bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficiencies of Four Versions of the AMPLICOR HIV-1 MONITOR Test for Quantification of Different Subtypes of Human Immunodeficiency Virus Type 1
Authors: Triques K. , Coste J. , Perret J. L. , Segarra C. , Mpoudi E. , Reynes J. , Delaporte E. , Butcher A. , Dreyer K. , Herman S. , Spadoro J. , Peeters M. 
Published: December 2019

ABSTRACT

Three versions of a commercial human immunodeficiency virus (HIV) type 1 (HIV-1) load test (the AMPLICOR HIV-1 MONITOR Test versions 1.0, 1.0+, and 1.5; Roche Diagnostics, Branchburg, N.J.) were evaluated for their ability to detect and quantify HIV-1 RNA of different genetic subtypes. Plasma samples from 96 patients infected with various subtypes of HIV-1 (55 patients infected with subtype A, 9 with subtype B, 21 with subtype C, 2 with subtype D, 7 with subtype E, and 2 with subtype G) and cultured virus from 29 HIV-1 reference strains (3 of subtype A, 6 of subtype B, 5 of subtype C, 3 of subtype D, 8 of subtype E, 3 of subtype F, and 1 of subtype G) were tested. Detection of subtypes A and E was significantly improved with versions 1.0+ and 1.5 compared to that with version 1.0, whereas detection of subtypes B, C, D, and G was equivalent with the three versions. Versions 1.0, 1.0+, and 1.5 detected 65, 98, and 100% of the subtype A-infected samples from patients, respectively, and 71, 100, and 100% of the subtype E-infected samples from patients, respectively. Version 1.5 yielded a significant increase in viral load for samples infected with subtypes A and E (greater than 1 log
10
HIV RNA copies/ml). For samples infected with subtype B, C, and D and tested with version 1.5, only a slight increase in viral load was observed (<0.5 log
10
). We also evaluated a prototype automated version of the test that uses the same PCR primers as version 1.5. The results with the prototype automated test were highly correlated with those of the version 1.5 test for all subtypes, but were lower overall. The AMPLICOR HIV-1 MONITOR Test, version 1.5, yielded accurate measurement of the HIV load for all HIV-1 subtypes tested, which should allow the test to be used to assess disease prognosis and response to antiretroviral treatment in patients infected with a group M HIV-1 subtype.
Quantitative Analysis of Epstein-Barr Virus Load by Using a Real-Time PCR Assay
Authors: Kimura Hiroshi , Morita Makoto , Yabuta Yumi , Kuzushima Kiyotaka , Kato Koji , Kojima Seiji , Matsuyama Takaharu , Morishima Tsuneo 
Published: December 2019

ABSTRACT

To measure the virus load in patients with symptomatic Epstein-Barr virus (EBV) infections, we used a real-time PCR assay to quantify the amount of EBV DNA in blood. The real-time PCR assay could detect from 2 to over 10
7
copies of EBV DNA with a wide linear range. We estimated the virus load in peripheral blood mononuclear cells (PBMNC) from patients with symptomatic EBV infections. The mean EBV-DNA copy number in the PBMNC was 10
3.7
copies/μg of DNA in patients with EBV-related lymphoproliferative disorders, 10
4.1
copies/μg of DNA in patients with chronic active EBV infections, and 10
2.2
copies/μg of DNA in patients with infectious mononucleosis. These numbers were significantly larger than those in either posttransplant patients or immunocompetent control patients without EBV-related diseases. In a patient with infectious mononucleosis, the virus load decreased as the symptoms resolved. The copy number of EBV DNA in PBMNC from symptomatic EBV infections was correlated with the EBV-positive cell number determined by the in situ hybridization assay (
r
= 0.842;
P
< 0.0001). These results indicate that the real-time PCR assay is useful for diagnosing symptomatic EBV infection and for monitoring the virus load.
False-Positive Gen-Probe Direct
Mycobacterium tuberculosis
Amplification Test Results for Patients with Pulmonary
M. kansasii
and
M. avium
Infections
Authors: Jorgensen James H. , Salinas Jesse R. , Paxson Rosemary , Magnon Karen , Patterson Jan E. , Patterson Thomas F. 
Published: December 2019

ABSTRACT

The Gen-Probe Amplified Mycobacterium Tuberculosis Direct (MTD) test has been approved for use in the United States for the rapid diagnosis of pulmonary tuberculosis in patients with acid-fast smear-positive sputum samples since 1996. Four patients infected with human immunodeficiency virus and one chronic pulmonary-disease patient seen in our institutions with abnormal chest radiographs and fluorochrome stain-positive sputa were evaluated for tuberculosis, including performance of the MTD test on expectorated sputum samples. Three of these five patients’ sputa were highly smear-positive (i.e., more than 100 bacilli per high-power field), while two patient’s sputa contained 1 to 10 bacilli per field. MTD results on sputum specimens from these patients ranged from 43,498 to 193,858 relative light units (RLU). Gen-Probe has defined values of at least 30,000 RLU as indicative of a positive test, i.e., the presence of
Mycobacterium tuberculosis
RNA. Four of the patients’ sputum cultures yielded growth of
M. kansasii
within 6 to 12 days, and the fifth produced growth of
M. avium
only. One patient’s culture contained both
M. kansasii
and
M. avium
, but none of the initial or follow-up cultures from these five patients revealed
M. tuberculosis
. However, subsequent cultures from three of the patients again revealed
M. kansasii
. During the period of this study, in which MTD tests were performed on smear-positive sputum specimens from 82 patients, four of seven patients with culture-proven
M. kansasii
pulmonary infections yielded one or more false-positive MTD tests. The MTD sensitivity observed in this study was 93.8%, and the specificity was 85.3%. Five cultures of
M. kansasii
(including three of these patients’ isolates and
M. kansasii
ATCC 12478), and cultures of several other species were examined at densities of 10
5
to 10
7
viable CFU/ml by the MTD test. All five isolates of
M. kansasii
and three of three isolates of
M. simiae
yielded false-positive test results, with readings of 75,191 to 335,591 RLU. These findings indicate that low-level false-positive MTD results can occur due to the presence of
M. kansasii
,
M. avium
, and possibly other
Mycobacterium
species other than
M. tuberculosis
in sputum. Low-level positive MTD results of 30,000 to 500,000 RLU should be interpreted in light of these findings. It remains to be determined if the enhanced MTD test (MTD 2) recently released by Gen-Probe will provide greater specificity than that observed in this report with its first-generation test.
Comparison between PCR and Detection of Antigen in Sera for Diagnosis of Pulmonary Aspergillosis
Authors: Kawamura Sumio , Maesaki Shigefumi , Noda Tetsuhiro , Hirakata Youichi , Tomono Kazunori , Tashiro Takayoshi , Kohno Shigeru 
Published: December 2019

ABSTRACT

We evaluated the usefulness of PCR and antigen detection for the diagnosis of pulmonary aspergillosis. Forty-four serum samples from patients with pulmonary aspergillosis (33 with pulmonary aspergilloma, 4 with allergic bronchopulmonary aspergillosis, 4 with invasive pulmonary aspergillosis, and 3 with aspergillus pyothorax) were used in this study. PCR detection of
Aspergillus
DNA in serum samples was successful in 39 patients. Galactomannan antigen was detected by sandwich enzyme-linked immunosorbent assay in 25 patients and by latex agglutination test in 13 patients. Detection of
Aspergillus
DNA in serum samples by nested PCR had the highest sensitivity of the three methods tested for the diagnosis of pulmonary aspergillosis.
Rapid Identification of
Burkholderia pseudomallei
by Latex Agglutination Based on an Exopolysaccharide-Specific Monoclonal Antibody
Authors: Steinmetz I. , Reganzerowski A. , Brenneke B. , Häussler S. , Simpson A. , White N. J. 
Published: December 2019

ABSTRACT

We recently identified a constitutively expressed exopolysaccharide of
Burkholderia pseudomallei
which is composed of a unique linear tetrasaccharide repeating unit consisting of three galactose residues and one 3-deoxy-
d
-
manno
-2-octulosonic acid residue. In this study we developed a latex agglutination test based on monoclonal antibody 3015, which is specific for this exopolysaccharide, and evaluated this test for rapid identification of
B. pseudomallei
grown on agar plates. All 74 environmental and clinical
B. pseudomallei
strains tested, originating from different areas of Southeast Asia, northern Australia, and Africa, showed a strong and specific agglutination.
B. pseudomallei
-like organisms and a variety of other bacteria did not react. In conclusion this monoclonal antibody-based test is a simple, rapid, and highly specific method for identifying
B. pseudomallei
culture isolates from different geographic areas.
Viral Superinfection in Previously Unrecognized Chronic Carriers of Hepatitis B Virus with Superimposed Acute Fulminant versus Nonfulminant Hepatitis
Authors: Chu Chia-Ming , Yeh Chau-Ting , Liaw Yun-Fan 
Published: December 2019

ABSTRACTThe role of viral superinfection in hepatitis B surface antigen carriers with superimposed fulminant (n= 60) versus nonfulminant (n= 90) acute hepatitis was studied. The frequency of hepatitis A virus (HAV) (0 versus 2.2%), HCV (18.3 versus 21.1%), HDV (15.0 versus 7.8%), and HEV (1.7 versus 4.4%) infection showed no significant difference, while simultaneous HCV and HDV infection was significantly more prevalent in the former (8.3 versus 0%). Only 3.6% of fulminant cases and 3.3% of nonfulminant controls were HGV RNA positive.
Ochrobactrum intermedium
Infection after Liver Transplantation
Authors: Möller Lieke V. M. , Arends Jan P. , Harmsen Hermie J. M. , Talens Adriaan , Terpstra Peter , Slooff Maarten J. H. 
Published: December 2019

ABSTRACT

A case of bacteremia due to
Ochrobactrum intermedium
, with concomitant liver abscesses, in an orthotopic liver transplant recipient is presented. Identical microorganisms were isolated from fecal specimens and from an aspirate of a liver abscess that was indicative of invasion of the graft by gastrointestinal spread. 16S DNA sequence analysis of the blood isolate revealed the recovery of the recently proposed new species
O. intermedium
, closely related to
Ochrobactrum anthropi
and
Brucella
spp.
Systemic Infection of an Immunocompromised Patient with
Methylobacterium zatmanii
Authors: Hornei B. , Lüneberg E. , Schmidt-Rotte H. , Maaß M. , Weber K. , Heits F. , Frosch M. , Solbach W. 
Published: December 2019

ABSTRACT

We describe the identification of
Methylobacterium zatmanii
as the causative agent of bacteremia and fever in an immunocompromised patient. The patient, a 60-year-old man, had a 5-month history of acute myeloid leukemia and had been on chemotherapy throughout this period. Seven days after the onset of neutropenia, the patient developed fever. The combination of ciprofloxacin, co-trimoxazole, imipenem, amikacin, and vancomycin led to a complete defervescence. On subculture from six positive blood cultures, the organism grew only on buffered charcoal yeast extract agar and not on standard agars. Identification by universal PCR and subsequent sequence analysis of the amplified 16S rRNA gene segment was achieved. This identification by molecular biology techniques was confirmed by conventional biochemical tests. To our knowledge, this is the first description of
M. zatmanii
isolated from patient material.
Serotyping of
Streptococcus pneumoniae
by Coagglutination with 12 Pooled Antisera
Authors: Lalitha M. K. , Thomas Kurien , Kumar R. Satish , Steinhoff Mark C. ,   the IBIS Study Group
Published: December 2019

ABSTRACT

We report on the performance of a recently introduced commercial chessboard method using 12 antisera, in comparison with that of the 55-antiserum panel used in determining the serogroups and types (SGTs) of
Streptococcus pneumoniae
, both of which were carried out by a coagglutination technique. Of a total of 150 strains of
S. pneumoniae
studied, 135 (90%) belonged to the SGTs represented in the 23-valent pneumococcal vaccine; of these, 130 (96.3%) were identified as the same SGTs by both typing methods. The remaining five strains showed cross-reactivity with more than two pools by the chessboard method, but could be assigned to a single SGT by the Quellung test. The 96.3% concordance of the chessboard method suggests it can be adopted for determination of the SGTs of
S. pneumoniae
in laboratories.
Klebsiella pneumoniaeLipopolysaccharide O Typing: Revision of Prototype Strains and O-Group Distribution among Clinical Isolates from Different Sources and Countries
Authors: Hansen Dennis S. , Mestre Francesca , Albertí Sebastián , Hernández-Allés Santiago , Álvarez Dolores , Doménech-Sánchez Antonio , Gil José , Merino Susana , Tomás Juan M. , Benedí Vicente J. 
Published: December 2019

ABSTRACTWe have previously described an inhibition enzyme-linked immunosorbent assay method for the O typing of O1 lipopolysaccharide fromKlebsiella pneumoniaewhich overcomes the technical problems and limitations of the classical O-typing method. In this study, we have extended the method to all of the currently recognized O types. The method was validated by studying the prototype strains that have defined the O groups by the classical tube agglutinatination O-typing method. Based on these results, we confirmed the O types of 60 of 64 typeable strains, and we propose a revised O-antigenic scheme, with minor but necessary changes, consisting of serogroups or serotypes O1, O2, O2ac, O3, O4, O5, O7, O8, and O12. Application of this typing method to 638K. pneumoniaeclinical isolates from Denmark, Spain, and the United States from different sources (blood, urine, and others) showed that up to 80% of these isolates belong to serotypes or serogroups O1, O2, O3, and O5, independently of the source of isolation, and that a major group of nontypeable isolates, representing about 17% of the total, consists of half O+and half O−strains. Differences were observed, however, in the prevalence of the lipopolysaccharide O types or groups, depending on the country and isolation source.
Quantitative Detection of Hepatitis B Virus DNA in Two International Reference Plasma Preparations
Authors: Heermann Klaus-Hinrich , Gerlich Wolfram H. , Chudy Michael , Schaefer Stephan , Thomssen Reiner ,   The Eurohep Pathobiology Group
Published: December 2019

ABSTRACT

Quantitative detection of hepatitis B virus (HBV) in serum or plasma is of significance for monitoring of therapy and establishment of the prognosis of the disease, as well as for infectivity assessment and quality control of the diagnosis. Unfortunately, various commercially available test kits for HBV DNA yielded conflicting quantitative results, with differences of up to a factor of 120. The Eurohep Pathobiology Group has established two reference samples of plasma from HBV carriers and determined as accurately as possible the number of HBV DNA molecules in these samples. Plasma donations from two single highly viremic carriers of HBV genotype A (HBV surface antigen subtype
adw2
) and genotype D (
ayw2/3
), respectively, were collected, and coded dilutions of these samples were analyzed by members of the Eurohep Pathobiology Group. Quantitative results from the seven laboratories reporting consistent results were initially divergent. Limiting dilution and nested PCR assays suffered from incomplete DNA extraction. Hybridization assays used inaccurately quantitated cloned DNA as a reference. Two hybridization assays could not be calibrated directly with cloned HBV DNA, because virion-derived DNA reacted much less efficiently. After identification and elimination of these problems, limiting-dilution assays from three laboratories and hybridization assays from two producers generated consistent and concordant results: 2.7 × 10
9
HBV DNA molecules/ml (range, 2.1 × 10
9
to 3.4 × 10
9
HBV DNA molecules/ml) in the plasma from the carrier of genotype A and 2.6 × 10
9
HBV DNA molecules/ml (range, 2.1 × 10
9
to 3.0 × 10
9
HBV DNA molecules/ml in the plasma from the carrier of genotype D. The two Eurohep reference plasma samples have already been used for the standardization of test kits and in quality control trials, and the plasma from the carrier of genotype A will probably be the basis of a World Health Organization reference sample.
Multicenter Evaluation of the Fully Automated COBAS AMPLICOR PCR Test for Detection of
Chlamydia trachomatis
in Urogenital Specimens
Authors: Vincelette Jean , Schirm Jurjen , Bogard Marc , Bourgault Anne-Marie , Luijt Dirk S. , Bianchi Anne , van Voorst Vader Pieter C. , Butcher Ann , Rosenstraus Maurice 
Published: December 2019

ABSTRACT

The fully automated COBAS AMPLICOR CT/NG test for the detection of
Chlamydia trachomatis
was evaluated in a multicenter trial. Test performance was evaluated for 2,014 endocervical swab and 1,278 urine specimens obtained from women and for 373 urethral swab and 254 urine specimens obtained from men. Culture served as the reference test. Culture-negative, COBAS AMPLICOR-positive specimens that tested positive in a confirmatory PCR test for an alternative target sequence within the
C. trachomatis
major outer membrane protein gene were resolved as true positives. The overall prevalence of chlamydia was 4.3% in cervical swabs and 11.0% in urethral swabs from men. When the results for each specimen type were considered separately, the resolved sensitivities were 96.5% (83 of 86) for endocervical swab specimens, 95.1% (39 of 41) for urine specimens from women, 100.0% (41 of 41) for urethral swab specimens from men, and 94.4% (17 of 18) for urine specimens from men; the resolved specificities were 99.4% (1,912 of 1,924) for endocervical swab specimens, 99.8% (1,204 of 1,207) for urine specimens from women, 98.5% (325 of 330) for urethral swab specimens from men, and 100.0% (236 of 236) for urine specimens from men. For the subset of patients from whom both swab and urine specimens were collected, the combined results for both specimen types were used to identify all infected patients. Using these combined reslts as criteria, the resolved sensitivities for the COBAS AMPLICOR test were 82.6% (38 of 46) for endocervical swab specimens, 84.4% (38 of 45) for urine specimens from women, 84.2% (16 of 19) for urethral swab specimens from men, and 89.5% (17 of 19) for urine specimens from men. In comparison, the sensitivity of culture was only 56.5% (26 of 46) for endocervical specimens and 63.2% (12 of 19) for urethral specimens from men. The internal control provided in the COBAS AMPLICOR test revealed that 2.9% of specimens were inhibitory when they were initially tested. Nevertheless, valid results were obtained for 99.1% of specimens because 68.7% of the inhibitory specimens were not inhibitory when a second aliquot of the original sample was tested. Two additional COBAS AMPLICOR-positive specimens were detected by retesting inhibitory specimens. The COBAS AMPLICOR CT/NG test for the detection of
C. trachomatis
exhibited equally high sensitivities and specificities with both urogenital swab and urine specimens and, thus, is well-suited for use in screening.
Rapid Identification of Clinically Relevant
Nocardia
Species to Genus Level by 16S rRNA Gene PCR
Authors: Laurent Frederic J. , Provost Frederique , Boiron Patrick 
Published: December 2019

ABSTRACT

Two regions of the gene coding for 16S rRNA in
Nocardia
species were selected as genus-specific primer sequences for a PCR assay. The PCR protocol was tested with 60 strains of clinically relevant
Nocardia
isolates and type strains. It gave positive results for all strains tested. Conversely, the PCR assay was negative for all tested species belonging to the most closely related genera, including
Dietzia
,
Gordona
,
Mycobacterium
,
Rhodococcus
,
Streptomyces
, and
Tsukamurella
. Besides, unlike the latter group of isolates, all
Nocardia
strains exhibited one
Mln
I recognition site but no
Sac
I restriction site. This assay offers a specific and rapid alternative to chemotaxonomic methods for the identification of
Nocardia
spp. isolated from pathogenic samples.
Comparative Evaluation of Ligation-Mediated PCR and Spoligotyping as Screening Methods for Genotyping of
Mycobacterium tuberculosis
Strains
Authors: Bonora Stefano , Gutierrez M. Cristina , Di Perri Giovanni , Brunello Francesca , Allegranzi Benedetta , Ligozzi Marco , Fontana Roberta , Concia Ercole , Vincent Veronique 
Published: December 2019

ABSTRACT

Spoligotyping has been suggested as a screening test in multistep genotyping of
Mycobacterium tuberculosis
strains. Relying on restriction fragment length polymorphism (RFLP) analysis with IS
6110
(IS
6110
RFLP analysis) as a “gold standard,” we performed a comparative evaluation of spoligotyping and ligation-mediated PCR (LMPCR), a recently described PCR-based typing method, as rapid screening tests for fingerprinting of 158
M. tuberculosis
strains collected in Verona, Italy. LMPCR seemed to be comparable to spoligotyping in terms both of feasibility with rapidly extracted DNA and of generation of software-analyzable images. Moreover, LMPCR grouped considerably fewer strains than spoligotyping (38 versus 67%) and was found to reduce the cluster overestimation rate (26.3 versus 58%) and to give a better discriminatory index (0.992 versus 0.970) compared to spoligotyping. In our geographical region, where there was no evidence of clustered strains carrying fewer than six IS
6110
copies, LMPCR was found to be more discriminatory than spoligotyping. We also evaluated two models of three-step typing strategies, involving the use of spoligotyping and LMPCR as screening methods and IS
6110
RFLP analysis as a further supporting test. LMPCR proved to be a more effective first-step test than spoligotyping, significantly reducing the need for subtyping. LMPCR should be considered an alternative to spoligotyping as a rapid screening method for
M. tuberculosis
fingerprinting, particularly in areas with a low prevalence of
M. tuberculosis
strains carrying few copies of IS
6110
.
The
cps
Genes of
Streptococcus suis
Serotypes 1, 2, and 9: Development of Rapid Serotype-Specific PCR Assays
Authors: Smith Hilde E. , Veenbergen Vincent , van der Velde Joeke , Damman Marloes , Wisselink Henk J. , Smits Mari A. 
Published: December 2019

ABSTRACT

We developed three type-specific PCR assays for the rapid and sensitive detection of
Streptococcus suis
serotype 1 (plus 14), serotype 2 (plus 1/2), and serotype 9 strains in tonsillar specimens from pigs. The PCR primers were based on the sequences of type-specific capsular genes of
S. suis
serotype 1, 2, and 9 strains. We recently characterized a major part of the capsular biosynthesis (
cps
) locus of
S. suis
serotype 2. Here we extended these studies and characterized major parts of the
cps
loci of
S. suis
serotypes 1 and 9. Type-specific genes were identified by cross-hybridization experiments between the individual
cps
genes and chromosomal DNAs from the 35 different serotypes. Four genes of
S. suis
serotype 1 specifically hybridized with serotype 1 and 14 strains only. Five genes of
S. suis
serotype 2 specifically hybridized with serotype 2 and 1/2 strains only, and two genes of
S. suis
serotype 9 specifically hybridized with serotype 9 strains. Until now rapid and sensitive diagnostic tests were available only for pathogenic strains of serotype 2 and highly pathogenic strains of serotype 1. The serotype-specific PCR assays can therefore be useful tools for the identification of serotype 1, 14, 2, 1/2, and 9 strains both for diagnostic purposes and in epidemiological and transmission studies. Therefore, these tests may facilitate control and eradication programs.