bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis
Authors: Palmer Sarah , Kearney Mary , Maldarelli Frank , Halvas Elias K. , Bixby Christian J. , Bazmi Holly , Rock Diane , Falloon Judith , Davey Richard T. , Dewar Robin L. , Metcalf Julia A. , Hammer Scott , Mellors John W. , Coffin John M. 
Published: January 2005

ABSTRACTTo investigate the extent to which drug resistance mutations are missed by standard genotyping methods, we analyzed the same plasma samples from 26 patients with suspected multidrug-resistant human immunodeficiency virus type 1 by using a newly developed single-genome sequencing technique and compared it to standard genotype analysis. Plasma samples were obtained from patients with prior exposure to at least two antiretroviral drug classes and who were on a failing antiretroviral regimen. Standard genotypes were obtained by reverse transcriptase (RT)-PCR and sequencing of the bulk PCR product. For single-genome sequencing, cDNA derived from plasma RNA was serially diluted to 1 copy per reaction, and a region encompassing p6, protease, and a portion of RT was amplified and sequenced. Sequences from 15 to 46 single viral genomes were obtained from each plasma sample. Drug resistance mutations identified by single-genome sequencing were not detected by standard genotype analysis in 24 of the 26 patients studied. Mutations present in less than 10% of single genomes were almost never detected in standard genotypes (1 of 86). Similarly, mutations present in 10 to 35% of single genomes were detected only 25% of the time in standard genotypes. For example, in one patient, 10 mutations identified by single-genome sequencing and conferring resistance to protease inhibitors (PIs), nucleoside analog reverse transcriptase inhibitors, and nonnucleoside reverse transcriptase inhibitors (NNRTIs) were not detected by standard genotyping methods. Each of these mutations was present in 5 to 20% of the 20 genomes analyzed; 15% of the genomes in this sample contained linked PI mutations, none of which were present in the standard genotype. In another patient sample, 33% of genomes contained five linked NNRTI resistance mutations, none of which were detected by standard genotype analysis. These findings illustrate the inadequacy of the standard genotype for detecting low-frequency drug resistance mutations. In addition to having greater sensitivity, single-genome sequencing identifies linked mutations that confer high-level drug resistance. Such linkage cannot be detected by standard genotype analysis.
Novel Assay Using Total Hepatitis C Virus (HCV) Core Antigen quantification for Diagnosis of HCV Infection in Dialysis Patients
Authors: Fabrizi Fabrizio , Lunghi Giovanna , Aucella Filippo , Mangano Stefano , Barbisoni Francesco , Bisegna Sergio , Vigilante Domenico , Limido Aurelio , Martin Paul 
Published: January 2005

ABSTRACTDialysis patients remain a high-risk group for hepatitis C virus (HCV) infection. The current diagnosis of HCV infection among dialysis patients includes serological assays and nucleic acid amplification technology (NAT) for assessing serum anti-HCV antibody and HCV viremia, respectively. However, current NAT techniques are expensive and labor-intensive and often lack standardization. An assay prototype designed to detect and quantify total HCV core antigen (total HCV core Ag) protein in serum and plasma in the presence or absence of anti-HCV antibodies has been recently developed. A comparison between a total anti-HCV core Ag enzyme-linked immunosorbent assay (ELISA) and a quantitative HCV RNA assay based on reverse transcription-PCR (RT-PCR) (Amplicor HCV Monitor test) was performed using a large (n= 305) cohort of ELISA HCV 3.0 HCV-negative and -positive patients on maintenance dialysis. The concentrations of HCV core Ag and HCV RNA levels (measured by RT-PCR) were significantly correlated (r= 0.471,P= 0.0001) over a wide range of HCV RNA levels and were maintained among different HCV genotypes (HCV genotype 1,r= 0.862,P= 0.0001; HCV genotype 2,r= 0.691,P= 0.0001). We estimated that 1 pg of total HCV core Ag per ml is equivalent to approximately 19.952 IU of HCV RNA per ml, even if the wide range in the ratio of core Ag to HCV RNA (95% confidence intervals, 2.8 × 103to 1.6 × 105IU/ml) precluded definitive conclusions. In summary, total HCV core Ag proved to be useful for performing HCV RNA measurement among dialysis patients in routine laboratories without the need for special equipment or training. The present study supports the use of the total anti-HCV core Ag ELISA for assessing viral load among dialysis patients with HCV infection.
Distribution of Major Genotypes among Methicillin-Resistant
Staphylococcus aureus
Clones in Asian Countries
Authors: Ko Kwan Soo , Lee Ji-Young , Suh Ji Yoeun , Oh Won Sup , Peck Kyong Ran , Lee Nam Yong , Song Jae-Hoon 
Published: January 2005

ABSTRACT

To investigate the evolutionary pattern and genotypic characteristics of methicillin-resistant
Staphylococcus aureus
(MRSA) strains in the Asian region, 74 MRSA strains isolated from 12 Asian countries were analyzed by multilocus sequence typing (MLST) and SCC
mec
typing. Overall, a total of 16 genotypes based on sequence type and SCC
mec
types were identified among MRSA strains from Asian countries. Data revealed two major genotypes of MRSA strains in Asia, with unique geographic distributions. By MLST analysis, all strains from Korea and Japan except one belonged to clonal complex 5 (CC5) while most MRSA isolates from other Asian countries belonged to CC239. SCC
mec
typing showed that most isolates from Korea and Japan were SS
mec
type II whereas SCC
mec
type III (or IIIA) was the most common type in strains from other Asian countries. Our data documented a unique geographic distribution and evolutionary pattern of MRSA clones in Asia.
Controlled Clinical Comparison of Plastic versus Glass Bottles of BacT/ALERT PF Medium for Culturing Blood from Children
Authors: Petti Cathy A. , Mirrett Stanley , Woods Christopher W. , Reller L. Barth 
Published: January 2005

ABSTRACT
The plastic pediatric BacT/ALERT (bioMérieux, Durham, N.C.) PF (PPF) is a new nonvented aerobic culture medium in a clear plastic bottle designed to prevent breakage. We compared the performance of the new PPF bottle to that of the present glass BacT/ALERT PF bottle for the recovery of microorganisms as well as for the time to detection of growth in samples of blood obtained for culture from children. We found that the PPF and PF bottles were comparable for recovery of microorganisms and that the safety advantage of plastic bottles can be achieved without compromising performance.
Clonal Diversity of Metallo-β-Lactamase-Possessing
Pseudomonas aeruginosa
in Geographically Diverse Regions of Japan
Authors: Kimura Soichiro , Alba Jimena , Shiroto Katsuaki , Sano Reiko , Niki Yoshihito , Maesaki Shigefumi , Akizawa Koji , Kaku Mitsuo , Watanuki Yuji , Ishii Yoshikazu , Yamaguchi Keizo 
Published: January 2005

ABSTRACT

The aim of this study was to determine the distribution of metallo-β-lactamase-producing
Pseudomonas aeruginosa
in Japan and to investigate the molecular characteristics of resistance gene cassettes including the gene encoding this enzyme. A total of 594 nonduplicate strains of
P. aeruginosa
isolated from 60 hospitals throughout Japan in 2002 were evaluated. This study indicated that although the prevalence of imipenem-resistant
P. aeruginosa
has not increased compared to that found in previous studies, clonal distribution of the same strain across Japan is evident.
Emerging Incidence of
Enterococcus faecium
among Hospital Isolates (1993 to 2002)
Authors: Treitman Adam N. , Yarnold Paul R. , Warren John , Noskin Gary A. 
Published: January 2005

ABSTRACT

Historically, most clinical microbiology laboratories report that 80 to 90% of enterococci are
Enterococcus faecalis
, whereas
E. faecium
accounts for 5 to 10% of isolates. At our medical center from 1993 to 2002, we evaluated the percentages of
E. faecium
among all enterococcal isolates and the percentages of
E. faecium
isolates that were vancomycin resistant. Over this 10-year period, the percentage of enterococci that were identified as
E. faecium
increased from 12.7 to 22.2% (
P
< 0.001) and the proportion of
E. faecium
that was vancomycin resistant increased from 28.9 to 72.4% (
P
< 0.001). Both the percentage of
E. faecium
among the enterococci and the proportion of vancomycin-resistant
E. faecium
increased significantly over this 10-year period.
Cryptococcus neoformans
Isolates from Transplant Recipients Are Not Selected for Resistance to Calcineurin Inhibitors by Current Immunosuppressive Regimens
Authors: Blankenship Jill R. , Singh Nina , Alexander Barbara D. , Heitman Joseph 
Published: January 2005

ABSTRACT

The immunosuppressants tacrolimus (FK506) and cyclosporine A inhibit calcineurin and have potent antifungal activity. In this study, 24% of
Cryptococcus neoformans
isolates from solid-organ transplant patients exhibited altered sensitivity to these drugs, which may have an impact on the infectious course but does not appear to be the consequence of immunosuppressive therapy.
Preliminary Evaluation of the API 20NE and RapID NF Plus Systems for Rapid Identification of
Burkholderia pseudomallei
and
B. mallei
Authors: Glass Mindy B. , Popovic Tanja 
Published: January 2005

ABSTRACT

We evaluated the API 20NE and the RapID NF Plus systems with 58
Burkholderia pseudomallei
and 23
B. mallei
strains for identification of these agents, but neither was reliable for confirmatory identification, with only 0 to 60% strains identified accurately. A greater diversity of strains in the system databases would be beneficial.
Analysis of Replication Kinetics of the Human Metapneumovirus in Different Cell Lines by Real-Time PCR
Authors: Deffrasnes Céline , Côté Stéphanie , Boivin Guy 
Published: January 2005

ABSTRACT
Human metapneumovirus (hMPV) is associated with acute respiratory tract disease especially in young children. Using a quantitative real-time TaqMan PCR, we analyzed the replication kinetics of hMPV in different cell lines. Our results indicate that hMPV replicates slightly more efficiently in LLC-MK2 than in Vero cells and poorly in HEp-2 cells.
Discrepancies and Interpretation Problems in Susceptibility Testing of VIM-1-Producing
Klebsiella pneumoniae
Isolates
Authors: Giakkoupi P. , Tzouvelekis L. S. , Daikos G. L. , Miriagou V. , Petrikkos G. , Legakis N. J. , Vatopoulos A. C. 
Published: January 2005

ABSTRACT

Susceptibilities to β-lactam antibiotics of five VIM-1-producing
Klebsiella pneumoniae
isolates were determined by broth microdilution, Etest, disk diffusion, and the automated systems Vitek 2, Phoenix, and MicroScan. Significant discrepancies were observed in the determination of susceptibility to imipenem and meropenem. Interpretation problems by the automated systems were also noted.
Low Proportion of Recent Human Immunodeficiency Virus (HIV) Infections among Newly Diagnosed Cases of HIV Infection as Shown by the Presence of HIV-Specific Antibodies of Low Avidity
Authors: Puchhammer-Stöckl Elisabeth , Schmied Brigitte , Rieger Armin , Sarcletti Mario , Geit Maria , Zangerle Robert , Hofmann Hanns 
Published: January 2005

ABSTRACT
The time between human immunodeficiency virus (HIV) infection and diagnosis is mostly unknown. Two hundred five newly diagnosed patients were investigated for the duration of their HIV infection by avidity testing. Recent HIV infection was identified in 27.3% of the cases. Early diagnosis was achieved significantly less frequently in heterosexually infected persons than in other patients.
Variation of the Polymorphic Region X of the Protein A Gene during Persistent Airway Infection of Cystic Fibrosis Patients Reflects Two Independent Mechanisms of Genetic Change in
Staphylococcus aureus
Authors: Kahl Barbara C. , Mellmann Alexander , Deiwick Susanne , Peters Georg , Harmsen Dag 
Published: January 2005

ABSTRACT

Variation of the polymorphic region of the protein A gene (
spa
) was observed during long-term persistence of
Staphylococcus aureus
in the airways of 10 cystic fibrosis patients and occurred at a rate of one genetic change every 70 months. Independent mutational events were observed eight times in 142 isolates: four deletions, two duplications of repeats, and two point mutations.
Evaluation of an Ultrasensitive p24 Antigen Assay as a Potential Alternative to Human Immunodeficiency Virus Type 1 RNA Viral Load Assay in Resource-Limited Settings
Authors: Respess Richard A. , Cachafeiro Ada , Withum David , Fiscus Susan A. , Newman Daniel , Branson Bernard , Varnier Oliviero E. , Lewis Kim , Dondero Timothy J. 
Published: January 2005

ABSTRACT
An inexpensive enzyme-linked immunosorbent assay method for human immunodeficiency virus type 1 quantitation, ultrasensitive p24 antigen assay (Up24), was compared with RNA viral load assay (VL). Up24 had 100% sensitivity of detection at a viral load of ≥30,000, with sensitivity of 46.4% at a viral load of <30,000 (232 specimens from 65 seropositive subjects). The assay was highly reproducible, with excellent correlation between duplicates and among three laboratories.
Comparison of the Mycoplasma Duo Test with PCR for Detection of
Ureaplasma
Species in Endotracheal Aspirates from Premature Infants
Authors: Cheah Fook-Choe , Anderson Trevor P. , Darlow Brian A. , Murdoch David R. 
Published: January 2005

ABSTRACT

We compared the Mycoplasma Duo kit (Sanofi Diagnostics Pasteur) with PCR for detection of
Ureaplasma
spp. in endotracheal aspirates from 60 premature neonates. The overall agreement between the two tests was 96%. The Mycoplasma Duo assay is a useful alternative to culture and PCR for detection of neonatal
Ureaplasma
infection.
Infant Botulism Acquired from Household Dust Presenting as Sudden Infant Death Syndrome
Authors: Nevas Mari , Lindström Miia , Virtanen Antti , Hielm Sebastian , Kuusi Markku , Arnon Stephen S. , Vuori Erkki , Korkeala Hannu 
Published: January 2005

ABSTRACT

Clostridium botulinum
type B was detected by multiplex PCR in the intestinal contents of a suddenly deceased 11-week-old infant and in vacuum cleaner dust from the patient's household.
C. botulinum
was also isolated from the deceased infant's intestinal contents and from the household dust. The genetic similarity of the two isolates was demonstrated by pulsed-field gel electrophoresis and randomly amplified polymorphic DNA analysis, thereby confirming that dust may act as a vehicle for infant botulism that results in sudden death.
Acute Hemorrhagic Pericarditis in a Child with Pneumonia Due to
Chlamydophila pneumoniae
Authors: Tenenbaum T. , Heusch A. , Henrich B. , MacKenzie C. R. , Schmidt K. G. , Schroten H. 
Published: January 2005

ABSTRACT

Chlamydophila pneumoniae
is mainly responsible for respiratory tract infections but has also been associated with endocarditis and myocarditis. We report a case of pneumonia in a child with hemorrhagic pericardial effusion with a positive result by a new
C. pneumoniae
TaqMan PCR, suggesting a pericardial inflammation directly induced by
C. pneumoniae
.
C. pneumoniae
should be suspected in patients with community-acquired pneumonia and concurrent pericarditis. Empirical treatment with azithromycin seems feasible.
Multiplex PCR-Identified Cutaneous Tuberculosis Evoked by
Mycobacterium bovis
BCG Vaccination in a Healthy Baby
Authors: Okazaki Tatsuma , Ebihara Satoru , Takahashi Hidenori , Asada Masanori , Sato Akimasa , Seki Masaaki , Ohto Hideyasu , Sasaki Hidetada 
Published: January 2005

ABSTRACT

This is the first identified case of
Mycobacterium bovis
bacillus Calmette-Guérin (BCG)-derived cutaneous tuberculosis that localizes at a place different from the vaccination site in hosts without immune deficiency. A healthy baby with a developing abscess is described. A multiplex PCR identified the abscess as originating from
M. bovis
BCG Tokyo 172.
Performance of the New VITEK 2 GP Card for Identification of Medically Relevant Gram-Positive Cocci in a Routine Clinical Laboratory
Authors: Funke Guido , Funke-Kissling Pascale 
Published: January 2005

ABSTRACTThe VITEK 2 gram-positive (GP) identification card (bioMérieux, Marcy l'Etoile, France) has been redesigned to achieve greater accuracy in the identification of gram-positive cocci. A total of 43 biochemical tests, including 17 enzymatic tests, are present in the card and interpreted in a kinetic mode, for up to 8 h. The VITEK 2 database, used in conjunction with the GP identification card, allows the identification of 115 different taxa. A total of 364 strains of GP cocci (217Streptococcaceaestrains and 147Micrococcaceaestrains) belonging to 31 taxa were tested with the new VITEK 2 GP identification card. Of the 364 strains, 105 were taken from routine primary plating media. A total of 344 strains (94.5%) were correctly identified to the species level and 17 strains (4.7%) were identified with low discrimination, requiring additional tests, whereas 1 strain (0.3%) was incorrectly identified and 2 strains (0.5%) remained unidentified. Within 7 h of the start of incubation, more than 90% of all strains were identified. Of the 105 primary cultures, 97% were correctly identified to the species level, 2% were identified with low discrimination, and 1% remained unidentified. Identification performance data were independent of each of the three plating media used. It is concluded that the new VITEK 2 GP identification card provides reliable results for the identification of GP cocci under routine laboratory conditions.
Sensitivities and Specificities of Spoligotyping and Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeat Typing Methods for Studying Molecular Epidemiology of Tuberculosis
Authors: Scott Allison N. , Menzies Dick , Tannenbaum Terry-Nan , Thibert Louise , Kozak Robert , Joseph Lawrence , Schwartzman Kevin , Behr Marcel A. 
Published: January 2005

ABSTRACT

The development of PCR-based genotyping modalities (spoligotyping and mycobacterial interspersed repetitive unit-variable-number tandem repeat [MIRU-VNTR] typing) offers promise for real-time molecular epidemiological studies of tuberculosis (TB). However, the utility of these methods depends on their capacity to appropriately classify isolates. To determine the operating parameters of spoligotyping and MIRU-VNTR typing, we have compared results generated by these newer tests to the standard typing method, IS
6110
restriction fragment length polymorphism, in analyses restricted to high-copy-number IS
6110
isolates. Sensitivities of the newer tests were estimated as the percentages of isolates with identical IS
6110
fingerprints that had identical spoligotypes and MIRU-VNTR types. The specificities of these tests were estimated as the percentages of isolates with unique IS
6110
fingerprints that had unique spoligotypes and MIRU-VNTR types. The sensitivity of MIRU-VNTR typing was 52% (95% confidence interval [CI], 31 to 72%), and the sensitivity of spoligotyping was 83% (95% CI, 63 to 95%). The specificity of MIRU-VNTR typing was 56% (95% CI, 51 to 62%), and the specificity of spoligotyping was 40% (95% CI, 35 to 46%). The proportion of isolates estimated to be due to recent transmission was 4% by identical IS
6110
patterns, 19% by near-identical IS
6110
patterns, 33% by MIRU-VNTR typing, and 53% by spoligotyping. The low calculated specificities of spoligotyping and MIRU-VNTR typing led to misclassification of cases, inflated estimates of TB transmission, and low positive predictive values, suggesting that these techniques have unsuitable operating parameters for population-based molecular epidemiology studies.
How physicians face ethical difficulties: a qualitative analysis
Authors: Hurst S A , Hull S C , DuVal G , Danis M 
Published: January 2005

Background:Physicians face ethical difficulties daily, yet they seek ethics consultation infrequently. To date, no systematic data have been collected on the strategies they use to resolve such difficulties when they do so without the help of ethics consultation. Thus, our understanding of ethical decision making in day to day medical practice is poor. We report findings from the qualitative analysis of 310 ethically difficult situations described to us by physicians who encountered them in their practice. When facing such situations, the physicians sought to avoid conflict, obtain assistance, and protect the integrity of their conscience and reputation, as well as the integrity of the group of people who participated in the decisions. These goals could conflict with each other, or with ethical goals, in problematic ways. Being aware of these potentially conflicting goals may help physicians to resolve ethical difficulties more effectively. This awareness should also contribute to informing the practice of ethics consultation.Objective:To identify strategies used by physicians in dealing with ethical difficulties in their practice.Design, setting, and participants:National survey of internists, oncologists, and intensive care specialists by computer assisted telephone interviews (n =  344, response rate  =  64%). As part of this survey, we asked physicians to tell us about a recent ethical dilemma they had encountered in their medical practice. Transcripts of their open-ended responses were analysed using coding and analytical elements of the grounded theory approach.Main measurements:Strategies and approaches reported by respondents as part of their account of a recent ethical difficulty they had encountered in their practice.Results:When faced with ethical difficulties, the physicians avoided conflict and looked for assistance, which contributed to protecting, or attempting to protect, the integrity of their conscience and reputation, as well as the integrity of the group of people who participated in the decisions. These efforts sometimes reinforced ethical goals, such as following patients’ wishes or their best interests, but they sometimes competed with them. The goals of avoiding conflict, obtaining assistance, and protecting the respondent’s integrity and that of the group of decision makers could also compete with each other.Conclusion:In resolving ethical difficulties in medical practice, internists entertained competing goals that they did not always successfully achieve. Additionally, the means employed were not always the most likely to achieve those aims. Understanding these aspects of ethical decision making in medical practice is important both for physicians themselves as they struggle with ethical difficulties and for the ethics consultants who wish to help them in this process.