemical profile to the biofilm. biofilm formation enhances the ability of the producer/s to persist in a given environment. pathogenic and spoilage bacterial species capable of forming biofilms are a significant problem ...201627803696
use of direct lamp screening of broiler fecal samples for campylobacter jejuni and campylobacter coli in the positive flock identification strategy.rapid identification of campylobacter-positive flocks before slaughter, following freezing and heat treatment for the campylobacter-positive carcasses at the slaughterhouses is an effective control strategy against foodborne campylobacteriosis. we evaluated a loop-mediated isothermal amplification (lamp) assay for the direct screening of naturally contaminated chicken cloacal swabs for c. jejuni/c. coli to compare this assay with conventional quantitative culture methods. in a comparison study o ...201627746777
extraction of total nucleic acids from bacterial isolates using the biomérieux nuclisens easymag total nucleic acid extractor.the biomerieux nuclisens easymag total nucleic acid extractor was evaluated for use on bacterial isolates in the clinical microbiology laboratory. forty eight isolates were extracted, yielding quantifiable amounts of dna for all isolates. the easymag is appropriate for dna extraction from bacterial isolates and will be incorporated in the clinical laboratory.201627658494
ethyl pyruvate: an anti-microbial agent that selectively targets pathobionts and biofilms.the microbiota has a strong influence on health and disease in humans. a causative shift favoring pathobionts is strongly linked to diseases. therefore, anti-microbial agents selectively targeting potential pathogens as well as their biofilms are urgently demanded. here we demonstrate the impact of ethyl pyruvate, so far known as ros scavenger and anti-inflammatory agent, on planktonic microbes and biofilms. ethyl pyruvate combats preferably the growth of pathobionts belonging to bacteria and fu ...201627658257
emergence of a potent multidrug efflux pump variant that enhances campylobacter resistance to multiple antibiotics.bacterial antibiotic efflux pumps are key players in antibiotic resistance. although their role in conferring multidrug resistance is well documented, the emergence of "super" efflux pump variants that enhance bacterial resistance to multiple drugs has not been reported. here, we describe the emergence of a resistance-enhancing variant (named re-cmeabc) of the predominant efflux pump cmeabc in campylobacter, a major zoonotic pathogen whose resistance to antibiotics is considered a serious antibi ...201627651364
prevalence and antibiotic resistance profile of thermophilic campylobacter spp. of slaughtered cattle and sheep in shiraz, iranalthough poultry meat is considered as the main source for human campylobacter infections, there is limited information about non-poultry sources. the present study was aimed to investigate the prevalence and the antibiotic resistance of thermophilic campylobacter spp. in fecal samples of the cattle and sheep in shiraz, iran. a total of 302 fecal samples were obtained from clinically healthy, slaughtered cattle and sheep from shiraz slaughterhouse. the animals were clinically healthy before bein ...201627872721
quantification of growth of campylobacter and extended spectrum β-lactamase producing bacteria sheds light on black box of enrichment procedures.campylobacter is well recognized as the leading cause of bacterial foodborne diarrheal disease worldwide, and is routinely found in meat originating from poultry, sheep, pigs, and cattle. effective monitoring of campylobacter contamination is dependent on the availability of reliable detection methods. the method of the international organization for standardization for the detection of campylobacter spp. in food (iso 10272-1:2006) recommends the use of bolton broth (bb) as selective enrichment ...201627672384
polyphosphate and associated enzymes as global regulators of stress response and virulence in campylobacter jejuni.campylobacter jejuni (c. jejuni), a gram-negative microaerophilic bacterium, is a predominant cause of bacterial foodborne gastroenteritis in humans worldwide. despite its importance as a major foodborne pathogen, our understanding of the molecular mechanisms underlying c. jejuni stress survival and pathogenesis is limited. inorganic polyphosphate (poly p) has been shown to play significant roles in bacterial resistance to stress and virulence in many pathogenic bacteria. c. jejuni contains the ...201627672264
point mutations in the major outer membrane protein drive hypervirulence of a rapidly expanding clone of campylobacter jejuni.infections due to clonal expansion of highly virulent bacterial strains are clear and present threats to human and animal health. association of genetic changes with disease is now a routine, but identification of causative mutations that enable disease remains difficult. campylobacter jejuni is an important zoonotic pathogen transmitted to humans mainly via the foodborne route. c. jejuni typically colonizes the gut, but a hypervirulent and rapidly expanding clone of c. jejuni recently emerged, ...201627601641
a new lab developed real time pcr assay for direct detection of c. difficle from stool sample without dna extraction.clostridium difficile is a major cause of nosocomial antibiotic-associated infectious diarrhea and pseudomembranous colitis. detection of c. difficile by anaerobic bacterial culture and/or cytotoxicity assays has been largely replaced by rapid enzyme immunoassays (eia). however, due to the lack of sensitivity of stool eia, we developed a multiplex real-time pcr assay targeting the c. difficile toxin genes tcdb. stool samples from hospitalized pediatric patients suspected of having c. difficile-a ...201627829823
antimicrobial resistance of campylobacter isolates from small scale and backyard chicken in kenya.thermophilic campylobacter species are a major cause of bacterial foodborne diarrhoea in humans worldwide. poultry and their products are the predominant source for human campylobacteriosis. resistance of campylobacter to antibiotics is increasing worldwide, but little is known about the antibiotic resistance in campylobacter isolated from chicken in kenya. in this study, 35 suspected campylobacter strains isolated from faeces and cloacal swabs of chicken were tested for their susceptibility to ...201627570543
whole-genome sequences of agricultural, host-associated campylobacter coli and campylobacter jejuni strains.we report here the genome sequences of four agricultural, multidrug-resistant campylobacter spp.: c. coli 11601 and c. jejuni 11601md, isolated from turkey cecum and jejunum, respectively, and c. coli 6067 and c. coli 6461, isolated from turkey-house water and swine feces, respectively. the genomes provide insights on campylobacter antimicrobial resistance and host adaptations.201627540063
mosaic tetracycline resistance genes encoding ribosomal protection proteins.first reported in 2003, mosaic tetracycline resistance genes are a subgroup of the genes encoding ribosomal protection proteins (rpps). they are formed when two or more rpp-encoding genes recombine resulting in a functional chimera. to date, the majority of mosaic genes are derived from sections of three rpp genes, tet(o), tet(w) and tet(32), with others comprising tet(m) and tet(s). in this first review of mosaic genes, we report on their structure, diversity and prevalence, and suggest that th ...201627494928
association of campylobacter jejuni ssp. jejuni chemotaxis receptor genes with multilocus sequence types and source of isolation.campylobacter jejuni's flagellar locomotion is controlled by eleven chemoreceptors. assessment of the distribution of the relevant chemoreceptor genes in the c. jejuni genomes deposited in the national center for biotechnology information (ncbi) database led to the identification of two previously unknown tlp genes and a tlp5 pseudogene. these two chemoreceptor genes share the same locus in the c. jejuni genome with tlp4 and tlp11, but the gene region encoding the periplasmic ligand binding doma ...201627766165
evaluation of various campylobacter-specific quantitative pcr (qpcr) assays for detection and enumeration of campylobacteraceae in irrigation water and wastewater via a miniaturized most-probable-number-qpcr assay.campylobacter spp. are the leading cause of bacterial gastroenteritis worldwide, and water is increasingly seen as a risk factor in transmission. here we describe a most-probable-number (mpn)-quantitative pcr (qpcr) assay in which water samples are centrifuged and aliquoted into microtiter plates and the bacteria are enumerated by qpcr. we observed that commonly used campylobacter molecular assays produced vastly different detection rates. in irrigation water samples, detection rates varied depe ...201627235434
subtyping of salmonella enterica subspecies i using single-nucleotide polymorphisms in adenylate cyclase.methods to rapidly identify serotypes of salmonella enterica subspecies i are of vital importance for protecting the safety of food. to supplement the serotyping method dkgb-linked intergenic sequence ribotyping (isr), single-nucleotide polymorphisms were characterized within adenylate cyclase (cyaa). the national center for biotechnology information (ncbi) database had 378 cyaa sequences from s. enterica subspecies i, which included 42 unique dna sequences and 19 different amino acid sequences. ...201627035032
campylobacter species and neutrophilic inflammatory bowel disease in cats.inflammatory bowel disease (ibd) is a common cause of signs of gastrointestinal disease in cats. a subset of cats with ibd has neutrophilic inflammation of the intestinal mucosa.201627362482
evidence of avian and possum fecal contamination in rainwater tanks as determined by microbial source tracking approaches.avian and possum fecal droppings may negatively impact roof-harvested rainwater (rhrw) water quality due to the presence of zoonotic pathogens. this study was aimed at evaluating the performance characteristics of a possum feces-associated (psm) marker by screening 210 fecal and wastewater samples from possums (n = 20) and a range of nonpossum hosts (n = 190) in southeast queensland, australia. the host sensitivity and specificity of the psm marker were 0.90 and 0.95 (maximum value, 1.00), respe ...201627208100
molecular epidemiology of campylobacter coli strains isolated from different sources in new zealand between 2005 and 2014.campylobacteriosis is one of the most important foodborne diseases worldwide and a significant health burden in new zealand. campylobacter jejuni is the predominant species worldwide, accounting for approximately 90% of human cases, followed by campylobacter coli most studies in new zealand have focused on c. jejuni; hence, the impact of c. coli strains on human health is not well understood. the aim of this study was to genotype c. coli isolates collected in the manawatu region of new zealand f ...201627208097
optimization of quantitative pcr methods for enteropathogen detection.detection and quantification of enteropathogens in stool specimens is useful for diagnosing the cause of diarrhea but is technically challenging. here we evaluate several important determinants of quantification: specimen collection, nucleic acid extraction, and extraction and amplification efficiency. first, we evaluate the molecular detection and quantification of pathogens in rectal swabs versus stool, using paired flocked rectal swabs and whole stool collected from 129 children hospitalized ...201627336160
potential use of fosfomycin-tromethamine for treatment of recurrent campylobacter species enteritis.we report 2 cases of recurrent campylobacter coli enteritis caused by macrolide- and fluoroquinolone-resistant strains in 2 patients with hypogammaglobulinemia, successfully treated with a prolonged course of fosfomycin-tromethamine with no side effects. fosfomycin-tromethamine may be a feasible alternative therapy for recurrent enteritis caused by campylobacter species resistant to first-line drugs.201627161640
identification of novel vaccine candidates against campylobacter through reverse vaccinology.campylobacteriosis is the most prevalent bacterial foodborne gastroenteritis affecting humans in the european union. human cases are mainly due to campylobacter jejuni or campylobacter coli, and contamination is associated with the handling and/or consumption of poultry meat. in fact, poultry constitutes the bacteria's main reservoir. a promising way of decreasing the incidence of campylobacteriosis in humans would be to decrease avian colonization. poultry vaccination is of potential for this p ...201627413761
pfge genotyping and molecular characterization of campylobacter spp. isolated from chicken meat.a total of 70 samples were collected from chicken meat obtained from 10 markets in tehran, iran from which 39 campylobacter coli were isolated. among 10 antibiotics used, maximum resistance was seen to trimethoprim-sulphamethoxazole (sxt) (97.36%), nalidixic acid (94.8%), ciprofloxacin (87.7%), streptomycin (89.72%), and tetracycline (97.4%). no resistance was to gentamycin was observed. none of the campylobacter strains under study harbored integron, suggesting the involvement of other resistan ...201627822247
optimized cultivation of campylobacter concisus from gut mucosal biopsies in inflammatory bowel disease.campylobacter concisus is a commensal of the human oral flora that has been linked to prolonged diarrhea and inflammatory bowel disease (ibd). it has been detected more often from intestinal biopsies in patients with ibd compared to healthy controls using pcr-based techniques, whereas the number of c. concisus culture-positive biopsies in previous studies has been very limited. determining the rate of viable isolates present in the gut mucosa is of great importance when evaluating the role in di ...201627252786
whole-genome sequencing of a campylobacter jejuni strain isolated from retail chicken meat reveals the presence of a megaplasmid with mu-like prophage and multidrug resistance genes.genome sequencing of campylobacter jejuni strain t1-21 isolated from retail chicken meat revealed the presence of a chromosome of 1,565,978 bp and a megaplasmid of 82,732 bp that contains mu-like prophage and multidrug resistance genes. this is the first reported sequence of a campylobacter megaplasmid >55 kb.201627231378
an overview of food safety and bacterial foodborne zoonoses in food production animals in the caribbean region.foodborne diseases (fbds) in the caribbean have a high economic burden. public health and tourism concerns rise along with the increasing number of cases and outbreaks registered over the last 20 years. salmonella spp., shigella spp., and campylobacter spp. are the main bacteria associated with these incidents. in spite of undertaking limited surveillance on fbd in the region, records related to bacterial foodborne zoonoses in food-producing animals and their associated epidemiologic significanc ...201627215411
seroprevalence of campylobacter-specific antibodies in two german duck farms - a prospective follow-up study.several studies have shown that about 60-100% of farmed ducks are colonized by campylobacter species. because of this, a higher risk of campylobacteriosis among duck farm workers can be assumed. to estimate the risk of campylobacter infections in duck farm workers, we investigated the prevalence of campylobacter spp. in ducks of two duck farms and the seroprevalence of anti-campylobacter antibodies (iga and igg) in two cohorts of workers. the first cohort consisted of high-exposed stable workers ...201627429794
hyperendemic campylobacter jejuni in guinea pigs (cavia porcellus) raised for food in a semi-rural community of quito, ecuador.domestic animals and animal products are the source of pathogenic campylobacter jejuni and c. coli in industrialized countries, yet little is known about the transmission of these bacteria in developing countries. guinea pigs (cavia porcellus) are commonly raised for food in the andean region of south america, however, limited research has characterized this rodent as a reservoir of zoonotic enteric pathogens. in this study, we examined the prevalence of campylobacter spp. in 203 fecal samples f ...201627043446
genotyping and antibiotic resistance of thermophilic campylobacter isolated from chicken and pig meat in vietnam.campylobacter species are recognized as the most common cause of foodborne bacterial gastroenteritis in humans. in this study nine campylobacter strains isolated from chicken meat and pork in hanoi, vietnam, were characterized using molecular methods and tested for antibiotic resistance.201627175218
bacteria in an intense competition for iron: key component of the campylobacter jejuni iron uptake system scavenges enterobactin hydrolysis product.to acquire essential fe(iii), bacteria produce and secrete siderophores with high affinity and selectivity for fe(iii) to mediate its uptake into the cell. here, we show that the periplasmic binding protein ceue of campylobacter jejuni, which was previously thought to bind the fe(iii) complex of the hexadentate siderophore enterobactin (kd ∼ 0.4 ± 0.1 µm), preferentially binds the fe(iii) complex of the tetradentate enterobactin hydrolysis product bis(2,3-dihydroxybenzoyl-l-ser) (h5-bisdhbs) (kd ...201627162326
detection of campylobacter jejuni in rectal swab samples from rousettus amplexicaudatus in the philippines.bats are the second diversity species of mammals and widely distributed in the world. they are thought to be reservoir and vectors of zoonotic pathogens. however, there is scarce report of the evidence of pathogenic bacteria kept in bats. the precise knowledge of the pathogenic bacteria in bat microbiota is important for zoonosis control. thus, metagenomic analysis targeting the v3-v4 region of the 16s rrna of the rectal microbiota in rousettus amplexicaudatus was performed using high throughput ...201627109214
application of alternative nucleic acid extraction protocols to progastro sscs assay for detection of bacterial enteric pathogens.as an alternative to automated extraction, fecal specimens were processed by investigational lysis/heating (i.e., manual) and by chromatography/centrifugation (i.e., column) methods. progastro ssc and shiga toxin-producing escherichia coli (i.e., stec) indeterminate rates for 101 specimens were 1.0% to 3.0% for automated, 11.9% for manual, and 24.8% to 37.6% for column methods. following freeze-thaw of 247 specimens, indeterminate rates were 1.6% to 2.4% for manual and 0.8 to 5.3% for column met ...201626935731
multicenter evaluation of clinical diagnostic methods for detection and isolation of campylobacter spp. from stool.the use of culture-independent diagnostic tests (cidts), such as stool antigen tests, as standalone tests for the detection of campylobacter in stool is increasing. we conducted a prospective, multicenter study to evaluate the performance of stool antigen cidts compared to culture and pcr for campylobacter detection. between july and october 2010, we tested 2,767 stool specimens from patients with gastrointestinal illness with the following methods: four types of campylobacter selective media, f ...201626962088
revisiting the roles of culture and culture-independent detection tests for campylobacter.culture-independent detection tests (cidts) for campylobacter have become an area of intense controversy and confusion among laboratorians in the field of clinical microbiology. to date, the true analytical and clinical performance of stool antigen cidts versus truly optimized culture conditions is unknown. in this issue of the journal of clinical microbiology, fitzgerald and colleagues (c. fitzgerald et al., j clin microbiol 54:1209-1215, 2016, http://dx.doi.org/10.1128/jcm.01925-15) report com ...201626912756
protein chips for detection of salmonella spp. from enrichment culture.food pathogens are the cause of foodborne epidemics, therefore there is a need to detect the pathogens in food productions rapidly. a pre-enrichment culture followed by selective agar plating are standard detection methods. molecular methods such as qpcr have provided a first rapid protocol for detection of pathogens within 24 h of enrichment culture. biosensors also may provide a rapid tool to individuate a source of salmonella contamination at early times of pre-enrichment culture. forty ml of ...201627110786
campylobacter in broiler slaughter samples assessed by direct count on mccda and campy-cefex agar.campylobacter spp. cause foodborne illnesses in humans primarily through the consumption of contaminated chicken. the aim of this study was to evaluate the united states department of agriculture's (usda) recommended methodology, protocol mlg 41.02, for the isolation, identification and direct plate counting of campylobacter jejuni and c. coli samples from the broiler slaughtering process. a plating method using both mccda and campy-cefex agars is recommended to recover campylobacter cells. it i ...201627237112
campylobacter growth rates in four different matrices: broiler caecal material, live birds, bolton broth, and brain heart infusion broth.the objective of this study was to characterise campylobacter growth in enrichment broths (bolton broth, brain heart infusion broth), caecal material (in vitro), and in the naturally infected live broilers (in vivo) in terms of mean lag periods and generation times as well as maximum growth rates and population (cell concentration) achieved.201627052025
genetic diversity of campylobacter jejuni and campylobacter coli isolates from conventional broiler flocks and the impacts of sampling strategy and laboratory method.the genetic diversity of campylobacter jejuni and campylobacter coliisolates from commercial broiler farms was examined by multilocus sequence typing (mlst), with an assessment of the impact of the sample type and laboratory method on the genotypes of campylobacter isolated. a total of 645c. jejuniand 106c. coli isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (sts) identified. the campylobacter jejuniisolates obtained by different sampling approaches and laboratory met ...201626873321
evaluation of luminex xtag gastrointestinal pathogen panel assay for detection of multiple diarrheal pathogens in fecal samples in vietnam.diarrheal disease is a complex syndrome that remains a leading cause of global childhood morbidity and mortality. the diagnosis of enteric pathogens in a timely and precise manner is important for making treatment decisions and informing public health policy, but accurate diagnosis is a major challenge in industrializing countries. multiplex molecular diagnostic techniques may represent a significant improvement over classical approaches. we evaluated the luminex xtag gastrointestinal pathogen p ...201626865681
the bacteriophage carrier state of campylobacter jejuni features changes in host non-coding rnas and the acquisition of new host-derived crispr spacer sequences.incorporation of self-derived crispr dna protospacers in campylobacter jejuni pt14 occurs in the presence of bacteriophages encoding a crispr-like cas4 protein. this phenomenon was evident in carrier state infections where both bacteriophages and host are maintained for seemingly indefinite periods as stable populations following serial passage. carrier state cultures of c. jejuni pt14 have greater aerotolerance in nutrient limited conditions, and may have arisen as an evolutionary response to s ...201627047470
whole-genome sequences of two campylobacter coli isolates from the antimicrobial resistance monitoring program in colombia.campylobacter coli, along with campylobacter jejuni, is a major agent of gastroenteritis and acute enterocolitis in humans. we report the whole-genome sequences of two multidrug-resistance c. coli strains, isolated from the colombian poultry chain. the isolates contain a variety of antimicrobial resistance genes for aminoglycosides, lincosamides, fluoroquinolones, and tetracycline.201626988048
a biotin biosynthesis gene restricted to helicobacter.in most bacteria the last step in synthesis of the pimelate moiety of biotin is cleavage of the ester bond of pimeloyl-acyl carrier protein (acp) methyl ester. the paradigm cleavage enzyme is escherichia coli bioh which together with the bioc methyltransferase allows synthesis of the pimelate moiety by a modified fatty acid biosynthetic pathway. analyses of the extant bacterial genomes showed that bioh is absent from many bioc-containing bacteria and is replaced by other genes. helicobacter pylo ...201626868423
in silico analysis of the cadf gene and development of a duplex polymerase chain reaction for species-specific identification of campylobacter jejuni and campylobacter coli.campylobacteriosis is a zoonotic infectious disease caused by campylobacter jejuni and c. coli. the cadf gene is considered as a genus-specific gene while other genes are mainly used for discrimination at the species level.201627127589
campylobacter jejuni and campylobacter coli in wild birds on danish livestock farms.reducing the occurrence of campylobacteriosis is a food safety issue of high priority, as in recent years it has been the most commonly reported zoonosis in the eu. livestock farms are of particular interest, since cattle, swine and poultry are common reservoirs of campylobacter spp. the farm environment provides attractive foraging and breeding habitats for some bird species reported to carry thermophilic campylobacter spp. we investigated the campylobacter spp. carriage rates in 52 wild bird s ...201626842400
campylobacter jejuni and campylobacter coli in wild birds on danish livestock farms.reducing the occurrence of campylobacteriosis is a food safety issue of high priority, as in recent years it has been the most commonly reported zoonosis in the eu. livestock farms are of particular interest, since cattle, swine and poultry are common reservoirs of campylobacter spp. the farm environment provides attractive foraging and breeding habitats for some bird species reported to carry thermophilic campylobacter spp. we investigated the campylobacter spp. carriage rates in 52 wild bird s ...201626842400
ebola or not? evaluating the ill traveler from ebola-affected countries in west africa.background.  the 2014-2015 ebola epidemic in west africa had global impact beyond the primarily affected countries of guinea, liberia, and sierra leone. other countries, including the united states, encountered numerous patients who arrived from highly affected countries with fever or other signs or symptoms consistent with ebola virus disease (evd). methods.  we describe our experience evaluating 25 travelers who met the us centers for disease control and prevention case definition for a person ...201626925428
oral phage therapy of acute bacterial diarrhea with two coliphage preparations: a randomized trial in children from bangladesh.antibiotic resistance is rising in important bacterial pathogens. phage therapy (pt), the use of bacterial viruses infecting the pathogen in a species-specific way, is a potential alternative.201626981577
prevalence and antimicrobial resistance of campylobacter isolated from dressed beef carcasses and raw milk in tanzania.campylobacter species are commonly transmitted to humans through consumption of contaminated foods such as milk and meat. the aim of this study was to investigate the prevalence, antimicrobial resistance, and genetic determinants of resistance of campylobacter isolated from raw milk and beef carcasses in tanzania. the antimicrobial resistance genes tested included blaoxa-61 (ampicillin), aph-3-1 (aminoglycoside), tet(o) (tetracycline), and cmeb (multi-drug efflux pump). the prevalence of campylo ...201626153978
the campylobacter jejuni oxidative stress regulator rrpb is associated with a genomic hypervariable region and altered oxidative stress resistance.campylobacter jejuni is the leading cause of bacterial foodborne diarrhoeal disease worldwide. despite the microaerophilic nature of the bacterium, c. jejuni can survive the atmospheric oxygen conditions in the environment. bacteria that can survive either within a host or in the environment like c. jejuni require variable responses to survive the stresses associated with exposure to different levels of reactive oxygen species. the marr-type transcriptional regulators rrpa and rrpb have recently ...201628082970
antibodies from multiple sclerosis patients preferentially recognize hyperglucosylated adhesin of non-typeable haemophilus influenzae.in autoimmune diseases, there have been proposals that exogenous "molecular triggers", i.e., specific this should be 'non-self antigens' accompanying infectious agents, might disrupt control of the adaptive immune system resulting in serious pathologies. the etiology of the multiple sclerosis (ms) remains unclear. however, epidemiologic data suggest that exposure to infectious agents may be associated with increased ms risk and progression may be linked to exogenous, bacterially-derived, antigen ...201628008952
zika virus: a review from the virus basics to proposed management strategies.this review aims to summarize the body of knowledge available on zika virus to date. a comprehensive review of the scientific literature on zika virus was performed with the aim to stress relevant aspects for healthcare professionals in the non-endemic areas. for several years, the zika virus infection was considered an extremely rare exotic disease with poor clinical relevance. however, zika virus has recently gained the attention of the scientific community and public opinion since the virus s ...201627872736
multiplex-touchdown pcr to simultaneously detect cryptosporidium parvum, giardia lamblia, and cyclospora cayetanensis, the major causes of traveler's diarrhea.this study aimed to develop a multiplex-touchdown pcr method to simultaneously detect 3 species of protozoan parasites, i.e., cryptosporidium parvum, giardia lamblia, and cyclospora cayetanensis, the major causes of traveler's diarrhea and are resistant to standard antimicrobial treatments. the target genes included the cryptosporidium oocyst wall protein for c. parvum, glutamate dehydrogenase for g. lamblia, and 18s ribosomal rna (18s rrna) for c. cayetanensis. the sizes of the amplified fragme ...201627853120
application of probiotics for the production of safe and high-quality poultry meat.poultry industry has always been a dynamic and integral part of national economies in many countries. economic losses incur especially in large-scale rearing facilities, often attributed to the deterioration of environmental conditions, poultry exposure to stressors and development of diseases. while antibiotics have been commonly used for prophylactic purposes and as growth stimulants, extensive documentation of antimicrobial resistance among pathogenic bacteria due to indiscriminate utilizatio ...201627857531
complementation of an aglb mutant of methanococcus maripaludis with heterologous oligosaccharyltransferases.the oligosaccharyltransferase is the signature enzyme for n-linked glycosylation in all domains of life. in archaea, this enzyme termed aglb, is responsible for transferring lipid carrier-linked glycans to select asparagine residues in a variety of target proteins including archaellins, s-layer proteins and pilins. this study investigated the ability of a variety of aglbs to compensate for the oligosaccharyltransferase activity in methanococcus maripaludis deleted for aglb, using archaellin flab ...201627907170
metagenome phylogenetic profiling of microbial community evolution in a tetrachloroethene-contaminated aquifer responding to enhanced reductive dechlorination protocols.chlorinated solvent contamination of potable water supplies is a serious problem worldwide. biostimulation protocols can successfully remediate chlorinated solvent contamination through enhanced reductive dechlorination pathways, however the process is poorly understood and sometimes stalls creating a more serious problem. whole metagenome techniques have the potential to reveal details of microbial community changes induced by biostimulation. here we compare the metagenome of a tetrachloroethen ...201627980706
concurrency of guillain-barre syndrome and acute transverse myelitis: a case report and review of literature.guillain-barré syndrome and acute transverse myelitis manifest as demyelinating diseases of the peripheral and central nervous system. concurrency of these two disorders is rarely documented in literature. a 4-year-old girl presenting with cough, fever, and an impaired walking ability was admitted to hospital. she had no previous complaints in her medical history. a physical examination revealed lack of muscle strength of the lower extremities and deep tendon reflexes. mri could not be carried o ...201628018472
the two-component system arlrs and alterations in metabolism enable staphylococcus aureus to resist calprotectin-induced manganese starvation.during infection the host imposes manganese and zinc starvation on invading pathogens. despite this, staphylococcus aureus and other successful pathogens remain capable of causing devastating disease. however, how these invaders adapt to host-imposed metal starvation and overcome nutritional immunity remains unknown. we report that arlrs, a global staphylococcal virulence regulator, enhances the ability of s. aureus to grow in the presence of the manganese-and zinc-binding innate immune effector ...201627902777
dcite: measuring necessary cladistic information can help you reduce polytomy artefacts in trees.biologists regularly create phylogenetic trees to better understand the evolutionary origins of their species of interest, and often use genomes as their data source. however, as more and more incomplete genomes are published, in many cases it may not be possible to compute genome-based phylogenetic trees due to large gaps in the assembled sequences. in addition, comparison of complete genomes may not even be desirable due to the presence of horizontally acquired and homologous genes. a decision ...201627898695
the minor flagellin of campylobacter jejuni (flab) confers defensive properties against bacteriophage infection.a screen of bacteriophages infecting a panel of campylobacter jejuni pt14 gene knock-out mutants identified a role for the minor flagellin encoded by the flab gene, in the defense of the host against cp8unalikevirus bacteriophage cp_f1 infection. inactivation of the flab gene resulted in an increase in the susceptibility of pt14 cultures to infection by cp_f1 and an increase in bacteriophage yields. infection of wild type pt14 with cp_f1 produces turbid plaques in bacterial lawns, from which 78% ...201627965643
evaluation and selection of bacillus species based on enzyme production, antimicrobial activity, and biofilm synthesis as direct-fed microbial candidates for poultry.social concern about misuse of antibiotics as growth promoters (agp) and generation of multidrug-resistant bacteria have restricted the dietary inclusion of antibiotics in livestock feed in several countries. direct-fed microbials (dfm) are one of the multiple alternatives commonly evaluated as substitutes of agp. sporeformer bacteria from the genus bacillus have been extensively investigated because of their extraordinary properties to form highly resistant endospores, produce antimicrobial com ...201627812526
variations of phosphorous accessibility causing changes in microbiome functions in the gastrointestinal tract of chickens.the chicken gastrointestinal tract (git) harbours a complex microbial community, involved in several physiological processes such as host immunomodulation and feed digestion. for the first time, the present study analysed dietary effects on the protein inventory of the microbiome in crop and ceca of broilers. we performed quantitative label-free metaproteomics by using 1-d-gel electrophoresis coupled with lc-ms/ms to identify the structural and functional changes triggered by diets supplied with ...201627760159
azithromycin vs. placebo for the clinical outcome in campylobacter concisus diarrhoea in adults: a randomized, double-blinded, placebo-controlled clinical trial.campylobacter concisus has been associated with prolonged mild diarrhoea, but investigations regarding the efficacy of antimicrobial treatment have not been reported previously. we initiated a phase 3, single-centre, randomized, double-blinded, placebo-controlled study comparing the efficacy of 500 mg once-daily dose of azithromycin with a 500 mg once-daily dose of placebo for three days, for the treatment of c. concisus diarrhoea in adult patients with a follow-up period of ten days. if symptom ...201627893820
exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes.fatigue, mood disturbances, under performance and gastrointestinal distress are common among athletes during training and competition. the psychosocial and physical demands during intense exercise can initiate a stress response activating the sympathetic-adrenomedullary and hypothalamus-pituitary-adrenal (hpa) axes, resulting in the release of stress and catabolic hormones, inflammatory cytokines and microbial molecules. the gut is home to trillions of microorganisms that have fundamental roles ...201627924137
altered intestinal microbiota-host mitochondria crosstalk in new onset crohn's disease.intestinal microbial dysbiosis is associated with crohn's disease (cd). however, the mechanisms leading to the chronic mucosal inflammation that characterizes this disease remain unclear. in this report, we use systems-level approaches to study the interactions between the gut microbiota and host in new-onset paediatric patients to evaluate causality and mechanisms of disease. we report an altered host proteome in cd patients indicative of impaired mitochondrial functions. in particular, mitocho ...201627876802
classification of a hypervirulent aeromonas hydrophila pathotype responsible for epidemic outbreaks in warm-water fishes.lineages of hypervirulent aeromonas hydrophila (vah) are the cause of persistent outbreaks of motile aeromonas septicemia in warm-water fishes worldwide. over the last decade, this virulent lineage of a. hydrophila has resulted in annual losses of millions of tons of farmed carp and catfish in the people's republic of china and the united states (us). multiple lines of evidence indicate us catfish and asian carp isolates of a. hydrophila affiliated with sequence type 251 (st251) share a recent c ...201627803692
epidemiological and clinical profile of adult patients with blastocystis sp. infection in barcelona, spain.blastocystis spp. are among the most frequently observed intestinal parasites in humans. despite the discovery of blastocystis approximately 100 years ago, limited information is available regarding its pathogenesis, genetic diversity, and available treatment options. the aim of this study was to describe the epidemiological and clinical characteristics of patients with blastocystis sp. infections diagnosed at vall d'hebron university hospital (barcelona, spain).201627741951
beyond antimicrobial resistance: evidence for a distinct role of the acrd efflux pump in salmonella biology.for over 20 years, bacterial multidrug resistance (mdr) efflux pumps have been studied because of their impact on resistance to antimicrobials. however, critical questions remain, including why produce efflux pumps under non-antimicrobial treatment conditions, and why have multiple pumps if their only purpose is antimicrobial efflux? salmonella spp. possess five efflux pump families, including the resistance-nodulation-division (rnd) efflux pumps. notably, the rnd efflux pump acrd has a unique s ...201627879336
catabolite and oxygen regulation of enterohemorrhagic escherichia coli virulence.the biogeography of the gut is diverse in its longitudinal axis, as well as within specific microenvironments. differential oxygenation and nutrient composition drive the membership of microbial communities in these habitats. moreover, enteric pathogens can orchestrate further modifications to gain a competitive advantage toward host colonization. these pathogens are versatile and adept when exploiting the human colon. they expertly navigate complex environmental cues and interkingdom signaling ...201627879335
spyb, a small heme-binding protein, affects the composition of the cell wall in streptococcus pyogenes.streptococcus pyogenes (group a streptococcus or gas) is a hemolytic human pathogen associated with a wide variety of infections ranging from minor skin and throat infections to life-threatening invasive diseases. the cell wall of gas consists of peptidoglycan sacculus decorated with a carbohydrate comprising a polyrhamnose backbone with immunodominant n-acetylglucosamine side-chains. all gas genomes contain the spyba operon, which encodes a 35-amino-acid membrane protein spyb, and a membrane-bo ...201627790410
comparison of proteomics profiles of campylobacter jejuni strain bf under microaerobic and aerobic conditions.campylobacter jejuni accounts for one of the leading causes of foodborne bacterial enteritis in humans. despite being considered an obligate microaerobic microorganism, c. jejuni is regularly exposed to oxidative stress. however, its adaptive strategies to survive the atmospheric oxygen level during transmission to humans remain unclear. recently, the clinical c. jejuni strain bf was singled out for its unexpected ability to grow under ambient atmosphere. here, we aimed to understand better the ...201627790195
spatial and temporal shifts in bacterial biogeography and gland occupation during the development of a chronic infection.gland colonization may be one crucial route for bacteria to maintain chronic gastrointestinal infection. we developed a quantitative gland isolation method to allow robust bacterial population analysis and applied it to the gastric pathobiont helicobacter pylori after infections in the murine model system, h. pylori populations multiply both inside and outside glands in a manner that requires the bacteria to be motile and chemotactic. h. pylori is able to achieve gland densities averaging 25 to ...201627729513
the type b flagellin of hypervirulent clostridium difficile is modified with novel sulfonated peptidylamido-glycans.glycosylation of flagellins is a well recognized property of many bacterial species. in this study, we describe the structural characterization of novel flagellar glycans from a number of hypervirulent strains of c. difficile we used mass spectrometry (nano-lc-ms and ms/ms analysis) to identify a number of putative glycopeptides that carried a variety of glycoform substitutions, each of which was linked through an initial n-acetylhexosamine residue to ser or thr. detailed analysis of a lldgsstei ...201627758867
the gut microbiome as therapeutic target in central nervous system diseases: implications for stroke.research on commensal microbiota and its contribution to health and disease is a new and very dynamically developing field of biology and medicine. recent experimental and clinical investigations underscore the importance of gut microbiota in the pathogenesis and course of stroke. importantly, microbiota may influence the outcome of cerebral ischemia by modulating central nervous system antigen-specific immune responses. in this review we summarize studies linking gut microbiota with physiologic ...201627714645
complete genomic sequence of campylobacter jejuni subsp. jejuni hs:19 strain rm1285 isolated from packaged chicken.poultry products serve as the main source of campylobacter jejuni subsp. jejuni infections in humans. c. jejuni subsp. jejuni infections are a leading cause of foodborne gastroenteritis and are a prevalent antecedent to guillain-barré syndrome. this study describes the genome of c. jejuni subsp. jejuni hs:19 strain rm1285, isolated from packaged chicken in california.201627795263
identification of ompa-like protein of tannerella forsythia as an o-linked glycoprotein and its binding capability to lectins.bacterial glycoproteins are associated with physiological and pathogenic functions of bacteria. it remains unclear whether bacterial glycoproteins can bind to specific classes of lectins expressed on host cells. tannerella forsythia is a gram-negative oral anaerobe that contributes to the development of periodontitis. in this study, we aimed to find lectin-binding glycoproteins in t. forsythia. we performed affinity chromatography of wheat germ agglutinin, which binds to n-acetylglucosamine (glc ...201627711121
age-related differences in the luminal and mucosa-associated gut microbiome of broiler chickens and shifts associated with campylobacter jejuni infection.despite the importance of gut microbiota for broiler performance and health little is known about the composition of this ecosystem, its development and response towards bacterial infections. therefore, the current study was conducted to address the composition and structure of the microbial community in broiler chickens in a longitudinal study from day 1 to day 28 of age in the gut content and on the mucosa. additionally, the consequences of a campylobacter (c.) jejuni infection on the microbia ...201627921008
one-step pcr detection of salmonella pullorum/gallinarum using a novel target: the flagellar biosynthesis gene flhb.salmonella enterica serovar pullorum/gallinarum is an important infectious pathogen that has caused widespread problems for chicken industry. traditional salmonella serotyping is an expensive and time-consuming process. in this study, we developed a rapid one-step polymerase chain reaction (pcr) method to identify s. pullorum/gallinarum. the pcr-based assay focuses on flhb, which shows a deficient region only in s. pullorum/gallinarum, compared with that of other serovars. the specificity and se ...201627920764
development of multiple cross displacement amplification label-based gold nanoparticles lateral flow biosensor for detection of shigella spp.shigella spp., the etiological agent of shigellosis or "bacillary dysentery," are responsible for considerable morbidity and mortality in excess of a million deaths globally per year. although pcr-based techniques (such as pcr-based dipstick biosensors) have been used for the molecular diagnosis of infectious disease, these assays were restricted due to the need for a sophisticated thermal cycling apparatus to denature target templates. to facilitate simple and rapid detection of target pathogen ...201627917160
patient-specific bacteroides genome variants in pouchitis.a 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). oligotyping and metagenomic short-read annotation identified bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. targeted cultivation of bacteroides isolates from ...201627935837
effects of seasonal meteorological variables on e. coli persistence in livestock faeces and implications for environmental and human health.agriculture contributes significant volumes of livestock faeces to land. understanding how faecal microbes respond to shifts in meteorological patterns of contrasting seasons is important in order to gauge how environmental (and human health) risks may alter under a changing climate. the aim of this study was to: (i) quantify the temporal pattern of e. coli growth within dairy faeces post defecation; and (ii) derive e. coli seasonal population change profiles associated with contrasting environm ...201627845409
unique and universal features of epsilonproteobacterial origins of chromosome replication and dnaa-dnaa box interactions.in bacteria, chromosome replication is initiated by the interaction of the initiator protein dnaa with a defined region of a chromosome at which dna replication starts (oric). while dnaa proteins share significant homology regardless of phylogeny, oric regions exhibit more variable structures. the general architecture of orics is universal, i.e., they are composed of a cluster of dnaa binding sites, a dna-unwinding element, and sequences that bind regulatory proteins. however, detailed structure ...201627746772
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