bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of Penicillin-Susceptible, Multidrug-Resistant Serotype 6B Pneumococci Isolated from Children in Greece
Authors: Syrogiannopoulos G. A. , Bogaert D. , Grivea I. N. , Beratis N. G. , De Groot R. , Hermans P. W. M. 
Published: July 2002

ABSTRACT
Since January 1996, and over a 3-year time span, a significant spread of serotype 6B multidrug-resistant (MDR) pneumococci, susceptible to penicillin and resistant to erythromycin, clindamycin, tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole, was noted in young carriers living in central and southern Greece. Using restriction fragment end labeling and penicillin binding protein (PBP) genotyping, we studied 41 serotype 6B penicillin-susceptible MDR pneumococci isolated during two independent studies in Greece. Forty (98%) of these 41 isolates were strongly related, representing a single lineage (genetic relatedness, ≥91%). The Greek isolates were closely related (genetic relatedness, ∼91%) to the penicillin-resistant MDR clone of serotype 6B that spread from Spain to Iceland in the late 1980s. Moreover, the Greek group of isolates was genetically distinct (genetic relatedness, ≤83%) from other penicillin-susceptible or -resistant serotype 6B strains from various parts of the world. All serotype 6B penicillin-susceptible MDR isolates displayed a penicillin-susceptible PBP 1A-2B-2X genotype. Our findings suggest that the penicillin-susceptible MDR 6B clone that was found in Greece between the years 1996 and 1999 represents the ancestor of the pandemic penicillin-resistant MDR clone 6B.
Peritonitis Due to
Thermoascus taitungiacus
(Anamorph
Paecilomyces taitungiacus
)
Authors: Korzets Asher , Weinberger Miriam , Chagnac Avry , Goldschmied-Reouven Anna , Rinaldi Michael G. , Sutton Deanna A. 
Published: July 2002

ABSTRACT

The first case of human disease due to the thermophilic ascomycete
Thermoascus taitungiacus
(the teleomorph of
Paecilomyces taitungiacus
) is presented.
T. taitungiacus
was recovered from four dialysate fluid specimens of a 57-year-old patient undergoing chronic peritoneal dialysis. Identification was based upon cylindrical conidia, reddish orange nonostiolate ascomata, lack of growth at 20°C, thermotolerance, and ascospores that appeared pale yellow, elliptical, thick walled, and predominately echinulate by light microscopy but irregularly verrucose by scanning electron microscopy.
Evaluation of a Rapid Optical Immunoassay for Influenza Viruses (FLU OIA Test) in Comparison with Cell Culture and Reverse Transcription-PCR
Authors: Boivin Guy , Hardy Isabelle , Kress Andrew 
Published: July 2002

ABSTRACT
The FLU OIA test was evaluated with 146 throat swab specimens from subjects with a flu-like illness in six Canadian clinics during the 1999–2000 flu season. The rate of positivity of the FLU OIA test (41.5%) was significantly lower than that of cell culture (55.2%) or reverse transcription-PCR (55.9%) during a season in which only influenza A virus was detected.
Serology of Typhoid Fever in an Area of Endemicity and Its Relevance to Diagnosis
Authors: House Deborah , Wain John , Ho Vo A. , Diep To S. , Chinh Nguyen T. , Bay Phan V. , Vinh Ha , Duc Minh , Parry Christopher M. , Dougan Gordon , White Nicholas J. , Hien Tran Tinh , Farrar Jeremy J. 
Published: July 2002

ABSTRACT

Currently, the laboratory diagnosis of typhoid fever is dependent upon either the isolation of
Salmonella enterica
subsp.
enterica
serotype Typhi from a clinical sample or the detection of raised titers of agglutinating serum antibodies against the lipopolysaccharide (LPS) (O) or flagellum (H) antigens of serotype Typhi (the Widal test). In this study, the serum antibody responses to the LPS and flagellum antigens of serotype Typhi were investigated with individuals from a region of Vietnam in which typhoid is endemic, and their usefulness for the diagnosis of typhoid fever was evaluated. The antibody responses to both antigens were highly variable among individuals infected with serotype Typhi, and elevated antibody titers were also detected in a high proportion of serum samples from healthy subjects from the community. In-house enzyme-linked immunosorbent assays (ELISAs) for the detection of specific classes of anti-LPS and antiflagellum antibodies were compared with other serologically based tests for the diagnosis of typhoid fever (Widal TO and TH, anti-serotype Typhi immunoglobulin M [IgM] dipstick, and IDeaL TUBEX). At a specificity of ≥0.93, the sensitivities of the different tests were 0.75, 0.55, and 0.52 for the anti-LPS IgM, IgG, and IgA ELISAs, respectively; 0.28 for the antiflagellum IgG ELISA; 0.47 and 0.32 for the Widal TO and TH tests, respectively; and 0.77 for the anti-serotype Typhi IgM dipstick assay. The specificity of the IDeaL TUBEX was below 0.90 (sensitivity, 0.87; specificity, 0.76). The serological assays based on the detection of IgM antibodies against either serotype Typhi LPS (ELISA) or whole bacteria (dipstick) had a significantly higher sensitivity than the Widal TO test when used with a single acute-phase serum sample (
P
≤ 0.007). These tests could be of use for the diagnosis of typhoid fever in patients who have clinical typhoid fever but are culture negative or in regions where bacterial culturing facilities are not available.
Epidemiological Usefulness of Anti-Opacity Factor Antibody Screening in Schoolchildren
Authors: Kim Sunjoo , Lee Nam Yong 
Published: July 2002

ABSTRACT
The presence of the anti-opacity factor (anti-OF) antibody (Ab) in the serum used for identifying the OF antigen (Ag) type represents previous or current infection with group A streptococci (GAS) of the OF Ag type. Throat cultures were taken from 172 elementary schoolchildren in Chinju, Korea, and venous blood samples were collected at the same time to screen for the frequency of the anti-OF Ab. After isolation of GAS, the OF Ag of each GAS was identified by inhibition of the opacity reaction with recognized anti-OF sera. The anti-OF Abs in the sera were screened with the six most common OF Ag types. OF22 and OF28 were high in prevalence (28.2 and 20.5%, respectively) among OF Ag types, while anti-OF types 4, 28, and 22 were frequently identified (39.5, 29.7, and 15.7%, respectively) in the sera. Thirty-two of 39 (82.1%) OF Ag-producing GAS carriers, 25 of 34 (73.5%) GAS carriers not producing OF Ag, and 72 of 99 (72.7%) throat culture-negative children harbored the anti-OF Ab. Forty-five (26.2%) of 172 children had two different anti-OF Abs, and 11 (6.4%) had more than three anti-OF Abs. Seventy-five percent of 172 elementary schoolchildren were shown to be previously or currently infected with GAS. The percentages of children positive for the anti-OF Ab were very high regardless of the result of throat culture or OF Ag production of GAS. We could also demonstrate (i) that the prevalent strains of GAS changed according to the time span by determining the difference between the frequencies of OF Ag and anti-OF Ab and (ii) that repeated infections were not uncommon in schoolchildren, as one-third had more than two different anti-OF Abs.
Development of a Genomics-Based PCR Assay for Detection of
Mycoplasma pneumoniae
in a Large Outbreak in New York State
Authors: Waring Alfred L. , Halse Tanya A. , Csiza Charles K. , Carlyn Cynthia J. , Musser Kimberlee Arruda , Limberger Ronald J. 
Published: July 2002

ABSTRACT

A genomics-based PCR method was developed and used to test specimens from patients involved in a large outbreak of
Mycoplasma pneumoniae
in a closed religious community in New York State. New P1 adhesin gene primers were designed to bind to 9 of 10 target sequences in the repetitive-element sequences obtained from the whole genome sequence of
M. pneumoniae
. This PCR method had a sensitivity of 0.006 CFU and a specificity of 100% for
M. pneumoniae
. The PCR was validated by testing a subset of patient samples by culture and comparing the results to those obtained by PCR. Of the initial 280 samples tested, 73 were positive by PCR and 22 were positive by culture. All samples positive by culture were also positive by PCR. Follow-up testing of selected patients 3 to 6 weeks after antibiotic treatment revealed that eight samples remained positive by PCR and that three samples remained positive by culture. Additionally, no nonspecific PCR inhibition was detected as a result of the specimen type, transport medium, or sample preparation methodology. The study demonstrates that the PCR described here is a rapid, sensitive, and specific method for the identification of
M. pneumoniae
and was helpful for the detection and monitoring of the outbreak.
Outbreak of Vancomycin-Resistant
Enterococcus faecium
of the Phenotype VanB in a Hospital in Warsaw, Poland: Probable Transmission of the Resistance Determinants into an Endemic Vancomycin-Susceptible Strain
Authors: Kawalec Magdalena , Gniadkowski Marek , Zaleska Maria , Ozorowski Tomasz , Konopka Lech , Hryniewicz Waleria 
Published: July 2002

ABSTRACT

The first outbreak caused by vancomycin-resistant enterococci of the VanB phenotype in Poland was analyzed. It occurred in a single ward of a Warsaw hospital which is a specialized center for the treatment of hematological disorders. Between July 1999 and February 2000, 11 patients in the ward were found to be infected and/or colonized by
Enterococcus faecium
that was resistant in vitro to vancomycin and susceptible to teicoplanin. PCR analysis confirmed that the vancomycin-resistant
E. faecium
(VREM) isolates carried the
vanB
gene, which is responsible for the VanB phenotype. Pulsed-field gel electrophoresis (PFGE) typing revealed that the isolates belonged to four distinct PFGE types and that one of these was clearly predominant, including isolates collected from seven different patients. The isolates contained one or more copies of the
vanB
gene cluster of the identical, unique
Dra
I/
Pag
I (
Bsp
HI) restriction fragment length polymorphism type, which resided in either the same or different plasmid molecules or chromosomal regions. All this data suggested that the outbreak was due to both clonal spread of a single strain and horizontal transfer of resistance genes among nonrelated strains, which could be mediated by plasmids and/or by
vanB
gene cluster-containing transposons. The comparative analysis of vancomycin-susceptible
E. faecium
(VSEM) isolates collected from infections in the same ward at the time of the VREM outbreak has led to identification of a widespread VSEM strain that was possibly related to the major VREM clone. It is very likely that this endemic VSEM strain has acquired vancomycin-resistance determinants and that the acquisition occurred more than once during the outbreak.
Replicate PCR Testing and Probit Analysis for Detection and Quantitation of
Chlamydia pneumoniae
in Clinical Specimens
Authors: Smieja M. , Mahony J. B. , Goldsmith C. H. , Chong S. , Petrich A. , Chernesky M. 
Published: July 2002

ABSTRACT

Nucleic acid amplification of clinical specimens with low target concentration has variable sensitivity. We examined whether testing multiple aliquots of extracted DNA increased the sensitivity and reproducibility of
Chlamydia pneumoniae
detection by PCR. Nested and non-nested
C. pneumoniae
PCR assays were compared using 10 replicates of 16 serial dilutions of
C. pneumoniae
ATCC VR-1310. The proportion positive versus the
C. pneumoniae
concentration was modeled by probit regression analysis. To validate the model, 10 replicates of 26 previously positive patient specimens of peripheral blood mononuclear cells (PBMC), sputum, or nasopharyngeal swabs (NPS) were tested. The proportion of replicates that were positive varied with the concentration of
C. pneumoniae
in the sample. At concentrations above 5 infection-forming units (IFU)/ml, both nested and non-nested PCR assay sensitivities were 90% or greater. The nested PCR was more sensitive (median detection, 0.35 versus 0.61 IFU/ml; relative median detection, 0.58; 95% confidence interval, 0.31 to 0.99;
P
= 0.04). In clinical specimens, replicate PCR detected 15 of 26 (nested) versus 1 of 26 (non-nested,
P
< 0.001). For PBMC specimens, testing 1, 3, or 5 replicates detected 3, 5, or 9 of 10 positive specimens, respectively. Median
C. pneumoniae
concentrations were estimated at 0.07 IFU/ml for PBMC and at <0.03 IFU/ml for NPS specimens. We conclude that performing 5 or 10 replicates considerably increased the sensitivity and reproducibility of
C. pneumoniae
PCR and enabled quantitation for clinical specimens. Due to sampling variability, PCR tests done without replication may miss a large proportion of positive specimens, particularly for specimens with small amounts of target
C. pneumoniae
DNA present.
One-Tube Real-Time Isothermal Amplification Assay To Identify and Distinguish Human Immunodeficiency Virus Type 1 Subtypes A, B, and C and Circulating Recombinant Forms AE and AG
Authors: de Baar Michel P. , Timmermans Eveline C. , Bakker Margreet , de Rooij Esther , van Gemen Bob , Goudsmit Jaap 
Published: July 2002

ABSTRACT

To halt the human immunodeficiency virus type 1 (HIV-1) epidemic requires interventions that can prevent transmission of numerous HIV-1 subtypes. The most frequently transmitted viruses belong to the subtypes A, B, and C and the circulating recombinant forms (CRFs) AE and AG. A fast one-tube assay that identifies and distinguishes among subtypes A, B, and C and CRFs AE and AG of HIV-1 was developed. The assay amplifies a part of the
gag
gene sequence of the genome of all currently known HIV-1 subtypes and can identify and distinguish among the targeted subtypes as the reaction proceeds, because of the addition of subtype-specific molecular beacons with multiple fluorophores. The combination of isothermal nucleic acid sequence-based amplification and molecular beacons is a new approach in the design of real-time assays. To obtain a sufficiently specific assay, we developed a new strategy in the design of molecular beacons, purposely introducing mismatches in the molecular beacons. The subtype A and CRF AG isolates reacted with the same molecular beacon. We tested the specificity and sensitivity of the assay on a panel of the culture supernatant of 34 viruses encompassing all HIV-1 subtypes: subtypes A through G, CRF AE and AG, a group O isolate, and a group N isolate. Assay sensitivity on this panel was 92%, with 89% correct subtype identification relative to sequence analysis. A linear relationship was found between the amount of input RNA in the reaction mixture and the time that the reaction became positive. The lower detection level of the assay was approximately 10
3
copies of HIV-1 RNA per reaction. In 38% of 50 serum samples from HIV-1-infected individuals with a detectable amount of virus, we could identify subtype sequences with a specificity of 94% by using sequencing and phylogenetic analysis as the “gold standard.” In conclusion, we showed the feasibility of the approach of using multiple molecular beacons labeled with different fluorophores in combination with isothermal amplification to identify and distinguish subtypes A, B, and C and CRFs AE and AG of HIV-1. Because of the low sensitivity, the assay in this format would not be suited for clinical use but can possibly be used for epidemiological monitoring as well as vaccine research studies.
Use of Recommended Laboratory Testing Methods among Patients with Tuberculosis in California
Authors: Kellam Steffi , Pascopella Lisa , Desmond Edward , Reingold Arthur , Chin Daniel P. 
Published: July 2002

ABSTRACT
This study assessed the extent to which laboratory methods recommended by the Centers for Disease Control and Prevention were used in tuberculosis testing of patients in California in 1998. While recommended methods were used for most patients, there was room for improvement by hospital and independent non-health maintenance organization laboratories.
Use of the Gen-Probe Amplified Mycobacterium Tuberculosis Direct Test for Early Detection of
Mycobacterium tuberculosis
in BACTEC 12B Medium
Authors: Desmond E. P. , Loretz K. 
Published: July 2002

ABSTRACT

To achieve better sensitivity than direct testing and better turnaround time than current culture and identification methods, the Gen-Probe Mycobacterium Tuberculosis Direct method was used to detect
Mycobacterium tuberculosis
in BACTEC 12B medium cultures when they first gave a growth index (GI) of at least 10 (MTD/BACTEC method). Of 179 acid-fast, smear-positive specimens that were culture positive for
M. tuberculosis
, all were positive by the MTD/BACTEC method (sensitivity, 100%). Positive results were obtained only with tuberculosis patients. For diagnostic specimens from untreated patients, the mean time to achieve a GI of 10 was 6 days.
Capnocytophaga cynodegmi
Cellulitis, Bacteremia, and Pneumonitis in a Diabetic Man
Authors: Sarma Podila S. , Mohanty Smruti 
Published: July 2002

ABSTRACT

Capnocytophaga cynodegmi
(formerly “DF-2 like organism”), a commensal organism of the canine oral cavity, is a capnophilic, gram-negative, facultative bacillus.
C. cynodegmi
has rarely been encountered in human diseases. We report the first known case of cellulitis, bacteremia, and pneumonitis caused by
C. cynodegmi
in a diabetic man from central India following a dog bite.
Differentiation of Mycobacterial Species by PCR-Restriction Analysis of DNA (342 Base Pairs) of the RNA Polymerase Gene (
rpoB
)
Authors: Kim Bum-Joon , Lee Keun-Hwa , Park Bo-Na , Kim Seo-Jeong , Bai Gill-Han , Kim Sang-Jae , Kook Yoon-Hoh 
Published: July 2002

ABSTRACT

PCR amplification-restriction analysis (PRA) of
rpoB
DNA (342 bp), which comprises the Rif
r
region, was used for the differential identification of 49 mycobacteria. The DNA had been used previously for the identification of mycobacterial species by comparative sequence analysis (B. J. Kim et al., J. Clin. Microbiol. 37:1714–1720, 1999). Digestion with four restriction enzymes (
Hae
III,
Hin
dII,
Mva
I, and
Acc
II), which were selected on the basis of
rpoB
DNA sequences, generated distinctive PRA patterns that allowed not only the reference strains but also the clinical isolates of mycobacteria to be distinguished. Both rapidly and slowly growing mycobacteria were distinctly differentiated by
Hae
III digestion of the amplified
rpoB
DNA. By
Hin
dII digestion the
Mycobacterium tuberculosis
complex was distinguished from the other mycobacteria. Furthermore, six subspecies of
Mycobacterium kansasii
(subspecies I to VI) as well as the closely related
Mycobacterium gastri
, and other closely related species, were distinguished by simultaneous digestion of
Mva
I and
Acc
II. According to the
rpoB
PRA scheme, 240 strains of clinical isolates could be identified. It was also possible to detect and identify
M. tuberculosis
directly from sputa and bronchoalveolar lavage specimens. These results suggest that PRA of
rpoB
DNA is a simple and feasible method not only for the differentiation of culture isolates but also for the rapid detection and identification of pathogenic mycobacteria in primary clinical specimens.
Prevalence of Iron Transport Gene on Pathogenicity-Associated Island of Uropathogenic
Escherichia coli
in
E. coli
O157:H7 Containing Shiga Toxin Gene
Authors: Ye Changyun , Xu Jianguo 
Published: July 2002

ABSTRACT

Uropathogenc
Escherichia coli
(UPEC) CFT073 has a pathogenicity-associated island (PAI
CFT073
), which causes pyelonephritis and cystitis. Using PCR method, we found the
prrA
gene of PAI
CFT073
in
E. coli
O157:H7 EDL933. Further detailed PCR screening of 38 open reading frames, the right and left junction sequences of PAI
CFT073
, revealed that it is the
prrA-modD-yc73-fepC
gene cluster but not the PAI
CFT073
present in
E. coli
O157:H7 EDL933. A rapid preliminary analysis suggested that the
prrA-modD-yc73-fepC
gene cluster of the PAI
CFT073
, is present in 43 strains of
E. coli
O157:H7 containing Shiga toxin (Stx) gene but absent in 19 strains of
E. coli
O157:H7 without Stx gene. A strict co-occurrence of the
prrA-modD-yc73-fepC
gene cluster and Stx genes was observed, regardless of their origin. The
prrA-modD-yc73-fepC
gene cluster encode proteins probably involved in iron uptake system, which strongly suggests the importance of iron metabolism in the Stx-mediated virulence. In addition, the
prrA-modD-yc73-fepC
gene cluster may be used as a diagnostic marker to distinguish
E. coli
O157:H7 strains containing Stx gene from that without Stx gene, and possibly to quickly detect other pathogenic gram-negative bacteria containing the Stx gene.
Comparison of a Polymer Conjugate-Enhanced Enzyme Immunoassay to Ligase Chain Reaction for Diagnosis of
Chlamydia trachomatis
in Endocervical Swabs
Authors: Chernesky Max , Jang Dan , Copes Debby , Patel Jay , Petrich Astrid , Biers Kathleen , Sproston Arlene , Kapala Julius 
Published: July 2002

ABSTRACT

Two endocervical swabs from each of 1,123 women were collected into manufacturer-supplied transport tubes and tested for
Chlamydia trachomatis
by a polymer conjugate-enhanced (PCE) enzyme immunoassay (EIA) (IDEIA PCE Chlamydia; DAKO) and a ligase chain reaction assay (LCx Chlamydia; Abbott). After confirmation by the EIA blocking test, the sensitivity of the IDEIA PCE remained at 91.8% and the specificity increased from 98.2 to 99.8% compared to LCx.
Liver Abscess Caused by
Klebsiella pneumoniae
in Siblings
Authors: Chiu Cheng-Hsun , Su Lin-Hui , Wu Tsu-Lan , Hung Iou-Jih 
Published: July 2002

ABSTRACT

Klebsiella pneumoniae
has been emerging as the leading cause of liver abscess in diabetic patients. Results of molecular typing of
K. pneumoniae
isolates from two siblings with liver abscess, their family members, and the environment suggest a possibility of cross infection of liver abscess by the fecal-oral route within diabetic patients.
rpoB
Sequence Analysis of Cultured
Tropheryma whippelii
Authors: Drancourt Michel , Carlioz Antoine , Raoult Didier 
Published: July 2002

ABSTRACT

Until recently no isolate of
Tropheryma whippelii
was available, and therefore genetic studies were limited to those based on PCR amplification of conserved genes. In this study we determined the nucleotide sequence of
rpoB
(encoding the β-subunit of RNA polymerase) from a cultured strain of
T. whippelii
using degenerate consensus PCR and genome walking. The
T. whippelii rpoB
consists of 3,657 bp with a 50.4% GC content and encodes 1,218 amino acids with a calculated molecular mass of 138 kDa. Comparison of
T. whippelii
RpoB with other eubacterial RpoB proteins indicated sequence similarity ranging from 57.19 (
Mycoplasma pneumoniae
) to 74.63% (
Mycobacterium tuberculosis
). Phylogenetic analysis of
T. whippelii
based on comparison of its RpoB sequence with sequences available for other bacteria was consistent with that previously derived from the 16S ribosomal DNA (rDNA) sequence, indicating that it belongs to the actinomyces clade. The sequence comparison allowed the design of a primer pair, TwrpoB.F and TwrpoB.R, specific for
T. whippelii rpoB.
When incorporated into a PCR, this primer pair allowed the detection of
T. whippelii rpoB
in three of three 16S rDNA PCR-positive biopsy specimens and zero of seven negative controls.
rpoB
could therefore be targeted in PCR-mediated detection and identification of this emerging bacterial species. This approach has previously been shown useful for the identification of related mycobacteria. This study underscores that a method involving isolation and then propagation of emerging bacteria is a useful way to quickly achieve extensive molecular knowledge of these pathogens.