bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of Multidrug-Resistant
Salmonella enterica
Serovar Typhimurium Phage Types DT102, DT104, and U302 by Multiplex PCR
Authors: Chiu Cheng-Hsun , Su Lin-Hui , Chu Chi-Hong , Wang Mei-Hwei , Yeh Chia-Ming , Weill Francois-Xavier , Chu Chishih 
Published: July 2006

ABSTRACT

Salmonella enterica
serovar Typhimurium is a common cause of nontyphoidal salmonellosis in humans and animals. Multidrug-resistant serovar Typhimurium phage type DT104, which emerged in the 1990s, has become widely distributed in many countries. A total of 104 clinical isolates of
Salmonella
serogroup B were collected from three major hospitals in Taiwan during 1997 to 2003 and were examined by a multiplex PCR targeting the resistance genes and the
spv
gene of the virulence plasmid. A total of 51 isolates (49%) were resistant to all drugs (ACSSuT [resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline]), and all contained a 1.25-kb PCR fragment of integron that is part of the 43-kb
Salmonella
genomic island 1 (SGI1). The second group was resistant to SSu (28%), and the third was susceptible to all five drugs (13%). Fifty-nine isolates were serotyped to be serovar Typhimurium by the tube agglutination method using H antisera. The virulence plasmid was found in 54 (91.5%) of the 59 serovar Typhimurium isolates. A majority (94.1%) of the
Salmonella
serogroup B isolates with the ACSSuT resistance pattern harbored a virulence plasmid. Phage typing identified three major phage types: DT104, DT120, and U302. Analysis of the isolates by pulsed-field gel electrophoresis showed six genotypes. We found two genotypes in DT104 strains, two in DT120, and the other two in U302. The presence of a monophasic serovar (4,5,12:i:−) has added difficulty in the determination of the serovars of multidrug-resistant
Salmonella
serogroup B isolates. Nevertheless, the multiplex PCR devised in the present study appears to be efficient and useful in the rapid identification of ACSSuT-type serovar Typhimurium with SGI1, irrespective of their phage types.
Comparison of Real-Time PCR Assays with Fluorescent-Antibody Assays for Diagnosis of Respiratory Virus Infections in Children
Authors: Kuypers Jane , Wright Nancy , Ferrenberg James , Huang Meei-Li , Cent Anne , Corey Lawrence , Morrow Rhoda 
Published: July 2006

ABSTRACT

Conventional fluorescent-antibody (FA) methods were compared to real-time PCR assays for detection of respiratory syncytial virus (RSV), influenza virus type A (FluA), parainfluenza virus types 1, 2, and 3 (PIV1, PIV2, and PIV3), human metapneumovirus (MPV), and adenovirus (AdV) in 1,138 specimens from children with respiratory illnesses collected over a 1-year period. At least one virus was detected in 436 (38.3%) specimens by FA and in 608 (53.4%) specimens by PCR (
P
< 0.001). Specimen quality was inadequate for FA in 52 (4.6%) specimens; 13 of these (25%) were positive by PCR. In contrast, 18 (1.6%) specimens could not be analyzed by PCR; 1 of these was positive by FA. The number of specimens positive only by PCR among specimens positive by PCR and/or FA was 18 (7.0%) of 257 for RSV, 18 (13.4%) of 134 for FluA, 25 (64.1%) of 39 for PIV1, 8 (88.9%) of 9 for PIV2, 17 (30.1%) of 55 for PIV3, and 101 (76.5%) of 132 for AdV. MPV was detected in 6.6% of all specimens and in 9.5% of the 702 specimens negative by FA. The mean number of virus copies per milliliter in specimens positive by both PCR and FA was significantly higher, at 6.7 × 10
7
, than that in specimens positive only by PCR, at 4.1 × 10
4
(
P
< 0.001). The PCR assays were significantly more sensitive than FA assays for detecting respiratory viruses, especially parainfluenza virus and adenovirus. Use of real-time PCR to identify viral respiratory pathogens in children will lead to improved diagnosis of respiratory illness.
Rapid Increase in Total Torquetenovirus (TTV) Plasma Viremia Load Reveals an Apparently Transient Superinfection by a TTV of a Novel Group 2 Genotype
Authors: Maggi Fabrizio , Andreoli Elisabetta , Lanini Letizia , Meschi Silvia , Rocchi Jara , Fornai Claudia , Vatteroni Maria Linda , Pistello Mauro , Bendinelli Mauro 
Published: July 2006

ABSTRACT
An apparently transient infection by a superimposed torquetenovirus (TTV) in a subject who already carried three different genotypes of the virus is described. The superinfection induced a rapid increase in the plasma TTV load and a decline in immunocomplexed virus. The superinfecting TTV was a novel group 2 genotype.
First Case Report of
Neisseria lactamica
Causing Cavitary Lung Disease in an Adult Organ Transplant Recipient
Authors: Zavascki Alexandre Prehn , Fritscher Leandro , Superti Silvana , Dias Cícero , Kroth Leonardo , Traesel Moacir Alexandre , Antonello Ivan Carlos Ferreira , Saitovitch David 
Published: July 2006

ABSTRACT

We describe a case of an adult organ recipient patient with a pulmonary cavitary lesion due to
Neisseria lactamica
, a harmless commensal organism that rarely causes human infection. To our knowledge, this is the first report of pulmonary disease caused by this organism and the second case of
N. lactamica
infection in an adult patient.
Etiological Misidentification by Routine Biochemical Tests of Bacteremia Caused by
Gordonia terrae
Infection in the Course of an Episode of Acute Cholecystitis
Authors: Gil-Sande E. , Brun-Otero M. , Campo-Cerecedo F. , Esteban E. , Aguilar L. , García-de-Lomas J. 
Published: July 2006

ABSTRACT

Gordonia terrae
has been reported to be a rare cause of bacteremia. We report the first case of bacteremia associated with acute cholecystitis. Commercial biochemical testing was not able to identify the strain at the genus level, classifying it instead as
Rhodococcus
sp. Definitive identification was obtained by sequencing of the 16S rRNA gene.
Blinded, Multicenter Comparison of Methods To Detect a Drug-Resistant Mutant of Human Immunodeficiency Virus Type 1 at Low Frequency
Authors: Halvas Elias K. , Aldrovandi Grace M. , Balfe Peter , Beck Ingrid A. , Boltz Valerie F. , Coffin John M. , Frenkel Lisa M. , Hazelwood J. Darren , Johnson Victoria A. , Kearney Mary , Kovacs Andrea , Kuritzkes Daniel R. , Metzner Karin J. , Nissley Dwight V. , Nowicki Marek , Palmer Sarah , Ziermann Rainer , Zhao Richard Y. , Jennings Cheryl L. , Bremer James , Brambilla Don , Mellors John W. 
Published: July 2006

ABSTRACT
We determined the abilities of 10 technologies to detect and quantify a common drug-resistant mutant of human immunodeficiency virus type 1 (lysine to asparagine at codon 103 of the reverse transcriptase) using a blinded test panel containing mutant-wild-type mixtures ranging from 0.01% to 100% mutant. Two technologies, allele-specific reverse transcriptase PCR and a Ty1HRT yeast system, could quantify the mutant down to 0.1 to 0.4%. These technologies should help define the impact of low-frequency drug-resistant mutants on response to antiretroviral therapy.
Comparison of the Gen-Probe APTIMA Combo 2 Assay to the AMPLICOR CT/NG Assay for Detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
in Urine Samples from Australian Men and Women
Authors: Lowe Peter , O'Loughlin Peter , Evans Kathryn , White Michael , Bartley Paul B. , Vohra Renu 
Published: July 2006

ABSTRACT

The performance of the APTIMA Combo 2 assay (AC2) for the detection of
Chlamydia trachomatis
and
Neisseria gonorrhoeae
infections in urine samples was compared to that of the AMPLICOR CT/NG assay (AMP). The AC2 performance was superior to that of AMP for both organisms in this study.
Multispacer Typing To Study the Genotypic Distribution ofBartonella henselaePopulations
Authors: Li Wenjun , Chomel Bruno B. , Maruyama Soichi , Guptil Lynn , Sander Anna , Raoult Didier , Fournier Pierre-Edouard 
Published: July 2006

ABSTRACTBartonella henselae, a worldwide fastidious bacterium, has a feline reservoir and is pathogenic for humans. However, the relationship between human and cat isolates ofB. henselae, as well as its population dynamics and geographic heterogeneity, is not fully understood, in part because of the absence of appropriate typing methods. Multilocus sequence typing (MLST), the most discriminatory genotyping method forB. henselae, identified seven genotypes and suggested that human isolates arose from a limited number of cat isolates. Herein, we estimated the discriminatory power of multispacer typing (MST) by studying 126B. henselaecat isolates from various areas of Europe, Asia, and the United States. We identified the nine most variable intergenic spacers conserved by bothB. henselaeandBartonella quintanagenomes. By comparing the sequences obtained from these nine spacers for each studied isolate, we identified 39 MST genotypes. The distribution of isolates into MST genotypes matched their phylogenetic organization into four clusters. MST showed that European and Asian isolates were different, in contrast with American isolates, but failed to identify pandemic strains. Our study demonstrated that MST is a powerful method for genotypingB. henselaeat the strain level and may serve in studying the population dynamics of this bacterium and understanding the relationships between cat and human isolates. Finally, we provide a free-access MST-Rick online software program (http://ifr48.timone.univ-mrs.fr/MST_BHenselae/mst) that investigators may use to compare their own MST sequences to our database.
Rapid Genotypic Detection of Rifampin- and Isoniazid-Resistant
Mycobacterium tuberculosis
Directly in Clinical Specimens
Authors: Bang Didi , Bengård Andersen Åse , Thomsen Vibeke Østergaard 
Published: July 2006

ABSTRACT

A multiplex PCR DNA strip assay (Genotype MTBDR) designed to detect rifampin (
rpoB
) and high-level isoniazid (
katG
) resistance mutations in
Mycobacterium tuberculosis
isolates was optimized for clinical specimens. Successful genotypic results were achieved with 36 of 38 (95%) smear-positive respiratory specimens, allowing rapid therapeutic adjustments in transmittable drug-resistant tuberculosis.
Progression Toward an Improved DNA Amplification-Based Typing Technique in the Study of
Mycobacterium tuberculosis
Epidemiology
Authors: Gopaul Krishna K. , Brown Timothy J. , Gibson Andrea L. , Yates Malcolm D. , Drobniewski Francis A. 
Published: July 2006

ABSTRACT

While high-copy-number IS
6110
-based restriction fragment length polymorphism (HCN-RFLP) is the gold standard for typing most
Mycobacterium tuberculosis
strains, the time taken for culturing and low throughput make it impractical for large-scale prospective typing of large numbers of isolates. The development of a new method, mycobacterial interspersed repetitive units (MIRU), a variation of the original variable-number tandem repeat (VNTR) technique, may provide a viable alternative. Panels based on the original 12-loci MIRU (12MIRU), a combination of 12MIRU and remaining ETR loci (15MIRU-VNTR), and an extended panel with an additional 10 novel regions (25VNTR) were used to study three populations with varying degrees of epidemiological data. MIRU discrimination increased with panel size and the addition of spoligotyping. Combining these two techniques enabled a reduction in the panel size from 25 to 14 loci without a significant loss in discrimination. However, 25VNTR alone or in combination with spoligotyping still possessed weaker discrimination than RFLP for high-copy-number isolates.
Use of 16S rRNA Gene Profiling by Terminal Restriction Fragment Length Polymorphism Analysis To Compare Bacterial Communities in Sputum and Mouthwash Samples from Patients with Cystic Fibrosis
Authors: Rogers G. B. , Carroll M. P. , Serisier D. J. , Hockey P. M. , Jones G. , Kehagia V. , Connett G. J. , Bruce K. D. 
Published: July 2006

ABSTRACT
The bacterial communities present in the oral cavity and the lungs of 19 adult cystic fibrosis (CF) patients were compared by using terminal restriction fragment length polymorphism analysis of 16S rRNA gene PCR products amplified from nucleic acids extracted directly from bacteria in clinical samples. Sputum samples were not found to be subject to profound contamination by oral cavity bacteria. Evidence of colonization of the CF lung by certain oral bacterial species was found.
Multilocus Variable-Number Tandem-Repeat Analysis for Investigation of
Clostridium difficile
Transmission in Hospitals
Authors: Marsh Jane W. , O'Leary Mary M. , Shutt Kathleen A. , Pasculle A. William , Johnson Stuart , Gerding Dale N. , Muto Carlene A. , Harrison Lee H. 
Published: July 2006

ABSTRACT

Clostridium difficile
is a major cause of antibiotic-associated gastrointestinal illness. Recently, an increased incidence of hospital-acquired infections with severe outcomes has been reported in North America and Europe. Current molecular-typing methods for detection of outbreaks and nosocomial transmission are labor-intensive, subjective, or insufficiently discriminatory to differentiate between closely related strains. This report describes the development of multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) for molecular subtyping of
C. difficile
. Seven VNTR loci were identified from the
C. difficile
630 genome by screening an isolate collection of various restriction endonuclease analysis (REA) types. The stability of the loci for short-term epidemiologic investigations was determined by performing MLVA on consecutive isolates of the same REA type from individual patients collected over as many as 90 days. Validation of MLVA for molecular genotyping was performed by direct comparison with REA results obtained from Hines Veterans Affairs Hospital on a combined collection of 40
C. difficile
isolates from two different sources. The ability of MLVA to detect outbreaks was demonstrated on a collection of tertiary-care hospital isolates from a defined
C. difficile
outbreak in 2001. MLVA successfully clustered
C. difficile
isolates of the same REA type and discriminated isolates of unique REA type. Thus, MLVA is an objective, portable genotyping method that permits reliable detection of
C. difficile
outbreaks and can aid epidemiologic investigations of nosocomial transmission.
Survey of Dogs in Japan for Group 2 Canine Coronavirus Infection
Authors: Yachi Akiko , Mochizuki Masami 
Published: July 2006

ABSTRACT
Specimens obtained from 96 dogs with respiratory and enteric clinical signs in Japan were retrospectively examined for group 2 coronavirus by reverse transcription-PCR. Two dogs were found to be positive. Phylogenetic analysis of the spike gene indicated that they were most probably related to the canine respiratory coronavirus recently described in the United Kingdom.
Assessment of MagNA Pure LC Extraction System for Detection of Human Papillomavirus (HPV) DNA in PreservCyt Samples by the Roche AMPLICOR and LINEAR ARRAY HPV Tests
Authors: Stevens Matthew P. , Rudland Elice , Garland Suzanne M. , Tabrizi Sepehr N. 
Published: July 2006

ABSTRACT

Roche Molecular Systems recently released two PCR-based assays, AMPLICOR and LINEAR ARRAY (LA), for the detection and genotyping, respectively, of human papillomaviruses (HPVs). The manual specimen processing method recommended for use with both assays, AmpliLute, can be time-consuming and labor-intensive and is open to potential specimen cross-contamination. We evaluated the Roche MagNA Pure LC (MP) as an alternative for specimen processing prior to use with either assay. DNA was extracted from cervical brushings, collected in PreservCyt media, by AmpliLute and MP using DNA-I and Total Nucleic Acid (TNA) kits, from 150 patients with histologically confirmed cervical abnormalities. DNA was amplified and detected by AMPLICOR and the LA HPV test. Concordances of 96.5% (139 of 144) (κ = 0.93) and 95.1% (135 of 142) (κ = 0.90) were generated by AMPLICOR when we compared DNA extracts from AmpliLute to MP DNA-I and TNA, respectively. The HPV genotype profiles were identical in 78.7 and 74.7% of samples between AmpliLute and DNA-I or TNA, respectively. To improve LA concordance, all 150 specimens were extracted by MP DNA-I protocol after the centrifugation of 1-ml PreservCyt samples. This modified approach improved HPV genotype concordance levels between AmpliLute and MP DNA-I to 88.0% (
P
= 0.043) without affecting AMPLICOR sensitivity. Laboratories that have an automated MP extraction system would find this procedure more feasible and easier to handle than the recommended manual extraction method and could substitute such extractions for AMPLICOR and LA HPV tests once internally validated.
Decrease in eccentric hamstring strength in runners in the Tirol Speed Marathon
Authors: Koller A , Sumann G , Schobersberger W , Hoertnagl H , Haid C 
Published: July 2006

Background:The local muscular endurance of knee flexors, during eccentric work in particular, is important in preventing or delaying kinematic changes associated with fatigue during treadmill running. This result, however, may not be transferable to overground running.Objective:To test the hypothesis that overground running is associated with eccentric hamstring fatigue.Methods:Thirteen runners (12 male and one female) performed an isokinetic muscle test three to four days before and 18 hours after a marathon. Both legs were tested. The testing protocol consisted of concentric and eccentric quadriceps and hamstring contractions.Results:There were no significant differences between peak torque before and after the race, except that eccentric peak hamstring torque (both thighs) was reduced.Conclusion:Overground running (running a marathon) is associated with eccentric hamstring fatigue. Eccentric hamstring fatigue may be a potential risk factor for knee and soft tissue injuries during running. Eccentric hamstring training should therefore be introduced as an integral part of the training programme of runners.
Toll-Like Receptor 9 Agonists Promote Cellular Invasion by Increasing Matrix Metalloproteinase Activity
Authors: Merrell Melinda A. , Ilvesaro Joanna M. , Lehtonen Niko , Sorsa Timo , Gehrs Bradley , Rosenthal Eben , Chen Dongquan , Shackley Brit , Harris Kevin W. , Selander Katri S. 
Published: July 2006

Abstract
Toll-like receptor 9 (TLR9) recognizes microbial DNA. We show here that TLR9 protein is expressed in human breast cancer cells and clinical breast cancer samples. Stimulation of TLR9-expressing breast cancer cells with the TLR9 agonistic CpG oligonucleotides (1-10 μmol/L) dramatically increased their in vitro invasion in both Matrigel assays and three-dimensional collagen cultures. Similar effects on invasion were seen in TLR9-expressing astrocytoma and glioblastoma cells and in the immortalized human breast epithelial cell line MCF-10A. This effect was not, however, dependent on the CpG content of the TLR9 ligands because the non-CpG oligonucleotides induced invasion of TLR9-expressing cells. CpG or non-CpG oligonucleotide-induced invasion in MDA-MB-231 cells was blunted by chloroquine and they did not induce invasion of TLR9− breast cancer cells. Treatment of MDA-MB-231 cells with CpG or non-CpG oligonucleotides induced the formation of ∼50-kDa gelatinolytic band in zymograms. This band and the increased invasion were abolished by a matrix metalloproteinase (MMP) inhibitor GM6001 but not by a serine proteinase inhibitor aprotinin. Furthermore, CpG oligonucleotide treatment decreased tissue inhibitor of metalloproteinase-3 expression and increased levels of active MMP-13 in TLR9-expressing but not TLR9− breast cancer cells without affecting MMP-8. Neutralizing anti-MMP-13 antibodies inhibited the CpG oligonucleotide-induced invasion. These findings suggest that infections may promote cancer progression through a novel TLR9-mediated mechanism. They also propose a new molecular target for cancer therapy, because TLR9 has not been associated with cancer invasiveness previously. (Mol Cancer Res 2006;4(7):437–47)
“Translating” Tumor Hypoxia: Unfolded Protein Response (UPR)–Dependent and UPR-Independent Pathways
Authors: Koumenis Constantinos , Wouters Bradly G. 
Published: July 2006

Abstract
Poor oxygenation (hypoxia) is present in the majority of human tumors and is associated with poor prognosis due to the protection it affords to radiotherapy and chemotherapy. Hypoxia also elicits multiple cellular response pathways that alter gene expression and affect tumor progression, including two recently identified separate pathways that strongly suppress the rates of mRNA translation during hypoxia. The first pathway is activated extremely rapidly and is mediated by phosphorylation and inhibition of the eukaryotic initiation factor 2α. Phosphorylation of this factor occurs as part of a coordinated endoplasmic reticulum stress response program known as the unfolded protein response and activation of this program is required for hypoxic cell survival and tumor growth. Translation during hypoxia is also inhibited through the inactivation of a second eukaryotic initiation complex, eukaryotic initiation factor 4F. At least part of this inhibition is mediated through a Redd1 and tuberous sclerosis complex 1/2–dependent inhibition of the mammalian target of rapamycin kinase. Inhibition of mRNA translation is hypothesized to affect the cellular tolerance to hypoxia in part by promoting energy homeostasis. However, regulation of translation also results in a specific increase in the synthesis of a subset of hypoxia-induced proteins. Consequently, both arms of translational control during hypoxia influence gene expression and phenotype. These hypoxic response pathways show differential activation requirements that are dependent on the level of oxygenation and duration of hypoxia and are themselves highly dynamic. Thus, the severity and duration of hypoxia can lead to different biological and therapeutic consequences. (Mol Cancer Res 2006;4(7):423–36)
Cardioprotection Via Activation of Protein Kinase C-δ Depends on Modulation of the Reverse Mode of the Na+/Ca2+Exchanger
Authors: Bouwman R. Arthur , Salic Kanita , Padding F. Gieneke , Eringa Etto C. , van Beek-Harmsen Brechje J. , Matsuda Toshio , Baba Akemichi , Musters René J.P. , Paulus Walter J. , de Lange Jaap J. , Boer Christa 
Published: July 2006

Background—Pretreatment with the volatile anesthetic sevoflurane protects cardiomyocytes against subsequent ischemic episodes caused by a protein kinase C (PKC)-δ mediated preconditioning effect. Sevoflurane directly modulates cardiac Ca2+handling, and because Ca2+also serves as a mediator in other cardioprotective signaling pathways, possible involvement of the Na+/Ca2+exchanger (NCX) in relation with PKC-δ in sevoflurane-induced cardioprotection was investigated.Methods and Results—Isolated right ventricular rat trabeculae were subjected to simulated ischemia and reperfusion (SI/R), consisting of superfusion with hypoxic glucose-free buffer for 40 minutes after rigor development, followed by reperfusion with normoxic glucose containing buffer. Preconditioning with sevoflurane before SI/R improved isometric force development during contractile recovery at 60 minutes after the end of hypoxic superfusion (83±7% [sevo] versus 57±2% [SI/R];n=8;P<0.01). Inhibition of the reverse mode of the NCX by KB-R7943 (10 μmol/L) or SEA0400 (1 μmol/L) during preconditioning attenuated the protective effect of sevoflurane. KB-R7943 and SEA0400 did not have intrinsic effects on the contractile recovery. Furthermore, inhibition of the NCX in trabeculae exposed to sevoflurane reduced sevoflurane-induced PKC-δ translocation toward the sarcolemma, as demonstrated by digital imaging fluorescent microscopy. The degree of PKC-δ phosphorylation at serine643as determined by western blot analysis was not affected by sevoflurane.Conclusions—Sevoflurane-induced cardioprotection depends on the NCX preceding PKC-δ translocation presumably via increased NCX-mediated Ca2+influx. This may suggest that increased myocardial Ca2+load triggers the cardioprotective signaling cascade elicited by volatile anesthetic agents similar to other modes of preconditioning.