bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a New Method for Diagnosis of Rubella Virus Infection by Reverse Transcription-Loop-Mediated Isothermal Amplification
Authors: Mori Nobuo , Motegi Yoshie , Shimamura Yasushi , Ezaki Takashi , Natsumeda Tomo , Yonekawa Toshihiro , Ota Yoshinori , Notomi Tsugunori , Nakayama Tetsuo 
Published: September 2006

ABSTRACT
We developed a useful method for the detection of rubella virus genome RNA by reverse transcription loop-mediated isothermal amplification (RT-LAMP) and compared the sensitivity of RT-LAMP with that of other virological tests: reverse transcription-PCR (RT-PCR) and virus isolation. The rubella virus genome was amplified by RT-LAMP from clinical isolates obtained between 1987 and 2004 with similar sensitivities to the Takahashi vaccine strain. The detection limit of RT-LAMP was compared with that of RT-PCR using the Takahashi vaccine strain. We detected rubella virus genome material corresponding to 30 PFU/ml in a culture fluid sample by RT-LAMP within 60 min after the extraction of RNA with equal sensitivity to RT-nested PCR. The positive result rates of RT-LAMP, RT-PCR, and virus isolation were also compared using throat swabs obtained from patients who were clinically diagnosed with acute rubella virus infection in 2004 in Tochigi, Japan. Among nine patients with clinical rubella, the positive result rates were three/nine (33.3%) for virus isolation, six/nine (66.7%) for RT-PCR, and seven/nine (77.8%) for RT-LAMP. Consequently, RT-LAMP for rubella virus would be expected to be a reliable rapid diagnostic tool in the clinical setting.
Nosocomial Spread of
Enterococcus faecium
Resistant to Vancomycin and Linezolid in a Tertiary Care Medical Center
Authors: Dobbs Thomas E. , Patel Mukesh , Waites Ken B. , Moser Stephen A. , Stamm Alan M. , Hoesley Craig J. 
Published: September 2006

ABSTRACT

In May 2004 our institution encountered its first clinical isolate of linezolid-resistant, vancomycin-resistant
Enterococcus faecium
(LRVRE). Between October 2004 and July 2005, 40 patients from whom LRVRE organisms were recovered in clinical specimens were characterized. Epidemiologic investigation and pulsed-field gel electrophoresis patterns indicated a clonal outbreak related to nosocomial spread.
Aspergillus
Galactomannan Enzyme-Linked Immunosorbent Assay Cross-Reactivity Caused by Invasive
Geotrichum capitatum
Authors: Giacchino Mareva , Chiapello Nadia , Bezzio Stefania , Fagioli Franca , Saracco Paola , Alfarano Alda , Martini Vincenza , Cimino Giuseppe , Martino Pietro , Girmenia Corrado 
Published: September 2006

ABSTRACT

We report three cases of invasive
Geotrichum capitatum
infection in patients with acute leukemia for which an enzyme-linked immunosorbent assay (ELISA) for
Aspergillus
galactomannan was positive, with no evidence of aspergillosis. Supernatants obtained from suspensions of 17
G. capitatum
strains gave positive reactions with the
Aspergillus
galactomannan ELISA. These clinical and laboratory data seem to suggest that
G. capitatum
produces a soluble antigen that is cross-reactive with
Aspergillus
galactomannan.
Capsule Production in
Bacillus cereus
Strains Associated with Severe Pneumonia
Authors: Sue David , Hoffmaster Alex R. , Popovic Tanja , Wilkins Patricia P. 
Published: September 2006

ABSTRACT

We identified three encapsulated
Bacillus cereus
strains, isolated from patients with severe pneumonia, in a collection of
B. cereus
isolates associated with human illness. We found that the extent of capsule expression was influenced by culturing conditions. Our findings highlight consequent clinical and laboratory diagnostic challenges posed by such isolates.
Staphylococcus aureus
Throat Colonization Is More Frequent than Colonization in the Anterior Nares
Authors: Nilsson Peter , Ripa Torvald 
Published: September 2006

ABSTRACT

The aim of this study was to determine the frequency and persistence of
Staphylococcus aureus
carriage in the throat in relation to anterior naris carriage. By use of a sensitive enrichment broth,
S. aureus
was cultured from the two sites from 259 patients upon admission to an orthopedic ward and from 87 staff members of the same ward. The throat was the most common carriage site in both groups. Forty percent of the patients and 54% of the staff were positive for
S. aureus
in the throat, compared to 31% and 36%, respectively, in the anterior nares. To determine the persistence of carriage, 67 individuals were repeatedly sampled from the anterior nares and the throat over 2 years (5 to 10 sampling occasions; mean, 7.8). The majority, 58% (39/67), were defined as persistent carriers of
S. aureus
, considering culture results from both sites. Of the 39 persistent carriers, 15 individuals were culture positive from only the throat on more than half of the sampling occasions (these are called preferential throat carriers) while only 5% (two individuals) were preferential anterior naris carriers by use of the same definition. Typing of the collected
S. aureus
isolates by pulsed-field gel electrophoresis revealed that the same strain of
S. aureus
was present, over time, in the throat of an individual at least to the same extent as in the anterior nares. Throat carriage was at least as persistent as carriage in the anterior nares.
Effectiveness of Cephalosporins in the Sputum of Patients with Nosocomial Bronchopneumonia
Authors: Klekner Almos , Bagyi Kinga , Bognar Laszlo , Gaspar Attila , Andrasi Melinda , Szabo Judit 
Published: September 2006

ABSTRACT
Nosocomial bronchopneumonia is a frequent complication in patients with chronic intratracheal intubation. Despite targeted antibiotic treatment, production of abundant bronchial secretion containing pathogen bacteria often tends to be chronic, and so mortality drastically increases. This problem led to an investigation of the penetration of five cephalosporin antibiotics into the sputum. Serum and sputum were collected from 24 chronically intubated patients having purulent nosocomial bronchopneumonia treated in an intensive care unit (ICU). Patients received the following doses intravenously every 24 h: five received 70 mg/kg of body weight cefuroxime, four received 110 mg/kg cefamandole, six received 80 mg/kg ceftriaxone, four received 80 mg/kg ceftazidime, and five received 80 mg/kg cefepime. Antibiotic concentrations in the serum and sputum were evaluated by capillary electrophoresis. MICs were determined for bacteria isolated from the purulent bronchial secretions. The mean levels of the cephalosporins in the sputum did not reach the MICs for the bacteria isolated from the same samples. Ceftriaxone was the only one of the investigated five cephalosporins that had a measurable concentration in the sputum (1.4 ± 1.2 mg/liter). The low concentration of antibiotics in the purulent tracheobronchial secretion can be one of the many reasons for ineffective therapy of nosocomial bronchopneumonia in intubated patients in the ICUs. In the case of intubated or mechanically ventilated patients having chronic bronchopneumonia, determination of drug concentration in the bronchial secretion might be considered when selecting an antibiotic for treatment.
Real-Time Reverse Transcription-PCR for Detection of Rotavirus and Adenovirus as Causative Agents of Acute Viral Gastroenteritis in Children
Authors: Logan Catriona , O'Leary John J. , O'Sullivan Niamh 
Published: September 2006

ABSTRACT
Viral pathogens are the most common cause of gastroenteritis in developed countries. Human rotavirus and adenovirus infections are major causes of acute outbreaks and sporadic cases of gastroenteritis, occurring primarily among children less than 2 years of age. Patient hospitalization is often required, with enormous infection control implications. This work describes the development of real-time PCR assays for the detection of group F adenovirus, rotavirus A, and rotavirus C from stool specimens. Two hundred twenty stool samples from pediatric patients exhibiting symptoms of diarrhea and/or vomiting were examined. PCR results were compared with those of virus detection by electron microscopy and latex agglutination antigen detection. The incorporation of an internal-control RNA that was spiked into individual stool extracts functioned as an internal validation for the reporting of PCR-negative results. Rotavirus C was not detected by real-time PCR in the patient stool samples examined. Real-time reverse transcription-PCR resulted in 175% and 111% increases in the rates of detection of adenovirus F and rotavirus A, respectively, compared with latex agglutination testing. Molecular detection increased the number of stool specimens in which causative agents of gastroenteritis were identified by 155% compared to electron microscopy. Genotyping of a proportion of the rotavirus and adenovirus strains identified only genotype G1 rotavirus and both adenovirus genotypes 40 and 41 in circulation within the patient cohort examined. The results highlight the significance of rapid molecular methods for the routine screening of stool samples in hospital laboratories to provide rapid definitive diagnoses.
Identification of Genotype 1 Hepatitis E Virus in Samples from Swine in Cambodia
Authors: Caron M. , Enouf V. , Than S. C. , Dellamonica L. , Buisson Y. , Nicand E. 
Published: September 2006

ABSTRACT
Hepatitis E virus (HEV) is a major enterically transmitted pathogen in many developing countries, where it causes outbreaks and sporadic cases of acute hepatitis. A study conducted with pigs from several livestock farms in Cambodia identified one swine genotype 1 HEV isolate as being associated with prevalent swine genotype 3 HEV.
A Modified Christensen's Urea and CLSI Broth Microdilution Method for Testing Susceptibilities of SixMalasseziaSpecies to Voriconazole, Itraconazole, and Ketoconazole
Authors: Rincón S. , Cepero de García M. C. , Espinel-Ingroff A. 
Published: September 2006

ABSTRACTTwo supplemented broths (Christensen's urea with 0.1% Tween 80 and 0.5% Tween 40 and RPMI 1640 with 1% glycerol, 1% peptone, 1.8% glucose, and 0.05% Tween 80) were evaluated to determine voriconazole, itraconazole, and ketoconazole MICs for 200Malasseziasp. isolates.Malassezia globosaandM. restrictawere the least susceptible species (MICs at which 90% of the isolates tested were inhibited, 1 to ≥8 μg/ml versus 0.25 to 1 μg/ml).
Invader Plus Method Detects Herpes Simplex Virus in Cerebrospinal Fluid and Simultaneously Differentiates Types 1 and 2
Authors: Allawi Hatim T. , Li Haijing , Sander Tamara , Aslanukov Azamat , Lyamichev Victor I. , Blackman Amondrea , Elagin Slava , Tang Yi-Wei 
Published: September 2006

ABSTRACT
We report here on the development and validation of a prototype Invader Plus method for the qualitative detection of herpes simplex virus types 1 and 2 in cerebrospinal fluid (CSF). The method combines PCR and Invader techniques in a single, closed-tube, continuous-reaction format that gives an analytical sensitivity of approximately 10 copies per reaction. The clinical sensitivity and specificity were 100.0% and 98.6%, respectively, when the results of the method were validated against the results obtained with a PCR colorimetric microtiter plate system by use of clinical CSF specimens.
Antibiotic Susceptibility and Molecular Diversity of
Bacillus anthracis
Strains in Chad: Detection of a New Phylogenetic Subgroup
Authors: Maho Angaya , Rossano Alexandra , Hächler Herbert , Holzer Anita , Schelling Esther , Zinsstag Jakob , Hassane Mahamat H. , Toguebaye Bhen S. , Akakpo Ayayi J. , Van Ert Matthew , Keim Paul , Kenefic Leo , Frey Joachim , Perreten Vincent 
Published: September 2006

ABSTRACT

We genotyped 15
Bacillus anthracis
isolates from Chad, Africa, using multiple-locus variable-number tandem repeat analysis and three additional direct-repeat markers. We identified two unique genotypes that represent a novel genetic lineage in the A cluster. Chadian isolates were susceptible to 11 antibiotics and free of 94 antibiotic resistance genes.
Molecular Epidemiology of Adenovirus Isolates from Patients Diagnosed with Intussusception in Melbourne, Australia
Authors: Selvaraj Gowri , Kirkwood Carl , Bines Julie , Buttery Jim 
Published: September 2006

ABSTRACT
Twenty-one intussusception (IS)-associated and 59 temporally linked adenoviral isolates from clinical infections were compared. Species C (15/21 IS- and 32/59 non-IS-associated isolates) dominated. Of these, serotype 2 (AdV-2) (7/15 IS-associated isolates) and serotype 1 (AdV-1) (16/32 non-IS-associated isolates) were the most commonly identified serotypes. DNA restriction analysis of AdV-2 isolates identified six genomic types; of these, type D2 (3/7 IS- and 8/11 non-IS-associated isolates) was the dominant type after BamHI and SmaI digestion. IS-associated isolates are similar to circulating non-IS-associated strains.
Evaluation of Real-Time and Conventional PCR Targeting Complex 85 Genes for Detection of
Mycobacterium leprae
DNA in Skin Biopsy Samples from Patients Diagnosed with Leprosy
Authors: Martinez Alejandra N. , Britto Constança F. P. C. , Nery José A. C. , Sampaio Elizabeth P. , Jardim Márcia R. , Sarno Euzenir N. , Moraes Milton O. 
Published: September 2006

ABSTRACT

In spite of the decrease in the number of registered leprosy patients, the number of new cases diagnosed each year (400,000) has remained essentially unchanged. Leprosy diagnosis is difficult due to the low sensitivity of current methodologies to identify new cases. In this study, conventional and TaqMan real-time PCR assays for detection of
Mycobacterium leprae
DNA were compared to current classification based on clinical, bacteriological, and histological evaluation.
M. leprae
DNA was extracted from frozen skin biopsy specimens from 69 leprosy patients enrolled in the study and was amplified using specific primers for either the antigen 85B-coding gene or the 85A-C intergenic region by using conventional and real-time PCR. The detection rate was 100% among multibacillary (MB) patients and ranged from 62.5% to 79.2% among paucibacillary (PB) patients according to the assay used. The TaqMan system for 85B gene amplification showed the highest sensitivity, although conventional PCR using the 85A-C gene as a target was also efficient. The cycle threshold (

C
T

) values obtained using the TaqMan system were able to statistically (
P
< 0.0001) differentiate MB (mean

C
T

, 28.06; standard deviation [SD], 4.51) from PB (mean

C
T

, 33.06; SD, 2.24) patients. Also, there was a correlation between

C
T

values and the bacteriological index for MB patients (Pearson's
r
, −0.444;
P
= 0.008). Within the PB patients' group, we tested normal skin from six patients exhibiting the pure neuritic form of leprosy (PNL). Five out of six PNL patients were positive for the presence of
M. leprae
DNA, even in the absence of skin lesions. In conclusion, the TaqMan real-time PCR developed here seems to be a useful tool for rapidly detecting and quantifying
M. leprae
DNA in clinical specimens in which bacilli were undetectable by conventional histological staining.
Pulmonary Cholera Due to Infection with a Non-O1
Vibrio cholerae
Strain
Authors: Shannon Jack D. , Kimbrough Robert C. 
Published: September 2006

ABSTRACT

We present 2 cases of primary pulmonary non-O1
Vibrio cholerae
infection. We believe that these are the first documented cases of primary pulmonary infection due to this organism from a freshwater source.
Loss of Catabolic Function in
Streptococcus agalactiae
Strains and Its Association with Neonatal Meningitis
Authors: Domelier Anne-Sophie , van der Mee-Marquet Nathalie , Grandet Adeline , Mereghetti Laurent , Rosenau Agnès , Quentin Roland 
Published: September 2006

ABSTRACT

The abilities of 151
Streptococcus agalactiae
strains to oxidize 95 carbon sources were studied using the Biolog system. Two populations were constituted: one with a high risk of causing meningitis (HR group; 63 strains), and the other with a lower risk of causing meningitis (LR group; 46 strains). Strains belonging to the HR group were significantly less able to use four carbon sources, i.e., α-
d
-glucose-1-phosphate,
d
-ribose, β-methyl-
d
-glucoside, and
d
,
l
-α-glycerol phosphate, than strains from the LR group (
P
≤ 0.004). Moreover, strains in the HR group significantly more frequently possessed one of several mobile genetic elements or genome deletions previously shown to be associated with strains responsible for neonatal meningitis than strains in the LR group (
P
< 0.001). These findings suggest that genetic disruption might have occurred in virulent clones of
S. agalactiae
. Fifteen biotypes (B1 to B15) were identified from the results of oxidation of the four carbon sources, of which six (B1 to B6) included 92% of the isolates belonging to the HR group. Strains of biotypes B1 to B6 are thus 13 times more likely to be able to invade the central nervous system of neonates than strains of biotypes B7 to B15. In addition, 86% of strains recently associated with neonatal meningitis (42 strains studied) were identified as being of biotypes B1 to B6. Identification of particular
S. agalactiae
biotypes may therefore be one of the criteria to assist clinicians in assessing the level of risk of neonatal meningitis when a mother and/or her neonate is colonized with
S. agalactiae
.
As a Bacterial Culture Medium, Citrated Sheep Blood Agar Is a Practical Alternative to Citrated Human Blood Agar in Laboratories of Developing Countries
Authors: Russell F. M. , Biribo S. S. N. , Selvaraj G. , Oppedisano F. , Warren S. , Seduadua A. , Mulholland E. K. , Carapetis J. R. 
Published: September 2006

ABSTRACT

Human blood agar (HuBA) is widely used in developing countries for the isolation of bacteria from clinical specimens. This study compared citrated sheep blood agar (CSBA) and HuBA with defibrinated horse blood agar and defibrinated sheep blood agar (DSBA) for the isolation and antibiotic susceptibility testing of reference and clinical strains of
Streptococcus pneumoniae
,
Streptococcus pyogenes
, and
Staphylococcus aureus
. Reference and clinical strains of all organisms were diluted in brain heart infusion and a clinical specimen of cerebrospinal fluid and cultured on all agars. Viable counts, colony morphology, and colony size were recorded. Susceptibility testing for
S. pneumoniae
and
S. pyogenes
was performed on defibrinated sheep blood Mueller-Hinton agar, citrated sheep blood Mueller-Hinton agar (CSB MHA), and human blood Mueller-Hinton agar plates. For all organisms, the colony numbers were similar on all agars. Substantially smaller colony sizes and absent or minimal hemolysis were noted on HuBA for all organisms. Antibiotic susceptibility results for
S. pneumoniae
were similar for the two sheep blood agars; however, larger zone sizes were displayed on HuBA, and quality control for the reference strain failed on HuBA. For
S. pyogenes
, larger zone sizes were demonstrated on HuBA and CSBA than on DSBA. Poor hemolysis made interpretation of the zone sizes difficult on HuBA. CSBA is an acceptable alternative for the isolation of these organisms. The characteristic morphology is not evident, and hemolysis is poor on HuBA; and so HuBA is not recommended for use for the isolation or the susceptibility testing of any of these organisms. CSB MHA may be suitable for use for the susceptibility testing of
S. pneumoniae
.
Effect of Primer Selection on Estimates of GB Virus C (GBV-C) Prevalence and Response to Antiretroviral Therapy for Optimal Testing for GBV-C Viremia
Authors: Souza I. E. , Allen J. B. , Xiang J. , Klinzman D. , Diaz R. , Zhang S. , Chaloner K. , Zdunek D. , Hess G. , Williams C. F. , Benning L. , Stapleton J. T. 
Published: September 2006

ABSTRACT
GB virus C (GBV-C; also called hepatitis G virus) is a common cause of infection associated with prolonged survival among HIV-infected individuals. The prevalences of GBV-C viremia vary widely in different studies, and there has been poor agreement among different laboratories performing GBV-C RNA detection in quality control studies. To determine the optimal method of measuring GBV-C RNA in clinical samples, samples obtained from 939 HIV-infected subjects were studied using reverse transcription (RT)-PCR methods amplifying four separate regions of the GBV-C genome. Primers amplifying the E2 coding region were 100% specific; however, their sensitivity was only 76.6%. In contrast, primers amplifying three additional conserved regions of the GBV-C genome (the 5′ nontranslated region and the nonstructural protein-coding regions 3 and 5A) were more sensitive but produced higher rates of false-positive results. Using low-specificity primer sets influenced the significance of association between GBV-C viremia and response to antiretroviral therapy. Using a quantitative GBV-C RNA method, the GBV-C RNA concentration did not correlate with baseline or set point HIV RNA levels; however, a correlation between negative, low, and high GBV-C RNA levels and increasing reduction in HIV RNA following antiretroviral therapy was observed. Subjects with both GBV-C E2 antibody and viremia had significantly lower GBV-C RNA levels than did viremic subjects without E2 antibody. These studies demonstrate that accurate detection of GBV-C RNA by nested RT-PCR requires the use of primers representing multiple genome regions. Analyses based on testing with single primers do not lead to reliable conclusions about the association between GBV-C infection and clinical outcomes.
Detection and Characterization of Bovine Coronaviruses in Fecal Specimens of Adult Cattle with Diarrhea during the Warmer Seasons
Authors: Park Su-Jin , Jeong Cheol , Yoon Soon-Seek , Choy Hyoun E. , Saif Linda J. , Park Sung-Hee , Kim You-Jung , Jeong Jae-Ho , Park Sang-Ik , Kim Ha-Hyun , Lee Bong-Joo , Cho Ho-Seong , Kim Sang-Ki , Kang Mun-Il , Cho Kyoung-Oh 
Published: September 2006

ABSTRACTBovine coronavirus (BCoV) is an etiological agent associated with winter dysentery (WD), prevalent in adult cattle during the winter. Although we previously detected, isolated, and characterized BCoV strains from adult cattle with WD (WD-BCoV strains) during the winter in South Korea, the precise epidemiology, as well as the causative agent of diarrhea in adult cattle in the warmer seasons, has not been examined. We examined 184 diarrheic fecal specimens collected from 75 herds of adult cattle from seven provinces during the spring (warm), autumn (warm), and summer (hot) seasons. Bovine coronavirus-positive reactions were detected for 107 (58.2%) diarrheic fecal samples (in 47/75 herds). Of these 107 positive samples, 90 fecal samples from 33 herds tested positive for BCoV alone and 17 fecal samples from 14 herds also tested positive for other pathogens. Biological comparisons between the 9 BCoV strains isolated in this study and the 10 previously isolated WD-BCoV strains revealed that there was no receptor-destroying enzyme (RDE) activity against mouse erythrocytes in the 9 BCoV strains but the 10 WD-BCoV strains had high RDE activity. Phylogenetic analysis of the spike (S) and hemagglutinin/esterase (HE) proteins revealed that all the Korean BCoVs clustered together regardless of season and were distinct from the other known BCoVs, suggesting a distinct evolutionary pathway for the Korean BCoVs. These and previous results revealed a high prevalence and widespread geographical distribution of BCoV, suggesting that this virus is endemic in adult cattle with diarrhea in all seasons in South Korea.