bluuebunny/crossref_metadata_2025_split huggingface dataset:
Amplified Fragment Length Polymorphism Reveals Genomic Variability among
Mycobacterium avium
subsp.
paratuberculosis
Isolates
Authors: O'Shea B. , Khare S. , Bliss K. , Klein P. , Ficht T. A. , Adams L. G. , Rice-Ficht A. C. 
Published: August 2004

ABSTRACT

Ninety-six primer sets were used for amplified fragment length polymorphism (AFLP) to characterize the genomes of 20
Mycobacterium avium
subsp.
paratuberculosis
field isolates, 1 American Type Culture Collection (ATCC)
M. avium
subsp.
paratuberculosis
isolate (ATCC 19698), and 2
M. avium
subsp.
avium
isolates (ATCC 35716 and Mac 104). AFLP analysis revealed a high degree of genomic polymorphism among
M. avium
subsp.
paratuberculosis
isolates that may be used to establish diagnostic patterns useful for the epidemiological tracking of
M. avium
subsp.
paratuberculosis
isolates. Four
M. avium
subsp.
paratuberculosis
-polymorphic regions revealed by AFLP were cloned and sequenced. Primers were generated internal to these regions for use in PCR analysis and applied to the
M. avium
subsp.
paratuberculosis
field isolates. An appropriate PCR product was obtained in 79 of 80 reactions, while the
M. avium
subsp.
avium
isolates failed to act as templates for PCR amplification in seven of eight reactions. This work revealed the presence of extensive polymorphisms in the genomes of
M. avium
subsp.
paratuberculosis
and
M. avium
subsp.
avium
, many of which are based on deletions. Of the
M. avium
subsp.
paratuberculosis
-specific sequences studied, one revealed a 5,145-bp region with no homologue in the
M. avium
subsp.
avium
genome. Within this region are genes responsible for integrase-recombinase function. Three additional
M. avium
subsp.
paratuberculosis
-polymorphic regions were cloned, revealing a number of housekeeping genes; all were evaluated for their diagnostic and epidemiological value.
Comparison of Two Urinary Antigen Tests for Establishment of Pneumococcal Etiology of Adult Community-Acquired Pneumonia
Authors: Strålin Kristoffer , Kaltoft Margit Staum , Konradsen Helle Bossen , Olcén Per , Holmberg Hans 
Published: August 2004

ABSTRACT

The Binax NOW immunochromatographic test (ICT) detecting the pneumococcal C polysaccharide and a serotype-specific latex agglutination (LA) test detecting 23 pneumococcal capsular antigens were evaluated for establishing pneumococcal etiology in community-acquired pneumonia (CAP) by use of nonconcentrated urine. ICT was considered to be strongly positive for result lines at least as intense as the control line and weakly positive for less intense result lines. When 215 adult CAP patients were tested, strong ICT, weak ICT, and LA positivity were found in 28, 24, and 16 patients, respectively; of these patients, 13 (46%), 6 (25%), and 13 (81%), respectively, had pneumococcal bacteremia and 27 (96%), 17 (71%), and 15 (94%), respectively, had
Streptococcus pneumoniae
isolated from blood, sputum, and/or nasopharynx. Among 108 controls tested, 2 (1.9%) were weakly ICT positive. When weak positivity was considered negative, the sensitivity of ICT decreased from 79% (19 of 24) to 54% (13 of 24), while the specificity increased from 83% (158 of 191) to 92% (176 of 191); no controls were false positive. The sensitivity and specificity of LA were 54% (13 of 24) and 98% (188 of 191), respectively. Eight of nine LA serotypes corresponded to culture serotypes. In conclusion, using nonconcentrated urine and dividing ICT-positive results into strongly and weakly positive results is a suitable way of performing ICT. While weak ICT positivity should be interpreted with caution, strong ICT positivity and LA positivity should be considered supportive of pneumococcal etiology in adult CAP. As such, these assays might have implications for antibiotic use in CAP. LA has promising potential for pneumococcal serotyping, although further evaluation is required.
MICs of Selected Antibiotics forBacillus anthracis,Bacillus cereus,Bacillus thuringiensis, andBacillus mycoidesfrom a Range of Clinical and Environmental Sources as Determined by the Etest
Authors: Turnbull Peter C. B. , Sirianni Nicky M. , LeBron Carlos I. , Samaan Marian N. , Sutton Felicia N. , Reyes Anatalio E. , Peruski Leonard F. 
Published: August 2004

ABSTRACTThis paper presents Etest determinations of MICs of selected antimicrobial agents for 76 isolates ofBacillus anthracischosen for their diverse histories and 67, 12, and 4 cultures, respectively, of its close relativesB. cereus,B. thuringiensis, andB. mycoidesderived from a range of clinical and environmental sources. NCCLS breakpoints are now available forB. anthracisand ciprofloxacin, penicillin, and tetracycline; based on these breakpoints, theB. anthracisisolates were all fully susceptible to ciprofloxacin and tetracycline, and all except four cultures, three of which had a known history of penicillin resistance and were thought to originate from the same original parent, were susceptible to penicillin. Based on NCCLS interpretive standards for gram-positive and/or aerobic bacteria, all cultures were susceptible to amoxicillin-clavulanic acid and gentamicin and 99% (one with intermediate sensitivity) of cultures were susceptible to vancomycin. No group trends were apparent among the different categories ofB. cereus(isolates from food poisoning incidents and nongastrointestinal infections and food and environmental specimens not associated with illness). Differences betweenB. anthracisand the other species were as expected for amoxicillin and penicillin, with allB. anthraciscultures, apart from the four referred to above, being susceptible versus high proportions of resistant isolates for the other three species. Four of theB. cereusand one of theB. thuringiensiscultures were resistant to tetracycline and a further sixB. cereusand oneB. thuringiensiscultures fell into the intermediate category. There was a slightly higher resistance to azithromycin among theB. anthracisstrains than for the other species. The proportion ofB. anthracisstrains fully susceptible to erythromycin was also substantially lower than for the other species, although just a singleB. cereusstrain was fully resistant. The Etest compared favorably with agar dilution in a subsidiary test set up to test the readings, and it compared with other published studies utilizing a variety of test methods.
Use of 16S rRNA Gene Sequencing for Rapid Confirmatory Identification of
Brucella
Isolates
Authors: Gee Jay E. , De Barun K. , Levett Paul N. , Whitney Anne M. , Novak Ryan T. , Popovic Tanja 
Published: August 2004

ABSTRACT

Members of the genus
Brucella
are categorized as biothreat agents and pose a hazard for both humans and animals. Current identification methods rely on biochemical tests that may require up to 7 days for results. We sequenced the 16S rRNA genes of 65
Brucella
strains along with 17 related strains likely to present a differential diagnostic challenge. All
Brucella
16S rRNA gene sequences were determined to be identical and were clearly different from the 17 related strains, suggesting that 16S rRNA gene sequencing is a reliable tool for rapid genus-level identification of
Brucella
spp. and their differentiation from closely related organisms.
Population Genetic Analysis ofBartonella bacilliformisIsolates from Areas of Peru Where Carrion's Disease Is Endemic and Epidemic
Authors: Hambuch Tina M. , Handley Scott A. , Ellis Barbara , Chamberlin Judith , Romero Sofia , Regnery Russell 
Published: August 2004

ABSTRACTCarrion's disease is caused by infection with the α-proteobacteriumBartonella bacilliformis. Distribution of the disease is considered coincident with the distribution of its known vector, the sand flyLutzomyia verrucarum. Recent epidemics ofB. bacilliformisinfections associated with atypical symptomatology in nonendemic regions have raised questions regarding the historic and present distribution of this bacterium and the scope of disease that infection causes. Phylogenetic relationships and genomic diversity of 18B. bacilliformisisolates (10 isolates from a region where Carrion's disease is epidemic, Cuzco, Peru, and 8 isolates from a region where Carrion's disease is endemic, Caraz, Peru) were assessed using genomic data generated by infrequent restriction site PCR and gene sequence analysis of the flagellingltAandialBgenes. A population genetic analysis of the genomic diversity suggests that what was once considered an epidemic region of Peru did not result from the recent introduction ofB. bacilliformis.
Evaluation of the QuickLab RSV Test, a New Rapid Lateral-Flow Immunoassay for Detection of Respiratory Syncytial Virus Antigen
Authors: Slinger Robert , Milk Rose , Gaboury Isabelle , Diaz-Mitoma Francisco 
Published: August 2004

ABSTRACT

Rapid respiratory syncytial virus (RSV) diagnosis is vital to the prevention of nosocomial RSV infections. We evaluated a new rapid lateral-flow RSV immunoassay, the QuickLab RSV test, that requires use of only one reagent. We compared QuickLab to the Directigen RSV (DIR) assay, which requires six reagents, and direct fluorescent antibody (DFA) testing. DFA results were considered the “gold standard.” For 133 nasopharyngeal aspirates tested, DFA results were 77 (57.8%) positive, 47 (35.3%) negative, and 9 (6.8%) indeterminate. The sensitivities, specificities, positive predictive values, and negative predictive values of QuickLab and DIR tests were 93.3% (70 of 75) and 80.8% (59 of 73), 95.6% (43 of 45) and 100.0% (46 of 46), 97.2% (70 of 72) and 100.0% (59 of 59), and 89.6% (43 of 48) and 76.7% (46 of 60), respectively. QuickLab was significantly (
P
= 0.02) more sensitive than DIR; the difference in specificities was not significant. DFA was more sensitive than DIR (
P
< 0.001) but not more sensitive than QuickLab (
P
= 0.45). The results of DIR testing were initially uninterpretable and required retesting with 15% of the specimens compared to 3% of QL results (
P
< 0.001). We conclude that the QuickLab RSV test has sensitivity similar to that of the DFA assay and better than that of the DIR assay. QuickLab testing is also simpler to perform and interpret than both DFA and DIR testing.
Use of Positive Blood Cultures for Direct Identification and Susceptibility Testing with the Vitek 2 System
Authors: de Cueto Marina , Ceballos Esther , Martinez-Martinez Luis , Perea Evelio J. , Pascual Alvaro 
Published: August 2004

ABSTRACT
In order to further decrease the time lapse between initial inoculation of blood culture media and the reporting of results of identification and antimicrobial susceptibility tests for microorganisms causing bacteremia, we performed a prospective study in which specially processed fluid from positive blood culture bottles from Bactec 9240 (Becton Dickinson, Cockeysville, Md.) containing aerobic media were directly inoculated into Vitek 2 system cards (bio-Mérieux, France). Organism identification and susceptibility results were compared with those obtained from cards inoculated with a standardized bacterial suspension obtained following subculture to agar; 100 consecutive positive monomicrobic blood cultures, consisting of 50 gram-negative rods and 50 gram-positive cocci, were included in the study. For gram-negative organisms, 31 of the 50 (62%) showed complete agreement with the standard method for species identification, while none of the 50 gram-positive cocci were correctly identified by the direct method. For gram-negative rods, there were 50% categorical agreements between the direct and standard methods for all drugs tested. The very major error rate was 2.4%, and the major error rate was 0.6%. The overall error rate for gram-negatives was 6.6%. Complete agreement in clinical categories of all antimicrobial agents evaluated was obtained for 19 of 50 (38%) gram-positive cocci evaluated; the overall error rate was 8.4%, with 2.8% minor errors, 2.4% major errors, and 3.2% very major errors. These findings suggest that the Vitek 2 cards inoculated directly from positive Bactec 9240 bottles do not provide acceptable bacterial identification or susceptibility testing in comparison with corresponding cards tested by a standard method.
Comparison of Real-Time PCR Signal-Amplified In Situ Hybridization and Conventional PCR for Detection and Quantification of Human Papillomavirus in Archival Cervical Cancer Tissue
Authors: Biedermann Karin , Dandachi Nadia , Trattner Maria , Vogl Georgia , Doppelmayr Hildegard , Moré Elena , Staudach Alfons , Dietze Otto , Hauser-Kronberger Cornelia 
Published: August 2004

ABSTRACT

Archival paraffin-embedded tumor specimens offer a wealth of information for both cancer research and for routine clinical applications. However, the use of formalin-fixed, paraffin-embedded specimens for quantitative real-time PCR is not yet a standard diagnostic method in many laboratories, in particular for the quantification of human papillomavirus (HPV). Particularly high-risk HPV types are involved in almost 100% of the carcinogenesis of cervical cancer. We compared the diagnostic applicability and sensitivity of real-time PCR to that of chromogenic tyramide-signal-amplified in situ hybridization and conventional PCR for the detection of HPV from archival tissue in 164 cases of carcinoma in situ and cervical cancer. Furthermore, we examined whether the viral load of HPV is of prognostic relevance. Our findings indicate that patients in tumor stage I with a lower viral load of HPV type 16 (HPV16; up to 1,000 copies/ng of DNA) had a significantly better survival than HPV 16-negative patients (
P
= 0.037). We observed a greater sensitivity of both real-time PCR and conventional PCR for the detection of HPV16 and -18 compared to signal amplified in situ hybridization. We found a considerable concordance between HPV16 (κ = 0.661) and HPV18 (κ = 0.781) status as measured by real-time PCR and conventional PCR, indicating similar sensitivities. We recognized an inhibitory effect of formalin fixation and paraffin embedding on the evaluation of real-time PCR quantification.
Use of DNA Microarrays for Rapid Genotyping of TEM Beta-Lactamases That Confer Resistance
Authors: Grimm Verena , Ezaki Satoshi , Susa Milorad , Knabbe Cornelius , Schmid Rolf. D. , Bachmann Till T. 
Published: August 2004

ABSTRACTStandard clinical procedures for pathogen resistance identification are laborious and usually require 2 days of cultivation before the resistance can be determined unequivocally. In contrast, clinicians and patients face increasing threats from antibiotic-resistant pathogenic bacteria in terms of their frequencies and levels of resistance. A major class of microbial resistance stems from the occurrence of beta-lactamases, which, if mutated, can cause the severe extended-spectrum beta-lactamase (ESBL) or inhibitor-resistant TEM (IRT) phenotype, which cause resistance to extended-spectrum cephalosporins, monobactams, and beta-lactamase inhibitors. We describe an oligonucleotide microarray for identification of the single nucleotide polymorphisms (SNPs) of 96% of the TEM beta-lactamase variants described to date which are related to the ESBL and/or IRT phenotype. The target DNA, originating fromEscherichia coli,Enterobacter cloacae, andKlebsiella pneumoniaecells isolated from clinical samples, was amplified and fluorescently labeled by PCR with consensus primers in the presence of cyanine 5-labeled nucleotides. The total assay, including PCR, hybridization, and image analysis, could be performed in 3.5 h. The microarray results were validated by standard clinical procedures. The microarray outperformed the standard procedures in terms of assay time and the depth of information provided. In conclusion, this array offers an attractive option for the identification and epidemiologic monitoring of TEM beta-lactamases in the routine clinical diagnostic laboratory.
High Prevalence of
Helicobacter
Species Detected in Laboratory Mouse Strains by Multiplex PCR-Denaturing Gradient Gel Electrophoresis and Pyrosequencing
Authors: Nilsson Hans-Olof , Ouis Ibn-Sina , Stenram Unne , Ljungh Åsa , Moran Anthony P. , Wadström Torkel , Al-Soud Waleed Abu 
Published: August 2004

ABSTRACT

Rodent models have been developed to study the pathogenesis of diseases caused by
Helicobacter pylori
, as well as by other gastric and intestinal
Helicobacter
spp., but some murine enteric
Helicobacter
spp. cause hepatobiliary and intestinal tract diseases in specific inbred strains of laboratory mice. To identify these murine
Helicobacter
spp., we developed an assay based on PCR-denaturing gradient gel electrophoresis and pyrosequencing. Nine strains of mice, maintained in four conventional laboratory animal houses, were assessed for
Helicobacter
sp. carriage. Tissue samples from the liver, stomach, and small intestine, as well as feces and blood, were collected; and all specimens (
n
= 210) were screened by a
Helicobacter
genus-specific PCR. Positive samples were identified to the species level by multiplex denaturing gradient gel electrophoresis, pyrosequencing, and a
H. ganmani
-specific PCR assay. Histologic examination of 30 tissue samples from 18 animals was performed. All mice of eight of the nine strains tested were
Helicobacter
genus positive;
H. bilis
,
H. hepaticus
,
H. typhlonius
,
H. ganmani
,
H. rodentium
, and a
Helicobacter
sp. flexispira-like organism were identified.
Helicobacter
DNA was common in fecal (86%) and gastric tissue (55%) specimens, whereas samples of liver tissue (21%), small intestine tissue (17%), and blood (14%) were less commonly positive. Several mouse strains were colonized with more than one
Helicobacter
spp. Most tissue specimens analyzed showed no signs of inflammation; however, in one strain of mice, hepatitis was diagnosed in livers positive for
H. hepaticus
, and in another strain, gastric colonization by
H. typhlonius
was associated with gastritis. The diagnostic setup developed was efficient at identifying most murine
Helicobacter
spp.
Scytalidium dimidiatum
Causing Recalcitrant Subcutaneous Lesions Produces Melanin
Authors: Morris-Jones R. , Youngchim S. , Hextall J. M. , Gomez B. L. , Morris-Jones S. D. , Hay R. J. , Casadevall A. , Nosanchuk J. D. , Hamilton A. J. 
Published: August 2004

ABSTRACT

Scytalidium dimidiatum
is a pigmented dematiaceous coelomycete that typically causes chronic superficial skin diseases and onychomycosis, as well as deeper infections, such as subcutaneous abscesses, mycetoma, and even fungemia in immunocompromised patients. A second species,
Scytalidium hyalinum
, has hyaline hyphae and arthroconidia and is considered by some authors to be an albino mutant of
S. dimidiatum
. This study aimed to confirm the presence of melanin or melanin-like compounds (which have been previously implicated in the virulence of other fungal pathogens) in
S. dimidiatum
from a patient with multiple subcutaneous nodules. Treatment of the hyphae and arthroconidia with proteolytic enzymes, denaturant, and concentrated hot acid yielded dark particles, which were stable free radicals, consistent with their identification as melanins. Extracted melanin particles from
S. dimidiatum
cultures were labeled by melanin-binding monoclonal antibodies (MAbs) from
Sporothrix schenckii
,
Aspergillus fumigatus
, and
Cryptococcus neoformans
. Lesional skin from the patient infected with
S. dimidiatum
contained fungal cells that were labeled by melanin-binding MAbs, and digestion of the tissue yielded dark particles that were also reactive.
S. hyalinum
was also subjected to the melanin extraction protocol, but no dark particles were yielded.
Assessment of a New Selective Chromogenic
Bacillus cereus
Group Plating Medium and Use of Enterobacterial Autoinducer of Growth for Cultural Identification of
Bacillus
Species
Authors: Reissbrodt R. , Raβbach A. , Burghardt B. , Rienäcker I. , Mietke H. , Schleif J. , Tschäpe H. , Lyte M. , Williams P. H. 
Published: August 2004

ABSTRACT

A new chromogenic
Bacillus cereus
group plating medium permits differentiation of pathogenic
Bacillus
species by colony morphology and color. Probiotic
B. cereus
mutants were distinguished from wild-type strains by their susceptibilities to penicillin G or cefazolin. The enterobacterial autoinducer increased the sensitivity and the speed of enrichment of
B. cereus
and
B. anthracis
spores in serum-supplemented minimal salts medium (based on the standard American Petroleum Institute medium) and buffered peptone water.
Comparison of Sequence Analysis and a Novel Discriminatory Real-Time PCR Assay for Detection and Quantification of Lamivudine-Resistant Hepatitis B Virus Strains
Authors: Wightman Fiona , Walters Tomos , Ayres Anna , Bowden Scott , Bartholomeusz Angeline , Lau Daryl , Locarnini Stephen , Lewin Sharon R. 
Published: August 2004

ABSTRACT
We report a rapid and accurate real-time PCR-based method to quantify wild-type and lamivudine-resistant hepatitis B virus by using a common forward primer paired with different reverse primers. Excellent concordance was demonstrated between sequencing and the discriminatory real-time assay; however, a mixture of quasispecies was more frequently detected by discriminatory real-time PCR.
Differentiation of the Major
Listeria monocytogenes
Serovars by Multiplex PCR
Authors: Doumith Michel , Buchrieser Carmen , Glaser Philippe , Jacquet Christine , Martin Paul 
Published: August 2004

ABSTRACT

A new multiplex PCR assay was developed to separate the four major
Listeria monocytogenes
serovars isolated from food and patients (1/2a, 1/2b, 1/2c, and 4b) into distinct groups. The PCR test, which constitutes a rapid and practical alternative to laborious classical serotyping, was successfully evaluated with 222
Listeria
strains.
Multicenter Evaluation of a New Screening Test That Detects
Clostridium difficile
in Fecal Specimens
Authors: Zheng L. , Keller S. F. , Lyerly D. M. , Carman R. J. , Genheimer C. W. , Gleaves C. A. , Kohlhepp S. J. , Young S. , Perez S. , Ye K. 
Published: August 2004

ABSTRACT

Clostridium difficile
causes approximately 25% of nosocomial antibiotic-associated diarrheas and most cases of pseudomembranous colitis. We evaluated
C. DIFF CHEK
, a new screening test that detects glutamate dehydrogenase of
C. difficile
. Our results showed that this test was comparable to PCR in sensitivity and specificity and outperformed bacterial culture.
Rapid and Specific Detection of the O15:K52:H1 Clonal Group of
Escherichia coli
by Gene-Specific PCR
Authors: Johnson James R. , Owens Krista , Sabate Montse , Prats Guillem 
Published: August 2004

ABSTRACT

Primers specific for
Escherichia coli
O15:K52:H1 were devised based on a novel single-nucleotide polymorphism identified within the housekeeping gene
fumC
, i.e., G594A. In experiments comparing various reference typing methods, the new primers provided 100% sensitivity and specificity for the O15:K52:H1 clonal group, including 162 diverse clinical and reference
E. coli
isolates.
Use of Rapid and Conventional Testing Technologies for Human Immunodeficiency Virus Type 1 Serologic Screening in a Rural Kenyan Reference Laboratory
Authors: Foglia Ginamarie , Royster G. Donald , Wasunna K. Monique , Kibaya Rukia , Malia Jennifer A. , Calero Eva K. , Sateren Warren , Renzullo Philip O. , Robb Merlin L. , Birx Deborah L. , Michael Nelson L. 
Published: August 2004

ABSTRACTWe report a prospective comparison of human immunodeficiency virus type 1 testing by enzyme immunoassay and Western blot with four rapid tests of 486 subjects performed in rural Kenya. Rapid test sensitivity was 100%. Specificity ranged from 99.1 to 100%. Combined use of two Food and Drug Administration-approved rapid tests yielded a single false-positive result.