bluuebunny/crossref_metadata_2025_split huggingface dataset:
Screening for Intermediately Vancomycin-Susceptible and Vancomycin-Heteroresistant Staphylococcus aureus by Use of Vancomycin-Supplemented Brain Heart Infusion Agar Biplates: Defining Growth Interpretation Criteria Based on Gold Standard Confirmation
Authors: Khatib Riad , Riederer Kathleen , Sharma Mamta , Shemes Stephen , Iyer Sugantha P. , Szpunar Susan 
Published: August 2015

ABSTRACT

BHI agars supplemented with vancomycin 4 (BHI-V4) and 3 (BHI-V3) mg/liter have been proposed for screening vancomycin intermediately susceptible
Staphylococcus aureus
(VISA) and heteroresistant (hVISA) phenotypes, respectively, but growth interpretation criteria have not been established. We reviewed the growth results (CFU) during population analysis profile-area under the curve (PAP-AUC) of consecutive methicillin-resistant
Staphylococcus aureus
(MRSA) blood isolates, which were saved intermittently between 1996 and 2012. CFU counts on BHI-V4 and BHI-V3 plates were stratified according to PAP-AUC interpretive criteria: <0.90 (susceptible [S-MRSA]), 0.90 to 1.3 (hVISA), and >1.3 (VISA). CFU cutoffs that best predict VISA and hVISA were determined with the use of receiver operating characteristic (ROC) curves. Mu3, Mu50, and methicillin-susceptible
S. aureus
(MSSA) controls were included. We also prospectively evaluated manufacturer-made BHI-V3/BHI-V4 biplates for screening of 2010-2012 isolates. The PAP-AUC of 616 clinical samples was consistent with S-MRSA, hVISA, and VISA in 550 (89.3%), 48 (7.8%), and 18 (2.9%) instances, respectively. For VISA screening on BHI-V4, a cutoff of 2 CFU/droplet provided 100% sensitivity and 97.7% specificity. To distinguish VISA from hVISA, a cutoff of 16 CFU provided 83.3% sensitivity and 94.7% specificity; the specificity was lowered to 89.5% with a 12-CFU cutoff. For detecting hVISA/VISA on BHI-V3, a 2-CFU/droplet cutoff provided 98.5% sensitivity and 93.8% specificity. These results suggest that 2-CFU/droplet cutoffs on BHI-V4 and BHI-V3 best approximate VISA and hVISA gold standard confirmation, respectively, with minimal overlap in samples with borderline PAP-AUC. Simultaneous screening for VISA/hVISA on manufacturer-made BHI-V4/BHI-V3 biplates is easy to standardize and may reduce the requirement for PAP-AUC confirmation.
Comparison of the Carba NP, Modified Carba NP, and Updated Rosco Neo-Rapid Carb Kit Tests for Carbapenemase Detection
Authors: AbdelGhani Sameh , Thomson Gina K. , Snyder James W. , Thomson Kenneth S. 
Published: August 2015

ABSTRACT
The accurate detection of carbapenemase-producing organisms is a major challenge for clinical laboratories. The Carba NP test is highly accurate but inconvenient, as it requires frequent preparation of fresh imipenem solution. The current study was designed to compare the Carba NP test to two alternative tests for accuracy and convenience. These were a modified Carba NP test that utilized intravenous (i.v.) imipenem-cilastatin, which is less expensive than reference standard imipenem powder, and an updated version of the Rosco Neo-Rapid Carb kit, which does not require the preparation of imipenem solution and has a shelf life of 2 years. The comparison included 87 isolates that produced class A carbapenemases (including KPC-2, -3, -4, -5, -6, and -8, NMC-A, and SME type), 40 isolates that produced metallo-β-lactamases (including NDM-1, GIM-1, SPM-1, IMP-1, -2, -7, -8, -18, and -27, and VIM-1, -2, and -7), 11 isolates that produced OXA-48, and one isolate that produced OXA-181. Negative controls consisted of 50 isolates that produced extended-spectrum β-lactamases (ESBLs), AmpCs (including hyperproducers), K1, other limited-spectrum β-lactamases, and porin and efflux mutants. Each test exhibited 100% specificity and high sensitivity (Carba NP, 100%; Rosco, 99% using modified interpretation guidelines; and modified Carba NP, 96%). A modified approach to interpretation of the Rosco test was necessary to achieve the sensitivity of 99%. If the accuracy of the modified interpretation is confirmed, the Rosco test is an accurate and more convenient alternative to the Carba NP test.
Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage
Authors: Octavia Sophie , Wang Qinning , Tanaka Mark M. , Sintchenko Vitali , Lan Ruiting 
Published: August 2015

ABSTRACT

Salmonella enterica
serovar Typhimurium is an important foodborne human pathogen that often causes self-limiting but severe gastroenteritis. Prolonged excretion of
S
. Typhimurium after the infection can lead to secondary transmissions. However, little is known about within-host genomic variation in bacteria associated with asymptomatic shedding. Genomes of 35 longitudinal isolates of
S
. Typhimurium recovered from 11 patients (children and adults) with culture-confirmed gastroenteritis were sequenced. There were three or four isolates obtained from each patient. Single nucleotide polymorphisms (SNPs) were analyzed in these isolates, which were recovered between 1 and 279 days after the initial diagnosis. Limited genomic variation (5 SNPs or fewer) was associated with short- and long-term carriage of
S
. Typhimurium. None of the isolates was shown to be due to reinfection. SNPs occurred randomly, and the majority of the SNPs were nonsynonymous. Two nonsense mutations were observed. A nonsense mutation in
flhC
rendered the isolate nonmotile, whereas the significance of a nonsense mutation in
yihV
is unknown. The estimated mutation rate is 1.49 × 10
−6
substitution per site per year.
S
. Typhimurium isolates excreted in stools following acute gastroenteritis in children and adults demonstrated limited genomic variability over time, regardless of the duration of carriage. These findings have important implications for the detection of possible transmission events suspected by public health genomic surveillance of
S
. Typhimurium infections.
Prevalence, Risk Factors, and Transmission Dynamics of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae: a National Survey of Cattle Farms in Israel in 2013
Authors: Adler Amos , Sturlesi Na'ama , Fallach Noga , Zilberman-Barzilai Deniz , Hussein Omar , Blum Shlomo E. , Klement Eyal , Schwaber Mitchell J. , Carmeli Yehuda 
Published: August 2015

ABSTRACT

Our objectives were to study the prevalence, risk factors for carriage, and transmission dynamics of extended-spectrum-β-lactamase (ESBL)-producing
Enterobacteriaceae
(ESBLPE) in a national survey of cattle. This was a point prevalence study conducted from July to October 2013 in Israel. Stool samples were collected from 1,226 cows in 123 sections on 40 farms of all production types. ESBLPE were identified in 291 samples (23.7%): 287 contained
Escherichia coli
and 4 contained
Klebsiella pneumoniae
. The number of ESBLPE-positive cows was the highest in quarantine stations and on fattening farms and was the lowest on pasture farms (
P
= 0.03). The number of ESBLPE-positive cows was the lowest in sections containing adult cows (age, >25 months) and highest in sections containing calves (age, <4 months) (
P
< 0.001). Infrastructure variables that were significant risk factors for ESBLPE carriage included crowding, a lack of manure cleaning, and a lack of a cooling (
P
< 0.001 for each), all of which were more common in sections containing calves. Antimicrobial prophylaxis was given almost exclusively to calves and was associated with a high number of ESBLPE carriers (
P
< 0.001). The 287
E. coli
isolates were typed into 106 repetitive extragenic palindromic (REP)-PCR types and mostly harbored
bla
CTX-M-1
or
bla
CTX-M-9
group genes. The isolates on the six farms with ≥15 isolates of ESBLPE were of 4 to 7 different REP-PCR types, with one dominant type being harbored by about half of the isolates. Fourteen types were identified on more than one farm, with only six of the farms being adjacent to each other. The prevalence of ESBLPE carriage is high in calves in cowsheds where the use of antimicrobial prophylaxis is common. ESBLPE disseminate within cowsheds mainly by clonal spread, with limited intercowshed transmission occurring.
Clinical Characteristics, Laboratory Identification, and
In Vitro
Antifungal Susceptibility of Yarrowia (Candida) lipolytica Isolates Causing Fungemia: a Multicenter, Prospective Surveillance Study
Authors: Zhao Ying , Chan Jasper Fuk-Woo , Tsang Chi-Ching , Wang He , Guo Dawen , Pan Yuhong , Xiao Yuling , Yue Na , Chen Jonathan Hon-Kwan , Lau Susanna Kar-Pui , Xu Yingchun , Woo Patrick Chiu-Yat 
Published: August 2015

ABSTRACT

Our case series showed that uncomplicated
Yarrowia lipolytica
fungemia might be treated with catheter removal alone. The Vitek 2 YST identification (ID) card system, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS), and internal transcribed spacer and 25S nuclear ribosomal DNA (nrDNA) gene sequencing provided reliable identification. All isolates had low MICs to voriconazole, echinocandins, and amphotericin B.
Multiplex Molecular Panels for Diagnosis of Gastrointestinal Infection: Performance, Result Interpretation, and Cost-Effectiveness
Authors: Binnicker Matthew J. 
Published: August 2015

ABSTRACT
Gastrointestinal disease is a major cause of morbidity and mortality worldwide, especially among young children and immunocompromised patients. Diarrhea may result from infection with a variety of microbial pathogens, including bacteria, viruses, or parasites. Historically, the diagnosis of infectious diarrhea has been made using microscopy, antigen tests, culture, and real-time PCR. A combination of these traditional tests is often required due to the inability to distinguish between infectious etiologies based on the clinical presentation alone. Recently, several multiplex molecular assays have been developed for the detection of gastrointestinal pathogens directly from clinical stool samples. These panels allow for the detection and identification of up to 20 pathogens in as little as 1 h. This review will focus on the multiplex molecular panels that have received clearance from the FDA for the diagnosis of diarrheal disease and will highlight issues related to test performance, result interpretation, and cost-effectiveness of these new molecular diagnostic tools.
Performance of Xpert MTB/RIF Assay in Diagnosis of Pleural Tuberculosis by Use of Pleural Fluid Samples
Authors: Rufai Syed Beenish , Singh Amit , Kumar Parveen , Singh Jitendra , Singh Sarman 
Published: August 2015

ABSTRACT
Prospectively, 162 pleural fluid samples from patients with probable tuberculous pleural effusion were tested by the Xpert MTB/RIF assay and the Bactec MGIT-960 culture system. Of these, 43 (26.5%) were positive in the MGIT-960 culture, and 23 (14.2%), in the Xpert MTB/RIF assay. The sensitivity and specificity of the Xpert MTB/RIF compared with the MGIT-960 culture were 54.8% and 100%, respectively.
Commentary: Fluoroquinolone Resistance in Salmonella and the Utility of Perfloxacin Disk Diffusion
Authors: Fang Ferric C. 
Published: August 2015

ABSTRACT

Fluoroquinolone resistance is a serious and increasingly common problem in
Salmonella
. Two companion studies in this issue of the
Journal of Clinical Microbiology
(E. Deak, R. Skov, J. A. Hindler, and R. M. Humphries, J Clin Microbiol 53:3405–3410, 2015,
http://dx.doi.org/10.1128/JCM.01393-15
; R. Skov, E. Matuschek, M. Sjölund-Karlsson, J. Åhman, A. Petersen, M. Stegger, M. Torpdahl, and G. Kahlmeter, J Clin Microbiol 53:3411–3417, 2015,
http://dx.doi.org/10.1128/JCM.01287-15
) provide data to support the use of perfloxacin disk diffusion as a convenient and inexpensive surrogate laboratory method to detect fluoroquinolone resistance in
Salmonella
when the direct measurement of fluoroquinolone MICs is not feasible. Recently updated CLSI and EUCAST susceptibility breakpoints will help to optimize clinical outcomes and reduce the likelihood of emergent resistance.
Role of the DNA Sensor STING in Protection from Lethal Infection following Corneal and Intracerebral Challenge with Herpes Simplex Virus 1
Authors: Parker Zachary M. , Murphy Aisling A. , Leib David A. 
Published: August 2015

ABSTRACT

STING is a protein in the cytosolic DNA and cyclic dinucleotide sensor pathway that is critical for the initiation of innate responses to infection by various pathogens. Consistent with this, herpes simplex virus 1 (HSV-1) causes invariable and rapid lethality in STING-deficient (STING
−/−
) mice following intravenous (i.v.) infection. In this study, using real-time bioluminescence imaging and virological assays, as expected, we demonstrated that STING
−/−
mice support greater replication and spread in ocular tissues and the nervous system. In contrast, they did not succumb to challenge via the corneal route even with high titers of a virus that was routinely lethal to STING
−/−
mice by the i.v. route. Corneally infected STING
−/−
mice also showed increased periocular disease and increased corneal and trigeminal ganglia titers, although there was no difference in brain titers. They also showed elevated expression of tumor necrosis factor alpha (TNF-α) and CXCL9 relative to control mice but surprisingly modest changes in type I interferon expression. Finally, we also showed that HSV strains lacking the ability to counter autophagy and the PKR-driven antiviral state had near-wild-type virulence following intracerebral infection of STING
−/−
mice. Together, these data show that while STING is an important component of host resistance to HSV in the cornea, its previously shown immutable role in mediating host survival by the i.v. route was not recapitulated following a mucosal infection route. Furthermore, our data are consistent with the idea that HSV counters STING-mediated induction of the antiviral state and autophagy response, both of which are critical factors for survival following direct infection of the nervous system.

IMPORTANCE
HSV infections represent an incurable source of morbidity and mortality in humans and are especially severe in neonatal and immunocompromised populations. A key step in the development of an immune response is the recognition of microbial components within infected cells. The host protein STING is important in this regard for the recognition of HSV DNA and the subsequent triggering of innate responses. STING was previously shown to be essential for protection against lethal challenge from intravenous HSV-1 infection. In this study, we show that the requirement for STING depends on the infection route. In addition, STING is important for appropriate regulation of the inflammatory response in the cornea, and our data are consistent with the idea that HSV modulates STING activity through inhibition of autophagy. Our results elucidate the importance of STING in host protection from HSV-1 and demonstrate the redundancy of host protective mechanisms, especially following mucosal infection.
Out of the Reservoir: Phenotypic and Genotypic Characterization of a Novel Cowpox Virus Isolated from a Common Vole
Authors: Hoffmann Donata , Franke Annika , Jenckel Maria , Tamošiūnaitė Aistė , Schluckebier Julia , Granzow Harald , Hoffmann Bernd , Fischer Stefan , Ulrich Rainer G. , Höper Dirk , Goller Katja , Osterrieder Nikolaus , Beer Martin 
Published: August 2015

ABSTRACT

The incidence of human cowpox virus (CPXV) infections has increased significantly in recent years. Serological surveys have suggested wild rodents as the main CPXV reservoir. We characterized a CPXV isolated during a large-scale screening from a feral common vole. A comparison of the full-length DNA sequence of this CPXV strain with a highly virulent pet rat CPXV isolate showed a sequence identity of 96%, including a large additional open reading frame (ORF) of about 6,000 nucleotides which is absent in the reference CPXV strain Brighton Red. Electron microscopy analysis demonstrated that the vole isolate, in contrast to the rat strain, forms A-type inclusion (ATI) bodies with incorporated virions, consistent with the presence of complete
ati
and
p4c
genes. Experimental infections showed that the vole CPXV strain caused only mild clinical symptoms in its natural host, while all rats developed severe respiratory symptoms followed by a systemic rash. In contrast, common voles infected with a high dose of the rat CPXV showed severe signs of respiratory disease but no skin lesions, whereas infection with a low dose led to virus excretion with only mild clinical signs. We concluded that the common vole is susceptible to infection with different CPXV strains. The spectrum ranges from well-adapted viruses causing limited clinical symptoms to highly virulent strains causing severe respiratory symptoms. In addition, the low pathogenicity of the vole isolate in its eponymous host suggests a role of common voles as a major CPXV reservoir, and future research will focus on the correlation between viral genotype and phenotype/pathotype in accidental and reservoir species.

IMPORTANCE
We report on the first detection and isolation of CPXV from a putative reservoir host, which enables comparative analyses to understand the infection cycle of these zoonotic orthopox viruses and the relevant genes involved.
In vitro
studies, including whole-genome sequencing as well as
in vivo
experiments using the Wistar rat model and the vole reservoir host allowed us to establish links between genomic sequences and the
in vivo
properties (virulence) of the novel vole isolate in comparison to those of a recent zoonotic CPXV isolated from pet rats in 2009. Furthermore, the role of genes present only in a reservoir isolate can now be further analyzed. These studies therefore allow unique insights and conclusions about the role of the rodent reservoir in CPXV epidemiology and transmission and about the zoonotic threat that these viruses represent.
Genome-Wide Screen Reveals Valosin-Containing Protein Requirement for Coronavirus Exit from Endosomes
Authors: Wong Hui Hui , Kumar Pankaj , Tay Felicia Pei Ling , Moreau Dimitri , Liu Ding Xiang , Bard Frédéric 
Published: August 2015

ABSTRACTCoronaviruses are RNA viruses with a large zoonotic reservoir and propensity for host switching, representing a real threat for public health, as evidenced by severe acute respiratory syndrome (SARS) and the emerging Middle East respiratory syndrome (MERS). Cellular factors required for their replication are poorly understood. Using genome-wide small interfering RNA (siRNA) screening, we identified 83 novel genes supporting infectious bronchitis virus (IBV) replication in human cells. Thirty of these hits can be placed in a network of interactions with viral proteins and are involved in RNA splicing, membrane trafficking, and ubiquitin conjugation. In addition, our screen reveals an unexpected role for valosin-containing protein (VCP/p97) in early steps of infection. Loss of VCP inhibits a previously uncharacterized degradation of the nucleocapsid N protein. This inhibition derives from virus accumulation in early endosomes, suggesting a role for VCP in the maturation of virus-loaded endosomes. The several host factors identified in this study may provide avenues for targeted therapeutics.IMPORTANCECoronaviruses are RNA viruses representing a real threat for public health, as evidenced by SARS and the emerging MERS. However, cellular factors required for their replication are poorly understood. Using genome-wide siRNA screening, we identified novel genes supporting infectious bronchitis virus (IBV) replication in human cells. The several host factors identified in this study may provide directions for future research on targeted therapeutics.
L Particles Transmit Viral Proteins from Herpes Simplex Virus 1-Infected Mature Dendritic Cells to Uninfected Bystander Cells, Inducing CD83 Downmodulation
Authors: Heilingloh Christiane S. , Kummer Mirko , Mühl-Zürbes Petra , Drassner Christina , Daniel Christoph , Klewer Monika , Steinkasserer Alexander 
Published: August 2015

ABSTRACTMature dendritic cells (mDCs) are known as the most potent antigen-presenting cells (APCs) since they are also able to prime/induce naive T cells. Thus, mDCs play a pivotal role during the induction of antiviral immune responses. Remarkably, the cell surface molecule CD83, which was shown to have costimulatory properties, is targeted by herpes simplex virus 1 (HSV-1) for viral immune escape. Infection of mDCs with HSV-1 results in downmodulation of CD83, resulting in reduced T cell stimulation. In this study, we report that not only infected mDCs but also uninfected bystander cells in an infected culture show a significant CD83 reduction. We demonstrate that this effect is independent of phagocytosis and transmissible from infected to uninfected mDCs. The presence of specific viral proteins found in these uninfected bystander cells led to the hypothesis that viral proteins are transferred from infected to uninfected cells via L particles. These L particles are generated during lytic replication in parallel with full virions, called H particles. L particles contain viral proteins but lack the viral capsid and DNA. Therefore, these particles are not infectious but are able to transfer several viral proteins. Incubation of mDCs with L particles indeed reduced CD83 expression on uninfected bystander DCs, providing for the first time evidence that functional viral proteins are transmitted via L particles from infected mDCs to uninfected bystander cells, thereby inducing CD83 downmodulation.IMPORTANCEHSV-1 has evolved a number of strategies to evade the host's immune system. Among others, HSV-1 infection of mDCs results in an inhibited T cell activation caused by degradation of CD83. Interestingly, CD83 is lost not only from HSV-1-infected mDCs but also from uninfected bystander cells. The release of so-called L particles, which contain several viral proteins but lack capsid and DNA, during infection is a common phenomenon observed among several viruses, such as human cytomegalovirus (HCMV), Epstein-Barr virus, and HSV-1. However, the detailed function of these particles is poorly understood. Here, we provide for the first time evidence that functional viral proteins can be transferred to uninfected bystander mDCs via L particles, revealing important biological functions of these particles during lytic replication. Therefore, the transfer of viral proteins by L particles to modulate uninfected bystander cells may represent an additional strategy for viral immune escape.
Oligomerization of Mumps Virus Phosphoprotein
Authors: Pickar Adrian , Elson Andrew , Yang Yang , Xu Pei , Luo Ming , He Biao 
Published: August 2015

ABSTRACT

The mumps virus (MuV) genome encodes a phosphoprotein (P) that is important for viral RNA synthesis. P forms the viral RNA-dependent RNA polymerase with the large protein (L). P also interacts with the viral nucleoprotein (NP) and self-associates to form a homotetramer. The P protein consists of three domains, the N-terminal domain (P
N
), the oligomerization domain (P
O
), and the C-terminal domain (P
C
). While P
N
is known to relax the NP-bound RNA genome, the roles of P
O
and P
C
are not clear. In this study, we investigated the roles of P
O
and P
C
in viral RNA synthesis using mutational analysis and a minigenome system. We found that P
N
and P
C
functions can be
trans
-complemented. However, this complementation requires P
O
, indicating that P
O
is essential for P function. Using this
trans
-complementation system, we found that P forms parallel dimers (P
N
to P
N
and P
C
to P
C
). Furthermore, we found that residues R231, K238, K253, and K260 in P
O
are critical for P's functions. We identified P
C
to be the domain that interacts with L. These results provide structure-function insights into the role of MuV P.

IMPORTANCE
MuV, a paramyxovirus, is an important human pathogen. The P protein of MuV is critical for viral RNA synthesis. In this work, we established a novel minigenome system that allows the domains of P to be complemented in
trans
. Using this system, we confirmed that MuV P forms parallel dimers. An understanding of viral RNA synthesis will allow the design of better vaccines and the development of antivirals.