bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monoclonal Antibodies Specific for Hippurate Hydrolase of
Campylobacter jejuni
Authors: Steele Marina , Gyles Carlton , Chan Voon Loong , Odumeru Joseph 
Published: July 2002

ABSTRACT

Eleven monoclonal antibodies raised against recombinant
Campylobacter jejuni
hippurate hydrolase were tested for binding to lysates from 19
C. jejuni
strains, 12 other
Campylobacter
strains, and 21 non-
Campylobacter
strains. Several monoclonal antibodies bound to
C. jejuni
but not to other
Campylobacter
species and may be useful in a species-specific immunoassay.
Use of PGMY Primers in L1 Consensus PCR Improves Detection of Human Papillomavirus DNA in Genital Samples
Authors: Coutlée François , Gravitt Patti , Kornegay Janet , Hankins Catherine , Richardson Harriet , Lapointe Normand , Voyer Hélène , Franco Eduardo 
Published: July 2002

ABSTRACT

The novel PGMY L1 consensus primer pair is more sensitive than the MY09 and MY11 primer mix for detection and typing with PCR of human papillomavirus (HPV) DNA in genital specimens. We assessed the diagnostic yield of PGMY primers for the detection and typing of HPV by comparing the results obtained with PGMY09/PGMY11 and MY09/MY11/HMB01 on 299 genital samples. Amplicons generated with PGMY primers were typed with the line blot assay (PGMY-line blot), while HPV amplicons obtained with the degenerate primer pool MY09/MY11/HMB01 were detected with type-specific radiolabeled probes in a dot blot assay (standard consensus PCR test). Cervicovaginal lavage samples (
N
= 272) and cervical scrape samples (
N
= 27) were tested in parallel with both PCR tests. The PGMY-line blot test detected the presence of HPV DNA more frequently than the standard consensus PCR assay. The concordance for HPV typing between the two assays was 84.3% (214 of 255 samples), for a good kappa value of 0.69. Of the 177 samples containing HPV DNA by at least one method, 40 samples contained at least one HPV type detected only with PGMY-line blot, whereas positivity exclusively with the standard consensus PCR test was found for only 7 samples (
P
< 0.001). HPV types 45 and 52 were especially more frequently detected with PGMY than MY primers. However, most HPV types were better amplified with PGMY primers, including HPV-16. Samples with discordant results between the two PCR assays more frequently contained multiple HPV types. Studies using PGMY instead of MY primers have the potential to report higher detection rates of HPV infection not only for newer HPV types but also for well-known genital types.
Genotyping of Human Papillomavirus in Liquid Cytology Cervical Specimens by the PGMY Line Blot Assay and the SPF
10
Line Probe Assay
Authors: van Doorn Leen-Jan , Quint Wim , Kleter Bernhard , Molijn Anco , Colau Brigitte , Martin Marie-Thérèse , Kravang-In  , Torrez-Martinez Norah , Peyton Cheri L. , Wheeler Cosette M. 
Published: July 2002

ABSTRACT

A comparison of two PCR-based human papillomavirus (HPV) DNA detection and genotyping systems (PGMY LBA and SPF
10
LiPA) was conducted in two laboratories. Both systems are based on broad-spectrum PCR for the detection of HPV DNA, followed by reverse hybridization with type-specific probes. A total of 400 selected cervical scrape specimens in PreservCyt solution (55% normal cytology, 18% atypical squamous cells of unknown significance, 14.8% low-grade squamous intraepithelial lesions [SIL], and 12.5% high-grade SIL) were tested for the presence of HPV DNA. In this selected group of specimens, the overall agreement between the two methods for the detection of any HPV DNA was high (κ = 0.859). When the 20 common HPV genotypes identified by both methods were considered (HPV types 6, 11, 16, 18, 31, 33, 35, 39, 40, 42, 45, 51, 52, 53, 54, 56, 58, 59, 66, and 68), compatible genotype-specific results were observed in 96.5% of the samples, even when multiple HPV genotypes were present. However, for some specific HPV genotypes, there were significant differences in HPV detection by the two methods. PGMY LBA detected more HPV type 42 (
P
= 0.002), HPV type 56 (
P
= 0.039), and HPV type 59 (
P
< 0.001), whereas SPF
10
LiPA detected more HPV type 31 (
P
< 0.001) and HPV type 52 (
P
= 0.031). For the remaining genotypes, including HPV types 16 and 18, the results obtained by the two methods were not significantly different. In general, both genotyping methods are highly suitable for clinical and epidemiological studies.
Polymorphic Amplified Typing Sequences Provide a Novel Approach to
Escherichia coli
O157:H7 Strain Typing
Authors: Kudva Indira T. , Evans Peter S. , Perna Nicole T. , Barrett Timothy J. , DeCastro G. Joel , Ausubel Frederick M. , Blattner Frederick R. , Calderwood Stephen B. 
Published: July 2002

ABSTRACT

Escherichia coli
O157:H7 (O157) strains are commonly typed by pulsed-field gel electrophoresis (PFGE) following digestion of genomic DNA with the restriction enzyme
Xba
I. We have shown that O157 strains differ from each other by a series of discrete insertions or deletions, some of which contain recognition sites for
Xba
I, suggesting that these insertions and deletions are responsible for the differences in PFGE patterns. We have devised a new O157 strain typing protocol, polymorphic amplified typing sequences (PATS), based on this information. We designed PCR primer pairs to amplify genomic DNA flanking each of 40 individual
Xba
I sites in the genomes of two O157 reference strains. These primer pairs were tested with 44 O157 isolates, 2 each from 22 different outbreaks of infection. Thirty-two primer pairs amplified identical fragments from all 44 isolates, while eight primer pairs amplified regions that were polymorphic between isolates. The isolates could be differentiated solely on the basis of which of the eight polymorphic amplicons was detected. PATS correctly identified 21 of 22 outbreak pairs as being identical or highly related, whereas PFGE correctly identified 14 of the 22 outbreak pairs as being identical or highly related; PATS was also able to type isolates from three outbreaks that were untypeable by PFGE. However, PATS was less sensitive than PFGE in discriminating between outbreaks. These data suggest that typing by PATS may provide a simple procedure for strain typing of O157 and other bacteria and that further evaluation of the utility of this method for epidemiologic investigations is warranted.
Recombinant BBK32 Protein in Serodiagnosis of Early and Late Lyme Borreliosis
Authors: Heikkilä Tero , Seppälä Ilkka , Saxén Harri , Panelius Jaana , Peltomaa Miikka , Julin Tiina , Carlsson Sten-Anders , Lahdenne Pekka 
Published: July 2002

ABSTRACT

Borrelial protein BBK32 was evaluated as an antigen in the serodiagnosis of early and disseminated Lyme borreliosis (LB).
bbk32
was cloned and sequenced from eight isolates of the three pathogenic
Borrelia
species. The identities between the amino acid sequences of the BBK32 proteins from
Borrelia burgdorferi
sensu stricto,
B. garinii
, and
B. afzelii
isolates were 71 to 100%. By immunoglobulin G (IgG) Western blotting (WB) or enzyme-linked immunosorbent assay (ELISA), up to 74 and 100% of acute- and convalescent-phase samples, respectively, from 23 patients with erythema migrans (EM) were positive for recombinant BBK32 protein from
B. afzelii
. In the serology of disseminated LB, the three variant BBK32 antigens cross-reacted. In total, 14 of 14 samples from patients with neuroborreliosis and 15 of 15 samples from patients with Lyme arthritis were positive. The specificities of the IgG ELISA with the variant BBK32 antigens for EM and disseminated borreliosis were 81 to 92% and 89 to 95%, respectively. Our findings indicate that the BBK32 proteins are promising serodiagnostic antigens for the detection of early and disseminated LB but that variant BBK32 proteins may be needed either in parallel or in combination with an immunoassay for LB to cover all the relevant borrelial species that cause the disease.
Genome Scale Comparison ofMycobacterium aviumsubsp.paratuberculosiswithMycobacterium aviumsubsp.aviumReveals Potential Diagnostic Sequences
Authors: Bannantine John P. , Baechler Emily , Zhang Qing , Li LingLing , Kapur Vivek 
Published: July 2002

ABSTRACTThe genetic similarity betweenMycobacterium aviumsubsp.paratuberculosisand other mycobacterial species has confounded the development ofM. aviumsubsp.paratuberculosis-specific diagnostic reagents. Random shotgun sequencing of theM. aviumsubsp.paratuberculosisgenome in our laboratories has shown >98% sequence identity withMycobacterium aviumsubsp.aviumin some regions. However, an in silico comparison of the largest annotatedM. aviumsubsp.paratuberculosiscontigs, totaling 2,658,271 bp, with the unfinishedM. aviumsubsp.aviumgenome has revealed 27 predictedM. aviumsubsp.paratuberculosiscoding sequences that do not align withM. aviumsubsp.aviumsequences. BLASTP analysis of the 27 predicted coding sequences (genes) shows that 24 do not match sequences in public sequence databases, such as GenBank. These novel sequences were examined by PCR amplification with genomic DNA from eight mycobacterial species and ten independent isolates ofM. aviumsubsp.paratuberculosis. From these analyses, 21 genes were found to be present in allM. aviumsubsp.paratuberculosisisolates and absent from all other mycobacterial species tested. One region of theM. aviumsubsp.paratuberculosisgenome contains a cluster of eight genes, arranged in tandem, that is absent in other mycobacterial species. This region spans 4.4 kb and is separated from other predicted coding regions by 1,408 bp upstream and 1,092 bp downstream. The gene upstream of this eight-gene cluster has strong similarity to mycobacteriophage integrase sequences. The GC content of this 4.4-kb region is 66%, which is similar to the rest of the genome, indicating that this region was not horizontally acquired recently. Southern hybridization analysis confirmed that this gene cluster is present only inM. aviumsubsp.paratuberculosis. Collectively, these studies suggest that a genomics approach will help in identifying novelM. aviumsubsp.paratuberculosisgenes as candidate diagnostic sequences.
Identification of Medically Relevant
Nocardia
Species with an Abbreviated Battery of Tests
Authors: Kiska Deanna L. , Hicks Karen , Pettit David J. 
Published: July 2002

ABSTRACT

Identification of
Nocardia
to the species level is useful for predicting antimicrobial susceptibility patterns and defining the pathogenicity and geographic distribution of these organisms. We sought to develop an identification method which was accurate, timely, and employed tests which would be readily available in most clinical laboratories. We evaluated the API 20C AUX yeast identification system as well as several biochemical tests and Kirby-Bauer susceptibility patterns for the identification of 75 isolates encompassing the 8 medically relevant
Nocardia
species. There were few biochemical reactions that were sufficiently unique for species identification; of note,
N. nova
were positive for arylsulfatase,
N. farcinica
were positive for opacification of Middlebrook 7H11 agar, and
N. brasiliensis
and
N. pseudobrasiliensis
were the only species capable of liquefying gelatin. API 20C sugar assimilation patterns were unique for
N. transvalensis
,
N. asteroides
IV, and
N. brevicatena
. There was overlap among the assimilation patterns for the other species. Species-specific patterns of susceptibility to gentamicin, tobramycin, amikacin, and erythromycin were obtained for
N. nova
,
N. farcinica
, and
N. brevicatena
, while there was overlap among the susceptibility patterns for the other isolates. No single method could identify all
Nocardia
isolates to the species level; therefore, a combination of methods was necessary. An algorithm utilizing antibiotic susceptibility patterns, citrate utilization, acetamide utilization, and assimilation of inositol and adonitol accurately identified all isolates. The algorithm was expanded to include infrequent drug susceptibility patterns which have been reported in the literature but which were not seen in this study.
Clonal Spread of
Staphylococcus aureus
Heterogeneously Resistant to Vancomycin in a University Hospital in Korea
Authors: Kim Mi-Na , Hwang Sang Hyun , Pyo Yeon-Jung , Mun Hyang-Mi , Pai Chik Hyun 
Published: July 2002

ABSTRACT

Since vancomycin-intermediate
Staphylococcus aureus
(VISA) was first reported in Japan in 1997, there has been great concern that heterogeneous vancomycin-intermediate
S. aureus
(hetero-VISA) is the putative precursor of VISA. To investigate the prevalence, clinical significance, and molecular epidemiology of
S. aureus
with reduced susceptibility to vancomycin, all consecutive isolates of
S. aureus
isolated from clinical specimens from December 1998 to August 1999 at Asan Medical Center were screened for VISA and hetero-VISA by using brain heart infusion agar containing 4 μg of vancomycin/ml. Screen-positive isolates were confirmed by susceptibility testing and population analysis of subpopulations with reduced susceptibility to vancomycin. The isolates confirmed as hetero-VISA were typed by pulsed-field gel electrophoresis (PFGE). Medical records were reviewed to evaluate the clinical significance and risk factors for the acquisition of hetero-VISA. Of the 4,483 isolates that were tested, 53 were screen positive; no VISA was detected, but 24 isolates (0.54%) from 22 patients were hetero-VISA. All but two strains appeared to be clones of the Korean VISA strain, AMC11094, in the PFGE analysis. A total of 18 patients were in intensive care units, and 16 underwent major surgeries during the same admission. Only 10 of the 22 patients had previous methicillin-resistant
S. aureus
infections and 11 had previous vancomycin or teicoplanin therapy. Only 7 of the 22 patients from whom hetero-VISA strains were isolated were infected, and the remaining 15 patients were colonized. All seven infected patients were successfully treated with vancomycin. These results suggest that hetero-VISA can be treated with vancomycin, but the spread of hetero-VISA clonal to VISA is of concern, since many believe that VISA can arise from hetero-VISA, although this phenomenon was not observed in this study.
Novel IS
6110
Insertion Sites in the Direct Repeat Locus of
Mycobacterium tuberculosis
Clinical Strains from the St. Petersburg Area of Russia and Evolutionary and Epidemiological Considerations
Authors: Mokrousov Igor , Narvskaya Olga , Limeschenko Elena , Otten Tatiana , Vyshnevskiy Boris 
Published: July 2002

ABSTRACT

A modification of spoligotyping with primers derived from the direct repeat (DR) and IS
6110
sequences was used to identify IS
6110
insertions in the DR locus of
Mycobacterium tuberculosis
clinical strains from the St. Petersburg area of Russia. Novel IS
6110
insertions were identified: (i) in two epidemiologically unlinked Beijing family strains, an asymmetrical direct insertion in DR37; (ii) in a non-Beijing strain, an asymmetrical insertion in the opposite orientation in DR38; (iii) in another non-Beijing strain, a direct insertion in DR38 and one in the opposite orientation in DR14 (DR numbering is according to standard spoligotyping). Our results strengthen an observation that the DR locus structure is extremely conserved in the Beijing genotype. Asymmetrical insertions prevented detection of the adjacent spacer by standard spoligotyping. This, therefore, should be taken into consideration when similar spoligoprofiles that differ only in signals 37 and 38 are interpreted.
Rapid Particle Agglutination Test for Human Immunodeficiency Virus: Hospital-Based Evaluation
Authors: Ramalingam Sandeep , Kannangai Rajesh , Raj A Antony , Jesudason Mary V. , Sridharan Gopalan 
Published: July 2002

ABSTRACT
The performance of a rapid particle agglutination test for human immunodeficiency virus (HIV) (Capillus HIV type 1 [HIV-1]/HIV-2) on hospital samples is compared with enzyme-linked immunosorbent assays. The test had a sensitivity and specificity of 99 and 98.9%, respectively. In addition, the test was reactive on plasma samples from all individuals infected with HIV-1 subtype C. This test can safely be used for voluntary counseling and testing in India.
Exposure of Laboratory Workers to
Francisella tularensis
despite a Bioterrorism Procedure
Authors: Shapiro Daniel S. , Schwartz Donald R. 
Published: July 2002

ABSTRACT

A rapidly fatal case of pulmonary tularemia in a 43-year-old man who was transferred to a tertiary care facility is presented. The microbiology laboratory and autopsy services were not notified of the clinical suspicion of tularemia by the service caring for the patient. Despite having a laboratory bioterrorism procedure in place and adhering to established laboratory protocol, 12 microbiology laboratory employees were exposed to
Francisella tularensis
and the identification of the organism was delayed due to lack of notification of the laboratory of the clinical suspicion of tularemia. A total of 11 microbiology employees and two persons involved in performing the patient's autopsy received prophylactic doxycycline due to concerns of transmission. None of them developed signs or symptoms of tularemia. One microbiology laboratory employee was pregnant and declined prophylactic antibiotics. As a result of this event, the microbiology laboratory has incorporated flow charts directly into the bench procedures for several highly infectious agents that may be agents of bioterrorism. This should permit more rapid recognition of an isolate for referral to a Level B laboratory for definitive identification and should improve laboratory safety.
The Human Immunodeficiency Virus Type 1 TAR RNA Upper Stem-Loop Plays Distinct Roles in Reverse Transcription and RNA Packaging
Authors: Harrich David , Hooker C. William , Parry Emma 
Published: July 2002

ABSTRACT
The human immunodeficiency virus type 1 (HIV-1) RNA genome is flanked by a repeated sequence (R) that is required for HIV-1 replication. The first 57 nucleotides of R form a stable stem-loop structure called the transactivation response element (TAR) that can interact with the virally encoded transcription activator protein, Tat, to promote high levels of gene expression. Recently, we demonstrated that TAR is also important for efficient HIV-1 reverse transcription, since HIV-1 mutated in the upper stem-loop of TAR showed a reduced ability both to initiate and to complete reverse transcription. We have analyzed a series of HIV-1 mutant viruses to better defined the structural or sequence elements required for natural endogenous reverse transcription and packaging of virion RNA. Our results indicate that the requirement for TAR in reverse transcription is conformation dependent, since mutants with mutations that alter the upper stem-loop orientation are defective for reverse transcription initiation and have minor defects in RNA packaging. In contrast, TAR mutations that allowed the formation of alternative upper stem-loop structure greatly reduced RNA packaging but did not affect reverse transcription efficiency. These results are consistent with direct involvement of the upper stem-loop structure in packaging of genomic RNA and suggest that the TAR RNA stem-loop from nucleotide +18 to +42 interacts with other components of the reverse transcription initiation complex to promote efficient reverse transcription.
Proteasome-Mediated Degradation of the Papillomavirus E2-TA Protein Is Regulated by Phosphorylation and Can Modulate Viral Genome Copy Number
Authors: Penrose Kerri J. , McBride Alison A. 
Published: July 2002

ABSTRACT
The bovine papillomavirus E2 proteins regulate viral transcription, replication, and episomal genome maintenance. We have previously mapped the major phosphorylation sites of the E2 proteins to serine residues 298 and 301 and shown that mutation of serine residue 301 to alanine leads to a dramatic (10- to 20-fold) increase in viral DNA copy number. In this study we analyzed how phosphorylation regulates E2 protein function. S301 is located in a PEST sequence; these sequences are often found in proteins with a short half-life and can be regulated by phosphorylation. We show here that the E2 protein is ubiquitinated and degraded by the proteasome. Mutation of serine 301 to alanine increases the half-life of E2 from approximately 50 min to 160 min. Furthermore, the A301 E2 protein shows greatly reduced ubiquitination and degradation by the proteasome. These results suggest that the E2 protein level is regulated by phosphorylation, which in turn determines viral episomal copy number.
Retargeting the Coxsackievirus and Adenovirus Receptor to the Apical Surface of Polarized Epithelial Cells Reveals the Glycocalyx as a Barrier to Adenovirus-Mediated Gene Transfer
Authors: Pickles Raymond J. , Fahrner Jill A. , Petrella JenniElizabeth M. , Boucher Richard C. , Bergelson Jeffrey M. 
Published: July 2002

ABSTRACT
Lumenal delivery of adenovirus vectors (AdV) results in inefficient gene transfer to human airway epithelium. The human coxsackievirus and adenovirus receptor (hCAR) was detected by immunofluorescence selectively at the basolateral surfaces of freshly excised human airway epithelial cells, suggesting that the absence of apical hCAR constitutes a barrier to adenovirus-mediated gene delivery in vivo. In transfected polarized Madin-Darby canine kidney cells, wild-type hCAR was expressed selectively at the basolateral membrane, whereas hCAR lacking the transmembrane and/or cytoplasmic domains was expressed on both the basolateral and apical membranes. Cells expressing apical hCAR still were not efficiently transduced by AdV applied to the apical surface. However, after the cells were treated with agents that remove components of the apical surface glycocalyx, AdV transduction occurred. These results indicate that adenovirus can infect via receptors located at the apical cell membrane but that the glycocalyx impedes interaction of AdV with apical receptors.
Simian Immunodeficiency Virus Rapidly Penetrates the Cervicovaginal Mucosa after Intravaginal Inoculation and Infects Intraepithelial Dendritic Cells
Authors: Hu Jinjie , Gardner Murray B. , Miller Christopher J. 
Published: July 2002

ABSTRACTDespite recent insights into mucosal human immunodeficiency virus (HIV) transmission, the route used by primate lentiviruses to traverse the stratified squamous epithelium of mucosal surfaces remains undefined. To determine if dendritic cells (DC) are used by primate lentiviruses to traverse the epithelial barrier of the genital tract, rhesus macaques were intravaginally exposed to cell-free simian immunodeficiency virus SIVmac251. We examined formalin-fixed tissues and HLA-DR+-enriched cell suspensions to identify the cells containing SIV RNA in the genital tract and draining lymph nodes within the first 24 h of infection. Using SIV-specific fluorescent in situ hybridization combined with immunofluorescent antibody labeling of lineage-specific cell markers, numerous SIV RNA+DC were documented in cell suspensions from the vaginal epithelium 18 h after vaginal inoculation. In addition, we determined the minimum time that the SIV inoculum must remain in contact with the genital mucosa for the virus to move from the vaginal lumen into the mucosa. We now show that SIV enters the vaginal mucosa within 60 min of intravaginal exposure, infecting primarily intraepithelial DC and that SIV-infected cells are located in draining lymph nodes within 18 h of intravaginal SIV exposure. The speed with which primate lentiviruses penetrate mucosal surfaces, infect DC, and disseminate to draining lymph nodes poses a serious challenge to HIV vaccine development.