bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive Multicenter Evaluation of a New Line Probe Assay Kit for Identification of Mycobacterium Species and Detection of Drug-Resistant Mycobacterium tuberculosis
Authors: Mitarai Satoshi , Kato Seiya , Ogata Hideo , Aono Akio , Chikamatsu Kinuyo , Mizuno Kazue , Toyota Emiko , Sejimo Akiko , Suzuki Katsuhiro , Yoshida Shiomi , Saito Takefumi , Moriya Ataru , Fujita Akira , Sato Shuko , Matsumoto Tomoshige , Ano Hiromi , Suetake Toshinori , Kondo Yuji , Kirikae Teruo , Mori Toru 
Published: December 2011

ABSTRACT

We evaluated a new line probe assay (LiPA) kit to identify
Mycobacterium
species and to detect mutations related to drug resistance in
Mycobacterium tuberculosis
. A total of 554 clinical isolates of
Mycobacterium tuberculosis
(
n
= 316),
Mycobacterium avium
(
n
= 71),
Mycobacterium intracellulare
(
n
= 51),
Mycobacterium kansasii
(
n
= 54), and other
Mycobacterium
species (
n
= 62) were tested with the LiPA kit in six hospitals. The LiPA kit was also used to directly test 163 sputum specimens. The results of LiPA identification of
Mycobacterium
species in clinical isolates were almost identical to those of conventional methods. Compared with standard drug susceptibility testing results for the clinical isolates, LiPA showed a sensitivity and specificity of 98.9% and 97.3%, respectively, for detecting rifampin (RIF)-resistant clinical isolates; 90.6% and 100%, respectively, for isoniazid (INH) resistance; 89.7% and 96.0%, respectively, for pyrazinamide (PZA) resistance; and 93.0% and 100%, respectively, for levofloxacin (LVX) resistance. The LiPA kit could detect target species directly in sputum specimens, with a sensitivity of 85.6%. Its sensitivity and specificity for detecting RIF-, PZA-, and LVX-resistant isolates in the sputum specimens were both 100%, and those for detecting INH-resistant isolates were 75.0% and 92.9%, respectively. The kit was able to identify mycobacterial bacilli at the species level, as well as drug-resistant phenotypes, with a high sensitivity and specificity.
Pediococcus acidilactici Endocarditis Successfully Treated with Daptomycin
Authors: Iwen Peter C. , Mindru Cezarina , Kalil Andre C. , Florescu Diana F. 
Published: December 2011

ABSTRACT

This report describes the first case of persistent bacteremia with endocarditis caused by
Pediococcus acidilactici
in a 32-year-old male with a history of short gut syndrome following a small bowel transplant. The results showed the utility of sequencing the intergenic spacer region for species identification and successful treatment using daptomycin.
Novel Real-Time Simultaneous Amplification and Testing Method To Accurately and Rapidly Detect Mycobacterium tuberculosis Complex
Authors: Cui Zhenling , Wang Yongzhong , Fang Liang , Zheng Ruijuan , Huang Xiaochen , Liu Xiaoqin , Zhang Gang , Rui Dongmei , Ju Jinliang , Hu Zhongyi 
Published: December 2011

ABSTRACT

The aim of this study was to establish and evaluate a simultaneous amplification and testing method for detection of the
Mycobacterium tuberculosis
complex (SAT-TB assay) in clinical specimens by using isothermal RNA amplification and real-time fluorescence detection. In the SAT-TB assay, a 170-bp
M. tuberculosis
16S rRNA fragment is reverse transcribed to DNA by use of Moloney murine leukemia virus (M-MLV) reverse transcriptase, using specific primers incorporating the T7 promoter sequence, and undergoes successive cycles of amplification using T7 RNA polymerase. Using a real-time PCR instrument, hybridization of an internal 6-carboxyfluorescein–4-[4-(dimethylamino)phenylazo] benzoic acid
N
-succinimidyl ester (FAM-DABCYL)-labeled fluorescent probe can be used to detect RNA amplification. The SAT-TB assay takes less than 1.5 h to perform, and the sensitivity of the assay for detection of
M. tuberculosis
H37Rv is 100 CFU/ml. The TB probe has no cross-reactivity with nontuberculous mycobacteria or other common respiratory tract pathogens. For 253 pulmonary tuberculosis (PTB) specimens and 134 non-TB specimens, the SAT-TB results correlated with 95.6% (370/387 specimens) of the Bactec MGIT 960 culture assay results. The sensitivity, specificity, and positive and negative predictive values of the SAT-TB test for the diagnosis of PTB were 67.6%, 100%, 100%, and 62.0%, respectively, compared to 61.7%, 100%, 100%, and 58.0% for Bactec MGIT 960 culture. For PTB diagnosis, the sensitivities of the SAT-TB and Bactec MGIT 960 culture methods were 97.6% and 95.9%, respectively, for smear-positive specimens and 39.2% and 30.2%, respectively, for smear-negative specimens. In conclusion, the SAT-TB assay is a novel, simple test with a high specificity which may enhance the detection rate of TB. It is therefore a promising tool for rapid diagnosis of
M. tuberculosis
infection in clinical microbiology laboratories.
Leptotrichia Bacteremia in Patients Receiving High-Dose Chemotherapy
Authors: Couturier Marc Roger , Slechta E. Susan , Goulston Claudia , Fisher Mark A. , Hanson Kimberly E. 
Published: December 2011

ABSTRACT

Leptotrichia
spp. are anaerobic, pencil-shaped, Gram-negative rods that are part of the normal oral and intestinal human flora. Although not typically considered pathogenic, invasive
Leptotrichia
infections have been reported in immunosuppressed patients. A perceived rise in the identification of
Leptotrichia
spp. at our institution prompted a retrospective evaluation of these infections. Laboratory and clinical records were reviewed to identify
Leptotrichia
culture-positive patients. Over a 5-year period, 68
Leptotrichia
-positive specimens were identified. Of these, 21% (14/68) were identified in original samples submitted from 13 different patients at our institution, and the remainder (79% [54/68]) were unknown isolates referred from outside hospitals for molecular identification. All in-house
Leptotrichia
were identified from blood cultures. Only 64% (9/14) of these grew on solid media, and 5 were a part of polymicrobial bacteremias containing other enteric pathogens. All local patients were receiving chemotherapy and a majority received hematopoietic stem cell transplant (HSCT) (11/13). All had neutropenic fever with symptoms of mucositis and/or enteritis. Most of the HSCT patients (73% [8/11]) were autologous recipients hospitalized after recent high-dose chemotherapy for multiple myeloma.
L. hongkongensis
, a novel species, was found in the majority of myeloma cases (63% [5/8]). In conclusion, we suggest that
Leptotrichia
spp. may be an underappreciated cause of bacteremia, particularly in multiple myeloma patients receiving cytotoxic chemotherapy for autologous HSCT. In our cohort, these infections were associated with neutropenic fever from an enteric source, and most isolates remained sensitive to standard antibiotics.
Molecular Diagnosis of Subcutaneous Pythium insidiosum Infection by Use of PCR Screening and DNA Sequencing
Authors: Salipante Stephen J. , Hoogestraat Daniel R. , SenGupta Dhruba J. , Murphey Donald , Panayides Kyriacos , Hamilton Emma , Castañeda-Sánchez Irene , Kennedy Jason , Monsaas Peter W. , Mendoza Leonel , Stephens Karen , Dunn James J. , Cookson Brad T. 
Published: December 2011

ABSTRACT

Pythium insidiosum
is an emerging human pathogen classified among brown algae and diatoms that can cause significant morbidity and mortality in otherwise healthy individuals. Here we describe a pediatric patient with pythiosis acquired in the southern United States, diagnosed by molecular screening and DNA sequencing of internal transcribed spacer region 1.
Legionella pneumophila Sequence Type 1/Paris Pulsotype Subtyping by Spoligotyping
Authors: Ginevra Christophe , Jacotin Nathalie , Diancourt Laure , Guigon Ghislaine , Arquilliere Romain , Meugnier Hélène , Descours Ghislaine , Vandenesch Francois , Etienne Jerome , Lina Gérard , Caro Valérie , Jarraud Sophie 
Published: December 2011

ABSTRACT

Endemic strains of
Legionella pneumophila
sequence type 1 (ST1), in particular the ST1/Paris pulsotype, are dispersed worldwide and represent about 10% of culture-proven clinical cases of Legionnaires' disease in France. The high rate of isolation of this strain from both clinical and environmental samples makes identification of the source of infection difficult during epidemiological investigations. The full-length genome sequence of this strain was recently determined, and it revealed the presence of a CRISPR/
cas
complex. The aim of this study was to develop and evaluate a spoligotyping tool based on the diversity of this CRISPR locus that would allow the accurate subtyping of the
L. pneumophila
serogroup 1 ST1/Paris pulsotype. The CRISPR loci of 28
L. pneumophila
ST1/Paris pulsotype isolates were sequenced, and 42 different spacers regions were characterized. A membrane-based spoligotyping method was developed and used to determine the subtypes of 406
L. pneumophila
isolates, including 233 with the ST1/Paris pulsotype profile that were collected in France from 2000 to 2011. A total of 46 different spoligotypes were detected, and 41 of these were specifically identified in the ST1/Paris pulsotype isolates. In 27 of 33 epidemiological investigations, the environmental source of contamination was confirmed by comparing spoligotypes of clinical isolates with those of environmental isolates. With an index of discrimination of 79.72% (95% confidence interval, 75.82 to 83.63), spoligotyping of the
L. pneumophila
ST1/Paris pulsotype has the potential to be a useful complementary genotyping tool for discriminating isolates with undistinguishable pulsed-field gel electrophoresis (PFGE) and ST genotypes, which could help to identify environmental sources of infection.
Presence of Genes Encoding Panton-Valentine Leukocidin Is Not the Primary Determinant of Outcome in Patients with Hospital-Acquired Pneumonia Due to Staphylococcus aureus
Authors: Sharma-Kuinkel Batu K. , Ahn Sun H. , Rude Thomas H. , Zhang Yurong , Tong Steven Y. C. , Ruffin Felicia , Genter Fredric C. , Braughton Kevin R. , DeLeo Frank R. , Barriere Steven L. , Fowler Vance G. 
Published: December 2011

ABSTRACT

The impact of Panton-Valentine leukocidin (PVL) on the outcome in
Staphylococcus aureus
pneumonia is controversial. We genotyped
S. aureus
isolates from patients with hospital-acquired pneumonia (HAP) enrolled in two registrational multinational clinical trials for the genetic elements carrying
pvl
and 30 other virulence genes. A total of 287 isolates (173 methicillin-resistant
S. aureus
[MRSA] and 114 methicillin-susceptible
S. aureus
[MSSA] isolates) from patients from 127 centers in 34 countries for whom clinical outcomes of cure or failure were available underwent genotyping. Of these,
pvl
was detected by PCR and its product confirmed in 23 isolates (8.0%) (MRSA, 18/173 isolates [10.4%]; MSSA, 5/114 isolates [4.4%]). The presence of
pvl
was not associated with a higher risk for clinical failure (4/23 [17.4%] versus 48/264 [18.2%];
P
= 1.00) or mortality. These findings persisted after adjustment for multiple potential confounding variables. No significant associations between clinical outcome and (i) presence of any of the 30 other virulence genes tested, (ii) presence of specific bacterial clone, (iii) levels of alpha-hemolysin, or (iv) delta-hemolysin production were identified. This study suggests that neither
pvl
presence nor
in vitro
level of alpha-hemolysin production is the primary determinant of outcome among patients with HAP caused by
S. aureus
.
The Geographic Origin of Helicobacter pylori Influences the Association of the
homB
Gene with Gastric Cancer
Authors: Kang Jieun , Jones Kathleen R. , Jang Sungil , Olsen Cara H. , Yoo Yun-Jung , Merrell D. Scott , Cha Jeong-Heon 
Published: December 2011

ABSTRACT

We found that South Korean
Helicobacter pylori
isolates predominantly carry
homB
at locus B and that there is no association between the
homB
allele and the
cagA
allele or the development of gastric cancer within this population. Uniquely, several East Asian strains carried multiple copies of the
hom
genes.
Evaluation of Swabs, Transport Media, and Specimen Transport Conditions for Optimal Detection of Viruses by PCR
Authors: Druce Julian , Garcia Katherine , Tran Thomas , Papadakis Georgina , Birch Chris 
Published: December 2011

ABSTRACT
Depletion of swabs and viral transport medium during epidemics may prompt the use of unvalidated alternatives. Swabs collected and transported dry or in saline were compared to commercially available swab/medium combinations for PCR detection of influenza, enterovirus, herpes simplex virus, and adenovirus. Each was detected at an ambient temperature (22°C) and 4°C for 7 days. Detection of influenza on dry or saline swabs is important because of its capacity to cause outbreaks involving large numbers of cases.
Severity of Human Rhinovirus Infection in Immunocompromised Adults Is Similar to That of 2009 H1N1 Influenza
Authors: Kraft Colleen S. , Jacob Jesse T. , Sears Marti H. , Burd Eileen M. , Caliendo Angela M. , Lyon G. Marshall 
Published: December 2011

ABSTRACTThis retrospective chart review of patients at a tertiary referral center compares characteristics and clinical features of patients diagnosed with human rhinovirus (HRV) infection to those of patients with 2009 H1N1 influenza A (pH1N1) during the pandemic respiratory season of 2009 to 2010. Hospital admission rates, intensive care unit (ICU) admissions, and mortality were not statistically different between the HRV and pH1N1 groups; however, more patients in the HRV group were considered immunocompromised.
Detection of Negative-Sense RNA in Packaged Hepatitis E Virions by Use of an Improved Strand-Specific Reverse Transcription-PCR Method
Authors: Chatterjee Subhashis N. , Devhare Pradip B. , Lole Kavita S. 
Published: December 2011

ABSTRACT
Current hepatitis E virus (HEV) negative-sense RNA detection assays have the drawback of false positivity. cDNA synthesis using tag-based primer and Superscript RT-III followed by exonuclease I treatment increased the specificity. Assays could detect as few as 10 copies of negative-sense RNA and could be used in detecting low levels of HEV replication in cells. Virus particles in stool samples of hepatitis E patients showed encapsidation of negative-sense RNA along with HEV genomic RNA.
Noncatalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial Double-Stranded RNA Virus ϕ6 from
De Novo
Initiation to Elongation
Authors: Wright Sam , Poranen Minna M. , Bamford Dennis H. , Stuart David I. , Grimes Jonathan M. 
Published: December 2011

ABSTRACT

RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage ϕ6 uses the bound noncatalytic Mn
2+
to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn
2+
, which must be replaced for elongation to occur. By inserting a dysfunctional Mg
2+
at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in ϕ6 RdRp, and pinpoint the previously unresolved Mn
2+
-dependent step in replication.
The Multibasic Cleavage Site of the Hemagglutinin of Highly Pathogenic A/Vietnam/1203/2004 (H5N1) Avian Influenza Virus Acts as a Virulence Factor in a Host-Specific Manner in Mammals
Authors: Suguitan Amorsolo L. , Matsuoka Yumiko , Lau Yuk-Fai , Santos Celia P. , Vogel Leatrice , Cheng Lily I. , Orandle Marlene , Subbarao Kanta 
Published: December 2011

ABSTRACT

Highly pathogenic avian influenza (HPAI) viruses of the H5 and H7 subtypes typically possess multiple basic amino acids around the cleavage site (MBS) of their hemagglutinin (HA) protein, a recognized virulence motif in poultry. To determine the importance of the H5 HA MBS as a virulence factor in mammals, recombinant wild-type HPAI A/Vietnam/1203/2004 (H5N1) viruses that possessed (H5N1) or lacked (ΔH5N1) the H5 HA MBS were generated and evaluated for their virulence in BALB/c mice, ferrets, and African green monkeys (AGMs) (
Chlorocebus aethiops
). The presence of the H5 HA MBS was associated with lethality, significantly higher virus titers in the respiratory tract, virus dissemination to extrapulmonary organs, lymphopenia, significantly elevated levels of proinflammatory cytokines and chemokines, and inflammation in the lungs of mice and ferrets. In AGMs, neither H5N1 nor ΔH5N1 virus was lethal and neither caused clinical symptoms. The H5 HA MBS was associated with mild enhancement of replication and delayed virus clearance. Thus, the contribution of H5 HA MBS to the virulence of the HPAI H5N1 virus varies among mammalian hosts and is most significant in mice and ferrets and less remarkable in nonhuman primates.
Influenza A Virus Infection Results in a Robust, Antigen-Responsive, and Widely Disseminated Foxp3
+
Regulatory T Cell Response
Authors: Betts Richard J. , Prabhu Nayana , Ho Adrian W. S. , Lew Fei Chuin , Hutchinson Paul E. , Rotzschke Olaf , Macary Paul A. , Kemeny D. Michael 
Published: December 2011

ABSTRACT

Foxp3
+
CD4
+
regulatory T cells (Tregs) represent a highly suppressive T cell subset with well-characterized immunosuppressive effects during immune homeostasis and chronic infections, although the role of these cells in acute viral infections is poorly understood. The present study sought to examine the induction of Foxp3
+
CD4
+
Tregs in a nonlethal murine model of pulmonary viral infection by the use of the prototypical respiratory virus influenza A. We establish that influenza A virus infection results in a robust Foxp3
+
CD4
+
T cell response and that regulatory T cell induction at the site of inflammation precedes the effector T cell response. Induced Foxp3
+
CD4
+
T cells are highly suppressive
ex vivo
, demonstrating that influenza virus-induced Foxp3
+
CD4
+
T cells are phenotypically regulatory. Influenza A virus-induced regulatory T cells proliferate vigorously in response to influenza virus antigen, are disseminated throughout the site of infection and primary and secondary lymphoid organs, and retain Foxp3 expression
in vitro
, suggesting that acute viral infection is capable of inducing a foreign-antigen-specific Treg response. The ability of influenza virus-induced regulatory T cells to suppress antigen-specific CD4
+
and CD8
+
T cell proliferation and cytokine production correlates closely to their ability to respond to influenza virus antigens, suggesting that virus-induced Tregs are capable of attenuating effector responses in an antigen-dependent manner. Collectively, these data demonstrate that primary acute viral infection is capable of inducing a robust, antigen-responsive, and suppressive regulatory T cell response.
Epstein-Barr Virus Downregulates MicroRNA 203 through the Oncoprotein Latent Membrane Protein 1: a Contribution to Increased Tumor Incidence in Epithelial Cells
Authors: Yu Haibo , Lu Jianhong , Zuo Lielian , Yan Qijia , Yu Zhengyuan , Li Xiayu , Huang Jin , Zhao Lian , Tang Hailin , Luo Zhaohui , Liao Qianjin , Zeng Zhaoyang , Zhang Junyi , Li Guiyuan 
Published: December 2011

ABSTRACT

The Epstein-Barr virus (EBV) is highly associated with nasopharyngeal carcinoma (NPC), and it regulates some microRNAs (miRNAs) that are involved in the development of cancer. The role of EBV in the deregulation of cellular miRNAs and how this affects the progression of NPC remain to be investigated. An analysis of the miRNA profile in an EBV-infected cell line revealed that miRNA 203 (miR-203) was downregulated. miR-203 is expressed specifically in epithelial cells. This downregulation of miR-203 was further verified and functionally analyzed. miR-203 was downregulated substantially in epithelial cells and NPC tissues that were latently infected with EBV. Downregulation of miR-203 also occurred during the early stage of EBV infection. Furthermore, the viral oncoprotein, latent membrane protein 1 (LMP1), was responsible for downregulation of miR-203. Removal of the latent EBV genome or suppression of LMP1 resulted in restoration of miR-203 expression. EBV-LMP1 mediated the downregulation of miR-203 at the primary transcript level. E2F3 and CCNG1 were identified as target genes of miR-203. Ectopic expression of miR-203 inhibited EBV-induced S-phase entry and transformation
in vivo
. Overexpression of the targets overcame the effects of miR-203 mimics on the cell cycle, and the expression of target genes in tumor models was inhibited by miR-203. Inhibitors of Jun N-terminal protein kinase (JNK) and NF-κB blocked miR-203 downregulation. These results imply that EBV promotes malignancy by downregulating cellular miR-203, which contributes to the etiology of NPC.
Macrophage Internal HIV-1 Is Protected from Neutralizing Antibodies
Authors: Koppensteiner Herwig , Banning Carina , Schneider Carola , Hohenberg Heinrich , Schindler Michael 
Published: December 2011

ABSTRACT
In macrophages, HIV-1 accumulates in intracellular vesicles designated virus-containing compartments (VCCs). These might play an important role in the constitution of macrophages as viral reservoirs and allow HIV-1 to evade the immune system by sequestration in an internal niche, which is difficult to access from the exterior. However, until now, evidence of whether internal virus accumulations are protected from the host's humoral immune response is still lacking. In order to be able to study the formation and antibody accessibility of VCCs, we generated HIV-1 with green fluorescent protein (GFP)-tagged Gag replicating in primary macrophages. Live-cell observations revealed faint initial cytosolic Gag expression and subsequent large intracellular Gag accumulations which stayed stable over days. Taking advantage of the opportunity to study the accessibility of intracellular VCCs via the cell surface, we demonstrate that macrophage internal HIV-1-containing compartments cannot be targeted by neutralizing antibodies. Furthermore, HIV-1 was efficiently transferred from antibody-treated macrophages to T cells. Three-dimensional reconstruction of electron microscopic slices revealed that Gag accumulations correspond to viral particles within enclosed compartments and convoluted membranes. Thus, although some VCCs were connected to the plasma membrane, the complex membrane architecture of the HIV-1-containing compartment might shield viral particles from neutralizing antibodies. In sum, our study provides evidence that HIV-1 is sequestered into a macrophage internal membranous web, posing an obstacle for the elimination of this viral reservoir.