bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Biodiversity of
Mycobacterium tuberculosis
Complex Strains from Patients with Pulmonary Tuberculosis in Cameroon
Authors: Niobe-Eyangoh Sara Ngo , Kuaban Christopher , Sorlin Philippe , Cunin Patrick , Thonnon Jocelyn , Sola Christophe , Rastogi Nalin , Vincent Veronique , Gutierrez M. Cristina 
Published: June 2003

ABSTRACT

We analyzed DNA polymorphisms in 455
Mycobacterium tuberculosis
complex isolates from 455 patients to evaluate the biodiversity of tubercle bacilli in Ouest province, Cameroon. The phenotypic and genotypic identification methods gave concordant results for 99.5% of
M. tuberculosis
isolates (413 strains) and for 90% of
Mycobacterium africanum
isolates (41 strains).
Mycobacterium bovis
was isolated from only one patient. Analysis of regions of difference (RD4, RD9, and RD10) proved to be an accurate and rapid method of distinguishing between unusual members of the
M. tuberculosis
complex. Whereas
M. africanum
strains were the etiologic agent of tuberculosis in 56% of cases 3 decades ago, our results showed that these strains now account for just 9% of cases of tuberculosis. We identified a group of closely genetically related
M. tuberculosis
strains that are currently responsible for >40% of smear-positive pulmonary tuberculosis cases in this region of Cameroon. These strains shared a spoligotype lacking spacers 23, 24, and 25 and had highly related IS
6110
ligation-mediated (LM) PCR patterns. They were designated the “Cameroon family.” We did not find any significant association between tuberculosis-causing species or strain families and patient characteristics (sex, age, and human immunodeficiency virus status). A comparison of the spoligotypes of the Cameroon strains with an international spoligotype database (SpolDB3) containing 11,708 patterns from >90 countries, showed that the predominant spoligotype in Cameroon was limited to West African countries (Benin, Senegal, and Ivory Coast) and to the Caribbean area.
Diagnosis of Pneumococcal Pneumonia by
psaA
PCR Analysis of Lung Aspirates from Adult Patients in Kenya
Authors: Scott J. Anthony G. , Marston Eric L. , Hall Andrew J. , Marsh Kevin 
Published: June 2003

ABSTRACT

psaA
is the gene encoding pneumococcal surface adhesin A (PsaA), a 37-kDa protein expressed on the surface of
Streptococcus pneumoniae
. PCR primers for
psaA
have been shown to amplify the target DNA sequence in all 90 serotypes of
S. pneumoniae
and in none of 67 heterologous pathogens and colonizing bacteria of the upper respiratory tract. Pathogenic bacteria identified in lung aspirate specimens cannot normally be dismissed as contaminants or colonizers, which limit the assay specificity of other respiratory tract specimens.
psaA
PCR analysis was evaluated in 171 lung aspirates from Kenyan adults with acute pneumonia. The limit of detection was one genome equivalent. Sensitivity, estimated in 35 culture-positive lung aspirates, was 0.83 (95% confidence interval, 0.70 to 0.95).
psaA
PCR analysis extended the number of identifications of
S. pneumoniae
in lung aspirates from 35 on culture to 61 by both methods. Of 26 new pneumococcal diagnoses, 19 were corroborated by results of blood culture or urine antigen detection. Sequences of the PCR products from 12 positive samples were identical to the
psaA
target gene fragment. Using an internal control for the PCR, inhibition of
psaA
PCR was demonstrated in 17% (8 of 47) of false-negative specimens. The results of a control PCR for the human gene β-actin suggested that false-negative
psaA
PCR results are attributable to problems of specimen collection, processing, or DNA extraction in 30% of cases (14 of 47).
psaA
PCR analysis is a sensitive tool for diagnosis of pneumococcal pneumonia in adults.
Nocardia veterana
as a Pathogen in North American Patients
Authors: Conville Patricia S. , Brown June M. , Steigerwalt Arnold G. , Lee Judy W. , Byrer Dorothy E. , Anderson Victoria L. , Dorman Susan E. , Holland Steven M. , Cahill Barbara , Carroll Karen C. , Witebsky Frank G. 
Published: June 2003

ABSTRACT

The molecular methodologies used in our laboratories have allowed us to define a group of
Nocardia
isolates from clinical samples which resemble the type strain of
Nocardia veterana
. Three patient isolates and the type strain of
N. veterana
gave identical and distinctive restriction fragment length polymorphisms (RFLPs) for an amplified portion of the 16S rRNA gene. These three isolates and the
N. veterana
type strain also gave identical RFLPs for an amplified portion of the 65-kDa heat shock protein gene, but this pattern was identical to that obtained for the
Nocardia nova
type strain. Sequence analysis of both a 1,359-bp region of the 16S rRNA gene and a 441-bp region of the heat shock protein gene of the patient isolates showed 100% identities with the same regions of the
N. veterana
type strain. DNA-DNA hybridization of the DNA of one of the patient isolates with the DNA of the
N. veterana
type strain showed a relative binding ratio of 82%, with 0% divergence, confirming that the isolate was
N. veterana
. Biochemical and susceptibility testing showed no significant differences among the patient isolates and the
N. veterana
type strain. Significantly, the results of antimicrobial susceptibility testing obtained for our isolates were similar to those obtained for
N. nova
, indicating that susceptibility testing alone cannot discriminate between these species. We present two case studies which show that
N. veterana
is a causative agent of pulmonary disease in immunocompromised patients residing in North America. We also describe difficulties encountered in using 16S rRNA gene sequences alone for discrimination of
N. veterana
from the related species
Nocardia africana
and
N. nova
because of the very high degree of 16S rRNA gene similarity among them.
Comparative Study Using Type Strains and Clinical and Food Isolates To Examine Hemolytic Activity and Occurrence of the
cyl
Operon in Enterococci
Authors: Semedo Teresa , Almeida Santos Margarida , Martins Paula , Silva Lopes Maria Fátima , Figueiredo Marques José J. , Tenreiro Rogério , Barreto Crespo Maria Teresa 
Published: June 2003

ABSTRACT

The hemolytic ability, the presence of
cyl
genes, and the diagnostic accuracy of cytolysin molecular detection were investigated in the genus
Enterococcus
by using 164 strains from 20 different species (26 reference strains, 42 clinical isolates from human and veterinary origin, and 96 isolates from ewe cheese and milk). Hemolysis was assayed with sheep and horse erythrocytes and under aerobic or anaerobic conditions. Screening of cytolysin genes (
cylL

L

,
cylL

S

,
cylM
,
cylB
, and
cylA
) was performed with new specific primers and the anaerobic assay of beta-hemolysis was used as the “gold standard” for the evaluation of
cyl
gene-based PCRs. Since beta-hemolysis and
cyl
genes were found in 10 and 14 species, respectively, the hemolytic ability seems to be spread throughout the genus
Enterococcus
. Beta-hemolysis was observed in 6 of 26 (23%) reference strains, 14 of 42 (33%) clinical isolates, and 6 of 96 (6%) food isolates. The presence of
cyl
genes was detected in 15 of 26 (58%) reference strains, 37 of 42 (88%) clinical isolates, and 67 of 96 (70%) food isolates. These data indicate a virulence potential in food isolates, reinforcing the need of their safety assessment. Analysis of phenotypic-genotypic congruence suggests a divergent sequence evolution of
cyl
genes and the effect of environmental factors in the regulation of cytolysin expression. Evaluation of the diagnostic accuracy of cytolysin molecular detection points to
cylL

L

-based PCR and
cylL

L

L

S

MBA
-based PCR as the most reliable approaches. Nevertheless, the low sensitivity (46%) and gene variability indicated by our study strongly recommend the phenotypic assay for the assessment of hemolytic ability in enterococci, followed by the molecular screening of
cyl
genes in nonhemolytic strains to evaluate their virulence potential.
Characterization of the 8-Kilodalton Antigens of
Taenia solium
Metacestodes and Evaluation of Their Use in an Enzyme-Linked Immunosorbent Assay for Serodiagnosis
Authors: Hancock Kathy , Khan Azra , Williams Fatima B. , Yushak Melinda L. , Pattabhi Sowmya , Noh John , Tsang Victor C. W. 
Published: June 2003

ABSTRACT

The Western blot for cysticercosis, which uses lentil lectin purified glycoprotein (LLGP) antigens extracted from the metacestode of
Taenia solium
, has been the “gold standard” serodiagnostic assay since it was first described in 1989. We report that the diagnostic antigens at 14, 18, and 21 kDa, as well as some larger disulfide-bonded antigens, are actually all members of a very closely related family of proteins, the 8-kDa antigens. The genes for 18 unique, mature proteins have been identified. Nine of these were chemically synthesized and tested in an enzyme-linked immunosorbent assay with a battery of defined serum samples, including 32 cysticercosis-positive serum samples reactive with the 8-kDa antigens of LLGP on Western blotting, 34 serum samples from patients with other parasitic infections, and 15 normal human serum samples. One of the 8-kDa antigens, TsRS1, is 100% sensitive and 100% specific. TsRS1 will be one component of a cocktail of three to four synthetic or recombinant antigens, based on the diagnostic bands of the Western blot, which will be used for the serodiagnosis of cysticercosis.
Phenotypic Description and Antimicrobial Susceptibilities of
Aerococcus sanguinicola
Isolates from Human Clinical Samples
Authors: Facklam Richard , Lovgren Marguerite , Shewmaker Patricia Lynn , Tyrrell Gregory 
Published: June 2003

ABSTRACT

This report describes the clinical sources and phenotypic characterization of 16 isolates of
Aerococcus sanguinicola
. Sixteen conventional tests were used to describe and differentiate the 16 isolates of
A. sanguinicola
from 30 strains of
Aerococcus viridans
, 27 strains of
Aerococcus urinae
, and a single strain each of
Aerococcus christensenii
and
Aerococcus urinaehominis
. The phenotypic characterizations of the type strains for each species and 14
A. sanguinicola
isolates were also compared in the two reference laboratories.
A. sanguinicola
are catalase-negative, vancomycin-susceptible, gram-positive cocci arranged in clusters and tetrads, as are all
Aerococcus
species except
A. christensenii
(which is arranged in short chains). All 16 isolates of
A. sanguinicola
were leucine aminopeptidase and pyrrolidonylarylamidase positive, which is unique to this species among the aerococci. All
A. sanguinicola
isolates grew in broth containing 6.5% NaCl, hydrolyzed hippurate, and were variable in the bile-esculin test. None of the isolates deaminated arginine or were Voges-Proskauer positive. The type strain of
A. sanguinicola
was isolated from a blood culture of a patient living in Denmark. Seven additional isolates were from patients living in Canada, all with urinary tract infections (six were female). Eight isolates were from patients living in five different states in the United States; five were from patients with urinary tract infections, and three were from blood cultures of one patient each with pneumonia, suspected endocarditis, and unknown clinical conditions. The antimicrobial susceptibility patterns were unremarkable; all isolates tested were susceptible to penicillin, amoxicillin, cefotaxime, cefuroxime, erythromycin, chloramphenicol, vancomycin, quinupristin-dalfopristin (Synercid), rifampin, linezolid, and tetracycline. Six of the 15 cultures were resistant to ciprofloxacin and levofloxacin, but all 15 strains were susceptible to sparfloxacin. High-level resistance was detected for meropenem (2 strains) and trimethoprim-sulfamethonazole (1 strain). Intermediate resistance was detected for trimethoprim-sulfamethoxazole (10 strains) and clindamycin (3 strains).
Prevalence of Human T-Lymphotropic Virus Type 1 among Blood Donors from Mashhad, Iran
Authors: Abbaszadegan Mohammad Reza , Gholamin Mehran , Tabatabaee Abbas , Farid Reza , Houshmand Massoud , Abbaszadegan Morteza 
Published: June 2003

ABSTRACT
The city of Mashhad is the capital of Khorasan, the northeastern province of Iran, which has been recognized as an area where human T-lymphotropic virus type 1 (HTLV-1) infection is endemic. All serum samples from blood donors are routinely screened for HTLV-1 by using enzyme-linked immunosorbent assay (ELISA). In the present study, 28,926 donors (81.86% male and 18.14% female) with a mean age of 32 years (range, 18 to 65 years) were screened in a 6 months period (July to December 1999). Of these donors in the primary screening, 228 (0.78%) tested positive by ELISA. The positive samples were confirmed by Western blot (WB) analysis. The WB results indicated that, of 228 positive ELISA specimens, 91.2% (208 specimens) were HTLV-1, 4.82% (11 specimens) were HTLV, 3.5% (8 specimens) were indeterminate, and 0.44% (1 specimen) was not confirmed. HTLV refers to samples in which the complete viral antigen banding patterns on WB strips were not present. In order to further evaluate the detection methodologies used, the HTLV-1-seropositive samples, the indeterminant samples, and/or HTLV samples were examined and confirmed by PCR. The HTLV samples were determined to be HTLV-1, the remaining samples were indeterminant, and the negative sample could not be confirmed for HTLV-1 by PCR. The prevalence of HTLV-1 infection in our study was 0.77% among blood bank donors, which reconfirms the city of Mashhad as an area where the virus is endemic compared to other regions in the world. The incidence was correlated with increasing age, and it was higher in females than in males.
Antimicrobial Susceptibility Testing of Porcine
Brachyspira
(
Serpulina
) Species Isolates
Authors: Karlsson M. , Fellström C. , Gunnarsson A. , Landén A. , Franklin A. 
Published: June 2003

ABSTRACT

No standardized method for susceptibility testing of
Brachyspira
spp. is currently available. A broth dilution procedure was evaluated and used to test the activities of six antimicrobial agents for 108 isolates of Swedish porcine
Brachyspira
spp. representing biochemical groups I, II, and III. Group I corresponds to
Brachyspira hyodysenteriae
, group II corresponds to
B
.
intermedia
, and group III corresponds to
B
.
murdochii
and
B
.
innocens
. A panel was designed with the antimicrobial agents dried in tissue culture trays with wells that allowed a liquid volume of 0.5 ml in each and agitation of the broth when incubated on a shaker. The MICs were determined by using brain heart infusion broth with 10% fetal calf serum. For 10 isolates, the results obtained in broth were compared to the MICs obtained on two different types of agar. Different inoculum densities and incubation times were also compared. The concentrations at which 90% of the
B
.
hyodysenteriae
isolates (
n
= 72) were inhibited in the broth dilution test by tiamulin (0.25 μg/ml), tylosin (>256 μg/ml), erythromycin (>256 μg/ml), clindamycin (>4 μg/ml), virginiamycin (4 μg/ml), and carbadox (0.06 μg/ml) were determined. The MICs tended to be lower in broth than on agar. Differences in inoculum densities and incubation times had little influence on the MICs. The evaluated broth dilution test was simple to perform, the end points were easily read, and the results were reproducible and reliable. No isolates with decreased susceptibility to tiamulin were found among the Swedish isolates tested.
Detection and Identification of
Mycobacterium
Species Isolates by DNA Microarray
Authors: Fukushima Masao , Kakinuma Kenichi , Hayashi Hiroshi , Nagai Hiroko , Ito Kunihiko , Kawaguchi Ryuji 
Published: June 2003

ABSTRACT

Rapid identification of
Mycobacterium
species isolates is necessary for the effective management of tuberculosis. Recently, analysis of DNA gyrase B subunit (
gyrB
) genes has been identified as a suitable means for the identification of bacterial species. We describe a microarray assay based on
gyrB
gene sequences that can be used for the identification of
Mycobacteria
species. Primers specific for a
gyrB
gene region common to all mycobacteria were synthesized and used for PCR amplification of DNA purified from clinical samples. A set of oligonucleotide probes for specific
gyrB
gene regions was developed for the identification of 14
Mycobacterium
species. Each probe was spotted onto a silylated glass slide with an arrayer and used for hybridization with fluorescently labeled RNA derived from amplified sample DNA to yield a pattern of positive spots. This microarray produced unique hybridization patterns for each species of mycobacteria and could differentiate closely related bacterial species. Moreover, the results corresponded well with those obtained by the conventional culture method for the detection of mycobacteria. We conclude that a
gyrB-
based microarray can rapidly detect and identify closely related mycobacterial species and may be useful in the diagnosis and effective management of tuberculosis.
Loop-Mediated Isothermal Amplification for Direct Detection of
Mycobacterium tuberculosis
Complex,
M. avium
, and
M. intracellulare
in Sputum Samples
Authors: Iwamoto Tomotada , Sonobe Toshiaki , Hayashi Kozaburo 
Published: June 2003

ABSTRACT

Loop-mediated isothermal amplification (LAMP) is a novel nucleic acid amplification method in which reagents react under isothermal conditions with high specificity, efficiency, and rapidity. We used LAMP for detection of
Mycobacterium tuberculosis
complex,
Mycobacterium avium
, and
Mycobacterium intracellulare
directly from sputum specimens as well as for detection of culture isolates grown in a liquid medium (MGIT; Nippon Becton Dickinson Co., Ltd., Tokyo, Japan) or on a solid medium (Ogawa's medium). Species-specific primers were designed by targeting the
gyrB
gene, and their specificities were validated on 24 mycobacterial species and 7 nonmycobacterial species. The whole procedure is quite simple, starting with the mixing of all reagents in a single tube, followed by an isothermal reaction during which the reaction mixture is held at 63°C. The resulting amplicons are visualized by adding SYBR Green I to the reaction tube. The only equipment needed for the amplification reaction is a regular laboratory water bath or heat block that furnishes a constant temperature of 63°C. The assay had a detection limit of 5 to 50 copies of purified DNA with a 60-min incubation time. The reaction time could be shortened to 35 min for the species identification of
M. tuberculosis
complex,
M. avium
, and
M. intracellulare
from a solid-medium culture. Residual DNA lysates prepared for the Amplicor assay (Roche Diagnostics GmbH) from 66 sputum specimens were tested in the LAMP assay. Although the sample size used for the latter assay was small, 2.75 μl of the DNA lysates, it showed a performance comparable with that of the Amplicor assay, which required 50 μl of the lysates. This LAMP-based assay is simple, rapid, and sensitive; a result is available in 35 min for a solid-medium culture and in 60 min for a liquid-medium culture or for a sputum specimen that contains a corresponding amount of DNA available for testing.
Genetic Diversity among Clinical Isolates of
Acremonium strictum
Determined during an Investigation of a Fatal Mycosis
Authors: Novicki Thomas J. , LaFe Karen , Bui Lynda , Bui Uyen , Geise Robert , Marr Kieren , Cookson Brad T. 
Published: June 2003

ABSTRACT

Primarily saprophytic in nature, fungi of the genus
Acremonium
are a well-documented cause of mycetoma and other focal diseases. More recently, a number of
Acremonium
spp. have been implicated in invasive infections in the setting of severe immunosuppression. During the course of routine microbiological studies involving a case of fatal mycosis in a nonmyeloablative hematopoietic stem cell transplant patient, we identified a greater-than-expected variation among strains previously identified as
Acremonium strictum
by clinical microbiologists. Using DNA sequence analysis of the ribosomal DNA intergenic transcribed spacer (ITS) regions and the D1-D2 variable domain of the 28S ribosomal DNA gene (28S), the case isolate and four other clinical isolates phenotypically identified as
A. strictum
were found to have <99% homology to the
A. strictum
type strain, CBS 346.70, at the ITS and 28S loci, while a sixth isolate phenotypically identified only as
Acremonium
sp
.
had >99% homology to the type strain at both loci. These results suggest that five out of the six clinical isolates belong to species other than
A. strictum
or that the
A. strictum
taxon is genetically diverse. Based upon these sequence data, the clinical isolates were placed into three genogroups.
Direct Isolation of
Candida
spp. from Blood Cultures on the Chromogenic Medium CHROMagar Candida
Authors: Horvath Lynn L. , Hospenthal Duane R. , Murray Clinton K. , Dooley David P. 
Published: June 2003

ABSTRACT

CHROMagar Candida is a selective and differential chromogenic medium that has been shown to be useful for identification of
Candida albicans
,
Candida krusei
,
Candida tropicalis
, and perhaps
Candida glabrata
. Colony morphology and color have been well defined when CHROMagar Candida has been used to isolate yeast directly from clinical specimens, including stool, urine, respiratory, vaginal, oropharyngeal, and esophageal sources. Direct isolation of yeast on CHROMagar Candida from blood cultures has not been evaluated. We evaluated whether the color and colony characteristics produced by
Candida
spp. on CHROMagar Candida were altered when yeasts were isolated directly from blood cultures. Fifty clinical isolates of
Candida
were inoculated into aerobic and anaerobic blood culture bottles and incubated at 35°C in an automated blood culture system. When growth was detected, an aliquot was removed and plated onto CHROMagar Candida. As a control, CHROMagar Candida plates were inoculated with the same isolate of yeast grown on Sabouraud dextrose agar simultaneously. No significant difference was detected in color or colony morphology between the blood and control isolates in any of the tested organisms. All
C. albicans
(
n
= 12),
C. tropicalis
(
n
= 12),
C. glabrata
(
n
= 9), and
C. krusei
(
n
= 5) isolates exhibited the expected species-specific colony characteristics and color, whether isolated directly from blood or from control cultures. CHROMagar Candida can be reliably used for direct isolation of yeast from blood cultures. Direct isolation could allow mycology laboratories to more rapidly identify
Candida
spp., enable clinicians to more quickly make antifungal agent selections, and potentially decrease patient morbidity and mortality.