bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of a Multilocus Sequence Typing Scheme for the Pig Pathogen
Streptococcus suis
: Identification of Virulent Clones and Potential Capsular Serotype Exchange
Authors: King Samantha J. , Leigh James A. , Heath Peter J. , Luque Inmaculada , Tarradas Carmen , Dowson Christopher G. , Whatmore Adrian M. 
Published: September 2002

ABSTRACT

Streptococcus suis
is an important pathogen of pigs and occasionally causes serious human disease. However, little is known about the
S. suis
population structure, the clonal relationships between strains, the potential of particular clones to cause disease, and the relevance of serotype as a marker for epidemiology. Here we describe a multilocus sequence typing (MLST) scheme for
S. suis
developed in order to begin to address these issues. Seven housekeeping gene fragments from each of 294
S. suis
isolates obtained from various
S. suis
diseases and from asymptomatic carriage representing 28 serotypes and nine distinct countries of origin were sequenced. Between 32 and 46 alleles per locus were identified, giving the ability to distinguish >1.6 × 10
11
sequence types (STs). However only 92 STs were identified in this study. Of the 92 STs 18 contained multiple isolates, the most common of which, ST1, was identified on 141 occasions from six countries. Assignment of the STs to lineages resulted in 37 being identified as unique and unrelated STs while the remaining 55 were assigned to 10 complexes. ST complexes ST1, ST27, and ST87 dominate the population; while the ST1 complex was strongly associated with isolates from septicemia, meningitis, and arthritis, the ST87 and ST27 complexes were found to contain significantly higher numbers of lung isolates. In agreement with the observed distribution of disease-causing isolates of
S. suis
, most isolates previously characterized as of high virulence in porcine infection models belong to ST1, while isolates belonging to other STs appear to be less virulent in general. Finally nine STs were found to contain isolates of multiple serotypes, and many isolates belonging to the same serotypes were found to have very disparate genetic backgrounds. As well as highlighting that the serotype can often be a poor indicator of genetic relatedness between
S. suis
isolates, these findings suggest that capsular genes may be moving horizontally through the
S. suis
population.
Improved Detection by DNA Amplification of
Trichomonas vaginalis
in Males
Authors: Schwebke Jane R. , Lawing Lisa F. 
Published: September 2002

ABSTRACT

Trichomoniasis is a sexually transmitted infection that is highly prevalent worldwide and has been linked to preterm birth and human immunodeficiency virus acquisition. In females, trichomoniasis causes vaginitis, while in males, it is frequently asymptomatic but can be a cause of urethritis. Control efforts have been hampered by the lack of a sensitive diagnostic technique for this infection in males. Men attending a sexually transmitted disease (STD) clinic for a new complaint were screened for
Trichomonas vaginalis
by culture and by PCR analysis of urine and urethral-swab specimens. The prevalence of
Trichomonas
determined by culture was 5% (15 of 300 specimens), compared to 17% (52 of 300) determined by PCR. Urine specimens yielded a greater number of positive results by PCR than did urethral-swab specimens. The sensitivity of PCR analysis of urine specimens in comparison to that of culture was 100%. The use of PCR techniques in urine specimen-based detection of
T. vaginalis
was highly sensitive and revealed a prevalence of infection more than three times that revealed by culture for men at high risk for STDs.
Analysis of Intratypic Variation Evident in an Ibaraki Virus Strain and Its Epizootic Hemorrhagic Disease Virus Serogroup
Authors: Ohashi Seiichi , Yoshida Kazuo , Yanase Tohru , Tsuda Tomoyuki 
Published: September 2002

ABSTRACTA new strain of Ibaraki virus (IBAV) was isolated from cattle showing atypical symptoms of Ibaraki disease. The isolate was genetically characterized, and the genetic diversity and evolution of the capsid proteins of viruses in the epizootic hemorrhagic disease virus (EHDV) serogroup were investigated. The nucleotide sequences of the isolate's viral RNA segments 2, 3, 6, and 7, which encode the viral structural proteins VP2, VP3, VP5, and VP7, respectively, were determined and were then compared against those of the existing strains of IBAV and EHDV, to which IBAV belongs serologically. The nucleotide sequences of segments 3 and 7 were conserved within the EHDV serogroup, particularly well among the strains of IBAV and Australian EHDV. The similarity of the sequence of segment 6 of the isolate to sequences of corresponding segments of the other strains of IBAV and EHDV was found to be about 93%. The similarity of segment 2 of the isolate to segments 2 of the other strains of IBAV and EHDV was less than 70%. Phylogenetic analysis based on the deduced amino acid sequences of segments 3 and 7 revealed that the viruses differed according to their geographical distributions. However, the new isolate of IBAV was categorized as having a distinct lineage in the phylogenetic tree of VP2. These results suggest that the isolate was modified by a reassortment of segment 2 and that it exhibits unique genetic and antigenic characteristics.
Evaluation of a Cytomegalovirus Glycoprotein B Recombinant Enzyme Immunoassay To Discriminate between a Recent and a Past Infection
Authors: Sipewa M. J. , Goubau P. , Bodéus M. 
Published: September 2002

ABSTRACT
Fetal damage following cytomegalovirus (CMV) intrauterine infection is mostly linked to primary infection. To differentiate primary infection from nonprimary infection, immunoglobulin M (IgM) tests are not reliable enough, and measurement of the IgG avidity appears to be the method that is the most widely used at present. In the present study the performance of the Vidas (bioMérieux) avidity assay was compared with that of a new enzyme immunoassay based on the use of a recombinant CMV glycoprotein B protein (Biotest).
Development of a Rapid Immunodiagnostic Test for
Haemophilus ducreyi
Authors: Patterson Kristine , Olsen Bonnie , Thomas Christopher , Norn Dora , Tam Milton , Elkins Christopher 
Published: September 2002

ABSTRACT

Haemophilus ducreyi
is the etiologic agent of chancroid, a sexually transmitted disease that increases the rate of transmission of human immunodeficiency virus. Chancroid ulcerations are difficult to distinguish from those produced by syphilis and herpes. Diagnosis based solely on clinical grounds is inaccurate, and culture is insensitive. Highly sensitive PCR has largely superseded culture as the preferred method of laboratory diagnosis; however, neither culture nor PCR is feasible where chancroid is endemic. We developed a rapid (15-min) diagnostic test based on monoclonal antibodies (MAbs) to the hemoglobin receptor of
H. ducreyi
, HgbA. This outer membrane protein is conserved in all strains of
H. ducreyi
tested and is required for the establishment of experimental human infection. MAbs to HgbA were generated and tested for cross-reactivity against a panel of geographically diverse strains. Three MAbs were found to be unique and noncompetitive and bound to all strains of
H. ducreyi
tested. Using an immunochromatography format, we evaluated the sensitivity and specificity of the test using geographically diverse strains of
H. ducreyi
, other
Haemophilus
strains, and other bacteria known to superinfect genital ulcers. All
H. ducreyi
strains were positive, and all other bacteria were negative, resulting in a specificity of 100%. The minimum number of CFU of
H. ducreyi
detected was 2 × 10
6
CFU, and the minimum amount of purified HgbA protein detected was 8.5 ng. Although this level of sensitivity may not be sufficient to detect
H. ducreyi
in all clinical specimens, further work to increase the sensitivity could potentially make this a valuable bedside tool in areas where chancroid is endemic.
Evaluation of the Etest ESBL and the BD Phoenix, VITEK 1, and VITEK 2 Automated Instruments for Detection of Extended-Spectrum Beta-Lactamases in Multiresistant
Escherichia coli
and
Klebsiella
spp
Authors: Leverstein-van Hall Maurine A. , Fluit Ad C. , Paauw Armand , Box Adrienne T. A. , Brisse Sylvain , Verhoef Jan 
Published: September 2002

ABSTRACT

Seventy-four isolates of multiresistant
Escherichia coli
and
Klebsiella
spp. recovered during a 3-year period and 17 control strains with genotypically identified beta-lactamases were tested for the production of extended-spectrum beta-lactamases (ESBLs) by using the Etest and the VITEK 1, VITEK 2, and Phoenix automated instruments. The use of the Etest was evaluated by investigating its accuracy in detecting the ESBLs of the control strains and by comparing interpretation results of laboratory technicians and experts. The accuracy of the Etest was 94%. With the Etest as the reference for the clinical strains and the genotype as the reference for the control strains, the automated instruments detected the ESBLs with accuracies of 78% (VITEK 2), 83% (VITEK 1), and 89% (Phoenix). No significant difference between the systems with regard to the control strains was detected. The VITEK 2 did, however, perform less well than the Phoenix (
P
= 0.03) on the collection of clinical isolates, mainly because of its high percentage of indeterminate test results (11%). No significant difference between the performances of the VITEK 1 and either the VITEK 2 or the Phoenix was found. However, because of its associated BDXpert system the Phoenix showed the best performance. The Etest was found to be an accurate test but was limited by its indeterminate results (4%), its inability to differentiate between K1 hyperproduction and ESBLs, questionable guidelines concerning mutants inside the inhibition zones, and the inability of the technicians to recognize subtle zone deformations.
IS
1311
and IS
1245
Restriction Fragment Length Polymorphism Analyses, Serotypes, and Drug Susceptibilities of
Mycobacterium avium
Complex Isolates Obtained from a Human Immunodeficiency Virus-Negative Patient
Authors: Dvorska Lenka , Bartos Milan , Ostadal Oldrich , Kaustova Jarmila , Matlova Ludmila , Pavlik Ivo 
Published: September 2002

ABSTRACT

Six isolates of
Mycobacterium avium
of genotype
dnaJ
+
IS
901
−
IS
1311
+
IS
1245
+
and serotypes 6 (
n
= 1), 6/9, (
n
= 2), and 9 (
n
= 3) were obtained within a 5-month period from a human immunodeficiency virus-negative patient treated for tuberculosis. The isolates were identified with
Pvu
II restriction fragment length polymorphism (RFLP) analysis as a single IS
1311
RFLP type and six different IS
1245
RFLP types. Six separate colonies/clones obtained by subculture from each of the six isolates were tested for MICs of a set of 10 drugs. This report documents the appearance of isolates that are resistant to antimycobacterial drugs as the duration of therapy increases. Because isolates recovered from the patient following longer duration of treatment were more likely to be resistant to more antimycobacterial drugs, we would conclude that there was selection for antimycobacterial drug-resistant isolates. Analyses of all 36 clones identified three IS
1311
and 22 IS
1245
types forming three clusters. Tests of 105 environmental samples collected in the home and the work place of the patient yielded 16 mycobacterial isolates, of which one
M. avium
from soil was of genotype
dnaJ
+
IS
901
+
IS
1311
+
IS
1245
+
and serotype 2, and the second
M. avium
from a vacuum cleaner was of genotype
dnaJ
+
IS
901
−
IS
1311
+
IS
1245
+
and serotype 9. Overall analyses of the results did not reveal any relation between serotype, RFLP type, and drug susceptibility. Based on the course of the disease in the patient and different serotypes, IS
1311
and IS
1245
RFLP types of isolates of
M. avium
we suppose represent polyclonal infection.
Real-Time Quantitative PCR for Detection ofHelicobacter pylori
Authors: He Qiang , Wang Jian-Ping , Osato Michael , Lachman Lawrence B. 
Published: September 2002

ABSTRACTHelicobacter pyloriis one of the most common chronic infections in humans, in whom it is a key etiological factor in peptic ulcer disease, gastric mucosa-associated lymphoid tissue lymphoma, and gastric adenocarcinoma. Humans are the bacterium's only host. Here we report the development of a real-time quantitative (Q) PCR-based assay to measureureCgene copy number to detectH. pylori,based on the fact that there is only one copy of theureCgene per bacterium. Upon optimization of LightCycler Q-PCR conditions, we obtained a standard curve with a linear range (correlation coefficient = 1) across six logs of DNA concentration. We were able to accurately quantify as few as 1,000 bacteria in our assay. Analysis of variance on 15 randomly selected clinical samples showed good reproducibility of this assay. Comparison of Q-PCR results with bacterial culture and histopathological results from an additional 85 clinical biopsy samples showed a significant difference for the presence ofH. pylori. Many samples that were negative forH. pyloriby culture and histopathology were positive by Q-PCR. Contamination of PCR byH. pyloriorH. pylorigenetic material could not be ruled out. In summary, we developed a rapid, sensitive, and real-time Q-PCR method for detectingH. pylori. This technique offers a significant improvement over other available methods for detectingH. pyloriin clinical and research samples.
Monitoring Drug Resistance in Chronic Hepatitis B Virus (HBV)-Infected Patients during Lamivudine Therapy: Evaluation of Performance of INNO-LiPA HBV DR Assay
Authors: Lok Anna S. F. , Zoulim Fabien , Locarnini Stephen , Mangia Alessandra , Niro Grazia , Decraemer Hilde , Maertens Geert , Hulstaert Frank , De Vreese Karen , Sablon Erwin 
Published: September 2002

ABSTRACTSensitive and early detection of emerging hepatitis B virus (HBV) drug resistance may not only help monitor the viral dynamics associated with lamivudine treatment but could also improve therapeutic decision making. This is especially important when new antivirals effective against lamivudine-resistant HBV become available. A total of 159 serum samples from 33 chronic HBV patients receiving lamivudine treatment were analyzed at four centers for the presence of lamivudine-resistant mutations at codons 528 [180] (proposed revised nomenclature according to Stuyver et al. [Hepatology33:751-757, 2001] shown in brackets), 552 [204], and 555 [207] of the HBV polymerase. Sequencing data were compared with results generated by the INNO-LiPA HBV DR line probe assay (LiPA), an assay based on reverse hybridization of amplified HBV DNA fragments with specific nucleotide probes immobilized on nitrocellulose strips. LiPA provided at least the same information as sequencing for 97.5% of all codons analyzed for codon 528 [180], 95% for codon 552 [204], and 100% for codon 555 [207]. The most common reason for discrepant or indeterminate results (0.4% and 1.5%, respectively) in a small percentage of the population tested could be attributed to polymorphisms not yet covered by LiPA probes. In at least five patients, a mutant could be detected earlier by LiPA than by sequencing. In 15 patients, LiPA detected mixed wild-type and mutant virus populations before viral breakthrough. These results demonstrate that INNO-LiPA HBV DR is a highly sensitive and easily applicable assay for the detection and monitoring of lamivudine-resistant mutations in chronic hepatitis B patients and that the assay is more sensitive than sequencing in detecting mixed mutant and wild-type sequences.
Trypanosoma cruziRecombinant Complement Regulatory Protein: a Novel Antigen for Use in an Enzyme-Linked Immunosorbent Assay for Diagnosis of Chagas' Disease
Authors: Meira Wendell S. F. , Galvão Lúcia M. C. , Gontijo Eliane D. , Machado-Coelho George L. L. , Norris Karen A. , Chiari Egler 
Published: September 2002

ABSTRACTCurrently, diagnosis of Chagas' disease is based on serological methods, but due to the high occurrence of inconclusive results, more reliable methods are needed. The use of recombinant antigens for serodiagnosis of Chagas' disease is recommended in order to increase the sensitivity and specificity of the serological tests. TheTrypanosoma cruzicomplement regulatory protein (CRP) is a surface glycoprotein present on the trypomastigote forms of the parasite, and the recombinant CRP (rCRP) was cloned in a mammalian expression system and purified by affinity chromatography. The purified recombinant protein was used as an antigen in an enzyme-linked immunosorbent assay (rCRP ELISA) in order to verify its sensitivity and specificity compared with other established methods. In this evaluation, a panel of 184 serum samples distributed among chronic chagasic patients (n= 65), blood bank donors (n= 100), and patients infected withLeishmaniaspp. (n= 19) was used. The sensitivity and specificity of the rCRP ELISA were 100% when compared to conventional serology and complement-mediated lysis tests from these groups. When hemoculture and PCR tests were evaluated for diagnosis of chronic chagasic patients, using the rCRP ELISA as a reference test, the positivities were found to be 64.62 and 81.54%, respectively, showing a higher degree of sensitivity of the test. The data demonstrate that rCRP ELISA was able to discriminate between chronic chagasic patients and nonchagasic individuals, such as blood donors and patients with leishmaniasis. Thus, the rCRP is an excellent antigen for use in Chagas' disease diagnosis, due to the absence of false-negative or false-positive results.
Molecular Epidemiology of
Neisseria gonorrhoeae
: Sequence Analysis of the
porB
Gene Confirms Presence of Two Circulating Strains
Authors: Unemo Magnus , Olcén Per , Berglund Torsten , Albert Jan , Fredlund Hans 
Published: September 2002

ABSTRACT

The phenotypic and genotypic characteristics of
Neisseria gonorrhoeae
strains fluctuate over time both locally and globally, and highly discriminative and precise characterization of the strains is essential. Conventional characterization of
N. gonorrhoeae
strains for epidemiological purposes is mostly based on phenotypic methods, which have some inherent limitations. In the present study sequence analysis of
porB1b
gene sequences was used for examination of the genetic relationships among
N. gonorrhoeae
strains. Substantial genetic heterogeneity was identified in the
porB
genes of serovar IB-2 isolates (8.1% of the nucleotide sites were polymorphic) and serovar IB-3 isolates (5.2% of the nucleotide sites were polymorphic) as well as between isolates of different serovars. The highest degree of diversity was identified in the gene segments encoding the surface-exposed loops of the mature PorB protein. Phylogenetic analysis of the
porB1b
gene sequences confirmed previous findings that have indicated the circulation of one
N. gonorrhoeae
strain each of serovar IB-2 and serovar IB-3 in the Swedish community. These strains caused the majority of the cases in two domestic core groups comprising homosexual men and young heterosexuals, respectively, and were also detected in other patients. The phylogenetic analyses of
porB
gene sequences in the present study showed congruence, but not complete identity, with previous results obtained by pulsed-field gel electrophoresis of the same isolates. In conclusion,
porB
gene sequencing can be used as a molecular epidemiological tool for examination of genetic relationships among emerging and circulating
N. gonorrhoeae
strains, as well as for confirmation or discrimination of clusters of gonorrhea cases.
Ability of the MicroScan Rapid Gram-Negative ID Type 3 Panel To Identify Nonenteric Glucose-Fermenting and Nonfermenting Gram-Negative Bacilli
Authors: O'Hara Caroline M. , Miller J. Michael 
Published: September 2002

ABSTRACT

The MicroScan Rapid Neg ID3 panel is designed for the identification of
Enterobacteriaceae
and nonenteric glucose-fermenting and nonfermenting gram-negative bacilli. We evaluated this panel for its ability to identify gram-negative non-
Enterobacteriaceae
bacteria. A total of 134 strains, representing 26 genera and 42 species, were taken from storage at −70
o
C, passaged three times before testing, and inoculated into the panels according to the manufacturer's directions before being inserted into a Walk/Away 96 instrument loaded with version 22.28 software. At the end of the initial 2.5-h incubation period, 89 isolates (66.4%) were correctly identified at a probability level of ≥85%. After additional testing recommended by the manufacturer was completed, another 11 isolates (8.2%) were correctly identified at probability levels of ≥85%. Twenty-five (18.7%) isolates were correctly identified after additional testing, but the probability levels were less than 85%. Two isolates were unidentified, and seven (5.2%) were incorrectly identified. The seven misidentified strains were not concentrated in any one genus. With an accuracy approaching 75%, this product may be used for the identification of the commonly isolated non-
Enterobacteriaceae
bacteria but may present problems in identification of other non-glucose-fermenting gram-negative bacilli.
Multicenter Evaluation of a Nonweekend Reading Schedule for Radiometric Pyrazinamide Susceptibility Testing of
Mycobacterium tuberculosis
Authors: Madison B. , Gross W. , George I. , Sloutsky A. , Washabaugh G. , Robinson-Dunn B. , Lipman H. , Metchock B. , Mazurek G. , Ridderhof J. 
Published: September 2002

ABSTRACT

Pyrazinamide (PZA) is an integral component of the short-course chemotherapy regimen for tuberculosis. The BACTEC 460TB PZA susceptibility test for
Mycobacterium tuberculosis
with a daily (D) reading schedule has been available for more than 10 years, but weekend laboratory staffing is necessary. A nonweekend (NW) reading schedule has not been validated in a multicenter study. This prospective multicenter study compares the interlaboratory reproducibility of PZA susceptibility results by following both the D and NW schedules. A total of 181 cultures were shared among four laboratories. Isolates were selected based on resistance or borderline resistance to at least one streptomycin-isoniazid-rifampin-ethambutol drug or PZA. One laboratory used a D reading schedule, and three laboratories used a NW schedule. Both reading schedules are based on the standard BACTEC 460TB PZA protocol. With the NW schedule, the growth index (GI) is not available for test interpretation on Saturday, Sunday, and Monday. Of the 181 shared cultures, 154 were found to be susceptible by all laboratories, 19 were found to be resistant, and 8 had discordant results. The overall pairwise interlaboratory agreement was 97.7%. The discrepancies were not associated with the type of reading schedule used. However, the median control GI was significantly higher for the NW schedule (321) than for the D schedule (259) (
P
< 0.0001) although results were available on average in about 7 days from setup for both schedules. These results show that the NW schedule is a suitable alternative for laboratories that do not read and interpret PZA susceptibility tests on weekends.