bluuebunny/crossref_metadata_2025_split huggingface dataset:
Head-to-Head Multicenter Comparison of DNA Probe and Nucleic Acid Amplification Tests for
Chlamydia trachomatis
Infection in Women Performed with an Improved Reference Standard
Authors: Black Carolyn M. , Marrazzo Jeanne , Johnson Robert E. , Hook Edward W. , Jones Robert B. , Green Timothy A. , Schachter Julius , Stamm Walter E. , Bolan Gail , St. Louis Michael E. , Martin David H. 
Published: September 2002

ABSTRACT

Few evaluations of tests for
Chlamydia trachomatis
have compared nucleic acid amplification tests (NAATs) with diagnostic tests other than those by culture. In a five-city study of 3,551 women, we compared the results of commercial ligase chain reaction (LCR) and PCR tests performed on cervical swabs and urine with the results of PACE 2 tests performed on cervical swabs, using independent reference standards that included both cervical swabs and urethral swab-urine specimens. Using cervical culture as a standard, the sensitivities of PACE 2, LCR, and PCR tests with cervical specimens were 78.1, 96.9, and 89.9%, respectively, and the specificities were 99.3, 97.5, and 98.2%, respectively. Using either cervical swab or urine LCR-positive tests as the standard decreased sensitivities to 60.8% for PACE 2 and to 75.8 and 74.9% for PCR with cervical swabs and urine, respectively. Specificities increased to 99.7% for PACE 2 and to 99.7 and 99.4% for PCR with cervical swabs and urine, respectively. Sensitivities with a cervical swab-urine PCR standard were 61.9% for PACE 2 and 85.5 and 80.8% for LCR with cervical swabs and urine, respectively. Specificities were 99.6% for PACE 2 and 99.0 and 98.9% for LCR with cervical swabs and urine, respectively. Cervical swab versus urine differences were significant only for PCR specificities (
P
= 0.034). Overall, LCR sensitivity exceeded that of PCR, and sensitivities obtained with cervical swabs exceeded those obtained with urine specimens by small amounts. These data have substantiated, using a large multicenter sample and a patient standard, that LCR and PCR tests performed on endocervical swabs and urine are superior to PACE 2 tests for screening
C. trachomatis
infections in women. In our study, NAATs improved the detection of infected women by 17 to 38% compared to PACE 2.
Comparison of Multilocus Sequence Typing and Pulsed-Field Gel Electrophoresis as Tools for Typing
Staphylococcus aureus
Isolates in a Microepidemiological Setting
Authors: Peacock S. J. , de Silva G. D. I. , Justice A. , Cowland A. , Moore C. E. , Winearls C. G. , Day N. P. J. 
Published: September 2002

ABSTRACT

Multilocus sequence typing (MLST) of
Staphylococcus aureus
is well suited to the study of global or long-term epidemiology, but its role in local epidemiology has not been defined. The present study has compared MLST with pulsed-field gel electrophoresis (PFGE) by using
S. aureus
isolates associated with carriage and disease in a busy regional renal unit. One hundred forty-four patients were prospectively recruited, of whom 103 were receiving hemodialysis and 41 were on continuous ambulatory peritoneal dialysis. Three nasal swab specimens were obtained 1 month apart on entering the study. A nasal swab was positive for
S. aureus
on at least one occasion in 50 patients (35%). Typing of the 104 carriage isolates demonstrated 21 PFGE types and 21 sequence types (STs). Thirty-one carriers had two or more positive nasal swabs; of these, the isolates in all swabs from a given carrier had identical PFGE types for 29 carriers; the isolates in all of the same 29 swabs had identical STs. The carriage strain in two patients changed both PFGE type and STs during the period of swabbing. Eight patients (6%) had an episode of
S. aureus
bacteremia during the 12-month study period, and two of these were nasal carriers. One of these invasive isolates had the same PFGE type and ST as the carriage isolate. There were no differences between Simpson's index of diversity for PFGE and Simpson's index of diversity for MLST for both invasive and carriage isolates, suggesting that the two methods have very similar discriminatory abilities. We conclude that PFGE and MLST performed equally in this study.
Evaluation of an Enzyme-Linked Immunosorbent Assay with Recombinant Rhoptry-Associated Protein 1 Antigen against
Babesia bovis
for the Detection of Specific Antibodies in Cattle
Authors: Boonchit Suthisak , Xuan Xuenan , Yokoyama Naoaki , Goff Will L. , Wagner Gale , Igarashi Ikuo 
Published: September 2002

ABSTRACT

The gene encoding
Babesia bovis
rhoptry-associated protein 1 (RAP-1) was used to develop an enzyme-linked immunosorbent assay (ELISA) to measure specific antibodies against
B. bovis.
The
B. bovis
RAP-1 gene was subcloned into a baculovirus transfer vector, and the RAP-1 protein was expressed in insect cells infected with a recombinant baculovirus. The recombinant
B. bovis
RAP-1 of 65 kDa was detected with anti-RAP-1 mouse serum by Western blotting, and this recombinant RAP-1 was used as an antigen in the ELISA. The ELISA was able to differentiate between
B. bovis
-infected sera and
B. bigemina
-infected sera or noninfected normal bovine sera. The results demonstrate that the recombinant RAP-1 expressed in insect cells might be a useful antigen for the detection of antibodies to
B. bovis.
Optimal Testing Conditions for Determining MICs and Minimum Fungicidal Concentrations of New and Established Antifungal Agents for Uncommon Molds: NCCLS Collaborative Study
Authors: Espinel-Ingroff A. , Chaturvedi V. , Fothergill A. , Rinaldi M. G. 
Published: September 2002

ABSTRACT

This collaborative three-center study evaluated NCCLS M38-A document testing conditions and other testing conditions for the antifungal susceptibility testing of 35 isolates of
Aspergillus nidulans
,
A. terreus
,
Bipolaris hawaiiensis
,
B. spicifera
,
Cladophialophora bantiana
,
Dactylaria constricta
,
Fusarium solani
,
Paecilomyces lilacinus
,
Scedosporium prolificans
,
Trichoderma longibrachiatum
, and
Wangiella dermatitidis
for itraconazole, three new triazoles (voriconazole, posaconazole, and ravuconazole), and amphotericin B. MICs and minimum fungicidal concentrations (MFCs) were determined in each center by using four media (standard RPMI-1640 [RPMI], RPMI with 2% dextrose [RPMI-2%], antibiotic medium 3 [M3], and M3 with 2% dextrose [M3-2%]) and two criteria of MIC determination (complete growth inhibition [MICs-0] and prominent growth inhibition [MICs-2]) at 24, 48 and 72 h. MFCs were defined as the lowest drug concentrations that yielded <3 colonies (approximately 99 to 99.5% killing activity). The reproducibility (within three wells) was higher among MICs-0 (93 to 99%) with either RPMI or M3 media than among all MICs-2 (86 to 95%) for the five agents at 48 to 72 h. The agreement for MFCs was lower (86 to 94%). Based on interlaboratory agreement, the optimal testing conditions were RPMI broth, 48 to 72 h of incubation and 100% growth inhibition (MIC-0); MFCs can be obtained after MIC determination with the above optimal testing parameters. These results warrant consideration for inclusion in the future version of the NCCLS M38 document. However, the role of these in vitro values as predictors of clinical outcome remains to be established in clinical trials.
Serodiagnosis of Tuberculosis: Comparison of Immunoglobulin A (IgA) Response to Sulfolipid I with IgG and IgM Responses to 2,3-Diacyltrehalose, 2,3,6-Triacyltrehalose, and Cord Factor Antigens
Authors: Julián Esther , Matas Lurdes , Pérez Andrés , Alcaide José , Lanéelle Marie-Antoinette , Luquin Marina 
Published: September 2002

ABSTRACT

Nonpeptidic antigens from the
Mycobacterium tuberculosis
cell wall are the focus of extensive studies to determine their potential role as protective antigens or serological markers of tuberculous disease. Regarding this latter role and using an enzyme-linked immunosorbent assay, we have made a comparative study of the immunoglobulin G (IgG), IgM, and IgA antibody responses to four trehalose-containing glycolipids purified from
M. tuberculosis
: diacyltrehaloses, triacyltrehaloses, cord factor, and sulfolipid I (SL-I). Sera from 92 tuberculosis patients (taken before starting antituberculosis treatment) and a wide group of control individuals (84 sera from healthy donors, including purified protein derivative-negative, -positive, healed, and vaccinated individuals, and 52 sera from nontuberculous pneumonia patients), all from Spain, were studied. The results indicated a significantly elevated IgG and IgA antibody response in tuberculosis patients, compared with controls, with all the antigens used. SL-I was the best antigen studied, showing test sensitivities and specificities for IgG of 81 and 77.6%, respectively, and of 66 and 87.5% for IgA. Using this antigen and combining IgA and IgG antibody detection, high test specificity was achieved (93.7%) with a sensitivity of 67.5%. Currently, it is widely accepted that it is not possible to achieve sensitivities above 80% in tuberculosis serodiagnosis when using one antigen alone. Thus, we conclude that SL-I, in combination with other antigenic molecules, could be a useful antigen for tuberculosis serodiagnosis.
Mutations in the
rpoB
and
katG
Genes Leading to Drug Resistance in
Mycobacterium tuberculosis
in Latvia
Authors: Tracevska T. , Jansone I. , Broka L. , Marga O. , Baumanis V. 
Published: September 2002

ABSTRACT

To characterize the genetic basis of drug resistance in
Mycobacterium tuberculosis
in Latvia, mutations involved in rifampin (
rpoB
gene) and isoniazid (
katG
gene) resistance in DNA from 19 drug-susceptible and 51 multidrug-resistant
M. tuberculosis
complex isolates were analyzed. The most frequent
rpoB
gene mutations found by the Line Probe assay were the S531L (14 of 34 isolates), D516V (7 of 34), H526D (4 of 34), and D516Y plus P535S (4 of 34) mutations. Direct sequencing of seven isolates with unclear results from Line Probe assay showed the presence of the L533P mutation and the Q510H plus H526Y (1 of 34) and D516V plus P535S (4 of 34) double mutations, neither of which has been described previously. Single-strand conformation polymorphism analysis showed strand mobility differences between the rifampin-susceptible and -resistant samples for the D516V, H526D, and D516Y plus P535S mutations but not for the S531L mutation. Nucleotide substitution at codon 315 (AGC→ACC) of the
katG
gene was found in 48 of 51 multidrug-resistant samples by sequencing. Furthermore,
katG
gene restriction fragment length polymorphism analysis with endonuclease
Aci
I confirmed the nucleotide change in codon 315.
Use of 16S rRNA Gene Sequencing for Identification of Nonfermenting Gram-Negative Bacilli Recovered from Patients Attending a Single Cystic Fibrosis Center
Authors: Ferroni Agnes , Sermet-Gaudelus Isabelle , Abachin Eric , Quesne Gilles , Lenoir Gerard , Berche Patrick , Gaillard Jean-Louis 
Published: September 2002

ABSTRACT

During 1999, we used partial 16S rRNA gene sequencing for the prospective identification of atypical nonfermenting gram-negative bacilli isolated from patients attending our cystic fibrosis center. Of 1,093 isolates of nonfermenting gram-negative bacilli recovered from 148 patients, 46 (4.2%) gave problematic results with conventional phenotypic tests. These 46 isolates were genotypically identified as
Pseudomonas aeruginosa
(19 isolates, 12 patients),
Achromobacter xylosoxidans
(10 isolates, 8 patients),
Stenotrophomonas maltophilia
(9 isolates, 9 patients),
Burkholderia cepacia
genomovar I/III (3 isolates, 3 patients),
Burkholderia vietnamiensis
(1 isolate),
Burkholderia gladioli
(1 isolate), and
Ralstonia mannitolilytica
(3 isolates, 2 patients), a recently recognized species.
Imipenem-EDTA Disk Method for Differentiation of Metallo-β-Lactamase-Producing Clinical Isolates of
Pseudomonas
spp. and
Acinetobacter
spp
Authors: Yong Dongeun , Lee Kyungwon , Yum Jong Hwa , Shin Hee Bong , Rossolini Gian Maria , Chong Yunsop 
Published: September 2002

ABSTRACT
Rapid detection of metallo-β-lactamase (MBL)-producing gram-negative bacilli is necessary to prevent their dissemination. The method using a disk with imipenem plus 750 μg of EDTA differentiated all MBL-producing pseudomonads, and the sensitivity and specificity for acinetobacters were 95.7 and 91.0%, respectively. The imipenem-EDTA disks were stable for 12 and 16 weeks at 4 and −20°C, respectively.
PCR Detection of
Borrelia burgdorferi
Sensu Lato, Tick-Borne Encephalitis Virus, and the Human Granulocytic Ehrlichiosis Agent in
Ixodes persulcatus
Ticks from Western Siberia, Russia
Authors: Morozova Olga V. , Dobrotvorsky Andrey K. , Livanova Natalya N. , Tkachev Sergey E. , Bakhvalova Valentina N. , Beklemishev Anatoly B. , Cabello Felipe C. 
Published: September 2002

ABSTRACT

PCR assays were used to test adult
Ixodes persulcatus
ticks from Western Siberia, Russia, for
Borrelia burgdorferi
sensu lato, tick-borne encephalitis virus (TBEV), and the human granulocytic ehrlichiosis (HGE) agent. Of the 150 ticks that were studied, 38% were infected with
B. burgdorferi
, 46% were infected with TBEV, and 8% were infected with the HGE agent. These three pathogens were distributed in the ticks independently of one another.
Rapid Detection of Human Immunodeficiency Virus Type 1 Subtype E Infection by PCR
Authors: Chen Mao-Yuan , Wang Wei-Kung , Lee Ming-Cheng , Twu Shing-Jer , Wu Shiow-Ing , Lee Chun-Nan 
Published: September 2002

ABSTRACT

The CRF01_AE (subtype E) strain of human immunodeficiency virus type 1 (HIV-1), originally reported in Thailand, spread rapidly to and showed prevalence in several countries in Southeast Asia, including Taiwan. This strain was also found in other regions of the world. Based on sequence analysis of the
vpu
gene, a nested PCR assay including an outer primer pair and a subtype E-specific inner primer pair was developed in this study for rapid detection of subtype E viruses. It was tested with 397 HIV-1-positive samples of known subtypes. For these samples, the sensitivity of detection of subtype E viruses was 100% (127 of 127), and the specificity was 97.8% (264 of 270). Although six samples of either subtype A or G showed a positive PCR, most of the cross-reactivity could be reduced by raising the annealing temperature from 54°C to 63°C. When tested with 195 HIV-positive samples of unknown subtypes, the assay had a sensitivity of 98.0% and a specificity of 98.6%. This is a simple, convenient, and sensitive method for rapid detection of subtype E viruses, especially in regions in which viruses of subtypes B and E are predominant.
Detection of
embB306
Mutations in Ethambutol-Susceptible Clinical Isolates of
Mycobacterium tuberculosis
from Northwestern Russia: Implications for Genotypic Resistance Testing
Authors: Mokrousov Igor , Otten Tatiana , Vyshnevskiy Boris , Narvskaya Olga 
Published: September 2002

ABSTRACT

A total of 183 epidemiologically unlinked
Mycobacterium tuberculosis
isolates collected in the St. Petersburg area of Russia from 1996 to 2001 were screened for alterations in codon 306 of the
embB
gene; mutations in this codon are reported to confer resistance to ethambutol (EMB). The
embB306
mutations were detected in 14 (48.3%) of 29 EMB-resistant strains and, quite surprisingly, in 48 (31.2%) of 154 EMB-susceptible strains. A discrepancy between the results of phenotypic and genotypic EMB resistance tests was restricted to the strains already resistant to other antitubercular (anti-TB) drugs. In particular, 40 (60%) of the 69 EMB-susceptible strains resistant to rifampin, isoniazid, and streptomycin but none of the 43 pansusceptible strains harbored an
embB306
mutation. We hypothesize that the phenomenon observed could reflect the presence of a target other than EmbB for the drug in tubercle bacilli; this unknown target could be sensitized and affected, sensu lato, by EMB during treatment with other first-line anti-TB drugs. Comparison with DNA fingerprinting data showed that, irrespectively of the phenotypic susceptibility profiles, 46 (50.6%) of 91 Beijing family strains and 16 (17.4%) of 92 strains of other genotypes had a mutation in
embB306
.
Direct Detection and Differentiation of
Legionella
spp. and
Legionella pneumophila
in Clinical Specimens by Dual-Color Real-Time PCR and Melting Curve Analysis
Authors: Reischl Udo , Linde Hans-Jörg , Lehn Norbert , Landt Olfert , Barratt Kevin , Wellinghausen Nele 
Published: September 2002

ABSTRACT

A dual-color LightCycler PCR assay targeting the 16S rDNA gene of
Legionella
spp. was established. By using two pairs of hybridization probes,
Legionella
spp. and
Legionella pneumophila
could be detected and differentiated simultaneously. With 26 culture-positive and 42 culture-negative respiratory specimens from patients with atypical pneumonia, 100% sensitivity and specificity was observed for
L. pneumophila
.
DNA Differential Diagnosis of Human Taeniid Cestodes by Base Excision Sequence Scanning Thymine-Base Reader Analysis with Mitochondrial Genes
Authors: Yamasaki Hiroshi , Nakao Minoru , Sako Yasuhito , Nakaya Kazuhiro , Sato Marcello Otake , Mamuti Wulamu , Okamoto Munehiro , Ito Akira 
Published: September 2002

ABSTRACT

For DNA differential diagnosis of human
Taenia
cestodes, a base excision sequence scanning thymine-base method using the cytochrome
c
oxidase subunit I and cytochrome
b
genes as targets was used. The characteristic thymine-base peak profiles provide four distinct types, unique for
T. saginata
,
T. asiatica
, and two genotypes of
T. solium
. This approach provides a useful tool for the identification and diagnosis of human taeniid cestodes without DNA sequencing if nucleotide sequence databases are available.
Assessment of a Combined Testing Strategy for Detection of Antibodies to Human Herpesvirus 8 (HHV-8) in Persons with Kaposi's Sarcoma, Persons with Asymptomatic HHV-8 Infection, and Persons at Low Risk for HHV-8 Infection
Authors: Casper Corey , Krantz Elizabeth , Taylor Heather , Dalessio Julie , Carrell David , Wald Anna , Corey Lawrence , Ashley Rhoda 
Published: September 2002

ABSTRACT
The performance of a human herpesvirus 8 (HHV-8) enzyme immunoassay (EIA) and selective subsequent use of an HHV-8 immunofluorescence assay (IFA) was tested in persons unlikely to be infected with HHV-8 and those who had HHV-8 detected in their saliva. The IFA was performed on samples within a range of EIA optical densities (0.15 to 0.35) where there was considerable overlap between HHV-8-infected and uninfected individuals. The sensitivity of the testing strategy was 88%, with a specificity of 97%.
Phylogenetic Analysis of Newcastle Disease Virus Genotypes Isolated in Japan
Authors: Mase Masaji , Imai Kunitoshi , Sanada Yasuyuki , Sanada Naoko , Yuasa Noboru , Imada Tadao , Tsukamoto Kenji , Yamaguchi Shigeo 
Published: September 2002

ABSTRACTWe genetically analyzed field isolates of the Newcastle disease (ND) virus isolated in Japan from 1930 to 2001. The coding region of the fusion protein was amplified by reverse transcriptase PCR and directly sequenced. Phylogenetic analysis revealed the presence of viruses belonging to six of the eight known genotypes. It can be concluded from this study that ND outbreaks in Japan have been of multiple etiologies.
Erythromycin-Resistant Group A Streptococcal Isolates Recovered in Sofia, Bulgaria, from 1995 to 2001
Authors: Detcheva Antoaneta , Facklam Richard R. , Beall Bernard 
Published: September 2002

ABSTRACT

The frequency of erythromycin resistance within group A streptococci in Sofia, Bulgaria, from 1995 to 2001 was 2.1% (26 isolates). Of this, 57.7% was macrolide-lincosamide-streptogramin (MLS) inducible, 7.7% was MLS constitutive, and 34.6% had the M phenotype. Eleven different
emm
sequence types were found among 25 erythromycin-resistant isolates tested. Nineteen of 26 erythromycin-resistant isolates were additionally resistant to tetracycline and/or chloramphenicol.
Association of the
prtF1
Gene (Encoding Fibronectin-Binding Protein F1) and the
sic
Gene (Encoding the Streptococcal Inhibitor of Complement) with
emm
Types of Group A Streptococci Isolated from Japanese Children with Pharyngitis
Authors: Ma Xiaoming , Kikuta Hideaki , Ishiguro Nobuhisa , Yoshioka Mikio , Ebihara Takashi , Murai Teiko , Kobayashi Intetu , Kobayashi Kunihiko 
Published: September 2002

ABSTRACT

A total of 66 clinical isolates of group A streptococci (GAS) were obtained from 66 Japanese children with pharyngitis. The
prtF1
gene (encoding fibronectin-binding protein F1) and the
sic
gene (encoding the streptococcal inhibitor of complement) were present in 51 (77.3%) and 48 (72.7%) of the 66 isolates, respectively. These results indicated that a high prevalence of two virulence genes,
prtF1
and
sic
, is characteristic of GAS in Japan.
Impact of Nasopharyngeal Swab Types on Detection of
Bordetella pertussis
by PCR and Culture
Authors: Cloud Joann L. , Hymas Weston , Carroll Karen C. 
Published: September 2002

ABSTRACT

A study was designed to assess the performance of various swabs and transport media routinely used to collect specimens submitted for
Bordetella
culture and PCR. Calcium-alginate swabs inhibited the PCR. No inhibition was detected in any PCRs with dacron or rayon swabs. All swab materials performed similarly for recovery of
Bordetella pertussis
in culture. The Amies with charcoal transport system performed poorly for culture. Calcium-alginate swabs are not recommended for PCR-based detection of
B. pertussis
. Dacron and rayon swabs are an excellent choice for both PCR and culture.
Comparison of the Antifungal Susceptibility Testing Subcommittee of the European Committee on Antibiotic Susceptibility Testing Proposed Standard and the E-Test with the NCCLS Broth Microdilution Method for Voriconazole and Caspofungin Susceptibility Testing of Yeast Species
Authors: Chryssanthou Erja , Cuenca-Estrella Manuel 
Published: September 2002

ABSTRACT

The proposed standard of the Antifungal Susceptibility Testing Subcommittee of the European Committee on Antibiotic Susceptibility Testing (AFST-EUCAST) and the E-test procedures were compared with the NCCLS reference broth microdilution method for voriconazole and caspofungin susceptibility testing of 102 clinical
Candida
species and
Saccharomyces cerevisiae
isolates. The voriconazole MIC at which 50% of strains were inhibited (MIC
50
) was ≤0.125 mg/liter for all yeast species except for
Candida glabrata
and
Candida krusei
, which yielded MIC
50
values of 0.25 to 1 mg/liter depending on the method. Caspofungin exhibited in vitro activity (MIC
50
of ≤0.125 to 2 mg/liter) against all yeast species except for
Candida guilliermondii
. The agreements between MICs within ±2 dilutions obtained by the NCCLS method and the EUCAST standard were 97% for voriconazole and 96% for caspofungin. Intraclass correlation coefficients were statistically significant (
P
< 0.05). The agreements between voriconazole MICs provided by the E-test and the NCCLS and between the E-test and the AFST-EUCAST method were 100 and 90%, respectively. Because of lower caspofungin MICs provided by the E-test, the agreement was slightly poorer with the NCCLS method (89%) than with the AFST-EUCAST procedure (94%). Both the EUCAST and the E-test procedures can be reliable techniques for susceptibility testing of yeasts to voriconazole and caspofungin.
Reduction of Contamination of Mycobacterial Growth Indicator Tubes with a Modified Antimicrobial Combination
Authors: Chang Chulhun Ludgerus , Park Tae Sung , Oh Seung Hwan , Kim Hyung Hoi , Lee Eun Yup , Son Han Chul , Kim Cheol Min 
Published: September 2002

ABSTRACT
Culture in the fluorimetric Mycobacteria Growth Indicator Tube (MGIT) treated with a combination of vancomycin, amphotericin B, and nalidixic acid (VAN) showed growth of most strains of 31 mycobacterial species with a less-than-1-day delay. The results were similar to those in the MGIT with polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin, but with respiratory specimens, the MGIT with VAN showed a lower contamination rate with no change in the detection rate or time.