bluuebunny/crossref_metadata_2025_split huggingface dataset:
Typing of
Campylobacter jejuni
Isolates from Dogs by Use of Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis
Authors: Parsons B. N. , Cody A. J. , Porter C. J. , Stavisky J. H. , Smith J. L. , Williams N. J. , Leatherbarrow A. J. H. , Hart C. A. , Gaskell R. M. , Dingle K. E. , Dawson S. 
Published: October 2009

ABSTRACT

Campylobacter
is a major cause of human gastroenteritis worldwide. Risk of
Campylobacter
infection in humans has been associated with many sources, including dogs. This study aimed to investigate whether
C. jejuni
carried by dogs could potentially be a zoonotic risk for humans and if there were common sources of
C. jejuni
infection for both humans and dogs. Multilocus sequence typing (MLST) together with macrorestriction analysis of genomic DNA using SmaI and pulsed-field gel electrophoresis (PFGE) were both used to analyze 33
C. jejuni
isolates obtained from various dog populations, including those visiting veterinary practices and from different types of kennels. MLST data suggested that there was a large amount of genetic diversity between dog isolates and that the majority of sequence types found in isolates from these dogs were the same as those found in isolates from humans. The main exception was ST-2772, which was isolated from four samples and could not be assigned to a clonal complex. The most commonly identified clonal complex was ST-45 (11 isolates), followed by ST-21 (4 isolates), ST-508 (4 isolates), and ST-403 (3 isolates). The profiles obtained by macrorestriction PFGE were largely in concordance with the MLST results, with a similar amount of genetic diversity found. The diversity of sequence types found within dogs suggests they are exposed to various sources of
C. jejuni
infection. The similarity of these sequence types to
C. jejuni
isolates from humans suggests there may be common sources of infection for both dogs and humans. Although only a small number of household dogs may carry
C. jejuni
, infected dogs should still be considered a potential zoonotic risk to humans, particularly if the dogs originate from kennelled or hunt kennel dog populations, where the prevalence may be higher.
Frequent Detection of Highly Diverse Variants of
Cardiovirus
,
Cosavirus
,
Bocavirus
, and
Circovirus
in Sewage Samples Collected in the United States
Authors: Blinkova O. , Rosario K. , Li L. , Kapoor A. , Slikas B. , Bernardin F. , Breitbart M. , Delwart E. 
Published: October 2009

ABSTRACT

Untreated sewage samples from 12 cities in the United States were screened for the presence of recently characterized RNA and DNA viruses found at high prevalence in the stool specimens of South Asian children. Genetic variants of human cosaviruses and cardioviruses in the
Picornaviridae
family and of DNA circoviruses and human bocaviruses were detected, expanding the known genetic diversity and geographic range of these newly identified viruses. All four virus groups were detected in sewage samples of less than a milliliter from multiple U.S. cities. PCR screening of particle-protected viral nucleic acid in sewage samples could therefore rapidly establish the presence and determine the diversity of four newly described enteric viruses in large urban populations. More frequent and deeper sampling of viral nucleic acids in sewage samples could be used to monitor changes in the prevalence and genetic composition of these and other novel enteric viruses.
Identification ofCryptococcus gattiiby Use ofl-Canavanine Glycine Bromothymol Blue Medium and DNA Sequencing
Authors: Klein K. R. , Hall L. , Deml S. M. , Rysavy J. M. , Wohlfiel S. L. , Wengenack N. L. 
Published: October 2009

ABSTRACTCryptococcus neoformansandCryptococcus gattiiare closely related pathogenic fungi.Cryptococcus neoformansis ecologically widespread and affects primarily immunocompromised patients, whileC. gattiiis traditionally found in tropical climates and has been reported to cause disease in immunocompetent patients.l-Canavanine glycine bromothymol blue (CGB) agar can be used to differentiateC. neoformansandC. gattii, but there are few reports of its performance in routine clinical practice. Growth ofC. gattiion CGB agar produces a blue color, indicating the assimilation of glycine, whileC. neoformansfails to cause a color change. Using reference and clinical strains, we evaluated the ability of CGB agar and D2 large ribosomal subunit DNA sequencing (D2 LSU) to differentiateC. neoformansandC. gattii.One hundred two yeast isolates were screened for urease activity, melanin production, and glycine assimilation on CGB agar as well as by D2 sequencing. Seventeen of 17 (100%)C. gattiiisolates were CGB positive, and 54 of 54C. neoformansisolates were CGB negative. Several yeast isolates other than theC. gattiiisolates were CGB agar positive, indicating that CGB agar cannot be used alone for identification ofC. gattii.D2 correctly identified and differentiated allC. gattiiandC. neoformansisolates. This study demonstrates that the use of CGB agar, in conjunction with urea hydrolysis and Niger seed agar, or D2 LSU sequencing can be reliably used in the clinical laboratory to distinguishC. gattiifromC. neoformans. We describe how CGB agar and D2 sequencing have been incorporated into the yeast identification algorithm in our laboratory.
Comparison of a Rapid Molecular Method, the BD GeneOhm Cdiff Assay, to the Most Frequently Used Laboratory Tests for Detection of Toxin-Producing
Clostridium difficile
in Diarrheal Feces
Authors: Terhes Gabriella , Urbán Edit , Sóki József , Nacsa Enikő , Nagy Elisabeth 
Published: October 2009

ABSTRACT

Six hundred diarrheal stool specimens were collected from inpatients and outpatients at local university hospitals for the detection of toxigenic
Clostridium difficile
using three parallel methods, the BD GeneOhm Cdiff assay, the tissue culture cytotoxicity assay, and a commercially available enzyme-linked fluorescence immunoassay (ELFA) (Vidas
C. difficile
toxin A and B assay; bioMérieux). Toxigenic
C. difficile
culture was also performed to further clarify discordant results. During a 3-month study period, 58 (9.7%) of the 600 diarrheal samples examined were positive by the BD GeneOhm Cdiff assay, while the Vidas
C. difficile
toxin A and B assay and the cytotoxicity assay performed directly on stool samples gave 4.7% and 6.3% positivity rates, respectively. In the case of four samples, BD GeneOhm Cdiff assay results were not evaluable at first because of the presence of PCR inhibitors, but upon repeat testing from the frozen lysates, all of these samples proved to be negative. After resolution with toxigenic culture, the cytotoxicity assay proved to be positive in 55 samples (9.2%), while the ELFA was positive in 37 samples (6.2%). Results of culture and repeated cytotoxicity assays emphasized the importance of the culture method, because the use of ELFA or enzyme immunoassay without a culture method may lead to a substantial portion of toxigenic
C. difficile
strains being missed.
Diagnosis of Endotoxemia with Gram-Negative Bacteremia Is Bacterial Species Dependent: a Meta-Analysis of Clinical Studies
Authors: Hurley James C. 
Published: October 2009

ABSTRACTEndotoxemia is undetectable for up to 60% of cases of bacteremia caused by gram-negative (GN) species, a discordance attributed to the limitations of theLimulusassay for endotoxemia. The lipid A structure of the endotoxin molecule is critical for the sensing of GN bacteria by the host immune system although not so for sensing by theLimulusassay. The lipid A structure of commensalEnterobacteriaceaeis hexa-acyl, whereas non-Enterobacteriaceaehave a broader range of structures. By using a previously published classification of lipid A structures (R. S. Munford, Infect. Immun. 76:454-465, 2008), the association of endotoxemia with bacteremia caused by GN organisms is reexamined for 580 GN bacteremic patients from 46 studies. Endotoxemia was less commonly detected for cases of bacteremia caused bySalmonellaentericaserovar Typhi (four studies; 15 of 55 cases of bacteremia [27%]) than for cases of bacteremia caused byNeisseria meningitidis(five studies; 69 of 84 cases [82%]) andPseudomonas pseudomallei(one study; 38 of 41 cases [93%]) among studies restricted to those with specified cases of bacteremia caused by GN organisms. Among 23 unrestricted studies, endotoxemia was less commonly detected for cases of bacteremia with a commensal member of theEnterobacteriaceae(104 of 240 cases [43%]) than with non-Enterobacteriaceae(59 of 100 cases [59%]) (summary odds ratio, 0.53 [90% confidence interval, 0.33 to 0.85]). This finding is consistent across all the unrestricted studies, even including studies with seemingly contrary results for endotoxemia diagnosis among cases of bacteremia caused by GN bacteria overall. Surprisingly, with bacteremia caused by commensalEnterobacteriaceae, the diagnosis of endotoxemia appears to be unrelated to theLimulusassay sensitivity. Across these 45 studies, the association of endotoxemia with GN bacteremia is variable but consistent for different types of GN bacteremia.
Failure of the BD GeneOhm StaphSR Assay for Direct Detection of Methicillin-Resistant and Methicillin-Susceptible
Staphylococcus aureus
Isolates in Positive Blood Cultures Collected in the United States
Authors: Snyder James W. , Munier Gina K. , Heckman Stacy A. , Camp Pamela , Overman Timothy L. 
Published: October 2009

ABSTRACT

Fifty-nine
Staphylococcus aureus
isolates from one hundred blood cultures containing gram-positive cocci in clusters were identified by conventional methods and the BD GeneOhm StaphSR assay (SR). The SR misidentified three methicillin (meticillin)-resistant
S. aureus
(MRSA) isolates as methicillin-susceptible
S. aureus
(MSSA), while one MSSA isolate tested negative for
S. aureus
. The three MRSA isolates were strains with MREJ types that cannot be detected by the currently available SR.
Screening of a Large Global
Aspergillus fumigatus
Species Complex Collection by Using a Species-Specific Microsphere-Based Luminex Assay
Authors: Etienne Kizee A. , Gade Lalitha , Lockhart Shawn R. , Diekema Daniel J. , Messer Shawn A. , Pfaller Michael A. , Balajee S. Arunmozhi 
Published: October 2009

ABSTRACT

A microsphere-based Luminex assay was developed and validated for rapid identification of
Aspergillus fumigatus
from the other species within the
A. fumigatus
species complex (section
Fumigati
). This molecular tool was then employed to screen 499 clinical
A. fumigatus
species complex isolates collected from multiple medical centers throughout the world with results demonstrating the exclusive presence of
A. fumigatus
.
Detection of Bocavirus in Saliva of Children with and without Respiratory Illness
Authors: Martin Emily T. , Taylor James , Kuypers Jane , Magaret Amalia , Wald Anna , Zerr Danielle , Englund Janet A. 
Published: October 2009

ABSTRACT
We evaluated saliva samples from 149 children 2 to 11 years old for human bocavirus (hBoV) DNA. hBoV was detected in saliva samples at asymptomatic enrollment in 3% (5/149) and during respiratory illness in 2% (2/106) of the cases. hBoV was detected in only 1/149 asymptomatic and 0/106 illness nasal samples.
Identification and Differentiation of Clinically Relevant Mycobacterium Species Directly from Acid-Fast Bacillus-Positive Culture Broth
Authors: Li Haijing , Turhan Vedat , Chokhani Laxmi , Stratton Charles W. , Dunbar Sherry A. , Tang Yi-Wei 
Published: October 2009

ABSTRACT

Mycobacterium
species cause a variety of clinical diseases, some of which may be species specific. Therefore, it is clinically desirable to rapidly identify and differentiate mycobacterial isolates to the species level. We developed a rapid and high-throughput system, MycoID, to identify
Mycobacterium
species directly from acid-fast bacillus (AFB)-positive mycobacterial culture broth. The MycoID system incorporated broad-range PCR followed by suspension array hybridization to identify 17 clinically relevant mycobacterial complexes, groups, and species in one single reaction. We evaluated a total of 271 AFB-positive culture broth specimens, which were identified by reference standard methods in combination with biochemical and molecular tests. The overall identification agreement between the standard and the MycoID system was 89.7% (perfect match) or 97.8% (one match in codetection). In comparison to the standard, the MycoID system possessed an overall sensitivity of 97.1% and specificity of 98.8%. The 159
Mycobacterium avium-M. intracellulare
complex isolates were further identified to the species level by MycoID as being
M. avium
(
n
= 98; 61.1%),
M. intracellulare
(
n
= 57; 35.8%), and mixed
M. avium
and
M. intracellulare
(
n
= 2; 1.3%).
M. avium
was recovered more frequently from sterile sites than
M. intracellulare
(odds ratio, 4.6;
P
= 0.0092). The entire MycoID procedure, including specimen processing, can be completed within 5 h, providing rapid and reliable identification and differentiation of mycobacterium species that is amenable to automation. Additional differentiation of
Mycobacterium avium-M. intracellulare
complex strains into
M. avium
and
M. intracellulare
may provide a tool to better understand the role of
Mycobacterium avium-M. intracellulare
complex isolates in human disease.
Acute Infection with Venezuelan Equine Encephalitis Virus Replicon Particles Catalyzes a Systemic Antiviral State and Protects from Lethal Virus Challenge
Authors: Konopka Jennifer L. , Thompson Joseph M. , Whitmore Alan C. , Webb Drue L. , Johnston Robert E. 
Published: October 2009

ABSTRACT
The host innate immune response provides a critical first line of defense against invading pathogens, inducing an antiviral state to impede the spread of infection. While numerous studies have documented antiviral responses within actively infected tissues, few have described the earliest innate response induced systemically by infection. Here, utilizing Venezuelan equine encephalitis virus (VEE) replicon particles (VRP) to limit infection to the initially infected cells in vivo, a rapid activation of the antiviral response was demonstrated not only within the murine draining lymph node, where replication was confined, but also within distal tissues. In the liver and brain, expression of interferon-stimulated genes was detected by 1 to 3 h following VRP footpad inoculation, reaching peak expression of >100-fold over that in mock-infected animals. Moreover, mice receiving a VRP footpad inoculation 6, 12, or 24 h prior to an otherwise lethal VEE footpad challenge were completely protected from death, including a drastic reduction in challenge virus titers. VRP pretreatment also provided protection from intranasal VEE challenge and extended the average survival time following intracranial challenge. Signaling through the interferon receptor was necessary for antiviral gene induction and protection from VEE challenge. However, VRP pretreatment failed to protect mice from a heterologous, lethal challenge with vesicular stomatitis virus, yet conferred protection following challenge with influenza virus. Collectively, these results document a rapid modulation of the host innate response within hours of infection, capable of rapidly alerting the entire animal to pathogen invasion and leading to protection from viral disease.
Populations of Genomic RNAs Devoted to the Replication or Spread of a Bipartite Plant Virus Differ in Genetic Structure
Authors: Lozano Gloria , Grande-Pérez Ana , Navas-Castillo Jesús 
Published: October 2009

ABSTRACTRNA viruses within a host exist as dynamic distributions of closely related mutants and recombinant genomes. These closely related mutants and recombinant genomes, which are subjected to a continuous process of genetic variation, competition, and selection, act as a unit of selection, termed viral quasispecies. Characterization of mutant spectra within hosts is essential for understanding viral evolution and pathogenesis resulting from the cooperative behavior of viral mutants within viral quasispecies. Furthermore, a detailed analysis of viral variability within hosts is needed to design control strategies, because viral quasispecies are reservoirs of viral variants that potentially can emerge with increased virulence or altered tropism. In this work, we report a detailed analysis of within-host viral populations in 13 field isolates of the bipartiteTomato chlorosis virus(ToCV) (genusCrinivirus, familyClosteroviridae). The intraisolate genetic structure was analyzed based on sequencing data for 755 molecular clones distributed in four genomic regions within the RNA-dependent RNA polymerase (RNA1) and Hsp70h, CP, and CPm (RNA2) open reading frames. Our results showed that populations of ToCV within a host plant have a heterogeneous and complex genetic structure similar to that described for animal and plant RNA viral quasispecies. Moreover, the structures of these populations clearly differ depending on the RNA segment considered, being more complex for RNA1 (encoding replication-associated proteins) than for RNA2 (encoding encapsidation-, systemic-movement-, and insect transmission-relevant proteins). These results support the idea that, in multicomponent RNA viruses, function can generate profound differences in the genetic structures of the different genomic segments.
The 5′ Leader of the mRNA Encoding the Marek's Disease Virus Serotype 1 pp14 Protein Contains an Intronic Internal Ribosome Entry Site with Allosteric Properties
Authors: Tahiri-Alaoui Abdessamad , Matsuda Daiki , Xu Hongtao , Panagiotis Panopoulos , Burman Luke , Lambeth Luke S. , Petherbridge Lawrence , James William , Mauro Vincent , Nair Venugopal 
Published: October 2009

ABSTRACT
We demonstrate the presence of a functional internal ribosome entry site (IRES) within the 5′ leader (designated 5L) from a variant of bicistronic mRNAs that encode the pp14 and RLORF9 proteins from Marek's disease virus (MDV) serotype 1. Transcribed as a 1.8-kb family of immediate-early genes, the mature bicistronic mRNAs have variable 5′ leader sequences due to alternative splicing or promoter usage. Consequently, the presence or absence of the 5L IRES in the mRNA dictates the mode of pp14 translation and leads to the production of two pp14 isoforms that differ in their N-terminal sequences. Real-time reverse transcription-quantitative PCR indicates that the mRNA variants with the 5L IRES is two to three times more abundant in MDV-infected and transformed cells than the mRNA variants lacking the 5L IRES. A common feature to all members of the 1.8-kb family of transcripts is the presence of an intercistronic IRES that we have previously shown to control the translation of the second open reading frame (i.e., RLORF9). Investigation of the two IRESs residing in the same bicistronic reporter mRNA revealed functional synergism for translation efficiency. In analogy with allosteric models in proteins, we propose IRES allostery to describe such a novel phenomenon. The functional implications of our findings are discussed in relation to host-virus interactions and translational control.
NKG2D Ligand MICA Is Retained in thecis-Golgi Apparatus by Human Cytomegalovirus Protein UL142
Authors: Ashiru Omodele , Bennett Neil J. , Boyle Louise H. , Thomas Mair , Trowsdale John , Wills Mark R. 
Published: October 2009

ABSTRACTHuman cytomegalovirus (HCMV) evades T-cell recognition by down-regulating expression of major histocompatibility complex (MHC) class I and II molecules on the surfaces of infected cells. Contrary to the “missing-self” hypothesis, HCMV-infected cells are refractory to lysis by natural killer (NK) cells. Inhibition of NK cell function is mediated by a number of HCMV immune evasion molecules, which operate by delivering inhibitory signals to NK cells and preventing engagement of activating ligands. One such molecule is UL142, which is an MHC class I-related glycoprotein encoded by clinical isolates and low-passage-number strains of HCMV. UL142 is known to down-modulate surface expression of MHC class I-related chain A (MICA), which is a ligand of the activating NK receptor NKG2D. However, the mechanism by which UL142 interferes with MICA is unknown. Here, we show that UL142 localizes predominantly to the endoplasmic reticulum (ER) andcis-Golgi apparatus. The transmembrane domain of UL142 mediates its ER localization, while we propose that the UL142 luminal domain is involved in itscis-Golgi localization. We also confirm that UL142 down-modulates surface expression of full-length MICA alleles while having no effect on the truncated allele MICA*008. However, we demonstrate for the first time that UL142 retains full-length MICA alleles in thecis-Golgi apparatus. In addition, we propose that UL142 interacts with nascent MICA en route to the cell surface but not mature MICA at the cell surface. Our data also demonstrate that the UL142 luminal and transmembrane domains are involved in recognition and intracellular sequestration of full-length MICA alleles.
Insertion of Enhanced Green Fluorescent Protein in a Hinge Region of Vesicular Stomatitis Virus L Polymerase Protein Creates a Temperature-Sensitive Virus That Displays No Virion-Associated Polymerase Activity In Vitro
Authors: Ruedas John B. , Perrault Jacques 
Published: October 2009

ABSTRACT

The RNA-dependent RNA polymerase of viruses belonging to the order
Mononegavirales
is part of a large multifunctional L protein that also catalyzes viral mRNA capping and cap methylation. The L protein of this diverse group of agents displays six blocks of conserved sequences. The precise relationship between these conserved regions and individual functions is largely unknown, except for “domain” VI that clearly encodes a viral mRNA cap methylase. The L protein of morbilliviruses (family
Paramyxoviridae
) was reported to tolerate insertion of the enhanced green fluorescent protein (EGFP) in a region just upstream of domain VI. Recombinant viruses with this insertion grow well in cell culture but are highly attenuated in animal hosts. We show here that the L protein of vesicular stomatitis virus (VSV), the prototype of the
Rhabdoviridae
family, also tolerates insertion of EGFP at a similar site. The modified protein (L
EGFP
) and the resultant recombinant virus both demonstrated a sharp temperature-sensitive phenotype for polymerase activity, with reduced activity at 37°C and no activity at 37.5°C. Neither translation nor methylation of mutant virus transcripts was affected at 37°C. Curiously, mutant virus grown at permissive temperature contained about threefold-less L protein than the wild-type virus did and displayed no virion-associated polymerase activity in vitro. These findings support the notion that a flexible “hinge” region separates the cap methylase domain of L proteins from upstream functions and open up a number of avenues for studies of L-protein function in the more-tractable VSV model system.