bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hepatitis C Virus Serotype-Specific Core and NS4 Antibodies in Injecting Drug Users Participating in the Amsterdam Cohort Studies
Authors: Beld Marcel , Penning Maarten , van Putten Marieke , van den Hoek Anneke , Lukashov Vladimir , McMorrow Martin , Goudsmit Jaap 
Published: December 2019

ABSTRACT
In the present study, the RIBA HCV serotyping SIA was evaluated with a cohort of injecting drug users. Serotyping may be a rapid and cost-effective method of determining genotypes in cohort studies. In this study, hepatitis C virus (HCV) antibody-positive sera from a cohort of 331 chronically infected injecting drug users, of which 167 were coinfected with human immunodeficiency virus (HIV), were serotyped by the RIBA HCV Serotyping SIA. Among the 331 specimens, serotype-specific antibodies were detected in 250 (sensitivity, 75.5%), in which serotype 1 was predominant (57.2%), followed by serotype 3 (26.8%). Among the 331 specimens, 164 were HIV negative, and serotype-specific antibodies were detected in 151 (sensitivity, 92.1%), in which serotype 1 was predominant (59.6%), followed by serotype 3 (33.8%). For a subset of 58 samples taken from 19 chronically infected HCV seroconverters with a mean follow-up of 5 years, serotypes were compared with genotypes, which were determined by a line probe assay (HCV LiPa) and by direct sequencing of the products obtained by nested PCR of the 5′ untranslated region. Among the 58 samples with known genotypes, serotype-specific antibodies were detected in 38 (total sensitivity, 65.5%), with a specificity of 78.9%. Thirty of these serotypeable samples revealed a serotype that corresponded to the genotype in the 58 samples (total positive predictive value, 51.7%). Of the 58 samples, 23 were coinfected with HIV, and when these were excluded, the total sensitivity increased to 76.5%, with a total specificity of 80.8% and a total positive predictive value of 61.8%. The serotyping assay showed a high total sensitivity (96.3%) for samples positive by HCV RIBA, version 3.0, with four bands. We conclude that the sensitivity of the RIBA HCV serotyping SIA is limited by the immunocompetence of the HCV-infected host. In general, samples from HIV-negative individuals containing genotype 1a had higher sensitivity, specificity, and concordance in the serotyping assay compared with genotyping, whereas samples containing genotype 3a were found to be more cross-reactive and untypeable. Therefore, the prevalence of genotypes other than genotype 1 could be underestimated if they are determined by serotyping, and improvements in specificity are recommended.
Evaluation of a Selective Transport Medium for Gastric Biopsy Specimens To Be Cultured for
Helicobacter pylori
Authors: Siu L. K. , Leung W. K. , Cheng A. F. B. , Sung J. Y. , Ling T. K. W. , Ling J. M. L. , Ng E. K. W. , Lau J. Y. W. , Chung S. C. S. 
Published: December 2019

ABSTRACT

Since the means of culturing
Helicobacter pylori
may not be available in some laboratories, prolonging the survival of this organism during transportation is a major concern in terms of improving detection rates. A selective transport medium was evaluated for the preservation of
H. pylori
from 254 gastric biopsy specimens collected from a rural area in China where culturing is not feasible. Gastric biopsy specimens were inoculated in sterile broth consisting of brain heart infusion (BHI) broth, horse serum, and yeast extract supplemented with vancomycin, amphotericin B, and nalidixic acid (VAN). Of the 254 biopsy specimens, 238 were identified by histology to have
H. pylori
infection. Total rates of recovery of
H. pylori
from the
H. pylori
-positive gastric biopsy specimens stored in the BHI-VAN broth ranged from 76 to 46% after storage of specimens for 5 to 9 days. In conclusion, the selective medium is useful for prolonging the survival of
H. pylori
in gastric biopsy specimens for which immediate culture is not feasible.
Genetic Relationship between Blood and Nonblood Isolates from Bacteremic Patients Determined by Pulsed-Field Gel Electrophoresis
Authors: Matsuda Junichi , Hirakata Yoichi , Iori Fumiaki , Mochida Chikako , Ozaki Yumi , Nakano Michiko , Izumikawa Kohichi , Yamaguchi Toshiyuki , Yoshida Ryoji , Miyazaki Yoshitsugu , Maesaki Shigefumi , Tomono Kazunori , Yamada Yasuaki , Kohno Shigeru , Kamihira Shimeru 
Published: December 2019

ABSTRACT

A total of 148 isolates from 55 bacteremic patients were examined by pulsed-field gel electrophoresis. Genetically different nonblood strains were isolated from 13.9% of patients with bacteremia caused by gram-positive cocci and 42.1% with
Pseudomonas aeruginosa
bacteremia, indicating that antibiograms of a single nonblood
P. aeruginosa
isolate are not always informative for treatment of bacteremia.
Identification of
Brucella
by Ribosomal-Spacer-Region PCR and Differentiation of
Brucella canis
from Other
Brucella
spp. Pathogenic for Humans by Carbohydrate Profiles
Authors: Fox Karen F. , Fox Alvin , Nagpal Madan , Steinberg Paul , Heroux Karen 
Published: December 2019

ABSTRACT

Molecular and chemical characteristics often provide complementary information in the differentiation of closely related organisms. The genus
Brucella
consists of a highly conserved group of organisms. Identification of the four species pathogenic in humans (
Brucella melitensis
,
Brucella abortus
,
Brucella suis
, and
Brucella canis
) is problematic for many clinical laboratories that depend primarily on serology and phenotypic characteristics to differentiate species. PCR amplification of the 16S-23S ribosomal DNA interspace region was evaluated for species-specific polymorphism.
B. abortus
,
B. melitensis
,
B. suis
, and
B. canis
produced identical PCR interspace profiles. However, these PCR products were unique to brucellae, allowing them to be readily distinguished from other gram-negative bacteria (including
Bartonella
spp. and
Agrobacterium
spp.). Carbohydrate profiles differentiated
B. canis
from the other three
Brucella
species due to the absence of the rare amino sugar quinovosamine in the three other species. PCR of the rRNA interspace region is useful in identification of the genus
Brucella
, while carbohydrate profiling is capable of differentiating
B. canis
from the other
Brucella
species.
Performance of the Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay in Detecting
Chlamydia trachomatis
in Endocervical and Urine Specimens from Women and Urethral and Urine Specimens from Men Attending Sexually Transmitted Disease and Family Planning Clinics
Authors: Ferrero Dennis V. , Meyers Holly N. , Schultz Diane E. , Willis Stephen A. 
Published: December 2019

ABSTRACT

The Gen-Probe AMPLIFIED Chlamydia Trachomatis Assay (AMP CT) uses transcription-mediated amplification and hybridization protection assay procedures to qualitatively detect
Chlamydia trachomatis
rRNA in urine, endocervical swab, and urethral specimens. The performance of the AMP CT was compared to that of cell culture for endocervical swab and urine specimens from women and urethral and urine specimens from men. Analysis of specimens with discrepant results was performed by a combination of reculture, direct fluorescent-antibody (DFA) staining of specimen sediment, and amplification which targeted a different chlamydial rRNA. A total of 800 urine samples were tested by the AMP CT (607 from women and 193 from men), and 7.1% were positive for
C. trachomatis
, with a sensitivity of 91.2% and a specificity of 99.6% upon discrepant analysis. A total of 926 swab specimens were tested by culture and AMP CT (717 endocervical swab specimens and 209 urethral swab specimens from men), and 7.7% were positive for
C. trachomatis
, with a sensitivity and specificity of 100% upon discrepant analysis. The AMP CT is a sensitive and specific nucleic acid hybridization assay for the detection of
C. trachomatis
in endocervical swab specimens from women, urethral swab specimens from men, and urine specimens from men and women.
Sequence Variation in the Small-Subunit rRNA Gene of
Plasmodium malariae
and Prevalence of Isolates with the Variant Sequence in Sichuan, China
Authors: Liu Qing , Zhu Shenghua , Mizuno Sahoko , Kimura Masatsugu , Liu Peina , Isomura Shin , Wang Xingzhen , Kawamoto Fumihiko 
Published: December 2019

ABSTRACT

By two PCR-based diagnostic methods,
Plasmodium malariae
infections have been rediscovered at two foci in the Sichuan province of China, a region where no cases of
P. malariae
have been officially reported for the last 2 decades. In addition, a variant form of
P. malariae
which has a deletion of 19 bp and seven substitutions of base pairs in the target sequence of the small-subunit (SSU) rRNA gene was detected with high frequency. Alignment analysis of
Plasmodium
sp. SSU rRNA gene sequences revealed that the 5′ region of the variant sequence is identical to that of
P. vivax
or
P. knowlesi
and its 3′ region is identical to that of
P. malariae
. The same sequence variations were also found in
P. malariae
isolates collected along the Thai-Myanmar border, suggesting a wide distribution of this variant form from southern China to Southeast Asia.
Molecular Characterization of
Bacillus
Strains Involved in Outbreaks of Anthrax in France in 1997
Authors: Patra Guy , Vaissaire Josée , Weber-Levy Martine , Le Doujet Claudine , Mock Michèle 
Published: December 2019

ABSTRACT

Outbreaks of anthrax zoonose occurred in two regions of France in 1997. Ninety-four animals died, and there were three nonfatal cases in humans. The diagnosis of anthrax was rapidly confirmed by bacteriological and molecular biological methods. The strains of
Bacillus anthracis
in animal and soil samples were identified by a multiplex PCR assay. They all belonged to the variable-number tandem repeat (VNTR) group (VNTR)
3
. A penicillin-resistant strain was detected. Nonvirulent bacilli related to
B. anthracis
, of all VNTR types, were also found in the soil.
Comparison of Four Serological Tests To Determine the CagA or VacA Status of
Helicobacter pylori
Strains
Authors: Yamaoka Yoshio , Kodama Tadashi , Graham David Y. , Kashima Kei 
Published: December 2019

ABSTRACT

We compared four tests for antibodies to CagA or VacA, HelicoBlot 2.0, RIDA Blot Helicobacter, CHIRON RIBA
H. pylori
SIA, and an enzyme-linked immunosorbent assay using recombinant CagA. Immunoblot assays were accurate for determining
Helicobacter pylori
status but poor for determining CagA or VacA status (accuracy, 66 to 80% for CagA status and 34 to 67% for VacA status). None can be recommended for determining CagA or VacA status.
Streptococcal Pharyngitis: Impact of a High-Sensitivity Antigen Test on Physician Outcome
Authors: Needham Cynthia A. , McPherson Kenneth A. , Webb Kenneth H. 
Published: December 2019

ABSTRACT
The purpose of the present study was to determine whether the availability of results from a high-sensitivity, rapid test for group A streptococci (Strep A OIA; BioStar, Inc., Boulder, Colo.) improves physician outcome. The study population included 465 consecutive patients with symptoms of acute pharyngitis seen in two outpatient clinics in a large suburban medical center; one clinic, a walk-in clinic (WIC), primarily saw adult patients, and one clinic, a pediatric and adolescent medicine clinic (PED), primarily saw pediatric patients. We measured improvement in physician outcome by comparing physician intent for prescribing an antibiotic based on clinical impression with physician practice once the results of the Strep A OIA were known. Based upon intent, the physicians seeing WIC patients (WIC physicians) would have prescribed an appropriate antibiotic course for 42% of patients with cultures positive for group A beta-hemolytic streptococci (GABHS) and 61% of patients with cultures negative for GABHS. After receiving the results of the Strep A OIA, WIC physicians prescribed an appropriate antibiotic course for 81% of patients with positive cultures and 72% of patients with negative cultures. Based upon intent, the physicians seeing PED patients (PED physicians) would have prescribed an appropriate antibiotic course for 35% of patients with positive cultures and 77% of patients with negative cultures. After receiving the results of the Strep A OIA, PED physicians prescribed an appropriate antibiotic course for 90% of patients with positive cultures and 81% of patients with negative cultures. Based on a 14.5% prevalence of GABHS among WIC patients, Strep A OIA improved the overall WIC physician outcome from 58 to 74%. Based on a 31.5% prevalence of GABHS among PED patients, Strep A OIA improved the PED physician outcome from 64 to 84%. Had Strep A OIA alone guided therapeutic choice, physicians would have prescribed an appropriate antibiotic course for 95% of the patients at the time of the initial encounter. We conclude that the use of Strep A OIA improves physician outcome.
Expanded Diversity among Californian
Borrelia
Isolates and Description of
Borrelia bissettii
sp. nov. (Formerly
Borrelia
Group DN127)
Authors: Postic D. , Ras N. Marti , Lane R. S. , Hendson M. , Baranton G. 
Published: December 2019

ABSTRACT

Up to now, the only species in the complex
Borrelia burgdorferi
sensu lato known to cause Lyme borreliosis in the United States has been
B. burgdorferi
sensu stricto. However, some atypical strains closely related to the previously designated genomic group DN127 have been isolated in the United States, mostly in California. To explore the diversity of
B. burgdorferi
sensu lato group DN127, we analyzed the nucleotide sequences of the
rrf-rrl
intergenic spacer regions from 19 atypical strains (18 from California and one from New York) and 13 North American
B. burgdorferi
sensu stricto strains (6 from California). The spacer region sequences from the entire
B. burgdorferi
sensu lato complex available in data banks were used for comparison. Phylogenetic analysis of sequences shows that the main species of the
B. burgdorferi
sensu lato complex (
B. afzelii
,
B. garinii
,
B. andersonii
,
B. japonica
,
B. burgdorferi
sensu stricto,
B. valaisiana
, and
B. lusitaniae
) each form a coherent cluster. A heterogeneous group comprising strains belonging to the previously designated group DN127 clustered separately from
B. burgdorferi
sensu stricto. Within this cluster, the deep branches expressing the distances between the
rrf-rrl
sequences reflect a high level of divergence. This unexpected diversity contrasts with the monomorphism exhibited by
B. burgdorferi
sensu stricto. To clarify the taxonomic status of this highly heterogeneous group, analysis of the
rrs
sequences of selected strains chosen from deeply separated branches was performed. The results show that these strains significantly diverge at a level that is compatible with several distinct genomic groups. We conclude that the taxonomy and phylogeny of North American
B. burgdorferi
sensu lato should be reevaluated. For now, we propose that the genomic group DN127 should be referred to as a new species,
B. bissettii
sp. nov., and that other related but distinct strains, which require further characterization, be referred to as
Borrelia
spp.
Clonal Distribution of Methicillin-Resistant
Staphylococcus aureus
in Poland
Authors: Leski T. , Oliveira D. , Trzcinski K. , Sanches I. Santos , de Sousa M. Aires , Hryniewicz W. , de Lencastre H. 
Published: December 2019

ABSTRACT

We report on a study of 158 methicillin-resistant
Staphylococcus aureus
(MRSA) clinical isolates obtained from 1990 to 1996 in 18 different hospitals in Poland. All isolates were recovered from infection and carriage sites of patients, carriage sites of health care personnel, and hospital environment samples. Fifty-seven MRSA strains described here were studied previously and these were divided into two different clusters according to the degree of heterogeneity of methicillin resistance expression. The aim of this study was to extend the correlation between the two clusters and identify the clonal identities among all isolates by a combination of different methodologies: (i) analysis of
mecA
polymorphs and Tn
554
insertion patterns and (ii) determination of pulsed-field gel electrophoresis patterns of chromosomal
Sma
I digests. Ninety-seven of 158 strains showed a heterogeneous expression of resistance to methicillin. Among these, 75 (77.3%) were
Cla
I-
mecA
type I,
Cla
I-Tn
554
type NH (NH, no homology with transposon Tn
554
), and pulsed-field gel electrophoresis (PFGE) pattern A (I::NH::A); 10 isolates were III::B::M (10.3%); and the remaining clones included a few or single isolates. The isolates with homogeneous expression of resistance to methicillin (
n
= 61) were predominantly
Cla
I-
mecA
type III (49 of 61 [80.3%]) but had great variability in their
Cla
I-Tn
554
and PFGE patterns. This study confirmed the existence of two main clusters of MRSA in Poland.
Antipneumococcal Activities of Levofloxacin and Clarithromycin as Determined by Agar Dilution, Microdilution, E-Test, and Disk Diffusion Methodologies
Authors: Clark Catherine L. , Jacobs Michael R. , Appelbaum Peter C. 
Published: December 2019

ABSTRACT

The activities of levofloxacin and clarithromycin against 199 penicillin- and macrolide-susceptible and -resistant pneumococci were tested by agar and microdilution methods in air and by disk diffusion and E-test methods in air and CO
2
. For levofloxacin, ≥99.0% of strains were susceptible at ≤2.0 μg/ml with zone diameters of ≥17 mm, regardless of incubation in air or CO
2
. Although zone sizes were smaller and E-test MICs were higher for clarithromycin in CO
2
than those in air, category differences were minor, and susceptibility rates for clarithromycin were similar to those obtained by agar and microdilution in air (range, 76.9 to 80.9% by all methods). For clarithromycin, adjustment of breakpoints based upon distribution of results resulted in susceptibility rates which were similar by all methods (75.8 to 76.9% susceptible, 0 to 1.5% intermediate, 22.6 to 23.1% resistant). Minor discrepancies were obtained with levofloxacin for one strain (0.5%) by microdilution and two strains (1.0%) by disk diffusion in CO
2
. For clarithromycin, minor discrepancies were found in three strains (1.5%) by microdilution, seven strains (3.5%) by agar dilution, four strains (2.0%) by E-test in air, six strains (3.0%) by disk diffusion in air, and five strains (2.5%) by disk diffusion in CO
2
. Major discrepancies occurred with levofloxacin in one strain (0.5%) by microdilution but were not found with clarithromycin. Very major discrepancies were not seen with levofloxacin, but occurred with clarithromycin in five strains (2.5%) by microdilution, three strains (1.5%) by agar dilution, two strains (1.0%) by E-test in air, eight strains (4.0%) by disk diffusion in air, and one strain (0.5%) by disk diffusion in CO
2
.
Pooling of Urine Samples for Screening for
Neisseria gonorrhoeae
by Ligase Chain Reaction: Accuracy and Application
Authors: Kacena Katherine A. , Quinn Sean B. , Hartman Suzanne C. , Quinn Thomas C. , Gaydos Charlotte A. 
Published: December 2019

ABSTRACT

The accuracy of detection of genital
Neisseria gonorrhoeae
infection in pooled urine samples by ligase chain reaction (LCR) was examined in three populations. Firstly, urine specimens from 300 female military recruits (FMR) were tested by LCR individually and in pools of four and six. Secondly, 300 urine specimens from middle-school students (MSS) were tested individually by LCR, and then the processed specimens were stored frozen for subsequent testing in pools of 4 and 10. Thirdly, 600 frozen urine specimens from high-school students (HSS) were tested by using the LCR pooling algorithm, i.e., testing processed specimens in pools of four in one test unit dose, and retesting individual specimens from positive pools. Finally, the pooling algorithm results were compared to culture results for a subset of 344 students from the original 600 HSS from whom cervical or urethral samples were taken at the discretion of the school nurse practitioners. Compared to individual testing of specimens by LCR in the FMR population, the pooling-by-four algorithm was 100% sensitive (5 of 5) and 100% pool specific (70 of 70), and the pool-by-six algorithm was 100% sensitive (5 of 5) and 100% pool specific (45 of 45). In the MSS population, the pool-by-4 algorithm was 95.8% sensitive (23 of 24) and 100% (52 of 52) pool specific, and the pool-by-10 algorithm was 95.8% sensitive (23 of 24) and 100% (17 of 17) pool specific. In the subset of 344 HSS from whom endocervical or urethral specimens were collected for culture, 31 were positive by LCR in urine and 26 were positive by culture. After results discrepant between culture and LCR were adjudicated by a confirmatory LCR test, the pooling algorithm was 93.8% (30 of 32) sensitive and 99.7% (311 of 312) specific. Culture from these 344 HSS was 81.3% (26 of 32) sensitive. The pooling algorithm reduced the cost of the
N. gonorrhoeae
LCR assay by 60% compared to individual testing of the HSS specimens and was both sensitive and specific.
Human Cytomegalovirus (HCMV) Encephalitis in an Immunocompetent Young Person and Diagnostic Reliability of HCMV DNA PCR Using Cerebrospinal Fluid of Nonimmunosuppressed Patients
Authors: Prösch Susanna , Schielke Eva , Reip Angela , Meisel Helga , Volk Hans-Dieter , Einhäupl Karl M. , Krüger Detlev H. 
Published: December 2019

ABSTRACT
Human cytomegalovirus (HCMV) encephalitis in adult nonimmunosuppressed patients has rarely been reported. We have diagnosed HCMV encephalitis in an anti-HCMV immunoglobulin G-negative, nonimmunosuppressed young woman by HCMV DNA PCR and virus isolation from cerebrospinal fluid (CSF). At the same time, HCMV antigen and HCMV DNA could be demonstrated in peripheral blood leukocytes, and the virus was isolated in fibroblast cultures. After 22 days of acute illness, the virus disappeared from the CSF. Remarkably, the patient did not generate detectable anti-HCMV antibodies within 5 months after the beginning of illness. To investigate the significance of HCMV DNA detection in CSF, samples of CSF, blood cells, and serum from 35 nonimmunosuppressed patients with various neurological disorders (but no herpes simplex virus central nervous system [CNS] disease) were tested for HCMV DNA, antigen, and antibodies. Eleven of these patients were found to be positive for virus DNA and/or antigen in peripheral blood leukocytes. Additionally, HCMV DNA was detected in the CSF of two patients with noninflammatory CNS diseases. A causative role of HCMV in the CNS diseases of these two patients was not evident. In summary, HCMV DNA amplification from CSF samples is a very suitable method to verify HCMV-associated encephalitis, but it should be taken into consideration that there are few cases of positive PCR with DNA from CSF without any known clinical correlative.