bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Evaluation of the Sensititre YeastOne Colorimetric Antifungal Plate for Antifungal Susceptibility Testing of the New Triazoles Voriconazole, Posaconazole, and Ravuconazole
Authors: Pfaller M. A. , Espinel-Ingroff A. , Jones R. N. 
Published: October 2004

ABSTRACT

A commercially prepared dried colorimetric microdilution panel (Sensititre YeastOne, TREK Diagnostic Systems, Cleveland, Ohio) was compared in three different laboratories with the National Committee for Clinical Laboratory Standards (NCCLS) reference microdilution method by testing two quality control strains and 300 clinical isolates of
Candida
spp. against fluconazole, voriconazole, posaconazole, and ravuconazole. Reference MIC endpoints were established after 48 h of incubation and YeastOne colorimetric endpoints were established after 24 h of incubation. YeastOne endpoints were determined to be the lowest concentration at which the color in the well changed from red (indicating growth) to purple (indicating growth inhibition) or blue (indicating no growth). Excellent agreement (within two dilutions) between the reference and colorimetric MICs was observed. Overall agreement was 95.4%. Agreement ranged from 92.3% with posaconazole to 98.0% with fluconazole. The YeastOne colorimetric method appears to be comparable to the NCCLS reference method for testing the susceptibility of
Candida
spp to the new triazoles voriconazole, posaconazole, and ravuconazole.
Performance Assessment of a Nested-PCR Assay (the RAPID BAP-MTB) and the BD ProbeTec ET System for Detection of
Mycobacterium tuberculosis
in Clinical Specimens
Authors: Wang Jann-Yuan , Lee Li-Na , Chou Chin-Sheng , Huang Chung-Yi , Wang Shu-Kuan , Lai Hsin-Chih , Hsueh Po-Ren , Luh Kwen-Tay 
Published: October 2004

ABSTRACT

The performance of a nested PCR-based assay (the RAPID BAP-MTB; AsiaGen, Taichung, Taiwan) and the BD ProbeTec ET (DTB) system (Becton Dickinson, Sparks, Md.) for detection of
Mycobacterium tuberculosis
was evaluated with 600 consecutive clinical samples. These samples, including 552 respiratory specimens and 48 nonrespiratory specimens, were collected from 333 patients treated at National Taiwan University Hospital from September to October 2003. The results of both assays were compared to the gold standard of combined culture results and clinical diagnosis. The overall sensitivity and specificity of the RAPID BAP-MTB assay for respiratory specimens were 66.7% and 97.2%, respectively, and for the DTB assay they were 56.7% and 95.3%, respectively. The positive and negative predictive values for the RAPID BAP-MTB were 74.1% and 96.0%, respectively, and for the DTB assay they were 59.6% and 94.7%, respectively. For smear-negative samples, the sensitivity of the RAPID BAP-MTB and DTB assays was 57.1% and 40.5%, respectively. The RAPID BAP-MTB assay produced 14 false-positive results in 14 samples, including one of the six samples yielding
Mycobacterium abscessus
, one of the six samples yielding
Mycobacterium avium intracellulare
, one sample from a patient with a history of pulmonary tuberculosis with complete treatment, and three samples from three patients with a previous diagnosis of tuberculosis who were under treatment at the time of specimen collection. Among the 48 nonrespiratory specimens, the RAPID BAP-MTB assay was positive in one biopsy sample from a patient with lumbar tuberculous spondylitis and one pus sample from a patient with tuberculous cervical lymphadenopathy. Our results showed that the RAPID BAP-MTB assay is better than the DTB assay for both respiratory specimens and nonrespiratory specimens. The overall time for processing this assay is only 5 h. In addition, its diagnostic accuracy in smear-negative samples is as high as in smear-positive samples.
Relative Importance of Nasopharyngeal versus Oropharyngeal Sampling for Isolation of
Streptococcus pneumoniae
and
Haemophilus influenzae
from Healthy and Sick Individuals Varies with Age
Authors: Greenberg David , Broides Arnon , Blancovich Irena , Peled Nechama , Givon-Lavi Noga , Dagan Ron 
Published: October 2004

ABSTRACT

Streptococcus pneumoniae
and
Haemophilus influenzae
carriage is a useful index for measuring the emergence of resistance and outcome in vaccination trials. We performed a study to determine which sampling site, nasopharynx (NP) or oropharynx (OP), yields the highest rate of
S. pneumoniae
and
H. influenzae
isolation at different ages. Both NP and OP cultures were obtained from 216 children aged <60 months and their mothers. The total
S. pneumoniae
carriage rate was 68% among children and 15% among mothers (
P
< 0.001). Using NP alone for the isolation of
S. pneumoniae
would have missed 2, 2, and 42% and using OP alone would have missed 77, 66, and 45% of
S. pneumoniae
in children aged 0 to 23 months, 24 to 59 months, and mothers, respectively. Using NP cultures alone for
H. influenzae
would have missed 23, 24, and 81% of the isolates, respectively. The respective figures for
H. influenzae
isolation from OP alone are 38, 29, and 9%. In children,
S. pneumoniae
was carried mainly in the NP while
H. influenzae
was equally carried in the NP and OP. In mothers,
S. pneumoniae
was carried equally in the NP and OP while
H. influenzae
was carried significantly more often in the OP. In children,
H. influenzae
colonization increased during illness, mainly in the NP. Culturing only one site significantly reduced the recovery of
H. influenzae
at all ages. NP cultures for
S. pneumoniae
detected close to 100% of isolates in children but only 58% of isolates in mothers.
Evidence of an Antigenic Shift among Palyam Serogroup Orbiviruses
Authors: Ohashi Seiichi , Matsumori Youichi , Yanase Tohru , Yamakawa Makoto , Kato Tomoko , Tsuda Tomoyuki 
Published: October 2004

ABSTRACT
The Japanese isolates of Palyam serogroup viruses isolated from 1985 to 2001 were investigated for the genome sequence of segments 2 and 7 and were phylogenetically analyzed in comparison with Australian and African isolates of the same serogroup. The nucleotide sequences of segment 7 were highly conserved within Japanese isolates (95.1 to 100%) and between Japanese and Taiwanese isolates (96.0 to 100%), whereas the identities between Japanese and Taiwanese isolates and Australian and African isolates were fairly conserved (84.2 to 92.0%). Phylogenetic analysis based on segment 7 revealed three clusters according to geographical origin. As a result of the nucleotide sequence analysis of segment 2, which encodes a serotype-specific antigen, Japanese isolates were classified into two groups by genome length and nucleotide identities. Four of the nine Japanese isolates were categorized into the same group as prototype strain K-47 of the Chuzan virus, and the remaining isolates were categorized into the same group as the D'Aguilar virus and Nyabira virus. Phylogenetic analysis based on segment 2 revealed two clusters, the cluster containing Chuzan virus and the cluster containing the D'Aguilar and Nyabira viruses. To examine the antigenic relationship among viruses categorized in different clusters, we conducted a cross-neutralization test. KSB-29/E/01, isolated in 2001 in Japan, was neutralized by antiserum not only to strain B8112 of D'Aguilar virus but also to Chuzan virus. These results indicated that genetically and antigenically unique characteristics of KSB-29/E/01 were attributed to genetic reassortment of segment 2 between Chuzan virus and D'Aguilar virus.
Evaluation of the Immunoglobulin G Avidity Test for Diagnosis of Toxoplasmic Lymphadenopathy
Authors: Montoya Jose G. , Huffman Heather B. , Remington J. S. 
Published: October 2004

ABSTRACT
Toxoplasmic lymphadenopathy (TL) is the most common clinical manifestation of acute acquired toxoplasma infection in normal individuals. The diagnosis is established by serologic methods and lymph node biopsy. Recently, tests for avidity of toxoplasma immunoglobulin G (IgG) antibodies have been introduced to help discriminate between recently acquired and distant infection with the parasite. We studied an avidity test to define the usefulness of this method and to determine the evolution of the IgG avidity in TL. Seventy-three consecutive patients diagnosed as having TL were studied. IgG avidity test titers were noted to be time dependent from the clinical onset of lymphadenopathy. Low IgG avidity test results were observed in patients who had developed lymphadenopathy from <1 month to 17 months prior to the sampling of sera, emphasizing that low IgG avidity test results are not reliable for diagnosis of recently acquired infection. In contrast, high IgG avidity test results were observed only in patients who had developed lymphadenopathy at least 4 months earlier. Thus, a high IgG avidity test result in an individual who has recent onset of lymphadenopathy (e.g., within 2 to 3 months of sera sampling) suggests a cause other than toxoplasmosis. In such cases, further workup is warranted in order to determine the cause of the lymphadenopathy.
High Prevalence of Genital Mycoplasmas among Sexually Active Young Adults with Urethritis or Cervicitis Symptoms in La Crosse, Wisconsin
Authors: Schlicht Michael J. , Lovrich Steven D. , Sartin Jeffrey S. , Karpinsky Patricia , Callister Steven M. , Agger William A. 
Published: October 2004

ABSTRACT

Sexually active young adults in the small college town of La Crosse, Wisconsin, were evaluated for conventional sexually transmitted pathogens and tested for infections with mycoplasmas. The prevalence in 65 symptomatic men or women and 137 healthy volunteers (67 men and 70 women) was compared. Urine specimens from both cohorts were tested by ligase chain reaction for
Chlamydia trachomatis
or
Neisseria gonorrhoeae
. In addition, the urethral or cervical swabs from the symptomatic subjects were tested by PCR for
Mycoplasma genitalium
and cultured for
Mycoplasma hominis
and the ureaplasmas. The results confirmed a relatively low prevalence of gonorrhea among symptomatic men (12%) and chlamydia among symptomatic men (15%) and normal women (3%). In contrast, infections with mycoplasmas, especially the ureaplasmas (57%), were common and the organisms were the only potential sexually transmitted pathogen detected in 40 (62%) symptomatic subjects. Because of the high prevalence, we also evaluated urethral swabs from an additional 25 normal female volunteers and recovered ureaplasmas from 4 (16%) subjects. Additionally, the participants rarely used protection during sexual intercourse and some symptomatic subjects apparently acquired their infections despite using condoms regularly. The findings demonstrate a strong association between abnormal urogenital findings and detection of myoplasmas, particularly ureaplasmas, and suggest the infections will remain common.
Tracking Methicillin-Resistant
Staphylococcus aureus
Clones during a 5-Year Period (1998 to 2002) in a Spanish Hospital
Authors: Pérez-Roth Eduardo , Lorenzo-Díaz Fabián , Batista Ninivé , Moreno Antonio , Méndez-Álvarez Sebastián 
Published: October 2004

ABSTRACT

Three hundred seventy-five consecutive methicillin-resistant
Staphylococcus aureus
(MRSA) clinical isolates recovered between 1998 and 2002 at the Nuestra Señora de Candelaria University Hospital in Tenerife, Spain, were analyzed by molecular fingerprinting techniques to determine MRSA clonal types and their prevalence over time. After determining antibiotic susceptibility, we used SmaI-digested genomic DNA separated by pulsed-field gel electrophoresis (PFGE) to characterize MRSA isolates and to establish PFGE types. Additionally, several selected isolates representative of each major PFGE type were tested by multilocus sequence typing (MLST) and by a multiplex PCR method capable of identifying the structural type of the staphylococcal cassette chromosome
mec
(SCC
mec
), generating the corresponding sequence type (ST)-SCC
mec
types. Results of PFGE, supported by those of MLST and SCC
mec
typing, allowed us to identify six MRSA clones within the five major PFGE types and document temporal shifts in the prevalence of these MRSA clones from 1998 to 2002. Four of the clones were the pandemic “Iberian” (designated ST247-MRSA-IA), EMRSA-15 (ST22-MRSA-IV), EMRSA-16 (ST36-MRSA-II), and the so-called pediatric (ST5-MRSA-IV) clones, while the other two (ST125-MRSA-IVA and ST146-MRSA-IVA) clones could be derived from the pediatric one. The most striking temporal shift in the dominance of MRSA clones was the replacement of the multidrug-resistant and highly epidemic Iberian clone by the so-called British EMRSA-16 clone during the 5-year surveillance period. Our results are in accordance with previously stated findings showing the worldwide hospital dominance of relatively few pandemic and presumably virulent MRSA clones. We report for the first time the detection in Spain of the British EMRSA-15 and pediatric clones, as well as the abrupt replacement of the Iberian by the EMRSA-16 as the major MRSA clone.
Evolutionary Genetic Analysis of the Emergence of Epidemic
Vibrio cholerae
Isolates on the Basis of Comparative Nucleotide Sequence Analysis and Multilocus Virulence Gene Profiles
Authors: O'Shea Yvonne A. , Reen F. Jerry , Quirke Anne Marie , Boyd E. Fidelma 
Published: October 2004

ABSTRACT

Vibrio cholerae
, the causative agent of cholera, is a natural inhabitant of the aquatic ecosystem. We examined a unique collection of
V. cholerae
clinical and environmental isolates of widespread geographic distribution recovered over a 60-year period to determine their evolutionary genetic relationships based on analysis of two housekeeping genes, malate dehydrogenase (
mdh
) and a chaperonin (
groEL
). In addition, the phylogenetic distribution of 12 regions associated with virulence was determined. Comparative sequence analysis of
mdh
revealed that all
V. cholerae
O1 and O139 serogroup isolates belonged to the same clonal lineage. Single-strand conformational polymorphism (SSCP) analysis of these O1 and O139 strains at
groEL
confirmed the presence of an epidemic clonal complex. Of the 12 virulence regions examined, only three regions,
Vibrio
seventh pandemic island 1 (VSP-I), VSP-II, and RS1, were absent from all classical
V. cholerae
isolates. Most
V. cholerae
El Tor biotype and O139 serogroup isolates examined encoded all 12 virulence regions assayed. Outside of
V. cholerae
O1/O139 serogroup isolates, only one strain, VO7, contained VSP-I. Two
V. cholerae
El Tor isolates, GP155 and 2164-78, lacked both VSP-I and VSP-II, and one El Tor isolate, GP43, lacked VSP-II. Five non-O1/non-O139 serogroup isolates had an
mdh
sequence identical to that of the epidemic O1 and O139 strains. These isolates, similar to classical strains, lack both VSP-I and VSP-II. Four of the 12 virulence regions examined were found to be present in all isolates:
hlyA
,
pilE
, MSHA and RTX. Among non-O1/non-O139 isolates, however, the occurrence of the additional eight regions was considerably lower. The evolutionary relationships and multilocus virulence gene profiles of
V. cholerae
natural isolates indicate that consecutive pandemic strains arose from a common O1 serogroup progenitor through the successive acquisition of new virulence regions.
Phylogeny, Clinical Associations, and Diagnostic Utility of the Pilin Subunit Gene (
sfpA
) of Sorbitol-Fermenting, Enterohemorrhagic
Escherichia coli
O157:H
−
Authors: Friedrich Alexander W. , Nierhoff Katja V. , Bielaszewska Martina , Mellmann Alexander , Karch Helge 
Published: October 2004

ABSTRACT

The plasmid-borne
sfpA
gene encodes the pilin subunit in sorbitol-fermenting (SF) enterohemorrhagic
Escherichia coli
(EHEC) O157:H
−
. We investigated the distribution of
sfpA
among 600
E. coli
isolates comprising the complete
E. coli
standard reference (ECOR) and diarrheagenic
E. coli
(DEC) strain collections and clinical isolates associated with enteric disease.
sfpA
was detected in DEC3F SF EHEC O157:H
−
strain 493/89, each of 107 SF EHEC O157:H
−
clinical isolates, and 14 Shiga toxin-negative SF
E. coli
O157:H
−
strains which contained
eae
, which encodes γ-intimin, and
fliC
, which encodes the H7 antigen.
sfpA
was absent from all other strains, including the ECOR strain collection, all non-SF EHEC O157:H7 strains, and all
E. coli
O55:H7 strains (
E. coli
O55:H7 is the postulated ancestor of Shiga toxin-producing
E. coli
[STEC] O157). These results suggest that there was a single acquisition of the
sfpA
gene in the nonmotile SF
E. coli
O157 branch, presumably after the
eae
-encoding pathogenicity island (the locus of enterocyte effacement) was acquired and motility was lost. We then applied the
sfpA
PCR in combination with
rfb
O157
,
stx
, and
eae
PCRs to screen 636 stool samples from patients with diarrhea or hemolytic-uremic syndrome for SF STEC O157:H
−
. In 27 cases, the simultaneous presence of the
sfpA
,
eae
, and
rfb
O157
amplicons indicated the presence of SF
E. coli
O157:H
−
strains, and the result was subsequently confirmed by isolation. All but two of these strains possessed
stx
2
. None of the other stool samples was positive by the
sfpA
PCR; 59 of these stool samples contained EHEC O157:H7. The
sfpA
gene can be recommended as a target for screening for SF
E. coli
O157:H
−
.
Differential Expression of Secretory Aspartyl Proteinase Genes (
SAP1
-
10
) in Oral
Candida albicans
Isolates with Distinct Karyotypes
Authors: Tavanti Arianna , Pardini Giacomo , Campa Daniele , Davini Paola , Lupetti Antonella , Senesi Sonia 
Published: October 2004

ABSTRACT

Two karyotypes of oral
Candida albicans
isolates, named b and c, constituted >80% of a collection from healthy carriers (22 b and 16 c isolates) and oral candidiasis patients who were either infected (31 b and 16 c isolates) or uninfected (13 b and 38 c isolates) with human immunodeficiency virus (HIV). The prevalence of the b and c karyotypes within HIV-positive and HIV-negative patients, respectively, who were suffering from oral candidiasis (
P
≤ 0.0001) suggested that these two types possessed different virulence potentials. Since
C. albicans
proteinases (Saps) are virulence factors in oral candidiasis, we evaluated whether the b and c karyotypes secreted different levels of Saps and expressed different patterns of Sap-encoding genes (
SAP1
-
10
). We found that the mean value of Sap activity was significantly lower (
P
= 0.003) in the commensal type than in the infectious b karyotype, whereas Sap activity in the commensal c type was as high as that registered for the infectious c strains. Marked differences in
SAP
mRNA expression were observed in commensal strains under non-Sap-inducing conditions, with all
SAP
genes being expressed only by strains with the c karyotype; interestingly, none of the commensal b strains expressed
SAP2
. In addition, while all of the
SAP1
-
10
genes were detectable under Sap-inducing conditions, the timing of their expression during growth differed significantly, with mRNAs of
SAP1
-
10
genes detected at 8 and 24 h postinoculation in c and b commensal strains, respectively. This provides the first evidence that commensal oral
C. albicans
isolates with distinct karyotypes are characterized by different patterns of
SAP1
-
10
gene expression and different levels of Sap secretion.
Genetic Diversity among Community Methicillin-Resistant
Staphylococcus aureus
Strains Causing Outpatient Infections in Australia
Authors: Coombs Geoffrey W. , Nimmo Graeme R. , Bell Jan M. , Huygens Flavia , O'Brien Frances G. , Malkowski Mary J. , Pearson Julie C. , Stephens Alex J. , Giffard Philip M. 
Published: October 2004

ABSTRACT

Increasing reports of the appearance of novel nonmultiresistant methicillin-resistant
Staphylococcus aureus
MRSA (MRSA) strains in the community and of the spread of hospital MRSA strains into the community are cause for public health concern. We conducted two national surveys of unique isolates of
S. aureus
from clinical specimens collected from nonhospitalized patients commencing in 2000 and 2002, respectively. A total of 11.7% of 2,498 isolates from 2000 and 15.4% of 2,486 isolates from 2002 were MRSA. Approximately 54% of the MRSA isolates were nonmultiresistant (resistant to less than three of nine antibiotics) in both surveys. The majority of multiresistant MRSA isolates in both surveys belonged to two strains (strains AUS-2 and AUS-3), as determined by pulsed-field gel electrophoresis (PFGE) and resistogram typing. The 3 AUS-2 isolates and 10 of the 11 AUS-3 isolates selected for multilocus sequence typing (MLST) and staphylococcal chromosomal cassette
mec
(SCC
mec
) analysis were ST239-MRSA-III (where ST is the sequence type) and thus belonged to the same clone as the eastern Australian MRSA strain of the 1980s, which spread internationally. Four predominant clones of novel nonmultiresistant MRSA were identified by PFGE, MLST, and SCC
mec
analysis: ST22-MRSA-IV (strain EMRSA-15), ST1-MRSA-IV (strain WA-1), ST30-MRSA-IV (strain SWP), and ST93-MRSA-IV (strain Queensland). The last three clones are associated with community acquisition. A total of 14 STs were identified in the surveys, including six unique clones of novel nonmultiresistant MRSA, namely, STs 73, 93, 129, 75, and 80slv and a new ST. SCC
mec
types IV and V were present in diverse genetic backgrounds. These findings provide support for the acquisition of SCC
mec
by multiple lineages of
S. aureus
. They also confirm that both hospital and community strains of MRSA are now common in nonhospitalized patients throughout Australia.
Two Novel Real-Time Reverse Transcriptase PCR Assays for Rapid Detection of Bacterial Contamination in Platelet Concentrates
Authors: Dreier Jens , Störmer Melanie , Kleesiek Knut 
Published: October 2004

ABSTRACT

The incidence of platelet bacterial contamination is approximately 1 per 2,000 units and has been acknowledged as the most frequent infectious risk from transfusion. In preliminary studies, the sterility of platelet concentrates (PCs) was tested with an automated bacterial blood culturing system and molecular genetic assays. Two real-time reverse transcriptase PCR (RT-PCR) assays performed in a LightCycler instrument were developed and compared regarding specificity and sensitivity by the use of different templates to detect the majority of the clinically important bacterial species in platelets. Primers and probes specific for the conserved regions of the eubacterial 23S rRNA gene or the
groEL
gene (encoding the 60-kDa heat shock protein Hsp60) were designed. During the development of the 23S rRNA RT-PCR, problems caused by the contamination of reagents with bacterial DNA were noted. Treatment with 8-methoxypsoralen and UV irradiation reduced the level of contaminating DNA. The sensitivity of the assays was greatly influenced by the enzyme system which was used. With r
Tth
DNA polymerase in a one-enzyme system, we detected 500 CFU of
Escherichia coli
or
Staphylococcus epidermidis
/ml. With a two-enzyme system consisting of Moloney murine leukemia virus RT and
Taq
DNA polymerase, we detected 16 CFU/ml. With
groEL
mRNA as the target of RT-PCR under optimized conditions, we detected 125 CFU of
E. coli
/ml, and no problems with false-positive results caused by reagent contamination or a cross-reaction with human nucleic acids were found. Furthermore, the use of mRNA as an indicator of viability was demonstrated. Here we report the application of novel real-time RT-PCR assays for the detection of bacterial contamination of PCs that are appropriate for transfusion services.