bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection ofChlamydia pneumoniae-Specific Antibodies Binding to the VD2 and VD3 Regions of the Major Outer Membrane Protein
Authors: Klein Marcus , Kötz Arne , Bernardo Katussevani , Krönke Martin 
Published: May 2003

ABSTRACTAlthoughChlamydia pneumoniaeis an important human pathogen, the antigens eliciting a specific humoral immune response remain elusive. We scrutinized several recombinant chlamydial surface proteins for species-specific recognition by a panel of human sera previously tested for the presence of anti-C. pneumoniaeand anti-C. trachomatisantibodies by microimmunofluorescence and enzyme-linked immunosorbent assay. The 15-kDa cysteine-rich protein (CrpA), porin-b (PorB), 9-kDa outer membrane protein (OMP3), 60-kDa outer membrane protein (OMP2), and four fragments of the major outer membrane protein (MOMP) representing each variable domain (VD) were overexpressed inEscherichia coli, affinity purified, and employed for Western blot analysis. None of the sera tested contained antibodies recognizing PorB and OMP3 ofC. pneumoniae. Sera fromC. pneumoniae-immune patients cross-reacted with OMP2 ofC. trachomatis, and sera fromC. trachomatis-immune patients cross-reacted with CrpA ofC. pneumoniae, indicating that some of chlamydial surface molecules share antigenic epitopes. In contrast, the VD2, as well as the VD3, regions of the MOMP ofC. pneumoniaewere only recognized byC. pneumoniae-positive sera, suggesting the existence of species-specific epitopes. The identification of such epitopes of cell surface molecules provides new insights intoC. pneumoniae-specific immune responses and may be of value for the improvement ofC. pneumoniae-specific diagnostic assay systems based on defined recombinant antigens.
Snapshot of Moving and Expanding Clones of
Mycobacterium tuberculosis
and Their Global Distribution Assessed by Spoligotyping in an International Study
Authors: Filliol Ingrid , Driscoll Jeffrey R. , van Soolingen Dick , Kreiswirth Barry N. , Kremer Kristin , Valétudie Georges , Anh Dang Duc , Barlow Rachael , Banerjee Dilip , Bifani Pablo J. , Brudey Karine , Cataldi Angel , Cooksey Robert C. , Cousins Debby V. , Dale Jeremy W. , Dellagostin Odir A. , Drobniewski Francis , Engelmann Guido , Ferdinand Séverine , Gascoyne-Binzi Deborah , Gordon Max , Gutierrez M. Cristina , Haas Walter H. , Heersma Herre , Kassa-Kelembho Eric , Ly Ho Minh , Makristathis Athanasios , Mammina Caterina , Martin Gerald , Moström Peter , Mokrousov Igor , Narbonne Valérie , Narvskaya Olga , Nastasi Antonino , Niobe-Eyangoh Sara Ngo , Pape Jean W. , Rasolofo-Razanamparany Voahangy , Ridell Malin , Rossetti M. Lucia , Stauffer Fritz , Suffys Philip N. , Takiff Howard , Texier-Maugein Jeanne , Vincent Véronique , de Waard Jacobus H. , Sola Christophe , Rastogi Nalin 
Published: May 2003

ABSTRACT

The present update on the global distribution of
Mycobacterium tuberculosis
complex spoligotypes provides both the octal and binary descriptions of the spoligotypes for
M. tuberculosis
complex, including
Mycobacterium bovis
, from >90 countries (13,008 patterns grouped into 813 shared types containing 11,708 isolates and 1,300 orphan patterns). A number of potential indices were developed to summarize the information on the biogeographical specificity of a given shared type, as well as its geographical spreading (matching code and spreading index, respectively). To facilitate the analysis of hundreds of spoligotypes each made up of a binary succession of 43 bits of information, a number of major and minor visual rules were also defined. A total of six major rules (A to F) with the precise description of the extra missing spacers (minor rules) were used to define 36 major clades (or families) of
M. tuberculosis
. Some major clades identified were the East African-Indian (EAI) clade, the Beijing clade, the Haarlem clade, the Latin American and Mediterranean (LAM) clade, the Central Asian (CAS) clade, a European clade of IS
6110
low banders (X; highly prevalent in the United States and United Kingdom), and a widespread yet poorly defined clade (T). When the visual rules defined above were used for an automated labeling of the 813 shared types to define nine superfamilies of strains (
Mycobacterium africanum
, Beijing,
M. bovis
, EAI, CAS, T, Haarlem, X, and LAM), 96.9% of the shared types received a label, showing the potential for automated labeling of
M. tuberculosis
families in well-defined phylogeographical families. Intercontinental matches of shared types among eight continents and subcontinents (Africa, North America, Central America, South America, Europe, the Middle East and Central Asia, and the Far East) are analyzed and discussed.
Improved Detection of Rhinoviruses by Nucleic Acid Sequence-Based Amplification after Nucleotide Sequence Determination of the 5′ Noncoding Regions of Additional Rhinovirus Strains
Authors: Loens K. , Ieven M. , Ursi D. , de Laat C. , Sillekens P. , Oudshoorn P. , Goossens H. 
Published: May 2003

ABSTRACT
The isothermal nucleic acid sequence-based amplification (NASBA) system was applied for the detection of rhinoviruses using primers targeted at the 5′ noncoding region (5′ NCR) of the viral genome. The nucleotide sequence of the 5′ NCRs of 34 rhinovirus isolates was determined to map the most conserved regions and design more appropriate primers and probes. The assay amplified RNA extracted from 30 rhinovirus reference strains and 88 rhinovirus isolates, it did not amplify RNA from 49 enterovirus isolates and other respiratory viruses. The assay allows one to discriminate between group A and B rhinoviruses. Sensitivities for the detection of group B and group A rhinoviruses was 20 and 200 50% tissue culture infective doses, respectively.
Microbial Population Diversity in the Urethras of Healthy Males and Males Suffering from Nonchlamydial, Nongonococcal Urethritis
Authors: Riemersma W. A. , van der Schee C. J. C. , van der Meijden W. I. , Verbrugh H. A. , van Belkum A. 
Published: May 2003

ABSTRACT

Nonchlamydial, nongonococcal urethritis (NCNGU) is suggested to be a sexually transmitted disease in men. NCNGU patients were compared to control subjects with regard to the presence of potentially infectious bacteria in the first void urine. Patients' pre- and post-antibiotic-treatment urine samples and two samples obtained 2 weeks apart from healthy volunteers, who did not receive antibiotic therapy, were analyzed with broad-spectrum PCR tests aiming at eubacterial small subunit rRNA genes. Restriction fragment length polymorphism analysis of the amplicons cloned from the mixtures of PCR products revealed that many different species of microorganisms were found to be colonizing the male urethra. We document here clear differences in the composition of the resident urethral flora between samples obtained from various individuals and between samples obtained at various points in time for a single individual. No major changes in population complexity were found upon antimicrobial treatment. In two of five patients a previously suggested pathogen (
Mycoplasma genitalium
or
Haemophilus parainfluenzae
) was accurately identified on the basis of DNA sequencing. No ubiquitous, azithromycin-sensitive organism was identified as a common pathogen in all patients, but up to 40% of all clones represented as-yet-unclassified bacterial species. Relatively often
Pseudomonas
spp. or
Pseudomonas-
like organisms were identified in the bacterial flora of patients. Interestingly, an as-yet-uncharacterized microbial species was identified as a negative predictor of NCNGU. This species was identified in all control subjects and was absent from all of the patient' samples (5 of 5 versus 0 of 5,
P
= 0.0079). This suggests that NCNGU might also be diagnosed by assessing the absence rather than the presence of certain bacterial species.
Controlled Comparison of BACTEC 13A, MYCO/F LYTIC, BacT/ALERT MB, and ISOLATOR 10 Systems for Detection of Mycobacteremia
Authors: Crump John A. , Tanner David C. , Mirrett Stanley , McKnight Celeste M. , Reller L. Barth 
Published: May 2003

ABSTRACT

To compare the performance of the BACTEC 13A (Becton Dickinson, Sparks, Md.), BACTEC MYCO/F LYTIC (Becton Dickinson), BacT/ALERT MB (bioMérieux, Durham, N.C.), and ISOLATOR 10 lysis-centrifugation (Wampole Laboratories, Cranbury, N.J.) systems for detection of mycobacteremia in adults, we inoculated 5-ml aliquots of blood from patients with suspected mycobacteremia into the bottle or tube required for each system. Of 600 sets tested, 85 (14%) yielded
Mycobacterium avium
complex (MAC) and 9 (2%) yielded other species of mycobacteria. Of 26 complete (three bottles and one tube) adequately filled (5 ± 1 ml) sets from which MAC was recovered, BACTEC 13A was positive for 19 (73%), BACTEC MYCO/F LYTIC was positive for 21 (81%), BacT/ALERT MB was positive for 22 (85%), and ISOLATOR 10 was positive for 21 (81%). Of the six possible two-way comparisons, the mean times to detection for the recovery of MAC from each bottle in positive adequately paired sets were 15.3 days for BACTEC 13A versus 12.8 days for MYCO/F LYTIC for 33 of 340 pairs, 14.1 days for BACTEC 13A versus 11.6 days for BacT/ALERT MB for 38 of 380 pairs, 12.6 days for BACTEC 13A versus 20.0 days for ISOLATOR 10 for 26 of 261 pairs, 12.8 days for BACTEC MYCO/F LYTIC versus 11.0 days for BacT/ALERT MB for 33 of 340 pairs, 13.2 days for BACTEC MYCO/F LYTIC versus 20.4 days for ISOLATOR 10 for 24 of 230 pairs, and 9.9 days for BacT/ALERT MB versus 19.0 days for ISOLATOR 10 for 24 of 257 pairs. There were no significant differences in yields between the systems. However, the mean time to detection differed significantly among the systems. The time to detection was shortest for BacT/ALERT MB, followed by BACTEC MYCO/F LYTIC and BACTEC 13A and then ISOLATOR 10. Although the numbers were too small for statistical comparison, the time to detection was substantially shorter for MAC than for
Mycobacterium tuberculosis
complex in the liquid systems. The continuously monitored systems (BACTEC MYCO/F LYTIC and BacT/ALERT MB) were as sensitive and, on balance, faster for the detection of MAC bacteremia than were the heretofore standard manual ISOLATOR 10 and radiometric BACTEC 13A systems.
Simple and Fast Lateral Flow Test for Classification of Leprosy Patients and Identification of Contacts with High Risk of Developing Leprosy
Authors: Bührer-Sékula S. , Smits H. L. , Gussenhoven G. C. , van Leeuwen J. , Amador S. , Fujiwara T. , Klatser P. R. , Oskam L. 
Published: May 2003

ABSTRACT

The interruption of leprosy transmission is one of the main challenges for leprosy control programs since no consistent evidence exists that transmission has been reduced after the introduction of multidrug therapy. Sources of infection are primarily people with high loads of bacteria with or without clinical signs of leprosy. The availability of a simple test system for the detection of antibodies to phenolic glycolipid-I (PGL-I) of
Mycobacterium leprae
to identify these individuals may be important in the prevention of transmission. We have developed a lateral flow assay, the ML Flow test, for the detection of antibodies to PGL-I which takes only 10 min to perform. An agreement of 91% was observed between enzyme-linked immunosorbent assay and our test; the agreement beyond chance (kappa value) was 0.77. We evaluated the use of whole blood by comparing 539 blood and serum samples from an area of high endemicity. The observed agreement was 85.9% (kappa = 0.70). Storage of the lateral flow test and the running buffer at 28°C for up to 1 year did not influence the results of the assay. The sensitivity of the ML Flow test in correctly classifying MB patients was 97.4%. The specificity of the ML Flow test, based on the results of the control group, was 90.2%. The ML Flow test is a fast and easy-to-perform method for the detection of immunoglobulin M antibodies to PGL-I of
M.
leprae
. It does not require any special equipment, and the highly stable reagents make the test robust and suitable for use in tropical countries.
Usefulness of the MicroSeq 500 16S Ribosomal DNA-Based Bacterial Identification System for Identification of Clinically Significant Bacterial Isolates with Ambiguous Biochemical Profiles
Authors: Woo Patrick C. Y. , Ng Kenneth H. L. , Lau Susanna K. P. , Yip Kam-tong , Fung Ami M. Y. , Leung Kit-wah , Tam Dorothy M. W. , Que Tak-lun , Yuen Kwok-yung 
Published: May 2003

ABSTRACT

Due to the inadequate automation in the amplification and sequencing procedures, the use of 16S rRNA gene sequence-based methods in clinical microbiology laboratories is largely limited to identification of strains that are difficult to identify by phenotypic methods. In this study, using conventional full-sequence 16S rRNA gene sequencing as the “gold standard,” we evaluated the usefulness of the MicroSeq 500 16S ribosomal DNA (rDNA)-based bacterial identification system, which involves amplification and sequencing of the first 527-bp fragment of the 16S rRNA genes of bacterial strains and analysis of the sequences using the database of the system, for identification of clinically significant bacterial isolates with ambiguous biochemical profiles. Among 37 clinically significant bacterial strains that showed ambiguous biochemical profiles, representing 37 nonduplicating aerobic gram-positive and gram-negative, anaerobic, and
Mycobacterium
species, the MicroSeq 500 16S rDNA-based bacterial identification system was successful in identifying 30 (81.1%) of them. Five (13.5%) isolates were misidentified at the genus level (
Granulicatella adiacens
was misidentified as
Abiotrophia defectiva
,
Helcococcus kunzii
was misidentified as
Clostridium hastiforme
,
Olsenella uli
was misidentified as
Atopobium rimae
,
Leptotrichia buccalis
was misidentified as
Fusobacterium mortiferum
, and
Bergeyella zoohelcum
was misidentified as
Rimerella anatipestifer
), and two (5.4%) were misidentified at the species level (
Actinomyces odontolyticus
was misidentified as
Actinomyces meyeri
and
Arcobacter cryaerophilus
was misidentified as
Arcobacter butzleri
). When the same 527-bp DNA sequences of these seven isolates were compared to the known 16S rRNA gene sequences in the GenBank, five yielded the correct identity, with good discrimination between the best and second best match sequences, meaning that the reason for misidentification in these five isolates was due to a lack of the 16S rRNA gene sequences of these bacteria in the database of the MicroSeq 500 16S rDNA-based bacterial identification system. In conclusion, the MicroSeq 500 16S rDNA-based bacterial identification system is useful for identification of most clinically important bacterial strains with ambiguous biochemical profiles, but the database of the MicroSeq 500 16S rDNA-based bacterial identification system has to be expanded in order to encompass the rarely encountered bacterial species and achieve better accuracy in bacterial identification.
Detection of Anti-West Nile Virus Immunoglobulin M in Chicken Serum by an Enzyme-Linked Immunosorbent Assay
Authors: Johnson Alison J. , Langevin Stanley , Wolff Katherine L. , Komar Nicholas 
Published: May 2003

ABSTRACTThe emergence of West Nile (WN) virus in New York and the surrounding area in 1999 prompted an increase in surveillance measures throughout the United States, including the screening of sentinel chicken flocks for antibodies. An enzyme-linked immunosorbent assay (ELISA) for the detection of chicken immunoglobulin M (IgM) to WN virus was developed, standardized, and characterized as a rapid and sensitive means to detect WN viral antibodies in sentinel flocks. Serum specimens from experimentally infected chickens were analyzed by using this assay, and IgM was detected as early as 3 to 7 days postinfection. Persistence of IgM varied from at least 19 to more than 61 days postinfection, which indicates the need to bleed sentinel flocks at least every 2 weeks for optimal results if this method is to be used as a screening tool. The ELISA was compared to hemagglutination-inhibition and plaque reduction neutralization tests and was found to be the method of choice when early detection of WN antibody is required. House sparrows and rock doves are potential free-ranging sentinel species for WN virus, and the chicken WN IgM-capture ELISA was capable of detecting anti-WN IgM in house sparrow serum samples from laboratory-infected birds but not from rock dove serum samples. The chicken WN IgM-capture ELISA detected anti-WN antibodies in serum samples from naturally infected chickens. It also detected IgM in serum samples from two species of geese and from experimentally infected ring-necked pheasants, American crows, common grackles, and redwinged blackbirds. However, the test was determined to be less appropriate than an IgG (IgY)-based assay for use with free-ranging birds. The positive-to-negative ratios in the ELISA were similar regardless of the strain of WN viral antigen used, and only minimal cross-reactivity was observed between the WN and St. Louis encephalitis (SLE) IgM-capture ELISAs. A blind-coded serum panel was tested, and the chicken WN IgM-capture ELISA produced consistent results, with the exception of one borderline result. A preliminary test was done to assess the feasibility of a combined SLE and WN IgM-capture ELISA, and results were promising.
DNA-Level Characterization ofHelicobacter pyloriStrains from Patients with Overt Disease and with Benign Infections in Bangladesh
Authors: Rahman Motiur , Mukhopadhyay Asish K. , Nahar Shamsun , Datta Simanti , Mashhud Ahmad Milan , Sarker Safique , Masud Ibna M. , Engstrand Lars , Albert M. John , Nair G. Balakrish , Berg Douglas E. 
Published: May 2003

ABSTRACTThe complex relation between the genotype ofHelicobacter pyloriand its association with clinical outcome is not well understood. Studies in the West have showed that strains expressing certain virulence factors (vacAs1,vacAm1, andcagA) are associated with duodenal ulcer disease. However, theH. pylorigenotype is known to vary with geographic region. In the present study, we compared several virulence markers (cagA,vacA, andiceA) and neutral markers (IS605, IS606, and IS608) inH. pyloristrains isolated from 65 adult patients with peptic ulcer (PU) and 50 patients with nonulcer dyspepsia (NUD). PCR tests indicated thatcagAis present in 75% of the strains from patients with PU compared to 55% in patients with NUD, and 80% of the isolates from patients with PU carried potentially toxigenicvacAs1alleles of the vacuolating cytotoxin gene (vacA) compared to 60% in isolates from patients with NUD. However, no significant difference in any other virulence marker was observed in isolates from both groups. Phylogenetic analysis of thevacAmiddle region and the 5′ end of thecagAgene indicates that Bangladeshi isolates are more closely related toH. pyloriisolates from India and are different from isolates from East Asia.
Molecular Epidemiology of
Mycobacterium avium
subsp.
paratuberculosis
: Evidence for Limited Strain Diversity, Strain Sharing, and Identification of Unique Targets for Diagnosis
Authors: Motiwala Alifiya S. , Strother Megan , Amonsin Alongkorn , Byrum Beverly , Naser Saleh A. , Stabel Judith R. , Shulaw William P. , Bannantine John P. , Kapur Vivek , Sreevatsan Srinand 
Published: May 2003

ABSTRACT

The objectives of this study were to understand the molecular diversity of animal and human strains of
Mycobacterium avium
subsp
. paratuberculosis
isolated in the United States and to identify
M. avium
subsp.
paratuberculosis
-specific diagnostic molecular markers to aid in disease detection, prevention, and control. Multiplex PCR of IS
900
integration loci (MPIL) and amplified fragment length polymorphism (AFLP) analyses were used to fingerprint
M. avium
subsp.
paratuberculosis
isolates recovered from animals (
n
= 203) and patients with Crohn's disease (
n
= 7) from diverse geographic localities. Six hundred bacterial cultures, including
M. avium
subsp.
paratuberculosis
(
n
= 303), non-
M. avium
subsp.
paratuberculosis
mycobacteria (
n
= 129), and other nonmycobacterial species (
n
= 168), were analyzed to evaluate the specificity of two IS
900
integration loci and a newly described
M. avium
subsp.
paratuberculosis
-specific sequence (locus 251) as potential targets for the diagnosis of
M. avium
subsp.
paratuberculosis
. MPIL fingerprint analysis revealed that 78% of bovine origin
M. avium
subsp.
paratuberculosis
isolates clustered together into a major node, whereas isolates from human and ovine sources showed greater genetic diversity. MPIL analysis also showed that the
M. avium
subsp.
paratuberculosis
isolates from ovine and bovine sources from the same state were more closely associated than were isolates from different geographic regions, suggesting that some of the strains are shared between these ruminant species. AFLP fingerprinting revealed a similar pattern, with most isolates from bovine sources clustering into two major nodes, while those recovered from sheep or humans were clustered on distinct branches. Overall, this study identified a high degree of genetic similarity between
M. avium
subsp.
paratuberculosis
strains recovered from cows regardless of geographic origin. Further, the results of our analyses reveal a relatively higher degree of genetic heterogeneity among
M. avium
subsp.
paratuberculosis
isolates recovered from human and ovine sources.
Two International Methicillin-Resistant
Staphylococcus aureus
Clones Endemic in a University Hospital in Patras, Greece
Authors: Aires de Sousa M. , Bartzavali C. , Spiliopoulou I. , Santos Sanches I. , Crisóstomo M. I. , de Lencastre H. 
Published: May 2003

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) of
Sma
I macrofragments and hybridization of
Cla
I digests with the
mecA
- and Tn
554
-specific DNA probes were used to define the endemic clones of methicillin-resistant
Staphylococcus aureus
(MRSA) among strains collected in 1993 and 1998 to 2000 at the University Hospital of Patras, Patras, Greece. Representatives of each clonal type were analyzed by
spaA
typing, multilocus sequence typing (MLST), and staphylococcal chromosomal cassette
mec
(SCC
mec
) typing. The results indicated the existence of two successive international MRSA clones: (i) a clonal type with PFGE type A, sequence type (ST) 30 (ST30), and SCC
mec
type IV, which was very similar to a clone widely spread in the United Kingdom, Mexico, and Finland, and (ii) a clonal type with PFGE type B, ST239, and SCC
mec
III, which was related to the Brazilian clone. Both clones seem to be widespread in Greece as well. A novel MRSA clone is also described and is characterized by a new MLST type (ST80) associated with SCC
mec
type IV and with the presence of Panton-Valentine leukocidin genes.
Characterization of Atypical Enteropathogenic
Escherichia coli
Strains Harboring the
astA
Gene That Were Associated with a Waterborne Outbreak of Diarrhea in Japan
Authors: Yatsuyanagi Jun , Saito Shioko , Miyajima Yoshimichi , Amano Ken-Ichi , Enomoto Katsuhiko 
Published: May 2003

ABSTRACT

The virulence traits of the
Escherichia coli
strain associated with a waterborne diarrhea outbreak were examined. Forty-one of 75 students (ages 12 to 15) in Akita Prefecture, Japan, showed clinical symptoms. Seven
E. coli
Ouk:K-:H45 isolates were isolated from the patients as the causative agent of this outbreak. One isolate (EC-3605) showed the presence of
E. coli
attaching-and-effacing (
eaeA
) and enteroaggregative
E. coli
heat-stable enterotoxin-1 (
astA
) genes and the absence of Shiga toxin (
stx1
and
stx2
) genes. A polymorphic enteropathogenic
E. coli
(EPEC) adherence factor plasmid was detected in EC-3605 with a major structural gene deletion and a regulatory gene frameshift mutation, revealing that EC-3605 represents an atypical EPEC strain harboring the
astA
gene. The role that atypical EPEC strains harboring the
astA
gene play in human disease is unclear. Our results, along with those of others, present a possibility that these strains comprise a distinct category of diarrheagenic
E. coli
and that
astA
affects the age distribution of atypical-EPEC infection.