bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Specimen Processing and Nucleic Acid Extraction by the Swab Extraction Tube System versus the MagNA Pure LC System for Laboratory Diagnosis of Herpes Simplex Virus Infections by LightCycler PCR
Authors: Issa N. C. , Espy M. J. , Uhl J. R. , Harmsen W. S. , Mandrekar J. N. , Gullerud R. E. , Davis M. D. , Smith T. F. 
Published: March 2005

ABSTRACT

A total of 563 specimens (234 dermal and 329 genital swabs) from patients suspected of having herpes simplex virus (HSV) infections were processed using two different extraction methods (the MagNA Pure LC system and the swab extraction tube system [SETS]); HSV DNA was amplified by LightCycler PCR. HSV DNA was detected in 157 of 563 specimens (27.9%) processed by the MagNA Pure LC system and in 179 of 563 specimens (31.8%) processed by SETS (
P
< 0.0001). There was no specimen processed by the MagNA Pure LC extraction method that was positive only for HSV DNA. Of 157 specimens positive by both methods, HSV DNA copy levels were higher (using cycle crossover points [cycle threshold {

C
T

}]) with SETS (mean

C
T

, 25.9 cycles) than with the MagNA Pure LC system (mean

C
T

, 32.0 cycles) (
P
< 0.0001). The time to process 32 samples was longer with the MagNA Pure LC extraction system (90 min) than with SETS (35 min). HSV DNA extraction using SETS is faster, less expensive, and more sensitive than the MagNA Pure LC system and could replace the latter for the laboratory diagnosis of HSV infections using LightCycler PCR.
Rapid Identification of the Coxsackievirus A24 Variant by Molecular Serotyping in an Outbreak of Acute Hemorrhagic Conjunctivitis
Authors: Park Sang-Won , Lee Chang-Seop , Jang Hee-Chang , Kim Eui-Chong , Oh Myoung-don , Choe Kang-Won 
Published: March 2005

ABSTRACT

We evaluated the clinical applicability of a molecular serotyping method for determination of the cause of epidemic acute hemorrhagic conjunctivitis. Seventy conjunctival swab specimens from individuals involved in a nationwide acute hemorrhagic conjunctivitis outbreak were tested. Viral culture and a molecular biology-based assay were compared by directly using clinical specimens. On the one hand, virus culture was done to isolate the enteroviruses, and serotyping was done by a coxsackievirus A24 variant-specific PCR. On the other hand, the original clinical specimens were directly screened for enterovirus by reverse transcription (RT)-PCR with panenterovirus-specific primers. Enterovirus screening-positive specimens were subjected to RT-PCR for detection of the VP1 region of enterovirus, and the amplicons were sequenced. Molecular serotyping was done by calculating the pairwise identity scores for the sequences with the maximum identities to the sequences of known prototype enteroviruses. Thirty-two specimens (45.7%) were culture positive, whereas 37 specimens (52.8%) were screening PCR positive (
P
< 0.001). The VP1 regions were amplified from 21 of the 37 specimens (56.8%), and the products amplified from 9 specimens were appropriately sequenced. These nine sequences were homologous with the sequence of the coxsackievirus A24 variant. Molecular serotyping by direct use of clinical specimens without cell culture could be applied for the rapid identification of the causative agent of epidemic acute hemorrhagic conjunctivitis.
Multiprefectural Spread of Gastroenteritis Outbreaks Attributable to a Single Genogroup II Norovirus Strain from a Tourist Restaurant in Nagasaki, Japan
Authors: Hirakata Yoichi , Arisawa Kokichi , Nishio Osamu , Nakagomi Osamu 
Published: March 2005

ABSTRACT
A series of gastroenteritis outbreaks caused by noroviruses (NVs) among tourist groups from several prefectures was associated with eating a lunch prepared by a restaurant in Nagasaki City, Japan, on 18 and 19 November 2003. A retrospective cohort study was performed to estimate the magnitude of the outbreak and identify the source of infection. Epidemiological information was obtained through the local public health centers in the areas where the illness occurred. Stool and vomit specimens and food and environmental samples were analyzed by reverse transcription-PCR with genogroup-specific primers. Positive samples were sequenced and analyzed phylogenetically. Of 1,492 tourists who ate a lunch prepared by the restaurant during the 2-day period, 660 (44.2%) developed illness, with an average incubation time of 31.2 h. Whereas NVs were not detected in any food samples, identical sequences most closely related to the Mexico genotype of genogroup II NV were found in specimens from case patients, restaurant staff, and the kitchen table. Food handlers were concluded to be the source of the outbreak as a result of the contamination of several meals. The series of outbreaks described here exemplifies the role of tourism as a contemporary way to distribute a single infectious agent to multiple and geographically remote areas.
Novel Antibody-Lectin Enzyme-Linked Immunosorbent Assay That Distinguishes Prion Proteins in Sporadic and Variant Cases of Creutzfeldt-Jakob Disease
Authors: Pan Tao , Li Ruliang , Wong Boon-Seng , Kang Shin-Chung , Ironside James , Sy Man-Sun 
Published: March 2005

ABSTRACTWe used different anti-prion protein (anti-PrP) monoclonal antibodies to capture either full-length or truncated PrP species and then used biotinylated lectin to compare the nature of the glycans on bound PrP species present in control, sporadic Creutzfeldt-Jakob disease (sCJD), or variant CJD (vCJD) brains. When full-length PrP species in these three groups were compared, no significant difference in the binding of concanavalin A orAleuria aurantialectin was detected. However, the binding ofRicinus communisagglutinin I (RCA) to sCJD and vCJD samples was significantly increased. In contrast, when only truncated PrP species were compared, only vCJD samples had more RCA binding activity. Therefore, while most of the RCA binding activity in sCJD is restricted to the full-length PrP species, the RCA binding activity in vCJD is associated with truncated and full-length PrP species. Furthermore, the RCA binding activity in sCJD and vCJD samples is mostly associated with proteinase K-resistant PrP species, a known signature of infectious prion. Therefore, PrP species in sCJD and vCJD have dissimilar lectin immunoreactivity, which reflects differences in their N-linked glycans. These differences may account for the distinct phenotypes of sCJD and vCJD.
Ascariasis Is a Zoonosis in Denmark
Authors: Nejsum Peter , Parker E. Davis , Frydenberg Jane , Roepstorff Allan , Boes Jaap , Haque Rashidul , Astrup Ingrid , Prag Jørgen , Skov Sørensen Uffe B. 
Published: March 2005

ABSTRACT

A preliminary epidemiological survey indicated an association between
Ascaris
infections in Danish patients and contact with pigs or pig manure. In the present study, we compared
Ascaris
worms collected from humans and
Ascaris
worms collected from pigs by amplified fragment length polymorphism (AFLP) analysis, a technique for whole-genome fingerprinting, and by PCR-linked restricted fragment length polymorphism (PCR-RFLP) analysis of the internal transcribed spacer region of nuclear rDNA. The AFLP data were analyzed by distance- and model-based clustering methods. These results assigned
Ascaris
worms from Danish patients to a cluster different from that for worms from humans in other geographic areas. In contrast, worms from humans and pigs in Denmark were assigned to the same cluster. These results were supported by the PCR-RFLP results. Thus, all of the examined Danish patients had acquired
Ascaris
infections from domestic pigs; ascariasis may therefore be considered a zoonotic disease in Denmark.
Rapid Identification of Staphylococcal Strains from Positive-Testing Blood Culture Bottles by Internal Transcribed Spacer PCR Followed by Microchip Gel Electrophoresis
Authors: Fujita Shin-Ichi , Senda Yasuko , Iwagami Thikako , Hashimoto Takuma 
Published: March 2005

ABSTRACT

PCR analysis of the 16S-23S rRNA gene internal transcribed spacer (ITS) followed by microchip gel electrophoresis (MGE) was evaluated for its usefulness in identification of staphylococci. Forty ITS PCR patterns were demonstrated among 228 isolated colonies of
Staphylococcus aureus
: 26 patterns for methicillin-susceptible
S. aureus
(MSSA; 91 strains), 11 patterns for methicillin-resistant
S. aureus
(MRSA; 99 strains), and 3 patterns for both MSSA and MRSA (38 strains). Thirty-seven control strains of coagulase-negative staphylococci (CNS) representing 16 species showed unique ITS PCR patterns (24 patterns) at the species and subspecies levels: two patterns for
S. caprae
,
S. cohnii
,
S. haemolyticus
, and
S. saprophyticus
; three patterns for
S. lugdunensis
; four patterns for
S. capitis
; and one pattern for each of the other CNS species. The combined PCR-MGE method was prospectively adapted to the positive blood culture bottles, and this method correctly identified MSSA and MRSA in 102 (89%) of 114 blood cultures positive for
S. aureus
on the basis of the ITS PCR patterns. Eight ITS PCR patterns were demonstrated from 166 blood culture bottles positive for CNS. The most frequent CNS species isolated from blood cultures were
S. epidermidis
(76%),
S. capitis
(11%), and
S. hominis
(8%). Overall, all 280 blood culture bottles shown to contain a single
Staphylococcus
species by routine phenotypic methods were correctly identified by the PCR-MGE method at the species level, whereas the organism failed to be identified in 8 culture bottles (3%) with mixed flora. The PCR-MGE method is useful not only for rapid identification (∼1.5 h) of staphylococci in positive blood culture bottles, but also for strain delineation of
S. aureus
.
Potential Limitations of the 16S-23S rRNA Intergenic Region for Molecular Detection of
Bartonella
Species
Authors: Maggi Ricardo G. , Breitschwerdt Edward B. 
Published: March 2005

ABSTRACT

PCR targeting the 16S-23S rRNA gene intergenic transcribed spacer (ITS) region has been proposed as a rapid and reliable method for the detection of
Bartonella
species DNA in clinical samples. Because of variation in ITS sequences among
Bartonella
species, a single PCR amplification can be used to detect different species within this genus. Therefore, by targeting the ITS region, multiple PCRs or additional sample-processing steps beyond the primary amplification can be avoided when attempting to achieve molecular diagnostic detection of
Bartonella
species. Although PCR amplification targeting this region is considered highly sensitive, amplification specificity obviously depends on primer design. We report evidence of nonspecific PCR amplification of
Mesorhizobium
species with previously published primers that were designed to amplify the
Bartonella
consensus ITS region. Use of these or other, less species-specific, primers could lead to a false-positive diagnostic test result when evaluating clinical samples. We also report the presence of
Mesorhizobium
species DNA as a contaminant in molecular-grade water, a series of homologous sequences in the ITS region that are common to
Bartonella
and
Mesorhizobium
species, the amplification of
Mesorhizobium
DNA with unpublished primers designed in our laboratory targeting the ITS region, and the subsequent design of unambiguous ITS primers that avoid nonspecific amplification of
Mesorhizobium
species. Our results define some potential limitations associated with the molecular detection of
Bartonella
species in patient samples and indicate that primer specificity is of critical importance if the ITS region is used as a diagnostic target for detection of
Bartonella
species.
Clinical Evaluation of the DiversiLab Microbial Typing System Using Repetitive-Sequence-Based PCR for Characterization of
Staphylococcus aureus
Strains
Authors: Shutt Cheryl K. , Pounder June I. , Page Sam R. , Schaecher Barbara J. , Woods Gail L. 
Published: March 2005

ABSTRACT

The DiversiLab System, which includes microfluidics-based detection, reagent kits, and software for data processing and analysis, is an automated method using repetitive sequence-based PCR (rep-PCR) for microbial strain typing. To assess the reliability of the DiversiLab System for strain characterization of
Staphylococcus aureus
, we tested clinical isolates sent to ARUP Laboratories for typing and compared results to those of pulsed field electrophoresis (PFGE) aided by the cluster analysis provided by BioNumerics software.
spa
typing was performed when the results of these two methods for an outbreak were not concordant. The study included 89
S. aureus
isolates (65
mecA
positive, 24
mecA
negative) from 19 outbreaks (2 to 11 isolates/outbreak). The DiversiLab and PFGE-BioNumerics results were concordant for 15 of the 19 outbreaks. For the remaining four outbreaks, there was partial concordance between the two methods.
spa
typing results were the same as or more similar to rep-PCR results for three of those outbreaks and were more similar to PFGE results for one. With regard to performance, the DiversiLab system was considerably less labor intensive than PFGE and provided results in less than 24 h, compared with 2 to 3 days for PFGE. Additionally, the Web-based DiversiLab software provides standardized comparisons among isolates almost instantaneously and generates user-friendly, customized reports.
Seroepidemiology of Human Metapneumovirus (hMPV) on the Basis of a Novel Enzyme-Linked Immunosorbent Assay Utilizing hMPV Fusion Protein Expressed in Recombinant Vesicular Stomatitis Virus
Authors: Leung Jessica , Esper Frank , Weibel Carla , Kahn Jeffrey S. 
Published: March 2005

ABSTRACT
Human metapneumovirus (hMPV) is a newly identified human respiratory virus now recognized as a major respiratory pathogen of infants and children. To define the seroepidemiology of hMPV, we developed a novel enzyme-linked immunosorbent assay (ELISA) based on expression of the fusion protein of hMPV (hMPV F) in recombinant vesicular stomatitis virus (VSV). Western blot analysis using an hMPV F-specific antiserum confirmed the expression of hMPV in recombinant VSV. The ELISA is specific for hMPV F; antibody specific for the most closely related human paramyxovirus, respiratory syncytial virus, does not bind to hMPV F. Overall, 216 serum specimens were tested. The percentages of seropositive individuals were 89.1% in children ≤5 months old, 55.0% in children 6 to 11 months old, 36.0% in children 12 to 23 months old, 45.0% in children 24 to 47 months old, 77.3% in children 48 to 59 months old, 91.3% in children 5 to 10 years old, and 95.5% for individuals 11 to 20 years old. This is the first seroepidemiological survey of hMPV in the United States and the first analysis to determine the prevalence of antibody to a specific hMPV protein. The data suggest that exposure to hMPV is common in childhood and that hMPV F is an antigenic determinant of hMPV.
Systematic Molecular Characterization of Multidrug-Resistant
Mycobacterium tuberculosis
Complex Isolates from Spain
Authors: Samper S. , Iglesias M. J. , Rabanaque M. J. , Gómez L. I. , Lafoz M. C. , Jiménez M. S. , Ortega A. , Lezcano M. A , Van Soolingen D. , Martín C. 
Published: March 2005

ABSTRACT

We used spoligotyping and restriction fragment length polymorphism (RFLP) of the IS
6110
-insertion sequence to study the molecular epidemiology of multidrug-resistant (MDR) tuberculosis in Spain. We analyzed 180
Mycobacterium tuberculosis
complex isolates collected between January 1998 and December 2000. Consecutive isolates from the same patients (
n
= 23) always had identical genotypes, meaning that no cases of reinfection occurred. A total of 105 isolates (58.3%) had unique RFLP patterns, whereas 75 isolates (41.7%) were in 20 different RFLP clusters. Characterization of the
katG
and
rpoB
genes showed that 14 strains included in the RFLP clusters did not actually cluster. Only 33.8% of the strains isolated were suggestive of MDR transmission, a frequency lower than that for susceptible strains in Spain (46.6%). We found that the Beijing/W genotype, which is prevalent worldwide, was significantly associated with immigrants. The 22 isolates in the largest cluster corresponded to the
Mycobacterium bovis
strain responsible for two nosocomial MDR outbreaks in Spain.
Analysis of the Influence of Tween Concentration, Inoculum Size, Assay Medium, and Reading Time on Susceptibility Testing of
Aspergillus
spp
Authors: Gomez-Lopez Alicia , Aberkane Amel , Petrikkou Eva , Mellado Emilia , Rodriguez-Tudela Juan Luis , Cuenca-Estrella Manuel 
Published: March 2005

ABSTRACT

The influence of several test variables on susceptibility testing of
Aspergillus
spp. was assessed. A collection of 28 clinical isolates was tested against amphotericin B, itraconazole, voriconazole, and terbinafine. Inoculum size (10
4
CFU/ml versus 10
5
CFU/ml) and glucose supplementation (0.2% versus 2%) did not have significant effects on antifungal susceptibility testing results and higher inoculum size and glucose concentration did not falsely elevate MICs. In addition, antifungal susceptibility testing procedure with an inoculum size of 10
5
CFU/ml distinctly differentiated amphotericin B or itraconazole-resistant
Aspergillus
strains in vivo from the susceptible ones. Time of incubation significantly affected the final values of MICs, showing major increases (two to six twofold dilutions,
P
< 0.01 by analysis of variance) between MIC readings at 24 and 48 h, but no differences were observed between antifungal susceptibility testing results obtained at 48 h and at 72 h. Significantly higher MICs were uniformly associated with higher concentrations of Tween (
P
< 0.01), used as a dispersing agent in the preparation of inoculum suspensions. The geometric mean MICs showed increases of between 1.5- and 10-fold when the Tween concentration varied from 0.1% (the geometric means for amphotericin B, itraconazole, voriconazole, and terbinafine were 1.29, 0.69, 1.06, and 0.64 μg/ml, respectively) to 5% (the geometric means for amphotericin B, itraconazole, voriconazole, and terbinafine were 1.97, 5.79, 1.60, and 4.66 μg/ml, respectively). The inhibitory effect of Tween was clearly increased with inoculum sizes of 10
5
CFU/ml and was particularly dramatic for itraconazole, terbinafine, and
Aspergillus terreus
. The inoculum effect was not observed when the Tween concentration was below 0.5% (
P
> 0.01).
Distribution ofMycobacterium aviumComplex Isolates in Tissue Samples of Pigs Fed Peat Naturally Contaminated with Mycobacteria as a Supplement
Authors: Matlova Ludmila , Dvorska Lenka , Ayele Wuhib Yayo , Bartos Milan , Amemori Takashi , Pavlik Ivo 
Published: March 2005

ABSTRACTIn early 1999, there was an increased incidence of tuberculous lesions in the lymph nodes of slaughtered pigs in the Czech Republic. In part 1 of this study, tuberculous lesions were detected in 140 (62%) tissue samples collected from pigs coming from 15 farms in 15 districts at routine veterinary meat inspections in abattoirs. Mycobacteria were isolated from 37 (16%) tissue samples: 34Mycobacterium aviumsubsp.hominissuisisolates and three environmentally derived mycobacteria. In search of infection sources,M. aviumsubsp.hominissuiswas isolated from 38 (79%) samples of peat used as a feed supplement. In part 2 of our study, the head, mesenteric, and inguinal lymph nodes of 117 randomly selected slaughtered pigs from one farm with young piglets fed peat as a supplement were investigated for mycobacterial infection. From 65 (56%) pigs, a total of 76 mycobacterial isolates were identified (56M. aviumsubsp.hominissuisisolates, 5M. aviumsubsp.aviumisolates, 3M. intracellulareisolates, and 12 environmentally derived mycobacterial isolates). IS1245restriction fragment length polymorphism (RFLP) types with >20 bands of 45 distinct RFLP types were found in 49M. aviumsubsp.hominissuisisolates from pigs (n= 31) and peat (n= 18). Identical RFLP types were found in only four pig isolates. Five randomly selected isolates from pigs and peat were subcultured to six independent clones or colonies. Among the IS1245RFLP types of 30 clones, identical RFLP types obtained from pigs and peat were identified, which confirmed the hypothesis that peat contaminated with mycobacteria represents a significant source of mycobacterial infection for pigs.
Molecular Epidemiology of Macrolide-Resistant
Streptococcus pneumoniae
Isolates in Europe
Authors: Reinert Ralf René , Ringelstein Adrian , van der Linden Mark , Cil Murat Yücel , Al-Lahham Adnan , Schmitz Franz-Josef 
Published: March 2005

ABSTRACT

In many European countries, the level of pneumococcal resistance to macrolides has now passed the level of resistance to penicillin G. A total of 82 erythromycin A-resistant isolates of
Streptococcus pneumoniae
were collected by 11 laboratories in seven European countries. All of the isolates were tested for antimicrobial susceptibility, analyzed for clonal relatedness by multilocus sequence typing, and characterized for macrolide resistance genotypes. The prevalence of the macrolide resistance genotypes varied substantially between countries. In France (87.5% of all strains), Spain (77.3%), Switzerland (80%), and Poland (100%), strains were predominantly
erm
(B) positive, whereas higher levels of
mef
(A)-positive strains were reported from Greece (100%) and Germany (33.3%). Macrolide resistance was caused by the oligoclonal spread of some multilocus sequence types, but significant differences in clonal distribution were noted between France and Spain, countries from which high levels of macrolide resistance have been reported. Overall, sequence type 81 (Spain23F-1 clone) was by far the most widespread. The mainly
erm
(B)-positive serotype 14 clone (sequence type 143), first reported in Poland in the mid-1990s, is now widespread in France.
Evaluation of a Point-of-Care Test, BVBlue, and Clinical and Laboratory Criteria for Diagnosis of Bacterial Vaginosis
Authors: Bradshaw C. S. , Morton A. N. , Garland S. M. , Horvath L. B. , Kuzevska I. , Fairley C. K. 
Published: March 2005

ABSTRACT
Bacterial vaginosis (BV) remains the most common cause of abnormal vaginal discharge in women of reproductive age and is associated with increased susceptibility to human immunodeficiency virus and sexually transmitted infections and preterm delivery. Present diagnostic methods require access to microscopy and laboratory expertise; however, the majority of women, particularly those in populations with a high prevalence of BV, do not have access to clinical services with on-site microscopy capabilities. We evaluated a point-of-care test for the diagnosis of BV, the BVBlue test, with 288 women attending a sexual health service with symptoms of abnormal vaginal discharge and/or odor. The BVBlue test performed well compared with conventional diagnostic methods for the assessment of women with symptoms suggestive of BV at the bedside and significantly better than other simple tests, such as vaginal pH determination and the amine test, that do not require microscopy. The BVBlue test was sensitive (88%; 95% confidence interval [CI], 81 to 93%) and specific (95%; 95% CI, 91 to 98%) compared to the method of Nugent et al. (R. P. Nugent, M. A. Krohn, and S. L. Hillier, J. Clin. Microbiol. 29:297-301, 1991) and performed well compared with the method of Amsel et al. (R. Amsel, P. A. Totten, C. A. Spiegel, K. C. Chen, D. Eschenbach, and K. K. Holmes, Am. J. Med. 74:14-22, 1983), with a sensitivity of 88% (95% CI, 81 to 93%) and a specificity of 91% (95% CI, 85 to 94%). The BVBlue test is a simple, rapid, and objective test for the diagnosis of BV and has the potential to facilitate prompt diagnosis and appropriate treatment of BV in the absence of microscopy. The majority of women at the greatest risk for the sequelae of BV are not in settings where the conventional diagnostic methods are either practical or possible, and they would greatly benefit from access to rapid and reliable point-of-care tests to improve the diagnosis and management of BV.