bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Assay for Simultaneous Detection and Differentiation of Immunoglobulin G Antibodies to Human Immunodeficiency Virus Type 1 (HIV-1) Group M, HIV-1 Group O, and HIV-2
Authors: Vallari Ana S. , Hickman Robert K. , Hackett John R. , Brennan Catherine A. , Varitek Vincent A. , Devare Sushil G. 
Published: December 2019

ABSTRACT
A rapid immunodiagnostic test that detects and discriminates human immunodeficiency virus (HIV) infections on the basis of viral type, HIV type 1 (HIV-1) group M, HIV-1 group O, or HIV-2, was developed. The rapid assay for the detection of HIV (HIV rapid assay) was designed as an instrument-free chromatographic immunoassay that detects immunoglobulin G (IgG) antibodies to HIV. To assess the performance of the HIV rapid assay, 470 HIV-positive plasma samples were tested by PCR and/or Western blotting to confirm the genotype of the infecting virus. These samples were infected with strains that represented a wide variety of HIV strains including HIV-1 group M (subtypes A through G), HIV-1 group O, and HIV-2 (subtypes A and B). The results showed that the HIV genotype identity established by the rapid assay reliably (469 of 470 samples) correlates with the HIV genotype identity established by PCR or Western blotting. A total of 879 plasma samples were tested for IgG to HIV by a licensed enzyme immunoassay (EIA) (470 HIV-positive samples and 409 HIV-negative samples). When they were tested by the rapid assay, 469 samples were positive and 410 were negative (99.88% agreement). Twelve seroconversion panels were tested by both the rapid assay and a licensed EIA. For nine panels identical results were obtained by the two assays. For the remaining three panels, the rapid assay was positive one bleed later in comparison to the bleed at which the EIA was positive. One hundred three urine samples, including 93 urine samples from HIV-seropositive individuals and 10 urine samples from seronegative individuals, were tested by the rapid assay. Ninety-one of the ninety-three urine samples from HIV-seropositive individuals were found to be positive by the rapid assay. There were no false-positive results (98.05% agreement). Virus in all urine samples tested were typed as HIV-1 group M. These results suggest that a rapid assay based on the detection of IgG specific for selected transmembrane HIV antigens provides a simple and reliable test that is capable of distinguishing HIV infections on the basis of viral type.
Comparison of Phenotypic and Genotypic Techniques for Identification of Unusual Aerobic Pathogenic Gram-Negative Bacilli
Authors: Tang Yi-Wei , Ellis Nicole M. , Hopkins Marlene K. , Smith Douglas H. , Dodge Deborah E. , Persing David H. 
Published: December 2019

ABSTRACT

Rapid and accurate identification of bacterial pathogens is a fundamental goal of clinical microbiology, but one that is difficult or impossible for many slow-growing and fastidious organisms. We used identification systems based on cellular fatty acid profiles (Sherlock; MIDI, Inc., Newark, Del.), carbon source utilization (Microlog; Biolog, Inc., Hayward, Calif.), and 16S rRNA gene sequence (MicroSeq; Perkin-Elmer Applied Biosystems Division, Foster City, Calif.) to evaluate 72 unusual aerobic gram-negative bacilli isolated from clinical specimens at the Mayo Clinic. Compared to lengthy conventional methods, Sherlock, Microlog, and MicroSeq were able to identify 56 of 72 (77.8%), 63 of 72 (87.5%), and 70 of 72 (97.2%) isolates to the genus level (
P
= 0.002) and 44 to 65 (67.7%), 55 of 65 (84.6%), and 58 of 65 (89.2%) isolates to the species level (
P
= 0.005), respectively. Four
Acinetobacter
and three
Bordetella
isolates which could not be identified to the species level by conventional methods were identified by MicroSeq. In comparison to the full 16S rDNA sequences, the first 527 bp provided identical genus information for all 72 isolates and identical species information for 67 (93.1%) isolates. These data show that MicroSeq provides rapid, unambiguous identification of clinical bacterial isolates. The improved turnaround time provided by genotypic identification systems may translate into improved clinical outcomes.
Effect of Serial Passage in Tissue Culture on Sequence ofomp1fromChlamydia trachomatisClinical Isolates
Authors: Stothard Diane R. , Van Der Pol Barbara , Smith Nancy J. , Jones Robert B. 
Published: December 2019

ABSTRACTPrevious epidemiological studies ofChlamydia trachomatisfrequently have required expansion of isolates in tissue culture. The possibility thatC. trachomatis omp1might undergo mutation during such expansion has not been examined systematically. We found no differences in theomp1sequences from 10 clinical specimens before and after 20 in vitro passages.
Rapid PCR Detection of
Helicobacter pylori
-Associated Virulence and Resistance Genes Directly from Gastric Biopsy Material
Authors: Björkholm Britta , Befrits Ragnar , Jaup Bernhard , Engstrand Lars 
Published: December 2019

ABSTRACT

We have developed a PCR-based method to detect macrolide resistance and the virulence gene
cagA
in
Helicobacter pylori
within 24 h, thereby improving the lengthy process of culture-based approaches. Total DNA was prepared directly from stomach biopsy specimens. The procedure proved to be rapid and reliable and could be utilized for diagnostic purposes.
Isolation of Blood-Borne
Mycobacterium avium
by Using the Nonradioactive BACTEC 9000 MB System and Comparison with a Solid-Culture System
Authors: Jacomo Véronique , Musso Didier , Gevaudan Marie-José , Drancourt Michel 
Published: December 2019

ABSTRACT

We conducted a 12-month prospective study comparing two approaches to the detection of
Mycobacterium avium
in the blood of human immunodeficiency virus type 1-infected patients, namely, a lytic centrifugation system combined with Middlebrook solid culture medium (the conventional procedure) and the nonradiometric BACTEC 9000 MB system. Species identification relied on 16S rRNA probe hybridization and cell wall fatty acids chromatography.
M. avium
was isolated in 17 of 345 (5%) blood specimens by the BACTEC 9000 MB automated system and in 14 of 345 (4%) blood specimens by the conventional procedure (nonsignificant, χ
2
test). Detection time was 16 ± 6 days by the BACTEC 9000 MB automated system and 27 ± 3 days by the conventional procedure (P < 0.001, Student t test). Non-
M. avium
mycobacteria were not recovered during the study period. Contamination rate was 8% (30 specimens) by the BACTEC 9000 MB system and 0% by the conventional procedure, indicating the necessity of using an antibiotic mixture (PANTA, consisting of polymyxin B, amphotericin B, nalidixic acid, trimethoprim, and azlocillin). Working time was 1 min 30 s by the BACTEC 9000 MB system and 8 min by the conventional procedure, which was 1.8 times more expensive than the BACTEC system. Use of the BACTEC 9000 MB system increased the sensitivity of
M. avium
detection and reduced detection time in blood culture.
Detection of Bovine Herpesvirus 1 Glycoprotein E Antibodies in Individual Milk Samples by Enzyme-Linked Immunosorbent Assays
Authors: Wellenberg G. J. , Verstraten E. R. A. M. , Mars M. H. , Van Oirschot J. T. 
Published: December 2019

ABSTRACT
The purpose of this study was to determine whether individual milk samples can replace serum samples for the detection of bovine herpesvirus 1 (BHV1) glycoprotein E (gE)-specific antibodies. Serum and milk samples were collected at the same time from cattle in BHV1-free herds, cattle in unvaccinated herds, and cattle in herds that were vaccinated twice with a BHV1 marker vaccine. The samples were tested in two gE enzyme-linked immunosorbent assay (ELISA) systems. In comparison to serum, the results showed that the gE-blocking ELISA was highly sensitive for testing milk samples (0.96). In contrast, the gE ELISA was less sensitive (0.79). The specificities of the gE-blocking ELISA and the gE ELISA for testing milk samples were very high (1.00 and 0.99, respectively). The presented results indicate that individual milk samples, which can be collected relatively easily and inexpensively, can be used instead of individual serum samples in the gE-blocking ELISA for the screening of cattle for BHV1 gE antibodies.
Detection ofTritrichomonas foetusby PCR and DNA Enzyme Immunoassay Based on rRNA Gene Unit Sequences
Authors: Felleisen Richard S. J. , Lambelet Natacha , Bachmann Philipp , Nicolet Jacques , Müller Norbert , Gottstein Bruno 
Published: December 2019

ABSTRACTTritrichomonas foetusis the causative agent of bovine tritrichomonosis, a sexually transmitted disease leading to infertility and abortion. Diagnosis is hampered by putative contamination of samples with intestinal or coprophilic trichomonadid protozoa which might be mistaken forT. foetus. Therefore, we developed a PCR test optimized for applicability in routine diagnosis. Amplification is based upon primers TFR3 and TFR4 directed to the rRNA gene units ofT. foetus. In order to avoid potential carryover contamination by products of previous amplification reactions, conditions were adapted to the use of the uracil DNA glycosylase system. Furthermore, documentation and interpretation of results were facilitated by including a DNA enzyme immunoassay for the detection of amplification products. Specificity was confirmed with genomic material from different related trichomonadid protozoa. The high sensitivity of the test allowed the detection of a singleT. foetusorganism in diagnostic culture medium or about 50 parasites per ml of preputial washing fluid. The present methods are thus proposed as (i) confirmatory tests for microscopic diagnosis following diagnostic in vitro cultivation and (ii) a directT. foetusscreening test with diagnostic samples.
Amplification of Full-Length Hepatitis B Virus Genomes from Samples from Patients with Low Levels of Viremia: Frequency and Functional Consequences of PCR-Introduced Mutations
Authors: Günther Stephan , Sommer Gunhild , Von Breunig Franziska , Iwanska Alicja , Kalinina Tatyana , Sterneck Martina , Will Hans 
Published: December 2019

ABSTRACTTo facilitate the investigation of hepatitis B virus (HBV) sequence variation, we recently established a method for functional analysis of PCR-amplified full-length HBV genomes. This study aimed at estimating the number of mutations introduced during amplification of genomes from samples from patients with low levels of viremia and their influence on replication and antigen expression. Wild-type HBV DNA template molecules in concentrations like those present in samples from patients with very low levels of viremia were amplified, sequenced (30 kb total), and functionally tested. We found thatTaqpolymerase and aTaq-Pwopolymerase mixture introduced an average of 5.7 and 3.1 mutations per genome, respectively, corresponding to polymerase error rates of 12.1 × 10−5and 6.0 × 10−5. One of 8 genomes (12%) amplified withTaqpolymerase, but 7 of 17 genomes amplified withTaq-Pwopolymerases (41%), remained replication competent. All replication-competent genomes expressed HBs and HBe antigens and had an average of only 0.9 mutations per genome. In contrast, replication-defective genomes had an average of 5.4 mutations, which frequently also disturbed viral antigen expression. From these data we conclude that many of the replication-competent HBV genomes from a clinical specimen will retain their replication and antigen expression phenotypes even after extensive amplification withTaq-Pwopolymerases. Because replication competence is highly sensitive to random mutations, it is the best marker for the identification of HBV genomes with few or no PCR-introduced mutations.
Oligonucleotide Ligation Assay for Detecting Mutations in the Human Immunodeficiency Virus Type 1
pol
Gene That Are Associated with Resistance to Zidovudine, Didanosine, and Lamivudine
Authors: Edelstein Reva E. , Nickerson Deborah A. , Tobe Vincent O. , Manns-Arcuino Laura A. , Frenkel Lisa M. 
Published: December 2019

ABSTRACT

This report describes the detection of mutations in the
pol
gene of human immunodeficiency virus type 1 associated with resistance to zidovudine, didanosine, and lamivudine by genotyping by an oligonucleotide ligation assay specific codons in the
pol
gene amplified by PCR. Our studies demonstrate the sensitivity, simplicity, and specificity of this genotyping system.
Prospective Study To Determine Clinical Relevance of Detection of Pneumococcal DNA in Sera of Children by PCR
Authors: Dagan Ron , Shriker Ofra , Hazan Inbal , Leibovitz Eugene , Greenberg David , Schlaeffer Francis , Levy Rachel 
Published: December 2019

ABSTRACT

We undertook a prospective study to evaluate the accuracy of PCR of serum (aimed at the pneumococcal pneumolysin gene) at detecting pneumococcal infections in infants and children. The assay was positive for all blood and cerebrospinal fluid culture-positive samples and for 38 and 44% of patients with lobar pneumonia and acute otitis media, respectively. It was positive for 17% of healthy controls. There was a marked effect of age on the rate of positivity among healthy controls, with the highest rate (33%) being in 2-year-old children, the age group with the highest rate of nasopharyngeal (NP) carriage; the lowest rate was found among infants <2 months of age (13%) and adults ages 18 to 50 years (0%), age groups with the lowest NP pneumococcal carriage rates. Carriers of pneumococci in the nasopharynges had a higher rate of positivity than noncarriers of pneumococci in the nasopharynges for all groups. Our results suggest that although PCR of serum is a sensitive test for the detection of
Streptococcus pneumoniae
in sterile fluids, its high rate of positivity for healthy controls, related to NP pneumococcal carriage, might exclude it from being useful in detecting deep-seated pneumococcal infections.
Evaluation of PCR for Diagnosis of
Bordetella pertussis
and
Bordetella parapertussis
Infections
Authors: Lind-Brandberg Lena , Welinder-Olsson Christina , Lagergård Teresa , Taranger John , Trollfors Birger , Zackrisson Gunilla 
Published: December 2019

ABSTRACT

PCR, using primers PIp1 and PIp2, was evaluated for the detection of DNA from
Bordetella pertussis
in bacterial strains and in nasopharyngeal samples from patients with a cough lasting at least 7 days. The assay could detect DNA from 6 CFU of
B. pertussis
/10 μl of sample. Results of the PCR assay were compared with those of cultures, a determination of serum antibodies against pertussis toxin and filamentous hemagglutinin, and a clinical evaluation of 2,442 coughing episodes. The overall sensitivity of PCR was 65% (623 of 956), which was higher than the sensitivity of cultures (58%) (
P
< 0.001). Factors influencing the sensitivity of PCR were the interval between the onset of symptoms and sampling and the vaccination status of the patient. The specificity of PCR was 98% (1,451 of 1,486). The positive and negative predictive values were 95 and 81%, respectively. Parapertussis PCR, using primers BPPA and BPPZ, was positive in 11 of 18 culture-positive cases and was confirmed by serology in another 4 cases. In conclusion, PCR is a valuable complement to cultures and can probably replace cultures for diagnosis of
B. pertussis
and
Bordetella parapertussis
infections.
Update on
Pneumocystis carinii
f. sp.
hominis
Typing Based on Nucleotide Sequence Variations in Internal Transcribed Spacer Regions of rRNA Genes
Authors: Lee Chao-Hung , Helweg-Larsen Jannik , Tang Xing , Jin Shaoling , Li Baozheng , Bartlett Marilyn S. , Lu Jang-Jih , Lundgren Bettina , Lundgren Jens D. , Olsson Mats , Lucas Sebastian B. , Roux Patricia , Cargnel Antonietta , Atzori Chiara , Matos Olga , Smith James W. 
Published: December 2019

ABSTRACT

Pneumocystis carinii
f. sp.
hominis
isolates from 207 clinical specimens from nine countries were typed based on nucleotide sequence variations in the internal transcribed spacer regions I and II (ITS1 and ITS2, respectively) of rRNA genes. The number of ITS1 nucleotides has been revised from the previously reported 157 bp to 161 bp. Likewise, the number of ITS2 nucleotides has been changed from 177 to 192 bp. The number of ITS1 sequence types has increased from 2 to 15, and that of ITS2 has increased from 3 to 14. The 15 ITS1 sequence types are designated types A through O, and the 14 ITS2 types are named types a through n. A total of 59 types of
P. carinii
f. sp.
hominis
were found in this study.
Detection of Cattle Naturally Infected with
Anaplasma marginale
in a Region of Endemicity by Nested PCR and a Competitive Enzyme-Linked Immunosorbent Assay Using Recombinant Major Surface Protein 5
Authors: Torioni de Echaide Susana , Knowles Donald P. , McGuire Travis C. , Palmer Guy H. , Suarez Carlos E. , McElwain Terry F. 
Published: December 2019

ABSTRACT

A competitive enzyme-linked immunosorbent assay using recombinant major surface protein 5 (rMSP5-cELISA) of
Anaplasma marginale
was validated in a naturally infected cattle herd in an area of eastern Oregon where
A. marginale
is endemic. The true positive and negative
A. marginale
infection status of 235 randomly selected cattle was determined by using a nested PCR (nPCR) coupled with
msp5
sequence analysis and hybridization. Judgment of the reliability of the nPCR and hybridization for detection of persistent infections was based on three observations. First, the nPCR was able to detect as few as 30 infected erythrocytes per ml. Second, the nPCR was able to consistently detect low levels of rickettsemia in seven carrier cattle experimentally infected with
A. marginale
. Third,
msp5
sequence analysis showed >95% identity among 30 nPCR amplicons from cattle naturally infected with field strains of
A. marginale
. The nPCR and hybridization identified 151 infected and 84 uninfected cattle among the 235 animals tested. With a cutoff point of 28%, the rMSP5-cELISA showed a sensitivity of 96% and a specificity of 95%. These results indicate that the rMSP5-cELISA can sensitively and specifically detect cattle with naturally acquired persistent
A. marginale
infections and suggest that it is an excellent assay for epidemiological studies, eradication programs, and regulation of international cattle movement.
Simultaneous Identification of Antibodies toBrucella abortusandStaphylococcus aureusin Milk Samples by Flow Cytometry
Authors: Iannelli Domenico , D’Apice Letizia , Fenizia Domenico , Serpe Luigi , Cottone Carlo , Viscardi Maurizio , Capparelli Rosanna 
Published: December 2019

ABSTRACTTwo flow cytometric assays are described herein. The single cytometric test (SCT) detects antibodies to eitherBrucella abortusorStaphylococcus aureusin the serum or milk of a cow or water buffalo. The double cytometric test (DCT) detects both anti-B. abortusand anti-S. aureusantibodies concurrently. In the SCT, the sample to be tested is incubated in succession with the antigen (eitherB. abortusorS. aureus) and the proper secondary antiserum (fluorescein isothiocyanate-labelled rabbit anti-cow immunoglobulin antiserum or rabbit anti-water buffalo immunoglobulin antiserum). In the DCT, the sample to be tested is incubated first withB. abortusandS. aureusantigens and then with the secondary antiserum. TheB. abortusantigen used in the DCT is covalently bound to 3-μm-diameter latex particles. The difference in size betweenB. abortusandS. aureuspermits the establishment of whether the antibodies are directed against one, the other, or both antigens. When compared to the complement fixation test, the SCT and DCT each show a specificity and a sensitivity of 100%. The SCT has been used previously to detect anti-S. aureusantibodies. Here its use is extended to the detection of anti-B. abortusantibodies. The DCT is described here for the first time. The DCT appears to be useful for large-scale brucellosis eradication programs. It offers the possibility of using one test to identify animals that are serologically positive for bothB. abortusandS. aureus.
Glycogen Assay for Diagnosis of Female Genital
Chlamydia trachomatis
Infection
Authors: Chun Yang , Yin Zhu Dao 
Published: December 2019

ABSTRACT

Chlamydia trachomatis
can synthesize glycogen at various stages in its developmental cycle. The glycogen content of female genital epithelial cells was detected by anthrone, and the results were compared with those from PCR. A total of 320 cervical samples were examined. Of 92 specimens that were positive by PCR, 78 were positive and 14 were negative by the glycogen assay. Of 228 specimens that were negative by PCR, 220 were negative and 8 were positive by the glycogen assay. The sensitivity and specificity of the glycogen assay obtained from these data were 84.8% (78 of 92) and 96.5% (220 of 228), respectively. Use of the glycogen assay to detect the glycogen content in genital epithelial cells may be helpful in the diagnosis of
C. trachomatis
infection. This is an easy, fast, and inexpensive assay and can be done in less-sophisticated labs.
Baculovirus Expression of the Fusion Protein Gene of Bovine Respiratory Syncytial Virus and Utility of the Recombinant Protein in a Diagnostic Enzyme Immunoassay
Authors: Pastey Manoj K. , Samal Siba K. 
Published: December 2019

ABSTRACTThe fusion (F) protein of bovine respiratory syncytial virus (BRSV) was expressed by using a baculovirus vector. Antigenicity was tested by immunofluorescence analysis with F-specific monoclonal and polyclonal antibodies. Antibodies to recombinant F protein raised in a rabbit neutralized BRSV and human respiratory syncytial virus infectivity when tested in a plaque reduction assay. The recombinant F protein was evaluated as a source of antigen in an enzyme-linked immunosorbent assay (ELISA), and this ELISA was compared with the virus neutralization (VN) test for detecting BRSV antibodies in 10 consecutive serum samples from four calves vaccinated with a live modified BRSV vaccine and from two nonvaccinated control calves. The ELISA with the baculovirus-expressed F protein as an antigen compared favorably with the VN test and is a rapid, sensitive, and specific method for detecting serum antibodies to BRSV.
Application of an Optimized and Highly Discriminatory Method Based on Arbitrarily Primed PCR for Epidemiologic Analysis of Methicillin-Resistant
Staphylococcus aureus
Nosocomial Infections
Authors: Olmos Antonio , Camarena Juan J. , Nogueira José M. , Navarro Juan C. , Risen Julia , Sánchez Roberto 
Published: December 2019

ABSTRACT

The optimization of an arbitrarily primed PCR method for typing 96 methicillin-resistant
Staphylococcus aureus
(MRSA) isolates was compared with pulsed-field gel electrophoresis. Identical results in the differentiation of MRSA clones and identification of the main cluster that included 82 strains (88% of patients) were obtained by both techniques.
Chromogenic Tube Test for Presumptive Identification or Confirmation of Isolates asCandida albicans
Authors: Merlino John , Tambosis Evanthia , Veal Duncan 
Published: December 2019

ABSTRACTThis report describes a new, modified, simple, and cost-effective method for the use of CHROMagar Candida (CHROMagar Company, Paris, France) for the presumptive identification of isolates asCandida albicansafter preliminary growth. Sixty randomly selected clinical isolates were evaluated, including 38 ofC. albicans. With incubation at 37°C for 24 h, the sensitivity and specificity appeared to be excellent and the test performed better than the traditional germ tube test. However, at earlier times,C. tropicalisisolates gave false-positive results.