bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of Molecular Methods for Typing
Vibrio parahaemolyticus
Authors: Marshall S. , Clark C. G. , Wang G. , Mulvey M. , Kelly M. T. , Johnson W. M. 
Published: December 2019

ABSTRACT

An outbreak of
Vibrio parahaemolyticus
gastroenteritis on Canada’s west coast in 1997 emphasized the need to develop molecular methods for differentiation and typing of these organisms. Isolates were analyzed by enterobacterial repetitive intergenic consensus sequence (ERIC) PCR, detection of restriction fragment length polymorphisms (RFLP) in rRNA genes (ribotyping), pulsed-field gel electrophoresis (PFGE), and RFLP analysis of the genetic locus encoding the polar flagellum (Fla locus RFLP analysis). ERIC PCR and ribotyping were the most informative typing methods, especially when used together, while Fla locus RFLP analysis was the least discriminatory. PFGE exhibited good discrimination but suffered from a high incidence of DNA degradation. ERIC PCR and ribotyping will be useful for the evaluation of genetic and epidemiological relationships among
V. parahaemolyticus
strains.
Osteomyelitis Caused by
Staphylococcus schleiferi
and Evidence of Misidentification of This
Staphylococcus
Species by an Automated Bacterial Identification System
Authors: Calvo Jorge , Hernández José L. , Fariñas Maria C. , García-Palomo Daniel , Agüero Jesús 
Published: December 2019

ABSTRACT

We report a case of sternal osteomyelitis due to
Staphylococcus schleiferi
in a patient who underwent thoracic surgery. This constitutes the first documented case of osteomyelitis caused by this
Staphylococcus
species. We also relate our experience in the utilization of commercially available MicroScan panels for the identification of this microorganism.
Rapid Detection of West Nile Virus from Human Clinical Specimens, Field-Collected Mosquitoes, and Avian Samples by a TaqMan Reverse Transcriptase-PCR Assay
Authors: Lanciotti Robert S. , Kerst Amy J. , Nasci Roger S. , Godsey Marvin S. , Mitchell Carl J. , Savage Harry M. , Komar Nicholas , Panella Nicholas A. , Allen Becky C. , Volpe Kate E. , Davis Brent S. , Roehrig John T. 
Published: December 2019

ABSTRACT
The authors report on the development and application of a rapid TaqMan assay for the detection of West Nile (WN) virus in a variety of human clinical specimens and field-collected specimens. Oligonucleotide primers and FAM- and TAMRA-labeled WN virus-specific probes were designed by using the nucleotide sequence of the New York 1999 WN virus isolate. The TaqMan assay was compared to a traditional reverse transcriptase (RT)-PCR assay and to virus isolation in Vero cells with a large number (≈500) of specimens obtained from humans (serum, cerebrospinal fluid, and brain tissue), field-collected mosquitoes, and avian tissue samples. The TaqMan assay was specific for WN virus and demonstrated a greater sensitivity than the traditional RT-PCR method and correctly identified WN virus in 100% of the culture-positive mosquito pools and 98% of the culture-positive avian tissue samples. The assay should be of utility in the diagnostic laboratory to complement existing human diagnostic testing and as a tool to conduct WN virus surveillance in the United States.
Detection and Quantification of
Plasmodium falciparum
in Blood Samples Using Quantitative Nucleic Acid Sequence-Based Amplification
Authors: Schoone Gerard J. , Oskam Linda , Kroon Nel C. M. , Schallig Henk D. F. H. , Omar Sabah A. 
Published: December 2019

ABSTRACT

A quantitative nucleic acid sequence-based amplification (QT-NASBA) assay for the detection of
Plasmodium
parasites has been developed. Primers and probes were selected on the basis of the sequence of the small-subunit rRNA gene. Quantification was achieved by coamplification of the RNA in the sample with one modified in vitro RNA as a competitor in a single-tube NASBA reaction. Parasite densities ranging from 10 to 10
8
Plasmodium falciparum
parasites per ml could be demonstrated and quantified in whole blood. This is approximately 1,000 times more sensitive than conventional microscopy analysis of thick blood smears. Comparison of the parasite densities obtained by microscopy and QT-NASBA with 120 blood samples from Kenyan patients with clinical malaria revealed that for 112 of 120 (93%) of the samples results were within a 1-log difference. QT-NASBA may be especially useful for the detection of low parasite levels in patients with early-stage malaria and for the monitoring of the efficacy of drug treatment.
Diagnostic Performance of the Roche AMPLICOR PCR in Detecting
Neisseria gonorrhoeae
in Genitourinary Specimens from Female Sex Workers in Cotonou, Benin
Authors: Mukenge-Tshibaka L. , Alary M. , Bernier F. , van Dyck E. , Lowndes C. M. , Guédou A. , Anagonou S. , Joly J. R. 
Published: December 2019

ABSTRACT

The objective of this study was to evaluate the diagnostic performance of the Roche multiplex AMPLICOR
Chlamydia trachomatis/Neisseria gonorrhoeae
PCR test for the detection of
Neisseria gonorrhoeae
infection in female urine specimens and wet and dry endocervical swabs. Endocervical swabs and urine specimens were collected from 342 female sex workers from Cotonou, Benin, and were tested using the AMPLICOR
C. trachomatis/N. gonorrhoeae
test (Roche Diagnostic Systems, Inc., Branchburg, N.J.) with internal control detection. Endocervical swabs were also cultured on Thayer-Martin medium. A series of alternate standards that included a combination of all the tests but not the test being evaluated was used to assess the performance of the test with each type of specimen. The sensitivity, specificity, and positive and negative predictive values for the urine were 53.8, 98.9, 93.5, and 87.5%, respectively. Corresponding figures for the wet swab were 91.5, 100, 100, and 97.4%, respectively. Those for the dry swab were 96.3, 96.2, 88.5, and 98.8%, respectively. Based on this study, the AMPLICOR PCR assay showed a low sensitivity for detection of
N. gonorrhoeae
infection in urine specimens, whereas the test was found to be highly sensitive and specific with endocervical specimens.
Peritonitis Due to
Brevibacterium otitidis
in a Patient Undergoing Continuous Ambulatory Peritoneal Dialysis
Authors: Wauters Georges , Van Bosterhaut Bernard , Avesani Véronique , Cuvelier René , Charlier Jacqueline , Janssens Michèle , Delmée Michel 
Published: December 2019

ABSTRACT

Brevibacterium otitidis
is a coryneform rod and, as far as is known, is isolated only from infected ears. We report the first known case of peritonitis caused by
B. otitidis
in a patient undergoing continuous ambulatory peritoneal dialysis.
Cryptic Genetic Diversity in
Dientamoeba fragilis
Authors: Johnson Jeanette A. , Clark C. Graham 
Published: December 2019

ABSTRACT

Uncertainty surrounding the role of
Dientamoeba fragilis
in human disease could be due in part to the existence of pathogenic and nonpathogenic variants. Evidence for two genetically distinct forms was obtained using PCR-restriction fragment length polymorphism analysis of ribosomal genes. Future studies in humans will need to take
D. fragilis
diversity into account.
Genetic Heterogeneities and Phenotypic Characteristics of Strains of the GenusAbiotrophiaand Proposal ofAbiotrophia para-adiacenssp. nov
Authors: Kanamoto Taisei , Sato Setsuko , Inoue Masakazu 
Published: December 2019

ABSTRACTThe genusAbiotrophiarepresents a heterogeneous group of fastidious cocci that show a dependence on pyridoxal hydrochloride analogs for growth. The genetic heterogeneity in the genusAbiotrophiawas examined by DNA-DNA hybridization, PCR assay of genomic DNA sequences, and restriction fragment length polymorphism and sequence homology analyses of the PCR-amplified 16S rRNA gene. Nine type or reference strains ofAbiotrophia defectiva,Abiotrophia adiacens, andAbiotrophia elegansand 36 oralAbiotrophiaisolates including the ones presumptively identified asGemella morbillorumby the rapid ID32 STREP system were divided into four groups:A. defectiva(genotype 1),A. adiacens(genotype 2),A. elegans(genotype 4), and a fourth species (genotype 3) which we propose be namedAbiotrophia para-adiacenssp. nov. A PCR assay specific for detection and identification of the novelAbiotrophiaspecies was developed.A. para-adiacensgenerally produced β-glucosidase but did not produce α- or β-galactosidase or arginine dihydrolase, did not ferment, trehalose, pullulan, or tagatose, and was serotype IV, V, or VI. Thus, it was distinguished phenotypically fromA. adiacens,A. elegans, andA. defectivaas well as, apparently, from the recently described speciesAbiotrophia balaenopteraesp. nov., which produces arginine dihydrolase and which ferments pullulan but not sucrose (P. A. Lawson et al., Int. J. Syst. Bacteriol. 49:503–506, 1999). Strain ATCC 27527, currently listed asG. morbillorum, was a member of the speciesA. para-adiacens.
A New Alkaline pH-Adjusted Medium Enhances Detection of β-Hemolytic Streptococci by Minimizing Bacterial Interference Due to
Streptococcus salivarius
Authors: Dierksen Karen P. , Ragland Nancy L. , Tagg John R. 
Published: December 2019

ABSTRACT

A new selective medium (CNA-P) that reduces or eliminates the inhibitory activity of bacteriocin-producing
Streptococcus salivarius
against β-hemolytic streptococci has been developed and compared with sheep blood agar (SBA) for the sensitive detection of small numbers of β-hemolytic streptococci in clinical specimens. CNA-P has as its basis a commercial medium (Difco Columbia CNA agar) supplemented with 5% (vol/vol) sheep blood, and the CNA is further modified by addition of 100 mM PIPES buffer [piperazine-
N
,
N
′-bis(2-ethanesulfonic acid)] (pH 7.5) to maintain cultures at an alkaline pH during incubation. CNA-P was shown to inhibit the production and/or release of four different types of
S. salivarius
bacteriocins or bacteriocin-like inhibitory molecules. The efficacies of CNA-P and SBA for detection of β-hemolytic streptococci in 1,352 pharyngeal samples from 376 children were compared. The β-hemolytic streptococcal isolates recovered from the samples included 314 group A (
S. pyogenes
), 61 group G, 33 group B, and 5 group C streptococci. Of 314 samples that yielded
S. pyogenes
, 300 were positive on CNA-P (96%) and 264 (86%) were positive on SBA. A significantly greater number of
S. pyogenes
isolates from these samples were recovered only on CNA-P (50 of 314) compared with the number of isolates recovered only on SBA (14 of 314). In addition, the degree of positivity, a measure of the total numbers of
S. pyogenes
isolates on the plate, was significantly higher on CNA-P than on SBA (2.40 versus 2.07;
P
< 0.001). Interestingly, CNA-P was also found to enhance the hemolytic activity of streptolysin O, allowing detection of streptolysin S-deficient
S. pyogenes
strains which might otherwise go undetected on SBA and other isolation media.
Presence of Type III Secretion Genes in
Burkholderia pseudomallei
Correlates with Ara
−
Phenotypes
Authors: Winstanley Craig , Hart C. Anthony 
Published: December 2019

ABSTRACT

Dot blot hybridization and PCR amplification of 14 Ara
+
and 8 Ara
−
Burkholderia pseudomallei
strains showed that type III secretion (TTS) genes were present in all the Ara
−
strains but absent from all but one of the Ara
+
strains. The link between TTS genes and an Ara
−
phenotype suggests a role for TTS in virulence.
Comparison of a New Neuraminidase Detection Assay with an Enzyme Immunoassay, Immunofluorescence, and Culture for Rapid Detection of Influenza A and B Viruses in Nasal Wash Specimens
Authors: Noyola Daniel E. , Clark Bruce , O'Donnell Frederick T. , Atmar Robert L. , Greer Jewel , Demmler Gail J. 
Published: December 2019

ABSTRACT
The performance of a new, rapid, easy-to-perform assay based on neuraminidase enzyme activity for detection of influenza virus types A and B was compared to detection by culture, indirect immunofluorescence, and enzyme immunoassay in 479 nasal wash specimens from children with respiratory infections. Compared to isolation of influenza virus by culture, the neuraminidase assay had a sensitivity of 70.1%, specificity of 92.4%, positive predictive value of 76.3%, and negative predictive value of 89.9%. There was a higher sensitivity for the detection of influenza A virus (76.4%) than for influenza B virus (40.9%). Indirect immunofluorescence showed a sensitivity of 59.8% and specificity of 97% compared to culture isolation for detection of influenza A and B viruses. Enzyme immunoassay showed a sensitivity of 89.7% and specificity of 98.1% for the detection of influenza A alone. The quality of the nasal wash specimen had a significant effect on the detection of influenza virus by all of the assays. A strong response of the neuraminidase assay was more likely to represent a culture-confirmed influenza infection. This new rapid neuraminidase assay was useful for the detection of influenza A and B viruses in nasal wash specimens.
Comparative Evaluation of Nine Different Enzyme-Linked Immunosorbent Assays for Determination of Antibodies against
Treponema pallidum
in Patients with Primary Syphilis
Authors: Schmidt Bruno L. , Edjlalipour Marzieh , Luger Anton 
Published: December 2019

ABSTRACT

Nine different enzyme-linked immunosorbent assays (ELISAs) with a sonicate or recombinant proteins of
Treponema pallidum
as antigen have been evaluated comparatively by testing 52 highly selected sera from patients with primary syphilis, all negative in the microhemagglutination test for
T. pallidum
(MHA-TP). Eight tests exhibited greater sensitivity (48.5 to 76.9%) than the commonly used Venereal Disease Research Laboratory test (44.2%). Higher sensitivity could be related to (i) the volume and dilution of the serum, (ii) the design of the assay (capture and competitive tests showed higher sensitivity than sandwich-based assays), and (iii) the ability to detected specific immunoglobulin M antibodies. The specificity of the ICE Syphilis and the Enzygnost Syphilis tests was 99.5 and 99.8%, respectively, as determined by routine testing of 2,053 unselected sera in comparison with the MHA-TP test. ELISAs tested offered high sensitivity in patients with primary syphilis; however, recommendations to use these tests as screening assays do need further data on specificity and reactivity in late stages of the disease.
A Panel of Monoclonal Antibodies Targeting the Rabies Virus Phosphoprotein Identifies a Highly Variable Epitope of Value for Sensitive Strain Discrimination
Authors: Nadin-Davis S. A. , Sheen M. , Abdel-Malik M. , Elmgren L. , Armstrong J. , Wandeler A. I. 
Published: December 2019

ABSTRACT
A recombinant rabies virus phosphoprotein fusion product (GST-P) was used to generate a series of monoclonal antibodies (MAbs) with anti-P reactivity. Competitive binding assays classified 27 of these MAbs into four groups (I to IV), and 24 of them were deemed to recognize linear epitopes, as judged by their reaction in immunoblots. The linear epitope recognized in each case was mapped by using two series of N- and C-terminally deleted recombinant phosphoproteins. Assessment of the reactivities of representative MAbs to a variety of lyssavirus isolates by an indirect fluorescent antibody test indicated that group I MAbs, which recognized a highly conserved N-terminal epitope, were broadly cross-reactive with all lyssaviruses assayed, while group III MAbs, which reacted with a site overlapping that of group I MAbs, exhibited variable reactivities and group IV MAbs reacted with most isolates of genotypes 1, 6, and 7 only. In contrast, group II MAbs, which recognized an epitope located within a highly divergent central portion of the protein, were exquisitely strain specific. These anti-P MAbs are potentially useful tools for lyssavirus identification and discrimination.
Phylogeny of
Porphyromonas gingivalis
by Ribosomal Intergenic Spacer Region Analysis
Authors: Rumpf Robert W. , Griffen Ann L. , Leys Eugene J. 
Published: December 2019

ABSTRACT

Periodontitis has been associated with the presence of
Porphyromonas gingivalis
, and previous studies have shown phenotypic differences in the pathogenicities of strains of
P. gingivalis
. An accurate and comprehensive phylogeny of strains of
P. gingivalis
would be useful in determining if there is an evolutionary basis to pathogenicity in this species. Previous phylogenies of
P. gingivalis
strains based on random amplified polymorphic DNA (RAPD) analysis and multilocus enzyme electrophoresis (MLEE) show little agreement. While the 16S ribosomal gene is the standard for phylogenetic reconstruction among bacterial species, it is insufficiently variable for this purpose. In the present study, the phylogeny of
P. gingivalis
was constructed on the basis of the sequence of the most variable region of the ribosomal operon, the intergenic spacer region (ISR). Heteroduplex analysis of the ISR has been used to study the variability of
P. gingivalis
strains in periodontitis. In the present study, typing by heteroduplex analysis was compared to ISR sequence-based phylogeny and close agreement was observed. The two strains of
P. gingivalis
whose heteroduplex types are strongly associated with periodontitis were found to be closely related and were well separated from strains whose heteroduplex types are less strongly associated with disease, suggesting a relationship between pathogenicity and phylogeny.
Pooling Cervical Swabs and Testing by Ligase Chain Reaction Are Accurate and Cost-Saving Strategies for Diagnosis of
Chlamydia trachomatis
Authors: Kapala J. , Copes D. , Sproston A. , Patel J. , Jang D. , Petrich A. , Mahony J. , Biers K. , Chernesky M. 
Published: December 2019

ABSTRACT

Specimen pooling to achieve efficiency when testing urine specimens for
Chlamydia trachomatis
nucleic acids has been suggested. We pooled endocervical swabs from 1,288 women and also tested individual swabs by ligase chain reaction (LCR). Out of 53 positive specimens, pools of 4 or 8 specimens missed two positives, providing 96.2% accuracy compared to individual test results. Dilution and positive-control spiking experiments showed that negative specimens with inhibitors of LCR in the pool reduced the signal. Conversely, two extra positives, detected only through pooling, were negative by individual testing but became positive after storage, suggesting that fresh positive specimens with labile inhibitors may be positive in a pool because of dilution of inhibitors. For this population of women with a 4% prevalence of
C. trachomatis
infection, substantial savings in cost of reagents (55 to 63%) and technologist time (50 to 63%) made pooling strategies a desirable alternative to individual testing.
False-Positive Results for
Mycobacterium celatum
with the AccuProbe
Mycobacterium tuberculosis
Complex Assay
Authors: Somoskövi Ákos , Hotaling Jacqueline E. , Fitzgerald Marie , Jonas Vivian , Stasik Denise , Parsons Linda M. , Salfinger Max 
Published: December 2019

ABSTRACT

Mycobacterium celatum
type 1 was found to cross-react in the AccuProbe
Mycobacterium tuberculosis
complex assay. Subsequently, we found a statistically significant increase in the relative light units with lower temperatures, suggesting that it is necessary to perform this AccuProbe assay at between 60 and 61°C. We also recommend the inclusion of
M. celatum
type 1 as a negative control.
Tracking Members of the Simian Immunodeficiency Virus deltaB670 Quasispecies Population In Vivo at Single-Cell Resolution
Authors: Reinhart Todd A. , Rogan Michael J. , Amedee Angela Martin , Murphey-Corb Michael , Rausch Dianne M. , Eiden Lee E. , Haase Ashley T. 
Published: December 2019

ABSTRACT

Genetically distinct lentiviruses constitute a quasispecies population that can evolve in response to selective forces. To move beyond characterization of the population as a whole to the behavior of individual members, we devised an in situ hybridization approach that uses genotype-specific probes. We used probes that detect simian immunodeficiency viruses (SIV) that differ in sequence in the V1 region of the surface envelope glycoprotein (
env
) gene to investigate the replication and cellular tropisms of four viral variants in the tissues of infected rhesus macaques. We found that the V1 genotypic variants replicated in spatially defined patterns and to different extents at each anatomic site. The two variants that replicated most extensively in animals with AIDS were detected in both macrophages and T lymphocytes in tissues. By extension of this approach, it will be possible to investigate the role of individual lentiviruses in a quasispecies in pathogenesis and to evaluate the effects of antiviral or immunotherapeutic treatment on select members of a quasispecies.
Inactivation of the RNase Activity of Glycoprotein E
rns
of Classical Swine Fever Virus Results in a Cytopathogenic Virus
Authors: Hulst M. M. , Panoto F. E. , Hoekman A. , van Gennip H. G. P. , Moormann R. J. M. 
Published: December 2019

ABSTRACT

Envelope glycoprotein E
rns
of classical swine fever virus (CSFV) has been shown to contain RNase activity and is involved in virus infection. Two short regions of amino acids in the sequence of E
rns
are responsible for RNase activity. In both regions, histidine residues appear to be essential for catalysis. They were replaced by lysine residues to inactivate the RNase activity. The mutated sequence of E
rns
was inserted into the p10 locus of a baculovirus vector and expressed in insect cells. Compared to intact E
rns
, the mutated proteins had lost their RNase activity. The mutated proteins reacted with E
rns
-specific neutralizing monoclonal and polyclonal antibodies and were still able to inhibit infection of swine kidney cells (SK6) with CSFV, but at a concentration higher than that measured for intact E
rns
. This result indicated that the conformation of the mutated proteins was not severely affected by the inactivation. To study the effect of these mutations on virus infection and replication, a CSFV mutant with an inactivated E
rns
(FLc13) was generated with an infectious DNA copy of CSFV strain C. The mutant virus showed the same growth kinetics as the parent virus in cell culture. However, in contrast to the parent virus, the RNase-negative virus induced a cytopathic effect in swine kidney cells. This effect could be neutralized by rescue of the inactivated E
rns
gene and by neutralizing polyclonal antibodies directed against E
rns
, indicating that this effect was an inherent property of the RNase-negative virus. Analyses of cellular DNA of swine kidney cells showed that the RNase-negative CSFV induced apoptosis. We conclude that the RNase activity of envelope protein E
rns
plays an important role in the replication of pestiviruses and speculate that this RNase activity might be responsible for the persistence of these viruses in their natural host.