bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain
Authors: Yang Xiang , Noyes Noelle R. , Doster Enrique , Martin Jennifer N. , Linke Lyndsey M. , Magnuson Roberta J. , Yang Hua , Geornaras Ifigenia , Woerner Dale R. , Jones Kenneth L. , Ruiz Jaime , Boucher Christina , Morley Paul S. , Belk Keith E. 
Published: February 2016

ABSTRACT

Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for
Salmonella enterica
,
Listeria monocytogenes
,
Escherichia coli
,
Staphylococcus aureus
,
Clostridium
spp. (
C. botulinum
and
C. perfringens
), and
Campylobacter
spp. (
C. jejuni
,
C. coli
, and
C. fetus
) decreased over subsequential processing steps. Furthermore, the normalized read counts for
S. enterica
,
E. coli
, and
C. botulinum
were greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.
Genetic Diversity of Campylobacter jejuni and Campylobacter coli Isolates from Conventional Broiler Flocks and the Impacts of Sampling Strategy and Laboratory Method
Authors: Vidal A. B. , Colles F. M. , Rodgers J. D. , McCarthy N. D. , Davies R. H. , Maiden M. C. J. , Clifton-Hadley F. A. 
Published: February 2016

ABSTRACT

The genetic diversity of
Campylobacter jejuni
and
Campylobacter coli
isolates 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 645
C. jejuni
and 106
C. coli
isolates were obtained from 32 flocks and 17 farms, with 47 sequence types (STs) identified. The
Campylobacter jejuni
isolates obtained by different sampling approaches and laboratory methods were very similar, with the same STs identified at similar frequencies, and had no major effect on the genetic profile of
Campylobacter
population in broiler flocks at the farm level. For
C. coli
, the results were more equivocal. While some STs were widely distributed within and among farms and flocks, analysis of molecular variance (AMOVA) revealed a high degree of genetic diversity among farms for
C. jejuni
, where farm effects accounted for 70.5% of variance, and among flocks from the same farm (9.9% of variance for
C. jejuni
and 64.1% for
C. coli
). These results show the complexity of the population structure of
Campylobacter
in broiler production and that commercial broiler farms provide an ecological niche for a wide diversity of genotypes. The genetic diversity of
C. jejuni
isolates among broiler farms should be taken into account when designing studies to understand
Campylobacter
populations in broiler production and the impact of interventions. We provide evidence that supports synthesis of studies on
C. jejuni
populations even when laboratory and sampling methods are not identical.
Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass
Authors: Mathieu Yann , Piumi Francois , Valli Richard , Aramburu Juan Carro , Ferreira Patricia , Faulds Craig B. , Record Eric 
Published: February 2016

ABSTRACT

Auxiliary activities family 3 subfamily 2 (AA3_2) from the CAZy database comprises various functions related to ligninolytic enzymes, such as fungal aryl alcohol oxidases (AAO) and glucose oxidases, both of which are flavoenzymes. The recent study of the
Pycnoporus cinnabarinus
CIRM BRFM 137 genome combined with its secretome revealed that four AA3_2 enzymes are secreted during biomass degradation. One of these AA3_2 enzymes, scf184803.g17, has recently been produced heterologously in
Aspergillus niger
. Based on the enzyme's activity and specificity, it was assigned to the glucose dehydrogenases (
P
.
cinnabarinus
GDH [
Pc
GDH]). Here, we analyze the distribution of the other three AA3_2 enzymes (scf185002.g8, scf184611.g7, and scf184746.g13) to assess their putative functions. These proteins showed the highest homology with aryl alcohol oxidase from
Pleurotus eryngii
. Biochemical characterization demonstrated that they were also flavoenzymes harboring flavin adenine dinucleotide (FAD) as a cofactor and able to oxidize a wide variety of phenolic and nonphenolic aryl alcohols and one aliphatic polyunsaturated primary alcohol. Though presenting homology with fungal AAOs, these enzymes exhibited greater efficiency in reducing electron acceptors (quinones and one artificial acceptor) than molecular oxygen and so were defined as aryl-alcohol:quinone oxidoreductases (AAQOs) with two enzymes possessing residual oxidase activity (
Pc
AAQO2 and
Pc
AAQO3). Structural comparison of
Pc
AAQO homology models with
P. eryngii
AAO demonstrated a wider substrate access channel connecting the active-site cavity to the solvent, explaining the absence of activity with molecular oxygen. Finally, the ability of
Pc
AAQOs to reduce radical intermediates generated by laccase from
P. cinnabarinus
was demonstrated, shedding light on the ligninolytic system of this fungus.
Systematic Mutational Analysis of Histidine Kinase Genes in the Nosocomial Pathogen Stenotrophomonas maltophilia Identifies BfmAK System Control of Biofilm Development
Authors: Zheng Liu , Wang Fang-Fang , Ren Bao-Zhen , Liu Wei , Liu Zhong , Qian Wei 
Published: February 2016

ABSTRACT

The Gram-negative bacterium
Stenotrophomonas maltophilia
lives in diverse ecological niches. As a result of its formidable capabilities of forming biofilm and its resistance to multiple antibiotic agents, the bacterium is also a nosocomial pathogen of serious threat to the health of patients whose immune systems are suppressed or compromised. Besides the histidine kinase RpfC, the two-component signal transduction system (TCS), which is the canonical regulatory machinery used by most bacterial pathogens, has never been experimentally investigated in
S. maltophilia
. Here, we annotated 62 putative histidine kinase genes in the
S. maltophilia
genome and successfully obtained 51 mutants by systematical insertional inactivation. Phenotypic characterization identified a series of mutants with deficiencies in bacterial growth, swimming motility, and biofilm development. A TCS, named here BfmA-BfmK (Smlt4209-Smlt4208), was genetically confirmed to regulate biofilm formation in
S. maltophilia
. Together with interacting partner prediction and chromatin immunoprecipitation screens, six candidate promoter regions bound by BfmA
in vivo
were identified. We demonstrated that, among them, BfmA acts as a transcription factor that binds directly to the promoter regions of
bfmA-bfmK
and
Smlt0800
(
acoT
), a gene encoding an acyl coenzyme A thioesterase that is associated with biofilm development, and positively controls their transcription. Genome-scale mutational analyses of histidine kinase genes and functional dissection of BfmK-BfmA regulation in biofilm provide genetic information to support more in-depth studies on cellular signaling in
S. maltophilia
, in the context of developing novel approaches to fight this important bacterial pathogen.
Direct Comparison of Physical Properties of Bacillus subtilis NCIB 3610 and B-1 Biofilms
Authors: Kesel Sara , Grumbein Stefan , Gümperlein Ina , Tallawi Marwa , Marel Anna-Kristina , Lieleg Oliver , Opitz Madeleine 
Published: February 2016

ABSTRACT

Many bacteria form surface-attached communities known as biofilms. Due to the extreme resistance of these bacterial biofilms to antibiotics and mechanical stresses, biofilms are of growing interest not only in microbiology but also in medicine and industry. Previous studies have determined the extracellular polymeric substances present in the matrix of biofilms formed by
Bacillus subtilis
NCIB 3610. However, studies on the physical properties of biofilms formed by this strain are just emerging. In particular, quantitative data on the contributions of biofilm matrix biopolymers to these physical properties are lacking. Here, we quantitatively investigated three physical properties of
B. subtilis
NCIB 3610 biofilms: the surface roughness and stiffness and the bulk viscoelasticity of these biofilms. We show how specific biomolecules constituting the biofilm matrix formed by this strain contribute to those biofilm properties. In particular, we demonstrate that the surface roughness and surface elasticity of 1-day-old NCIB 3610 biofilms are strongly affected by the surface layer protein BslA. For a second strain,
B. subtilis
B-1, which forms biofilms containing mainly γ-polyglutamate, we found significantly different physical biofilm properties that are also differently affected by the commonly used antibacterial agent ethanol. We show that B-1 biofilms are protected from ethanol-induced changes in the biofilm's stiffness and that this protective effect can be transferred to NCIB 3610 biofilms by the sole addition of γ-polyglutamate to growing NCIB 3610 biofilms. Together, our results demonstrate the importance of specific biofilm matrix components for the distinct physical properties of
B. subtilis
biofilms.
SaxA-Mediated Isothiocyanate Metabolism in Phytopathogenic Pectobacteria
Authors: Welte Cornelia U. , Rosengarten Jamila F. , de Graaf Rob M. , Jetten Mike S. M. 
Published: February 2016

ABSTRACT

Pectobacteria are devastating plant pathogens that infect a large variety of crops, including members of the family Brassicaceae. To infect cabbage crops, these plant pathogens need to overcome the plant's antibacterial defense mechanisms, where isothiocyanates are liberated by hydrolysis of glucosinolates. Here, we found that a
Pectobacterium
isolate from the gut of cabbage root fly larvae was particularly resistant to isothiocyanate and even seemed to benefit from the abundant
Brassica
root metabolite 2-phenylethyl isothiocyanate as a nitrogen source in an ecosystem where nitrogen is scarce. The
Pectobacterium
isolate harbored a naturally occurring mobile plasmid that contained a
sax
operon. We hypothesized that SaxA was the enzyme responsible for the breakdown of 2-phenylethyl isothiocyanate. Subsequently, we heterologously produced and purified the SaxA protein and characterized the recombinant enzyme. It hydrolyzed 2-phenylethyl isothiocyanate to yield the products carbonyl sulfide and phenylethylamine. It was also active toward another aromatic isothiocyanate but hardly toward aliphatic isothiocyanates. It belongs to the class B metal-dependent beta-lactamase fold protein family but was not, however, able to hydrolyze beta-lactam antibiotics. We discovered that several copies of the
saxA
gene are widespread in full and draft
Pectobacterium
genomes and therefore hypothesize that SaxA might be a new pathogenicity factor of the genus
Pectobacterium
, possibly compromising food preservation strategies using isothiocyanates.
Germs within Worms: Localization of Neorickettsia sp. within Life Cycle Stages of the Digenean Plagiorchis elegans
Authors: Greiman Stephen E. , Rikihisa Yasuko , Cain Jacob , Vaughan Jefferson A. , Tkach Vasyl V. 
Published: February 2016

ABSTRACT

Neorickettsia
spp. are bacterial endosymbionts of parasitic flukes (
Digenea
) that also have the potential to infect and cause disease (e.g., Sennetsu fever) in the vertebrate hosts of the fluke. One of the largest gaps in our knowledge of
Neorickettsia
biology is the very limited information available regarding the localization of the bacterial endosymbiont within its digenean host. In this study, we used indirect immunofluorescence microscopy to visualize
Neorickettsia
sp. within several life cycle stages of the digenean
Plagiorchis elegans
. Individual sporocysts, cercariae, metacercariae, and adults of
P. elegans
naturally infected with
Neorickettsia
sp. were obtained from our laboratory-maintained life cycle, embedded, sectioned, and prepared for indirect immunofluorescence microscopy using anti-
Neorickettsia
risticii
horse serum as the primary antibody.
Neorickettsia
sp. was found within the tegument of sporocysts, throughout cercarial embryos (germ balls) and fully formed cercariae (within the sporocysts), throughout metacercariae, and within the tegument, parenchyma, vitellaria, uteri, testes, cirrus sacs, and eggs of adults. Interestingly,
Neorickettsia
sp. was not found within the ovarian tissue. This suggests that vertical transmission of
Neorickettsia
within adult digeneans occurs via the incorporation of infected vitelline cells into the egg rather than direct infection of the ooplasm of the oocyte, as has been described for other bacterial endosymbionts of invertebrates (e.g.,
Rickettsia
and
Wolbachia
).
Direct and Indirect Horizontal Transmission of the Antifungal Probiotic Bacterium Janthinobacterium lividum on Green Frog (Lithobates clamitans) Tadpoles
Authors: Rebollar Eria A. , Simonetti Stephen J. , Shoemaker William R. , Harris Reid N. 
Published: February 2016

ABSTRACT

Amphibian populations worldwide are being threatened by the disease chytridiomycosis, which is caused by
Batrachochytrium dendrobatidis
. To mitigate the effects of
B. dendrobatidis
, bioaugmentation of antifungal bacteria has been shown to be a promising strategy. One way to implement bioaugmentation is through indirect horizontal transmission, defined as the transfer of bacteria from a host to the environment and to another host. In addition, direct horizontal transmission among individuals can facilitate the spread of a probiotic in a population. In this study, we tested whether the antifungal bacterium
Janthinobacterium lividum
could be horizontally transferred, directly or indirectly, in a laboratory experiment using
Lithobates clamitans
tadpoles. We evaluated the ability of
J. lividum
to colonize the tadpoles' skin and to persist through time using culture-dependent and culture-independent techniques. We also tested whether the addition of
J. lividum
affected the skin community in
L. clamitans
tadpoles. We found that transmission occurred rapidly by direct and indirect horizontal transmission, but indirect transmission that included a potential substrate was more effective. Even though
J. lividum
colonized the skin, its relative abundance on the tadpole skin decreased over time. The inoculation of
J. lividum
did not significantly alter the skin bacterial diversity of
L. clamitans
tadpoles, which was dominated by
Pseudomonas
. Our results show that indirect horizontal transmission can be an effective bioaugmentation method. Future research is needed to determine the best conditions, including the presence of substrates, under which a probiotic can persist on the skin so that bioaugmentation becomes a successful strategy to mitigate chytridiomycosis.
Longitudinal Transcriptome Analysis Reveals a Sustained Differential Gene Expression Signature in Patients Treated for Acute Lyme Disease
Authors: Bouquet Jerome , Soloski Mark J. , Swei Andrea , Cheadle Chris , Federman Scot , Billaud Jean-Noel , Rebman Alison W. , Kabre Beniwende , Halpert Richard , Boorgula Meher , Aucott John N. , Chiu Charles Y. 
Published: February 2016

ABSTRACT

Lyme disease is a tick-borne illness caused by the bacterium
Borrelia burgdorferi
, and approximately 10 to 20% of patients report persistent symptoms lasting months to years despite appropriate treatment with antibiotics. To gain insights into the molecular basis of acute Lyme disease and the ensuing development of post-treatment symptoms, we conducted a longitudinal transcriptome study of 29 Lyme disease patients (and 13 matched controls) enrolled at the time of diagnosis and followed for up to 6 months. The differential gene expression signature of Lyme disease following the acute phase of infection persisted for at least 3 weeks and had fewer than 44% differentially expressed genes (DEGs) in common with other infectious or noninfectious syndromes. Early Lyme disease prior to antibiotic therapy was characterized by marked upregulation of Toll-like receptor signaling but lack of activation of the inflammatory T-cell apoptotic and B-cell developmental pathways seen in other acute infectious syndromes. Six months after completion of therapy, Lyme disease patients were found to have 31 to 60% of their pathways in common with three different immune-mediated chronic diseases. No differential gene expression signature was observed between Lyme disease patients with resolved illness to those with persistent symptoms at 6 months post-treatment. The identification of a sustained differential gene expression signature in Lyme disease suggests that a panel of selected human host-based biomarkers may address the need for sensitive clinical diagnostics during the “window period” of infection prior to the appearance of a detectable antibody response and may also inform the development of new therapeutic targets.

IMPORTANCE
Lyme disease is the most common tick-borne infection in the United States, and some patients report lingering symptoms lasting months to years despite antibiotic treatment. To better understand the role of the human host response in acute Lyme disease and the development of post-treatment symptoms, we conducted the first longitudinal gene expression (transcriptome) study of patients enrolled at the time of diagnosis and followed up for up to 6 months after treatment. Importantly, we found that the gene expression signature of early Lyme disease is distinct from that of other acute infectious diseases and persists for at least 3 weeks following infection. This study also uncovered multiple previously undescribed pathways and genes that may be useful in the future as human host biomarkers for diagnosis and that constitute potential targets for the development of new therapies.
Electroacupuncture Relieves Labour Pain and Influences the Spinal Dynorphin/κ-Opioid Receptor System in Rats
Authors: Jiang Qiu-Yan , Wang Meng-Ying , Li Li , Mo Hai-Xia , Song Jin-Ling , Tang Qian-Li , Feng Xiao-Tao 
Published: February 2016

Background The dynorphin (DYN)/κ-opioid receptor (KOR) system plays a key role in the control of labour pain. Our previous clinical study reported that electroacupuncture (EA) provided intrapartum analgesia, but the underlying mechanisms of action have not been fully elucidated. Aims To observe the effect of EA on labour pain and to explore the underlying mechanisms of action in a rat model. Methods Copulation-confirmed pregnant rats (n=120) were given castor oil to induce labour. Rats remained untreated (control group, n=20) or received either meperidine (an opioid that is commonly used to treat labour pain, n=20) or EA at SP6, LI4, SP6+LI4 or SP10 (four groups, n=20 each). Labour pain was evaluated by the warm water tail-flick test. Serum DYN values were measured by ELISA. Protein and mRNA expression of prodynorphin (PDYN, the precursor protein of DYN) and KOR were analysed by Western blotting and real-time PCR, respectively. Results EA treatment at all acupuncture point combinations studied significantly relieved labour pain and increased serum DYN concentrations, to a degree similar to that achieved with meperidine. EA notably enhanced protein expression of KOR and PDYN and mRNA expression in the lumbar spinal cord but not in the cerebral cortex. The size of effect varied by EA group in the order: SP6>LI4>SP6+LI4>SP10 for all parameters measured, indicating differential effects relating to acupuncture point selection/combination. Conclusions The present study indicates that EA relieves labour pain, at least in part, by regulation of the spinal DYN/KOR system in a rat model.
Patient safety: the landscape of the global research output and gender distribution
Authors: Schreiber Moritz , Klingelhöfer Doris , Groneberg David A , Brüggmann Doerthe 
Published: February 2016

ObjectivesPatient safety is a crucial issue in medicine. Its main objective is to reduce the number of deaths and health damages that are caused by preventable medical errors. To achieve this, it needs better health systems that make mistakes less likely and their effects less detrimental without blaming health workers for failures. Until now, there is no in-depth scientometric analysis on this issue that encompasses the interval between 1963 and 2014. Therefore, the aim of this study is to sketch a landscape of the past global research output on patient safety including the gender distribution of the medical discipline of patient safety by interpreting scientometric parameters. Additionally, respective future trends are to be outlined.SettingThe Core Collection of the scientific database Web of Science was searched for publications with the search term ‘Patient Safety’ as title word that was focused on the corresponding medical discipline. The resulting data set was analysed by using the methodology implemented by the platform NewQIS. To visualise the geographical landscape, state-of-the-art techniques including density-equalising map projections were applied.Results4079 articles on patient safety were identified in the period from 1900 to 2014. Most articles were published in North America, the UK and Australia. In regard to the overall number of publications, the USA is the leading country, while the output ratio to the population of Switzerland was found to exhibit the best performance. With regard to the ratio of the number of publications to the Gross Domestic Product (GDP) per Capita, the USA remains the leading nation but countries like India and China with a low GDP and high population numbers are also profiting.ConclusionsThough the topic is a global matter, the scientific output on patient safety is centred mainly in industrialised countries.