bluuebunny/crossref_metadata_2025_split huggingface dataset:
VeA Is Associated with the Response to Oxidative Stress in the Aflatoxin Producer Aspergillus flavus
Authors: Baidya Sachin , Duran Rocio M. , Lohmar Jessica M. , Harris-Coward Pamela Y. , Cary Jeffrey W. , Hong Sung-Yong , Roze Ludmila V. , Linz John E. , Calvo Ana M. 
Published: June 2014

ABSTRACT

Survival of fungal species depends on the ability of these organisms to respond to environmental stresses. Osmotic stress or high levels of reactive oxygen species (ROS) can cause stress in fungi resulting in growth inhibition. Both eukaryotic and prokaryotic cells have developed numerous mechanisms to counteract and survive the stress in the presence of ROS. In many fungi, the HOG signaling pathway is crucial for the oxidative stress response as well as for osmotic stress response. This study revealed that while the osmotic stress response is only slightly affected by the master regulator
veA
, this gene, also known to control morphological development and secondary metabolism in numerous fungal species, has a profound effect on the oxidative stress response in the aflatoxin-producing fungus
Aspergillus flavus
. We found that the expression of
A. flavus
homolog genes involved in the HOG signaling pathway is regulated by
veA
. Deletion of
veA
resulted in a reduction in transcription levels of oxidative stress response genes after exposure to hydrogen peroxide. Furthermore, analyses of the effect of VeA on the promoters of
cat1
and
trxB
indicate that the presence of VeA alters DNA-protein complex formation. This is particularly notable in the
cat1
promoter, where the absence of VeA results in abnormally stronger complex formation with reduced
cat1
expression and more sensitivity to ROS in a
veA
deletion mutant, suggesting that VeA might prevent binding of negative transcription regulators to the
cat1
promoter. Our study also revealed that
veA
positively influences the expression of the transcription factor gene
atfB
and that normal formation of DNA-protein complexes in the
cat1
promoter is dependent on AtfB.
Aspergillus parasiticus SU-1 Genome Sequence, Predicted Chromosome Structure, and Comparative Gene Expression under Aflatoxin-Inducing Conditions: Evidence that Differential Expression Contributes to Species Phenotype
Authors: Linz John E. , Wee Josephine , Roze Ludmila V. 
Published: June 2014

ABSTRACT

The filamentous fungi
Aspergillus parasiticus
and
Aspergillus flavus
produce the carcinogenic secondary metabolite aflatoxin on susceptible crops. These species differ in the quantity of aflatoxins B
1
, B
2
, G
1
, and G
2
produced in culture, in the ability to produce the mycotoxin cyclopiazonic acid, and in morphology of mycelia and conidiospores. To understand the genetic basis for differences in biochemistry and morphology, we conducted next-generation sequence (NGS) analysis of the
A. parasiticus
strain SU-1 genome and comparative gene expression (RNA sequence analysis [RNA Seq]) analysis of
A. parasiticus
SU-1 and
A. flavus
strain NRRL 3357 (3357) grown under aflatoxin-inducing and -noninducing culture conditions. Although
A. parasiticus
SU-1 and
A. flavus
3357 are highly similar in genome structure and gene organization, we observed differences in the presence of specific mycotoxin gene clusters and differential expression of specific mycotoxin genes and gene clusters that help explain differences in the type and quantity of mycotoxins synthesized. Using computer-aided analysis of secondary metabolite clusters (antiSMASH), we demonstrated that
A. parasiticus
SU-1 and
A. flavus
3357 may carry up to 93 secondary metabolite gene clusters, and surprisingly, up to 10% of the genome appears to be dedicated to secondary metabolite synthesis. The data also suggest that fungus-specific zinc binuclear cluster (C6) transcription factors play an important role in regulation of secondary metabolite cluster expression. Finally, we identified uniquely expressed genes in
A. parasiticus
SU-1 that encode C6 transcription factors and genes involved in secondary metabolism and stress response/cellular defense. Future work will focus on these differentially expressed
A. parasiticus
SU-1 loci to reveal their role in determining distinct species characteristics.
Application of Coamplification at Lower Denaturation Temperature-PCR Sequencing for Early Detection of Antiviral Drug Resistance Mutations of Hepatitis B Virus
Authors: Wong Danny Ka-Ho , Tsoi Ottilia , Huang Fung-Yu , Seto Wai-Kay , Fung James , Lai Ching-Lung , Yuen Man-Fung 
Published: June 2014

ABSTRACTNucleoside/nucleotide analogue for the treatment of chronic hepatitis B virus (HBV) infection is hampered by the emergence of drug resistance mutations. Conventional PCR sequencing cannot detect minor variants of <20%. We developed a modifiedco-amplification atlowerdenaturation temperature-PCR (COLD-PCR) method for the detection of HBV minority drug resistance mutations. The critical denaturation temperature for COLD-PCR was determined to be 78°C. Sensitivity of COLD-PCR sequencing was determined using serially diluted plasmids containing mixed proportions of HBV reverse transcriptase (rt) wild-type and mutant sequences. Conventional PCR sequencing detected mutations only if they existed in ≥25%, whereas COLD-PCR sequencing detected mutations when they existed in 5 to 10% of the viral population. The performance of COLD-PCR was compared to conventional PCR sequencing and a line probe assay (LiPA) using 215 samples obtained from 136 lamivudine- or telbivudine-treated patients with virological breakthrough. Among these 215 samples, drug resistance mutations were detected in 155 (72%), 148 (69%), and 113 samples (53%) by LiPA, COLD-PCR, and conventional PCR sequencing, respectively. Nineteen (9%) samples had mutations detectable by COLD-PCR but not LiPA, while 26 (12%) samples had mutations detectable by LiPA but not COLD-PCR, indicating both methods were comparable (P= 0.371). COLD-PCR was more sensitive than conventional PCR sequencing. Thirty-five (16%) samples had mutations detectable by COLD-PCR but not conventional PCR sequencing, while none had mutations detected by conventional PCR sequencing but not COLD-PCR (P< 0.0001). COLD-PCR sequencing is a simple method which is comparable to LiPA and superior to conventional PCR sequencing in detecting minor lamivudine/telbivudine resistance mutations.
Use of Anidulafungin as a Surrogate Marker To Predict Susceptibility and Resistance to Caspofungin among 4,290 Clinical Isolates of Candida by Using CLSI Methods and Interpretive Criteria
Authors: Pfaller Michael A. , Diekema Daniel J. , Jones Ronald N. , Castanheira Mariana 
Published: June 2014

ABSTRACTThis study addressed the application of anidulafungin as a surrogate marker to predict the susceptibility ofCandidato caspofungin due to unacceptably high interlaboratory variation of caspofungin MIC values. CLSI reference broth microdilution methods and species-specific interpretive criteria were used to test 4,290 strains ofCandida(eight species), including 71 strains with documentedfksmutations. Caspofungin MIC values were compared with those of anidulafungin to determine the percentage of categorical agreement (CA) and very major (VME), major (ME), and minor error rates, as well as the ability to detectfksmutants. For all 4,290 isolates the CA was 97.1% (0.2% VME and ME, 2.5% minor errors) using anidulafungin as the surrogate. Among the 62 isolates ofCandida albicans(4 isolates),C. tropicalis(5 isolates),C. krusei(4 isolates),C. kefyr(2 isolates), andC. glabrata(47 isolates) that were nonsusceptible (NS; either intermediate [I] or resistant [R]) to both caspofungin and anidulafungin, 52 (83.8%) contained a mutation infks1orfks2. Eight mutants ofC. glabrata, two ofC. albicans, and one each ofC. tropicalisandC. kruseiwere classified as susceptible (S) to both antifungal agents. The remaining 7 mutants (2C. albicansand 5C. glabrata) were susceptible to one of the agents and either intermediate or resistant to the other. Using the epidemiological cutoff value (ECV) of 0.12 μg/ml for both caspofungin and anidulafungin to differentiate wild-type (WT) from non-WT strains ofC. glabrata, 42 of the 55 (76.4%)C. glabratamutants were non-WT and 8 of the 55 (14.5%) were WT for both agents (90.9% concordance). Anidulafungin can accurately serve as a surrogate marker to predict S and R ofCandidato caspofungin.
Extended Characterization of Corynebacterium pyruviciproducens Based on Clinical Strains from Canada and Switzerland
Authors: Goldenberger D. , Hinić V. , Turan S. , Schultheiss E. , Pacheco A. L. , Frei R. , Bernard K. 
Published: June 2014

ABSTRACT

The species
Corynebacterium pyruviciproducens
was described in 2010 based on the features of a single strain. In this report, we describe the chemotaxonomic and phenotypic characteristics of 11
C. pyruviciproducens
clinical strains isolated in Switzerland and Canada in comparison to the strain 06-17730
T
. Heterogeneities within the type strain were found in the 16S rRNA gene and in biochemical markers. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) identification of this species could not be achieved since currently this bacterial species is not included in the corresponding database. Reliable identification is obtained only with sequence-based identification tools. Results of antimicrobial susceptibility testing of this species with an extended panel of antimicrobials are presented here for the first time.
Improved Sensitivity for Molecular Detection of Bacterial and Candida Infections in Blood
Authors: Bacconi Andrea , Richmond Gregory S. , Baroldi Michelle A. , Laffler Thomas G. , Blyn Lawrence B. , Carolan Heather E. , Frinder Mark R. , Toleno Donna M. , Metzgar David , Gutierrez Jose R. , Massire Christian , Rounds Megan , Kennel Natalie J. , Rothman Richard E. , Peterson Stephen , Carroll Karen C. , Wakefield Teresa , Ecker David J. , Sampath Rangarajan 
Published: June 2014

ABSTRACT
The rapid identification of bacteria and fungi directly from the blood of patients with suspected bloodstream infections aids in diagnosis and guides treatment decisions. The development of an automated, rapid, and sensitive molecular technology capable of detecting the diverse agents of such infections at low titers has been challenging, due in part to the high background of genomic DNA in blood. PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) allows for the rapid and accurate identification of microorganisms but with a sensitivity of about 50% compared to that of culture when using 1-ml whole-blood specimens. Here, we describe a new integrated specimen preparation technology that substantially improves the sensitivity of PCR/ESI-MS analysis. An efficient lysis method and automated DNA purification system were designed for processing 5 ml of whole blood. In addition, PCR amplification formulations were optimized to tolerate high levels of human DNA. An analysis of 331 specimens collected from patients with suspected bloodstream infections resulted in 35 PCR/ESI-MS-positive specimens (10.6%) compared to 18 positive by culture (5.4%). PCR/ESI-MS was 83% sensitive and 94% specific compared to culture. Replicate PCR/ESI-MS testing from a second aliquot of the PCR/ESI-MS-positive/culture-negative specimens corroborated the initial findings in most cases, resulting in increased sensitivity (91%) and specificity (99%) when confirmed detections were considered true positives. The integrated solution described here has the potential to provide rapid detection and identification of organisms responsible for bloodstream infections.
Population Dynamics of an Acinetobacter baumannii Clonal Complex during Colonization of Patients
Authors: Wen Hanchun , Wang Ke , Liu Yang , Tay Martin , Lauro Federico M. , Huang Hong , Wu Huayu , Liang Hongjie , Ding Yichen , Givskov Michael , Chen Yiqiang , Yang Liang 
Published: June 2014

ABSTRACT

Acinetobacter baumannii
has emerged as one of the leading pathogens causing hospital-acquired infection. The success of
A. baumannii
as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of
A. baumannii
spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of
A. baumannii
within hosts. Here, whole-genome sequencing was used to analyze population dynamics of
A. baumannii
strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled
A. baumannii
strains belonged to the international clone II (CC92 clonal complex). While the
A. baumannii
strains were found to be stable in three patients, there was a change of
A. baumannii
strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between
A. baumannii
strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when
A. baumannii
colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing
A. baumannii
.
Whole-Genome Analysis of Exserohilum rostratum from an Outbreak of Fungal Meningitis and Other Infections
Authors: Litvintseva Anastasia P. , Hurst Steven , Gade Lalitha , Frace Michael A. , Hilsabeck Remy , Schupp James M. , Gillece John D. , Roe Chandler , Smith David , Keim Paul , Lockhart Shawn R. , Changayil Shankar , Weil M. Ryan , MacCannell Duncan R. , Brandt Mary E. , Engelthaler David M. 
Published: June 2014

ABSTRACT

Exserohilum rostratum
was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of
Exserohilum
infection had been reported, and very little was known about this dematiaceous fungus, which usually infects plants. Here, we report using whole-genome sequencing (WGS) for the detection of single nucleotide polymorphisms (SNPs) and phylogenetic analysis to investigate the molecular origin of the outbreak using 22 isolates of
E. rostratum
retrieved from 19 case patients with meningitis or epidural/spinal abscesses, 6 isolates from contaminated NECC vials, and 7 isolates unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of 8 SNPs were detected among the outbreak genomes, with no more than 2 SNPs separating any 2 of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by ∼136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in
E. rostratum
.
Detection of Methicillin-Resistant Coagulase-Negative Staphylococci by the Vitek 2 System
Authors: Johnson Kristen N. , Andreacchio Kathleen , Edelstein Paul H. 
Published: June 2014

ABSTRACT

The accurate performance of the Vitek 2 GP67 card for detecting methicillin-resistant coagulase-negative staphylococci (CoNS) is not known. We prospectively determined the ability of the Vitek 2 GP67 card to accurately detect methicillin-resistant CoNS, with
mecA
PCR results used as the gold standard for a 4-month period in 2012. Included in the study were 240 consecutively collected nonduplicate CoNS isolates. Cefoxitin susceptibility by disk diffusion testing was determined for all isolates. We found that the three tested systems, Vitek 2 oxacillin and cefoxitin testing and cefoxitin disk susceptibility testing, lacked specificity and, in some cases, sensitivity for detecting methicillin resistance. The Vitek 2 oxacillin and cefoxitin tests had very major error rates of 4% and 8%, respectively, and major error rates of 38% and 26%, respectively. Disk cefoxitin testing gave the best performance, with very major and major error rates of 2% and 24%, respectively. The test performances were species dependent, with the greatest errors found for
Staphylococcus saprophyticus
. While the 2014 CLSI guidelines recommend reporting isolates that test resistant by the oxacillin MIC or cefoxitin disk test as oxacillin resistant, following such guidelines produces erroneous results, depending on the test method and bacterial species tested. Vitek 2 cefoxitin testing is not an adequate substitute for cefoxitin disk testing. For critical-source isolates,
mecA
PCR, rather than Vitek 2 or cefoxitin disk testing, is required for optimal antimicrobial therapy.
Rothia Bacteremia: a 10-Year Experience at Mayo Clinic, Rochester, Minnesota
Authors: Ramanan Poornima , Barreto Jason N. , Osmon Douglas R. , Tosh Pritish K. 
Published: June 2014

ABSTRACT

Rothia
spp. are Gram-positive cocco-bacilli that cause a wide range of serious infections, especially in immunocompromised hosts. Risk factors for
Rothia mucilaginosa
(previously known as
Stomatococcus mucilaginosus
) bacteremia include prolonged and profound neutropenia, malignancy, and an indwelling vascular foreign body. Here, we describe 67 adults at the Mayo Clinic in Rochester, MN, from 2002 to 2012 with blood cultures positive for
Rothia
. Twenty-five of these patients had multiple positive blood cultures, indicating true clinical infection. Among these, 88% (22/25) were neutropenic, and 76% (19/25) had leukemia. Common sources of bacteremia were presumed gut translocation, mucositis, and catheter-related infection. One patient died with
Rothia
infection. Neutropenic patients were less likely to have a single positive blood culture than were nonneutropenic patients. Antimicrobial susceptibility testing was performed on 21% of the isolates. All of the tested isolates were susceptible to vancomycin and most beta-lactams; however, four of six tested isolates were resistant to oxacillin. There was no difference between the neutropenic and nonneutropenic patients in need of intensive care unit care, mortality, or attributable mortality.
Cluster of Escherichia coli Isolates Producing a Plasmid-Mediated OXA-48 β-Lactamase in a Spanish Hospital in 2012
Authors: Fernández Javier , Montero Ignacio , Fleites Ana , Rodicio M. Rosario 
Published: June 2014

ABSTRACT

Three unrelated sequence type 131 (ST131), ST58, and ST83
Escherichia coli
isolates with low-level resistance to imipenem and resistance to ertapenem were recovered in a Spanish hospital from July to October 2012. They were positive for
bla
OXA-48
carried by an IncL/M conjugative plasmid, which may have been acquired from
Klebsiella pneumoniae
.
Development of Two Molecular Approaches for Differentiation of Clinically Relevant Yeast Species Closely Related to Candida guilliermondii and Candida famata
Authors: Feng Xiaobo , Wu Jingsong , Ling Bo , Yang Xianwei , Liao Wanqing , Pan Weihua , Yao Zhirong 
Published: June 2014

ABSTRACT

The emerging pathogens
Candida palmioleophila
,
Candida fermentati
, and
Debaryomyces nepalensis
are often misidentified as
Candida guilliermondii
or
Candida famata
in the clinical laboratory. Due to the significant differences in antifungal susceptibilities and epidemiologies among these closely related species, a lot of studies have focused on the identification of these emerging yeast species in clinical specimens. Nevertheless, limited tools are currently available for their discrimination. Here, two new molecular approaches were established to distinguish these closely related species. The first approach differentiates these species by use of restriction fragment length polymorphism analysis of partial internal transcribed spacer 2 (ITS2) and large subunit ribosomal DNA with the enzymes BsaHI and XbaI in a double digestion. The second method involves a multiplex PCR based on the intron size differences of
RPL18
, a gene coding for a protein component of the large (60S) ribosomal subunit, and species-specific amplification. These two methods worked well in differentiation of these closely related yeast species and have the potential to serve as effective molecular tools suitable for laboratory diagnoses and epidemiological studies.
Isolation of West Nile Virus from Urine Samples of Patients with Acute Infection
Authors: Barzon Luisa , Pacenti Monia , Franchin Elisa , Squarzon Laura , Sinigaglia Alessandro , Ulbert Sebastian , Cusinato Riccardo , Palù Giorgio 
Published: June 2014

ABSTRACT
This study demonstrated that West Nile virus (WNV) excreted in the urine of patients with acute infection can be isolated in cell cultures. In addition, the protocols for WNV isolation from urine samples were standardized, and factors that may affect the efficiency of WNV isolation were identified.
Association of lifestyle factors and suboptimal health status: a cross-sectional study of Chinese students
Authors: Bi Jianlu , Huang Ying , Xiao Ya , Cheng Jingru , Li Fei , Wang Tian , Chen Jieyu , Wu Liuguo , Liu Yanyan , Luo Ren , Zhao Xiaoshan 
Published: June 2014

ObjectivesSuboptimal health status (SHS) is considered to be an intermediate status between disease and health, and is characterised by a decline in vitality, in physiological function and in the capacity for adaptation. Although the incidence of SHS is high, the underlying causes remain unclear. Lifestyle is one of the most important factors affecting health status; however, the relationship between SHS and lifestyle has not been elucidated.DesignCross-sectional survey.SettingA questionnaire, based on ‘Health Promoting Lifestyle Profile-II (HPLP-II)’ and ‘Sub-Health Measurement Scale V1.0 (SHMS V1.0)’, was sent to four colleges in four districts (Guangzhou, Foshan, Zhanjiang and Shaoguan) of China between May and July 2013.ParticipantsA total of 12 429 questionnaires were distributed during the study period, and 11 144 completed responses were received.ResultsThe prevalence rates for the ‘healthy’, ‘SHS’ and ‘disease’ groups of respondents (students) were 22.81% (2542), 55.9% (6234) and 21.25% (2368), respectively. Most of the students reported a ‘moderate’ or ‘good’ lifestyle. There were significant differences in lifestyle and health status between the two genders. It was notable that health status was significantly positively correlated with lifestyle (r=0.563). For every dimension of the HPLP-II model, the mean values were lower for those participants who reported as ‘SHS’ or ‘disease’ than for those who reported that they were ‘healthy’. The individual dimensions of the HPLP-II model, including ‘spiritual growth’, ‘health responsibility’, ‘physical activity’, ‘interpersonal relations’ and ‘stress management’ were all related to SHS.ConclusionsHealth status is significantly positively correlated with lifestyle. Poor lifestyle is a risk factor for SHS. Conversely, adopting a healthier lifestyle can improve SHS.Trial registration numberChiCTR-OCH-12002317.