bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multicenter Comparison of ESP Culture System II with BACTEC 460TB and with Lowenstein-Jensen Medium for Recovery of Mycobacteria from Different Clinical Specimens, Including Blood
Authors: Tortoli Enrico , Cichero Paola , Chirillo M. Gabriella , Gismondo M. Rita , Bono Letizia , Gesu Giampietro , Simonetti M. Tullia , Volpe Gisella , Nardi Giampietro , Marone Piero 
Published: December 2019

ABSTRACT

The recently developed ESP Culture System II (AccuMed, Chicago, Ill.) was compared with radiometric BACTEC 460TB (Becton Dickinson, Towson, Md.) and with Lowenstein-Jensen medium for recovery of mycobacteria from over 2,500 clinical specimens both of respiratory and nonrespiratory origin, including blood. The majority of the 219 mycobacterial isolates (129) belonged to the
Mycobacterium tuberculosis
complex, followed by 37 isolates of the
Mycobacterium avium
complex (MAC) and 53 isolates of eight other mycobacterial species. Rates of recovery obtained with BACTEC, ESP, and Lowenstein-Jensen medium were 89, 79, and 64%, respectively, with such differences being statistically significant. Different media and systems appeared to behave differently when the more frequently detected organisms were considered:
M. tuberculosis
complex isolates grew better with BACTEC, and MAC isolates grew better with ESP. An analysis of the combinations of Lowenstein-Jensen medium with BACTEC and with ESP did not reveal significant differences in recovery rates. With regard to the times needed for the detection of positive cultures, they were significantly longer on Lowenstein-Jensen medium (average, 28 days) than with the remaining two systems, between which there was no difference (average, 18 days). We conclude, therefore, that the ESP system, when used in combination with a solid medium, performs as well as the thoroughly validated radiometric BACTEC system and offers the advantages of full automation and absence of radioisotopes.
Use of Voriconazole in Treatment of
Scedosporium apiospermum
Infection: Case Report
Authors: Girmenia Corrado , Luzi Giovanni , Monaco Monica , Martino Pietro 
Published: December 2019

ABSTRACT

We report a case of disseminated
Scedosporium apiospermum
infection in a neutropenic patient with acute myeloid leukemia. Due to progression of the mycosis after 7 days of amphotericin B lipid complex therapy and to high susceptibility of the mold to voriconazole in vitro, the patient was treated with intravenous voriconazole. After a few days of therapy, fever disappeared and skin lesions improved. However, the patient died after 1 month due to intestinal bleeding. Despite a negative outcome, this case seems to indicate a promising role for voriconazole in the treatment of
S. apiospermum
infections.
Comparison of a 2,3-Bis(2-Methoxy-4-Nitro-5-Sulfophenyl)-5-[(Phenylamino)Carbonyl]-2
H
-Tetrazolium Hydroxide (XTT) Colorimetric Method with the Standardized National Committee for Clinical Laboratory Standards Method of Testing Clinical Yeast Isolates for Susceptibility to Antifungal Agents
Authors: Hawser S. P. , Norris H. , Jessup C. J. , Ghannoum M. A. 
Published: December 2019

ABSTRACT

MICs for clinical
Candida
and
Cryptococcus
isolates were determined by a method incorporating the colorimetric indicator 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2
H
-tetrazolium hydroxide (XTT), and the results were compared with MICs obtained by the National Committee for Clinical Laboratory Standards approved standard method (M27-A). One hundred percent of all isolates demonstrated agreement within 2 dilutions between the MICs of amphotericin B, fluconazole, itraconazole, ketoconazole, and flucytosine obtained by the two methods. These data suggest that an XTT-based method could provide a useful means for the determination of antifungal susceptibility of yeasts.
Comparison of Three Methods for Testing Azole Susceptibilities of
Candida albicans
Strains Isolated Sequentially from Oral Cavities of AIDS Patients
Authors: Tortorano Anna Maria , Viviani Maria Anna , Barchiesi Francesco , Arzeni Daniela , Rigoni Anna Lisa , Cogliati Massimo , Compagnucci Patrizia , Scalise Giorgio 
Published: December 2019

ABSTRACT

Three susceptibility testing procedures were compared to determine fluconazole, itraconazole, and ketoconazole MICs against 47
Candida albicans
strains isolated sequentially from the oral cavities of five AIDS patients undergoing azole therapy. They included the broth microdilution method (BM), performed according to the National Committee for Clinical Laboratory Standards’ tentative standard, the agar dilution method (AD), and the Etest; the latter two tests were performed both in Casitone agar (AD-Cas and Etest-Cas) and in RPMI (AD-RPMI and Etest-RPMI). Twenty-four- and 48-h MICs obtained by AD and Etest were compared with 48-h MICs obtained by BM. The MICs of all the azoles determined by BM were usually lower than those obtained by the other methods, mainly due to different reading criteria. In order to assess the most appropriate way of evaluating the agreement of MICs obtained by different methods with those produced by the proposed reference method (BM), we used the mean differences calculated according to Bland and Altman’s method. Comparison of fluconazole MICs obtained by BM and AD-Cas yielded a mean difference of 3, and the percentages of agreement within ±2 dilutions were 98 and 100% at 24 and 48 h, respectively. For ketoconazole and itraconazole MICs, lower mean differences were noted, and agreement ranged from 96 to 100%. Agreement between the AD-RPMI and BM results was poor for all azoles, and an increase in MICs was always observed between the 1st- and 2nd-day readings. Similarly, Etest-Cas gave better agreement with BM than did Etest-RPMI for all the azoles. BM, AD-Cas, and Etest-Cas each demonstrated a progressive increase in fluconazole MICs against strains isolated sequentially from a given patient, in accordance with the decreased clinical response to fluconazole.
Molecular Analysis of and Identification of Antibiotic Resistance Genes in Clinical Isolates of
Salmonella typhi
from India
Authors: Shanahan Philippa M. A. , Jesudason Mary V. , Thomson Christopher J. , Amyes Sebastian G. B. 
Published: December 2019

ABSTRACT

A representative sample of 21
Salmonella typhi
strains isolated from cultures of blood from patients at the Christian Medical College and Hospital, Vellore, India, were tested for their susceptibilities to various antimicrobial agents. Eleven of the
S. typhi
strains possessed resistance to chloramphenicol (256 mg/liter), trimethoprim (64 mg/liter), and amoxicillin (>128 mg/liter), while four of the isolates were resistant to each of these agents except for amoxicillin. Six of the isolates were completely sensitive to all of the antimicrobial agents tested. All the
S. typhi
isolates were susceptible to cephalosporin agents, gentamicin, amoxicillin plus clavulanic acid, and imipenem. The antibiotic resistance determinants in each
S. typhi
isolate were encoded by one of four plasmid types. Plasmid-mediated antibiotic resistance genes were identified with specific probes in hybridization experiments; the genes responsible for chloramphenicol, trimethoprim, and ampicillin resistance were chloramphenicol acetyltransferase type I, dihydrofolate reductase type VII, and TEM-1 β-lactamase, respectively. Pulsed-field gel electrophoresis analysis of
Xba
I-generated genomic restriction fragments identified a single distinct profile (18 DNA fragments) for all of the resistant isolates. In comparison, six profiles, different from each other and from the resistance profile, were recognized among the sensitive isolates. It appears that a single strain containing a plasmid conferring multidrug-resistance has emerged within the
S. typhi
bacterial population in Vellore and has been able to adapt to and survive the challenge of antibiotics as they are introduced into clinical medicine.
Rapid Identification of
Candida albicans
and Other Human Pathogenic Yeasts by Using Short Oligonucleotides in a PCR
Authors: Mannarelli B. M. , Kurtzman C. P. 
Published: December 2019

ABSTRACT

A PCR system that can quickly and accurately identify 14 species of human pathogenic yeasts was developed. The procedure distinguished between nine species of a closely related clade,
Lodderomyces elongisporus
,
Candida parapsilosis
, a new
Candida
sp.,
C. sojae
,
C. tropicalis
,
C. maltosa
,
C. viswanathii
,
C. albicans
, and
C. dubliniensis
and between another five more divergent species,
Pichia guilliermondii
,
C. glabrata
,
C. zeylanoides
,
C. haemulonii
, and
C. haemulonii
type II. A rapid DNA extraction procedure that yields purified DNA in about 1 h is also described. The system uses uniform conditions with four primers for each reaction, two 40- to 50-mer universal primers that serve as a positive control and two 23- to 30-mer species-specific primers. Species-specific primers were derived from a 600-nucleotide variable region (D1/D2) at the 5′ end of the large-subunit (26S) ribosomal DNA gene and were generally designed to use mismatches at the 3′ end. Universal primers were developed from conserved nucleotide sequences in the small-subunit (18S) rRNA gene. In this system, a control 1,200- to 1,300-base DNA fragment was produced in all reactions and a smaller 114- to 336-base DNA fragment was produced if the chromosomal DNA from the target species was present. The PCR procedure is rapid and easy to interpret and may be used with mixed cultures.
Tubulointerstitial Nephritis Due to a Mutant Polyomavirus BK Virus Strain, BKV(Cin), Causing End-Stage Renal Disease
Authors: Smith R. D. , Galla J. H. , Skahan K. , Anderson P. , Linnemann C. C. , Ault G. S. , Ryschkewitsch C. F. , Stoner G. L. 
Published: December 2019

ABSTRACTA renal biopsy from a 36-year-old man with AIDS showed a severe tubulointerstitial nephritis with intranuclear inclusions in epithelial cells. Electron microscopy revealed the characteristic findings of a polyomavirus (PyV) infection, and immunofluorescence indicated the presence of BK virus (BKV) antigen. Inoculation of rhesus monkey kidney cell cultures both with urine and with buffy coat blood cells resulted in a cytopathic response which was subsequently confirmed to be due to BKV. Further characterization of the viral DNA from the kidney by PCR amplification and Southern blot analysis with PyV and strain-specific primers and probes indicated that the virus was closely related to the BK(Dun) strain but different in its apparent sequence arrangement. Subsequent cycle sequencing showed a dinucleotide mutation of TG→AA which substitutes hydrophilic Gln for hydrophobic Leu in a sequence homologous to an origin DNA-binding domain of simian virus 40 T antigen. It is suggested that the mutation and a coding region rearrangement of this strain of BKV designated BKV(Cin) has the potential to alter viral DNA replication and enhance pathogenicity.
Antimicrobial Susceptibilities and Molecular Epidemiology ofSalmonella entericaSerotype Enteritidis Strains Isolated in Hong Kong from 1986 to 1996
Authors: Ling J. M. , Koo I. C. , Kam K. M. , Cheng A. F. 
Published: December 2019

ABSTRACTThe incidence of salmonellosis has been increasing in Hong Kong since 1989. The most commonSalmonella entericaserotype isolated in 1994 wasS. enteritidis. The antimicrobial susceptibilities and molecular epidemiology of 275S. enteritidisstrains isolated in this locality between 1986 and 1996 were studied. Over 99% of the isolates were susceptible to 17 of the 19 antimicrobial agents tested. One isolate harbored an autotransferring plasmid that confers resistance to tetracycline and trimethoprim-sulfamethoxazole. Another isolate harbored a mobilizable plasmid that confers resistance to ampicillin and cephalothin. This isolate was found to produce a β-lactamase with a pI of 5.2. A total of 264 isolates (96%) were found to harbor one to five plasmids, and the majority (254) harbored a 60-kb plasmid. Of these isolates, 94% contained identical 60-kb plasmids. Based on plasmid profiles, plasmid and chromosomal fingerprints, ribotypes, and randomly amplified polymorphic DNA (RAPD) patterns, 170 (62%) isolates were allocated to group 1b. About 90% of isolates had identical or similar DNA fingerprints, ribotypes, and RAPD patterns, suggesting that a predominant clone ofS. enteritidiswas circulating in Hong Kong during the period being studied.
Detection and Identification ofActinobacillus pleuropneumoniaeSerotype 5 by Multiplex PCR
Authors: Lo Terry M. , Ward Christine K. , Inzana Thomas J. 
Published: December 2019

ABSTRACTSerotyping ofActinobacillus pleuropneumoniaeis based on detection of the serotype-specific capsular antigen. However, not all isolates can be serotyped, and some may cross-react with multiple serotyping reagents. To improve sensitivity and specificity of serotyping and for early detection, a multiplex PCR assay was developed for detection ofA. pleuropneumoniaeand identification of serotype 5 isolates. DNA sequences specific to the conserved export and serotype-specific biosynthesis regions of the capsular polysaccharide ofA. pleuropneumoniaeserotype 5 were used as primers to amplify 0.7- and 1.1-kb DNA fragments, respectively. The 0.7-kb fragment was amplified from all strains ofA. pleuropneumoniaetested with the exception of serotype 4. The 0.7-kb fragment was not amplified from any heterologous species that are also common pathogens or commensals of swine. In contrast, the 1.1-kb fragment was amplified from all serotype 5 strains only. The assay was capable of amplifying DNA from less than 102CFU. TheA. pleuropneumoniaeserotype 5 capsular DNA products were readily amplified from lung tissues obtained from infected swine, although the 1.1-kb product was not amplified from some tissues stored frozen for 6 years. The multiplex PCR assay enabled us to detectA. pleuropneumoniaerapidly and to distinguish serotype 5 strains from other serotypes. The use of primers specific to the biosynthesis regions of otherA. pleuropneumoniaeserotypes would expand the diagnostic and epidemiologic capabilities of this assay.
Detection of
Bacteroides fragilis
Enterotoxin Gene by PCR
Authors: Shetab Razeq , Cohen Stuart H. , Prindiville Thomas , Tang Yajarayma J. , Cantrell Mary , Rahmani Darush , Silva Joseph 
Published: December 2019

ABSTRACT

Bacteroides fragilis
constitutes about 1% of the bacterial flora in intestines of normal humans. Enterotoxigenic strains of
B. fragilis
have been associated with diarrheal diseases in humans and animals. The enterotoxin produced by these isolates induces fluid changes in ligated intestinal loops and an in vitro cytotoxic response in HT-29 cells. We developed a nested PCR to detect the enterotoxin gene of
B. fragilis
in stool specimens. After DNA extraction, a 367-bp fragment was amplified with two outer primers. The amplicon from this reaction was subjected to a second round of amplification with a set of internal primers. With these inner primers, a 290-bp DNA fragment was obtained which was confirmed as part of the
B. fragilis
enterotoxin gene by Southern blotting with a nonradioactive internal probe and a chemiluminescence system. By this approach,
B. fragilis
enterotoxin gene sequences were detected in eight known enterotoxigenic human isolates and nine enterotoxigenic horse isolates. No amplification products were obtained from DNA extracted from 28 nonenterotoxigenic
B. fragilis
isolates or
B. distasonis
,
B. thetaiotaomicron
,
B. uniformis
,
B. ovatus
,
Escherichia coli
, or
Clostridium difficile
. The sensitivity of this assay allowed us to detect as little as 1 pg of enterotoxin DNA sequences or 100 to 1,000 cells of enterotoxigenic
B. fragilis
/g of stool. Enterotoxin production of all isolates was confirmed in vitro in HT-29 cells. A 100% correlation was obtained between enterotoxin detection by cytotoxin assay and the nested PCR assay. This rapid and sensitive assay can be used to identify enterotoxigenic
B. fragilis
and may be used clinically to determine the role of
B. fragilis
in diarrheal diseases.
Stabilized, Freeze-Dried PCR Mix for Detection of Mycobacteria
Authors: Klatser Paul R. , Kuijper Sjoukje , van Ingen Cor W. , Kolk Arend H. J. 
Published: December 2019

ABSTRACT

We report here the development of a freeze-drying procedure allowing stabilization at ambient temperature of preoptimized, premixed, and predispensed PCR mixes aimed at the detection of mycobacteria in clinical materials. The freeze-dried mixes retained activity at 4°C and at 20°C for 1 year and for 3 months at 37°C, as judged by their performance with 50 and 500 fg of purified
Mycobacterium bovis
BCG target DNA.
A PCR Specific for
Escherichia coli
O157 Based on the
rfb
Locus Encoding O157 Lipopolysaccharide
Authors: Desmarchelier Patricia M. , Bilge Sima S. , Fegan Narelle , Mills Leanne , Vary James C. , Tarr Phillip I. 
Published: December 2019

ABSTRACT

A PCR was developed for the detection of
Escherichia coli
O157 based on the
rfbE
O-antigen synthesis genes. A 479-bp PCR product was amplified specifically from
E. coli
O157 in cell lysates containing 200 or 2 CFU following crude DNA extraction. The PCR detected <1 CFU of
E. coli
O157 per ml in raw milk following enrichment.
Conservation of Restriction Sites in Isolates of
Streptococcus pneumoniae
with Diverse Restriction Fragment Patterns
Authors: Hall Lucinda M. C. , Duke Brigid 
Published: December 2019

ABSTRACT

Separation of large restriction fragments by pulsed-field gel electrophoresis is a commonly used method for epidemiological typing of
Streptococcus pneumoniae
and many other bacterial species. Information on the genetic changes underlying the restriction fragment polymorphisms that allow discrimination between isolates is scarce. In this study fragments adjacent to
Apa
I sites in a clinical isolate of
S. pneumoniae
were cloned and used to probe
Hin
dIII and
Hin
dIII-plus-
Apa
I genomic DNA digests from other isolates with very different
Apa
I fragment patterns. If for a given isolate the
Hin
dIII fragment detected by the probe was reduced in size on digestion with
Apa
I, it was deduced that the
Apa
I site was conserved in that isolate. The results demonstrate that of six
Apa
I sites in PN93/908 examined, five were retained in 11 genetically different isolates and one was retained in 2 isolates but lost in 9 others. It was concluded that point mutations at restriction sites are unlikely to account for the restriction fragment length polymorphism observed and that much of the polymorphism may be due to DNA rearrangements, possibly resulting from the insertion or deletion of mobile DNA elements.
Defective Human T-Cell Lymphotropic Virus Type I (HTLV-I) Provirus in 10 Chilean Seronegative Patients with Tropical Spastic Paraparesis or HTLV-I-Associated Myelopathy
Authors: Ramirez Eugenio , Cartier Luis , Rios Maritza , Fernandez Jorge 
Published: December 2019

ABSTRACT

We studied the presence of
tax
and
ltr
genes from human T-cell lymphotropic virus type I (HTLV-I) provirus in the peripheral blood mononuclear cells from 15 seronegative patients with tropical spastic paraparesis or HTLV-I-associated myelopathy by PCR. Only a region of the
tax
gene from 10 patients was amplified. The nucleotide homologies of six Chilean isolates to the ATK-1 clone ranged between 98.7 and 99.4%.
International Surveillance of Bloodstream Infections Due to
Candida
Species: Frequency of Occurrence and Antifungal Susceptibilities of Isolates Collected in 1997 in the United States, Canada, and South America for the SENTRY Program
Authors: Pfaller M. A. , Jones R. N. , Doern G. V. , Sader H. S. , Hollis R. J. , Messer S. A. , Group for The Sentry Participant 
Published: December 2019

ABSTRACT

An international program of surveillance of bloodstream infections (BSIs) in the United States, Canada, and South America between January and December 1997 detected 306 episodes of candidemia in 34 medical centers (22 in the United States, 6 in Canada, and 6 in South America). Eighty percent of the BSIs were nosocomial and 50% occurred in patients hospitalized in an intensive care unit. Overall, 53.3% of the BSIs were due to
Candida albicans
, 15.7% were due to
C. parapsilosis
, 15.0% were due to
C. glabrata
, 7.8% were due to
C. tropicalis
, 2.0% were due to
C. krusei
, 0.7% were due to
C. guilliermondii
, and 5.8% were due to
Candida
spp. However, the distribution of species varied markedly by country. In the United States, 43.8% of BSIs were due to non-
C. albicans
species.
C. glabrata
was the most common non-
C. albicans
species in the United States. The proportion of non-
C. albicans
BSIs was slightly higher in Canada (47.5%), where
C. parapsilosis
, not
C. glabrata
, was the most common non-
C. albicans
species.
C. albicans
accounted for 40.5% of all BSIs in South America, followed by
C. parapsilosis
(38.1%) and
C. tropicalis
(11.9%). Only one BSI due to
C. glabrata
was observed in South American hospitals. Among the different species of
Candida
, resistance to fluconazole (MIC, ≥64 μg/ml) and itraconazole (MIC, ≥1.0 μg/ml) was observed with
C. glabrata
and
C. krusei
and was observed more rarely among other species. Isolates of
C. albicans
,
C. parapsilosis
,
C. tropicalis
, and
C. guilliermondii
were all highly susceptible to both fluconazole (99.4 to 100% susceptibility) and itraconazole (95.8 to 100% susceptibility). In contrast, 8.7% of
C. glabrata
isolates (MIC at which 90% of isolates are inhibited [MIC
90
], 32 μg/ml) and 100% of
C. krusei
isolates were resistant to fluconazole, and 36.9% of
C. glabrata
isolates (MIC
90
, 2.0 μg/ml) and 66.6% of
C. krusei
isolates were resistant to itraconazole. Within each species there were no geographic differences in susceptibility to fluconazole or itraconazole.
Comparison of Roche Cobas Amplicor
Mycobacterium tuberculosis
Assay with In-House PCR and Culture for Detection of
M. tuberculosis
Authors: Eing Bodo R. , Becker Andrea , Sohns Arthur , Ringelmann Ronald 
Published: December 2019

ABSTRACT

The new Roche Cobas Amplicor
Mycobacterium tuberculosis
assay, which is a semiautomated version of the manually performed Roche Amplicor
M. tuberculosis
test, was compared to culture and an IS
6110
-based in-house PCR protocol. A total of 1,681 specimens from 833 patients, including specimen types other than sputum, were tested in parallel by both the in-house PCR and the Cobas Amplicor
M. tuberculosis
assay. After we resolved discrepant PCR results, the sensitivity, specificity, and positive and negative predictive values for the Cobas Amplicor
M. tuberculosis
assay were 66.33, 99.71, 94.36, and 97.66%, respectively. The corresponding values for the in-house PCR were 91.08, 99.85, 97.87, and 99.37%, respectively. For culture- and smear-positive specimens, the sensitivity of the Cobas Amplicor
M. tuberculosis
test was 96.42% (in-house PCR, 100%). If only smear-negative sputum specimens were considered, the Cobas Amplicor
M. tuberculosis
assay exhibited a sensitivity of 45.45% (in-house PCR, 63.63%) relative to that of culture. With a modified protocol for DNA extraction (washing of samples plus ultrasonication), both PCR methods performed better with gastric aspirates than with sputum samples (sensitivity of the Cobas Amplicor
M. tuberculosis
assay with smear-negative gastric aspirates, 70.00%; sensitivity of in-house PCR, 90.00%). With dithiothreitol being used for liquefaction of specimens in this study, the Cobas Amplicor
M. tuberculosis
assay exhibited an inhibition rate of 9.16%. In our view, the new Cobas Amplicor
M. tuberculosis
test (i) is well suited for typing of smear-positive specimens, (ii) may also be applied to gastric aspirates and other types of specimens if DNA extraction methods are modified appropriately, and (iii) exhibits a sensitivity with smear-negative sputum specimens which makes it recommendable that a minimum of three samples from the same patient be tested.