bluuebunny/crossref_metadata_2025_split huggingface dataset:
Duration of Persistence of Gonococcal DNA Detected by Ligase Chain Reaction in Men and Women following Recommended Therapy for Uncomplicated Gonorrhea
Authors: Bachmann Laura H. , Desmond Renee A. , Stephens Joan , Hughes Annalee , Hook Edward W. 
Published: September 2002

ABSTRACT

Neisseria gonorrhoeae
infection remains relatively common in the United States, representing a public health challenge. Ligase chain reaction (LCR) is both highly sensitive and specific for the detection of
N. gonorrhoeae
in urine and patient-obtained vaginal swab specimens. Because of the LCR test's exquisite sensitivity, it may potentially detect DNA from nonviable organisms following effective therapy, leading to false-positive test results and unnecessary additional treatment. The purpose of the present study was to determine the duration that gonococcal DNA is detectable by LCR following therapy for uncomplicated gonococcal infection. One hundred thirty men and women between the ages of 16 and 50 years presenting to a sexually transmitted disease clinic with urogenital gonorrhea were enrolled. After the standard history was taken and a genital examination was done, the patients were asked to submit either a urine specimen (men) or a urine specimen plus a self-obtained vaginal swab specimen (women) for
N. gonorrhoeae
testing by LCR at the initial visit and each day during the study period. At enrollment, patients were treated with single doses of ofloxacin, cefixime, or ceftriaxone. The median time to a negative urine LCR test result was 1 day for the men (mean, 1.6 ± 0.14 days) and 2 days for the women (mean, 1.7 ± 0.19 days). Among the women the clearance time was significantly longer for vaginal specimens (mean, 2.8 ± 0.30 days) than for urine specimens (mean, 1.7 ± 0.11 days). Irrespective of patient gender and specimen type, gonococcal DNA can be expected to be absent from urogenital specimens within 2 weeks following successful therapy.
Identification of
Candida glabrata
by a 30-Second Trehalase Test
Authors: Freydière A.-M. , Parant F. , Noel-Baron F. , Crepy M. , Treny A. , Raberin H. , Davidson A. , Odds F. C. 
Published: September 2002

ABSTRACT

Rapid (30-s) trehalase tests done with material from colonies of 482 yeasts suspended in a drop of trehalose solution on a commercially supplied glucose test strip were positive for 225 (99.1%) of 227
Candida glabrata
isolates grown on either of two differential media, Candida ID medium or CandiSelect medium. The test was positive for only 3 (1.2%) and 12 (4.7%) of 255 isolates of other medically important yeast species grown on the same two media, respectively. A rapid maltase test done with a subset of 255 yeast isolates was negative for all but 1 of 64 trehalase-positive
C. glabrata
isolates, raising the specificity of the rapid testing for
C. glabrata
to 98.4 to 100%, depending on the isolation medium used. Rapid trehalase and maltase tests done independently in two laboratories with 217 yeast isolates showed sensitivities of 96.0 to 98.0% and specificities of 98.2 to 99.4% for identification of
C. glabrata
from colonies grown on Candida ID medium. The specificity was much lower because of frequent false-positive trehalose test results when the source of colonies was Sabouraud agar formulated with 4% glucose. We conclude that direct recognition of
C. albicans
as blue colonies on Candida ID isolation medium coupled with the performance of the 30-s trehalase and maltase tests for
C. glabrata
among the white colonies on this medium will allow the rapid presumptive identification of the two yeast species most commonly encountered in clinical samples.
Identification of
Bartonella bacilliformis
Genotypes and Their Relevance to Epidemiological Investigations of Human Bartonellosis
Authors: Birtles Richard J. , Fry Norman K. , Ventosilla Palmira , Cáceres Abraham G. , Sánchez Eduardo , Vizcarra Hugo , Raoult Didier 
Published: September 2002

ABSTRACT

Genotypic diversity among 26 isolates of
Bartonella bacilliformis
obtained from different areas of Peru, and at different times, was assessed by comparison of DNA sequences derived from 16S-23S ribosomal DNA intergenic spacer regions (ISR) and a citrate synthase gene (
gltA
) fragment and by amplified fragment length polymorphism (AFLP) analysis.
gltA
comparison divided the isolates into two groups, whereas ISR comparison revealed six sequences. AFLP analysis using a selective primer delineated five profiles that correlated well with those obtained by sequence comparison. Combination of all three data sets divided the isolates into six genotypes. One of these genotypes was common to isolates collected from a large area in western Peru that corresponded to the region of endemicity for bartonellosis; however, isolates belonging to two other genotypes were also found within this region. Two of these genotypes were found in isolates isolated more than 35 years apart. The remaining three genotypes were each specifically associated with three outbreaks of bartonellosis that have recently occurred in areas where the disease had not previously been recognized. Demonstration of the unique nature of these isolates indicates that the outbreaks with which they were associated did not result from the introduction of disease by individuals who acquired their infection in the recognized region of endemicity. The sources of these outbreaks remain unknown. A consensus approach to bacterial typing using comparative sequence analysis of multiple genetic loci and the pan-genomic sampling of AFLP appears to offer a well-supported assessment of
B. bacilliformis
diversity, and the genotypic differences identified appear to have epidemiological significance.
Detection in
Escherichia coli
of the Genes Encoding the Major Virulence Factors, the Genes Defining the O157:H7 Serotype, and Components of the Type 2 Shiga Toxin Family by Multiplex PCR
Authors: Wang Gehua , Clark Clifford G. , Rodgers Frank G. 
Published: September 2002

ABSTRACT

Strains of Shiga toxin-producing
Escherichia coli
(STEC) have been associated with outbreaks of diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans. Most clinical signs of disease arise as a consequence of the production of Shiga toxin 1 (Stx1), Stx2 or combinations of these toxins. Other major virulence factors include enterohemorrhagic
E. coli
hemolysin (EHEC
hlyA
), and intimin, the product of the
eaeA
gene that is involved in the attaching and effacing adherence phenotype. In this study, a series of multiplex-PCR assays were developed to detect the eight most-important
E. coli
genes associated with virulence, two that define the serotype and therefore the identity of the organism, and a built-in gene detection control. Those genes detected were
stx
1
,
stx
2
,
stx
2c
,
stx
2d
,
stx
2e
,
stx
2f
, EHEC
hlyA
, and
eaeA
, as well as
rfbE
, which encodes the
E. coli
O157 serotype;
fliC
, which encodes the
E. coli
flagellum H7 serotype; and the
E. coli
16S rRNA, which was included as an internal control. A total of 129
E. coli
strains, including 81 that were O157:H7, 10 that were O157:non-H7, and 38 that were non-O157 isolates, were investigated. Among the 129 samples, 101 (78.3%) were
stx
positive, while 28 (21.7%) were lacked
stx
. Of these 129 isolates, 92 (71.3%) were EHEC
hlyA
positive and 96 (74.4%) were
eaeA
positive. All STEC strains were identified by this procedure. In addition, all Stx2 subtypes, which had been initially identified by PCR-restriction fragment length polymorphism, were identified by this method. A particular strength of the assay was the identification of these 11 genes without the need to use restriction enzyme digestion. The proposed method is a simple, reliable, and rapid procedure that can detect the major virulence factors of
E. coli
while differentiating O157:H7 from non-O157 isolates.
Improved Culture from Lymph Nodes of Patients with Cat Scratch Disease and Genotypic Characterization of
Bartonella henselae
Isolates in Australia
Authors: Fournier Pierre-Edouard , Robson Jenny , Zeaiter Zaher , McDougall Rodney , Byrne Shane , Raoult Didier 
Published: September 2002

ABSTRACT

Over a 4-year period we detected
Bartonella henselae
isolates in 104 of 297 specimens (35.1%) from Australian patients clinically suspected of having cat scratch disease by amplification of a fragment of the
htrA
gene. We isolated 17
B. henselae
strains (20.5%) from the 83 PCR-positive human specimens available for culture. Our culture method was based on prolonged incubation in a moist atmosphere of blood agar to which hemin was added. We obtained more
B. henselae
isolates than the number of all other isolates from lymph nodes reported in the literature. In order to identify and study the genetic variation of Australian
B. henselae
isolates, we determined the sequence of a fragment of the
pap31
gene from our 17 human isolates and also from 8 Australian cat isolates. Thirteen of the human
B. henselae
isolates belonged to the Houston genotype, variant Houston-1 (76.5%), and four belonged to the Marseille genotype, variant CAL-1 (23.5%). In contrast, seven cat isolates were classified as
B. henselae
Marseille, variant CAL-1 (87.5%), and one was classified as
B. henselae
Houston, variant Houston-1 (12.5%). Our study describes an efficient culture method for the diagnosis of cat scratch disease and contributes to the description of the genotypic distribution of
B. henselae
in Australia.
Comparative Sequence Analysis of the Core Protein and Its Frameshift Product, the F Protein, of Hepatitis C Virus Subtype 1b Strains Obtained from Patients with and without Hepatocellular Carcinoma
Authors: Ogata Satoshi , Nagano-Fujii Motoko , Ku Yonson , Yoon Seitetsu , Hotta Hak 
Published: September 2002

ABSTRACT
The core protein of hepatitis C virus (HCV) has been implicated in hepatocarcinogenesis. In order to determine whether there is a correlation between mutations of the core protein and the development of hepatocellular carcinoma (HCC), the core protein-coding sequence of the viral genome of HCV subtype 1b (HCV-1b) obtained from patients with and without HCC was analyzed. We found that 12 (40.0%) of 30 HCV-1b isolates from patients with HCC but none of 29 isolates from patients without HCC had a point mutation(s) in an N-terminal region of 20 residues. Similarly, 10 (33.3%) of 30 isolates from patients with HCC had mutations in a limited region between residues 141 and 160, whereas only 2 (6.9%) of 29 isolates from patients without HCC did. The differences between the two groups were statistically significant. The mutations were found in isolates from both cancerous and adjacent noncancerous tissues of patients with HCC, suggesting that the mutations were present before the development of HCC. The other regions of the core protein of some isolates also had mutations, but no significant difference was observed between isolates from patients with HCC and those from patients without HCC. The F protein, a frameshift product that is still hypothetical for HCV-1b strains, showed more sequence diversity than the core protein among the isolates analyzed, but there were no significant differences in the mutation rates or positions between isolates from patients with HCC and isolates from patients without HCC, except for a short N-terminal sequence of ∼11 residues that is shared with the core protein.
Quantification of
Chlamydia trachomatis
Elementary Bodies in Urine by Ligase Chain Reaction
Authors: Blocker Michael E. , Krysiak Robert G. , Behets Frieda , Cohen Myron S. , Hobbs Marcia M. 
Published: September 2002

ABSTRACT

Modification of the standard
Chlamydia trachomatis
ligase chain reaction (LCR) detection assay resulted in a quantitative test. Sample rates from
C. trachomatis
standards ranging from 32 to 1,048,576 elementary bodies (EB)/ml of urine exhibited a linear correlation with concentration. Quantitative LCR (qLCR) was used to measure the number of EB per milliliter in 158 urine samples from women in Madagascar that tested positive for
C. trachomatis
by the standard LCR detection assay.
C. trachomatis
concentrations displayed an apparent bimodal distribution, with approximately one-third of samples (37%) in a peak ranging from 32 to 1,015 EB/ml (median = 297 EB/ml) and the remainder (63%) in a grouping with relatively higher concentrations, ranging from 1,086 to 218,670 EB/ml (median = 7,389 EB/ml). qLCR will be useful for studies of chlamydial infection aimed at understanding the associations of organism burden with clinical manifestations and transmission.
Detection of Herpes Simplex Virus Type 2-Specific Immunoglobulin G Antibodies in African Sera by Using Recombinant gG2, Western Blotting, and gG2 Inhibition
Authors: Hogrefe Wayne , Su Xin , Song James , Ashley Rhoda , Kong Lilly 
Published: September 2002

ABSTRACT

Sera (
n
= 781) from four African countries were used to determine the prevalence of herpes simplex virus type 2 (HSV-2) antibodies by using the HerpeSelect HSV-2 enzyme-linked immunosorbent assay (ELISA; Focus Technologies) and Western blotting (WB). Also, an HSV inhibition assay was developed to evaluate the discordant sample results between HerpesSelect and WB. The seroprevalence of HSV-2 ranged from 17% in the South African panel to nearly 70% in panels from Kenya, Uganda, and Zimbabwe. Overall, HerpeSelect was 100% sensitive and 88% specific compared to WB and 100% sensitive and 96% specific compared to the inhibition assay. There was 100% concordance among all three assays for samples from South Africa and Zimbabwe. The discordant results occurred in samples from Kenya and Uganda.
Genetic Classification and Differentiation of
Bartonella
Species Based on Comparison of Partial
ftsZ
Gene Sequences
Authors: Zeaiter Zaher , Liang Zhongxing , Raoult Didier 
Published: September 2002

ABSTRACT

Currently, 19 species are recognized in the genus
Bartonella
, 7 of which are involved in an increasing variety of human diseases. Development of molecular tools for detection, identification, and subtyping of strains and isolates has promoted research on
Bartonella
spp. We amplified and sequenced the portion of the
ftsZ
gene encoding the N-terminal region of the cell division protein for 13
Bartonella
species:
Bartonella alsatica
,
B. birtlesii
,
B. doshiae
,
B. elizabethae
,
B. grahami
,
B. koehlerae
,
B. schoenbuchensis
,
B. taylorii
,
B. tribocorum
,
Bartonella vinsonii
subsp.
arupensis
,
Bartonella vinsonii
subsp.
berkhoffii
,
Bartonella vinsonii
subsp.
vinsonii
, and
B. bovis
Bermond et al.(“
B. weissii
”). Phylogenetically derived trees revealed four statistically supported groups, indicating that sequencing of the
ftsZ
gene is a useful tool for identifying evolutionary relationships among
Bartonella
species. Furthermore, we amplified and sequenced the portion of the
ftsZ
gene encoding the C-terminal region of the protein for 4
B. bacilliformis
isolates, 14
B. clarridgeiae
isolates, 14
B. quintana
isolates, and 30
B. henselae
isolates that were obtained from different geographic regions, hosts, and clinical specimens.
B. clarridgeiae
and
B. quintana
sequences were highly conserved, while those of the four
B. bacilliformis
isolates differed from the type strain at 5 positions. Among
B. henselae
strains isolated from cats and patients, only two genotypes were detected: Houston and Marseille. Among 80 clinical samples we detected
Bartonella
spp. in 35 (43.75%) and found the assay to be comparable to that of a combined intergenic-spacer-region- and
pap31
-based PCR assay. Our results show the usefulness of the portion of the
ftsZ
gene encoding the C-terminal region for diagnosis of
Bartonella
infections. More samples should be tested to study its usefulness for epidemiological investigations.
Molecular Follow-Up of
Salmonella enterica
subsp.
enterica
Serovar Agona Infection in Cattle and Humans
Authors: Lindqvist Nanna , Siitonen Anja , Pelkonen Sinikka 
Published: September 2002

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Agona was not frequently encountered in Finland until an increase in rates of isolation among animal and feed was seen in 1994. A small outbreak among cattle farms in the regions of Oulu and Vaasa in northwestern Finland in 1994-1995 included eight farms. After the outbreak, an increase in the number of serovar Agona infections in humans was seen in 1999: the number of annual microbiologically confirmed cases in humans increased from about 10 from 1990 to 1998 to 84 in 1999, including an outbreak in which more than 50 people were infected. To gather epidemiological data on serovar Agona and to trace the origin of the human infections, 110 serovar Agona isolates isolated from animal, feed, and other sources as well as from humans with cases of salmonellosis of domestic and foreign origin, which were recovered from 1984 to 1999, were analyzed for their pulsed-field gel electrophoresis (PFGE), plasmid, and IS
200
profiles and antibiograms. Of these typing methods, PFGE with restriction endonucleases
Xba
I,
Bln
I,
Not
I, and
Spe
I was the most useful. The PFGE profile of the strain causing an outbreak among cattle in Finland in 1994-1995 was not seen previously. The strain with this profile was later only sporadically found in human infections. The profile of the strain causing the human outbreak in 1999 was not found among isolates from cattle or any other sources. Molecular typing was valuable in showing that although the outbreaks in cattle and humans seemed to be related regionally, they were not related otherwise.
Plasma RNA Viral Load in Human Immunodeficiency Virus Type 2 Subtype A and Subtype B Infections
Authors: Damond Florence , Gueudin Marie , Pueyo Sophie , Farfara Isabelle , Robertson David L. , Descamps Diane , Chène Geneviève , Matheron Sophie , Campa Pauline , Brun-Vézinet Françoise , Simon François 
Published: September 2002

ABSTRACT

Human immunodeficiency virus type 2 (HIV-2) is much less pathogenic than HIV-1, and HIV-2 infection is associated with plasma viral loads significantly lower than those found in HIV-1 infection. We have developed a real-time quantitative PCR method for measuring the HIV-2 RNA load that covers the range of genetic diversity of HIV-2 isolates and that detects extremely low viral loads. Samples from 49 patients were studied. Proviral DNA was first detected and quantified. The strains that were detected were then genotyped: 21 patients were infected with HIV-2 subtype A and 15 patients were infected with HIV-2 subtype B; 1 patient was infected with a highly divergent strain.
Env
PCR failed for the remaining 12 patients, so subtypes could not be determined. For viral RNA quantification, a stock of HIV-2 strain NIHZ, which was counted by electron microscopy, was used as the standard. Several primer sets targeting the highly conserved
gag
region were evaluated. Various primer combinations failed to amplify subtype B strains. With the final primer pair selected, which detected both subtype A and subtype B strains, the sensitivity of the assay was 100% at a viral load of 250 copies/ml and 66% at a viral load of 125 copies/ml. We found a correlation between the CD4
+
-cell count, the clinical stage, and the plasma HIV-2 RNA level. The median plasma HIV-2 RNA value for the 33 asymptomatic patients was 2.14 log
10
, whereas it was 3.1 log
10
for the 16 patients with AIDS (
P
< 0.01). Proviral DNA was detectable in 18 symptom-free patients with high CD4
+
-cell counts, in whom viral RNA was undetectable.
Genotypes of Invasive Pneumococcal Isolates Recently Recovered from Italian Patients
Authors: Dicuonzo Giordano , Gherardi Giovanni , Gertz Robert E. , D'Ambrosio Fabio , Goglio Antonio , Lorino Giulia , Recchia Simona , Pantosti Annalisa , Beall Bernard 
Published: September 2002

ABSTRACT

We examined 73 recent invasive pneumococcal isolates within selected areas of Italy for genotypic variability. Thirty-three genomic macrorestriction types were found, three of which represented multiple serotypes. Restriction fragment patterns of
pbp2b
,
pbp2x
, and
pspA
were conserved within the majority of isolates that shared macrorestriction types. Of the nine macrorestriction types found among the 22 penicillin-nonsusceptible
Streptococus pneumoniae
(PNSP) isolates, seven comprised isolates with allelic profiles showing five to seven allelic matches to profiles in the multilocus sequence typing database (
www.mlst.net
); however, three of the seven profiles represented serotypes not previously associated with these clonal clusters. Two PNSP macrorestriction types represented new clones with unique allelic profiles. Allelic profiles obtained from isolates of 3 of the 25 macrorestriction types found among the 51 penicillin-susceptible
S. pneumoniae
(PSSP) isolates were closely related to previously described profiles. One PSSP isolate was a novel type 24F isolate related to the multiresistant clone France
9V
-3. This work reports new PNSP strains and new serotype-clone associations.
Rapid and Sensitive Routine Detection of All Members of the Genus
Enterovirus
in Different Clinical Specimens by Real-Time PCR
Authors: Nijhuis Monique , van Maarseveen Noortje , Schuurman Rob , Verkuijlen Sandra , de Vos Machiel , Hendriksen Karin , van Loon Anton M. 
Published: September 2002

ABSTRACT
We developed a rapid and sensitive method for the routine detection of all members of the enterovirus genus in different clinical specimens by using real-time TaqMan quantitative PCR. Multiple primer and probe sets were selected in the highly conserved 5′-untranslated region of the enterovirus genome. Our assay detected all 60 different enterovirus species tested, whereas no reactivity was observed with the viruses from the other genera of the picornaviridae family, e.g., hepatovirus and parechovirus. Weak cross-reactivity was observed with 7 of the 90 different high-titer rhinovirus stocks but not with rhinovirus-positive clinical isolates. Analysis of a well-characterized reference panel containing different enteroviruses at various concentrations demon-strated that the enterovirus real-time TaqMan PCR is as sensitive as most of the currently used molecular detection assays. Evaluation of clinical isolates demonstrated that the assay is more sensitive than the “gold standard” method, i.e., viral culture. Moreover, the PCR assay can be used on different clinical specimens, such as plasma, serum, nose and throat swabs, cerebrospinal fluid, and bronchoalveolar lavage, without apparent inhibition. Our data demonstrate that the real-time TaqMan PCR is a rapid and sensitive assay for the detection of enterovirus infection. The assay has a robust character and is easily standardized, which makes it an excellent alternative for the conventional time-consuming viral culture.