bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a Contaminating
Mycobacterium tuberculosis
Strain with a Transposition of an IS
6110
Insertion Element Resulting in an Altered Spoligotype
Authors: Benjamin William H. , Lok Kerry H. , Harris Randall , Brook Nancy , Bond Lisa , Mulcahy Donna , Robinson Nancy , Pruitt Virginia , Kirkpatrick deNay P. , Kimerling Michael E. , Dunlap Nancy E. 
Published: July 2002

ABSTRACT

Molecular fingerprinting with the IS
6110
insertion sequence is useful for tracking transmission of
Mycobacterium tuberculosis
within a population or confirming specimen contamination in the laboratory or through instrumentation. Secondary typing with other molecular methods yields additional information as to the relatedness of strains with similar IS
6110
fingerprints. Isolated, relatively rare, random events within the
M. tuberculosis
genome alter molecular fingerprinting patterns with any of the methods; therefore, strains which are different by two or more typing methods are usually not considered to be closely related. In this report, we describe two strains of
M. tuberculosis
, obtained from the same bronchoscope 2 days apart, that demonstrated unique molecular fingerprinting patterns by two different typing methods. They were closely linked through the bronchoscope by a traditional epidemiologic investigation. Genetic analysis of the two strains revealed that a single event, the transposition of an IS
6110
insertion sequence in one of the strains, accounted for both the differences in the IS
6110
pattern and the apparent deletion of a spacer in the spoligotype. This finding shows that a single event can change the molecular fingerprint of a strain in two different molecular typing systems, and thus, molecular typing cannot be the only means used to track transmission of this organism through a population. Traditional epidemiologic techniques are a necessary complement to molecular fingerprinting so that radical changes within the fingerprint pattern can be identified.
Unsatisfactory Performance of Flow Cytometer UF-100 and Urine Strips in Predicting Outcome of Urine Cultures
Authors: Zaman Zahur , Roggeman Sylvie , Verhaegen Jan 
Published: July 2002

ABSTRACT
UF-100 flow cytometer and urine strip results were cross-interpreted to predict culture outcomes. The best negative predictive value was obtained with bacteria at ≥1,000/μl, white blood cells at ≥20/μl, or leukocyte esterase positivity. Nine of 24 false negatives were clinically significant. Thus, UF-100 and urine strip results do not accurately predict the outcome of cultures.
No Evidence of Infectious Retroviruses in Measles Virus Vaccines Produced in Chicken Embryo Cell Cultures
Authors: Shahabuddin Muhammad , Sears Johnna F. , Khan Arifa S. 
Published: July 2002

ABSTRACT

All vaccines that are prepared in chicken embryo fibroblasts (CEFs) contain a low level of particle-associated reverse transcriptase (RT) activity, which is produced from the avian cell substrate. The RNAs present in the particles have sequence homology to viral DNAs belonging to the ancient endogenous avian virus (EAV) family or to the avian sarcoma-leukosis virus (ALV)-related subgroup E endogenous virus loci. Although no replication-competent retrovirus has been associated with the RT activity produced from CEFs, there have been some theoretical safety concerns regarding potential consequences of integration of EAV and ALV sequences in human DNA, which may result from nonproductive infection with replication-defective particles or infection with EAV and ALV pseudotypes bearing measles virus envelopes. To address these possibilities, we have analyzed EAV and ALV particles in a measles virus vaccine equivalent (MVVE) preparation, obtained from a U.S. manufacturer, for integration and for replication in human peripheral blood mononuclear cells (PBMCs). The results show the absence of EAV and ALV integrants in DNA prepared from MVVE-inoculated human cells by direct DNA PCR and
Alu
PCR assays and no propagation of retrovirus in 18-day cultures of MVVE-inoculated human PBMCs by a highly sensitive PCR-based RT assay. These results provide further confidence regarding the safety of chicken RT activity in live viral vaccines and support the continued use of chick-cell-derived vaccines in humans.
Nosocomial Spread of an Unusual Methicillin-Resistant
Staphylococcus aureus
Clone That Is Sensitive to All Non-β-Lactam Antibiotics, Including Tobramycin
Authors: Pournaras Spyros , Slavakis Aris , Polyzou Aleka , Sofianou Danai , Maniatis Antonios N. , Tsakris Athanassios 
Published: July 2002

ABSTRACT

Between January and December 1999, in Hippokration General Hospital, Thessaloniki, Greece, a large proportion of the methicillin-resistant
Staphylococcus aureus
isolates (34.4%) exhibited susceptibility to virtually all alternative non-β-lactam antibiotics, including tobramycin. Twenty-five of them were selected randomly for further testing; all belonged to a unique genotype and were characterized as heterogeneously resistant to oxacillin. The
aadD
gene, encoding tobramycin resistance, failed to be amplified in all cases, indicating absence of the gene or the entire plasmid pUB110 from the
mec
DNA.
Heterogeneity of
Pneumocystis
Sterol Profiles of Samples from Different Sites in the Same Pair of Lungs Suggests Coinfection by Distinct Organism Populations
Authors: Amit Zunika , Kaneshiro Edna S. 
Published: July 2002

ABSTRACT

Sterol profiles of samples taken from different sites of a
Pneumocystis
-infected human lung showed large variations in pneumocysterol similar to those that occur among samples from different patients. Thus, the influence of diet or drugs on pneumocysterol accumulation was ruled out, suggesting distinct phenotypic populations as the basis for the heterogeneity.
Phage Types and Genotypes of Shiga Toxin-Producing
Escherichia coli
O157 in Finland
Authors: Saari Marjut , Cheasty Thomas , Leino Kirsikka , Siitonen Anja 
Published: July 2002

ABSTRACT

This study examined Shiga toxin-producing
Escherichia coli
(STEC) O157, using phage typing, pulsed-field gel electrophoresis, and typing of Shiga toxin variant genes by PCR with restriction fragment length polymorphism in an epidemiological survey of STEC O157 isolated from humans in Finland between 1990 and 1999.
Novel Mycobacterium Related to
Mycobacterium triplex
as a Cause of Cervical Lymphadenitis
Authors: Hazra Rohan , Floyd Margaret M. , Sloutsky Alexander , Husson Robert N. 
Published: July 2002

ABSTRACT

The
Mycobacterium avium
complex (MAC) is an important cause of cervical lymphadenitis in children, and its incidence appears to be increasing in the United States and elsewhere. In areas where
Mycobacterium tuberculosis
is not prevalent,
M. avium
causes the vast majority of cases of mycobacterial lymphadenitis, although several other nontuberculous mycobacterial species have been reported as etiologic agents. This report describes the case of a child with cervical lymphadenitis caused by a nontuberculous mycobacterium that could not be identified using standard methods, including biochemical reactions and genetic probes. Direct 16S ribosomal DNA sequencing showed greater than 99% homology with
Mycobacterium triplex
, but sequence analysis of the 283-bp 16S-23S internal transcribed spacer (ITS) sequence showed only 95% identity, suggesting that it is a novel species or subspecies within a complex of organisms that includes
M. triplex
. Mycolic acid high-performance liquid chromatography analysis also identified this isolate as distinct from
M. triplex
, and differences in susceptibility to streptomycin and rifampin between this strain and
M. triplex
were also observed. These data support the value of further testing of clinical isolates that test negative with the MAC nucleic acid probes and suggest that standard methods used for the identification of mycobacteria may underestimate the complexity of the genus
Mycobacterium
. ITS sequence analysis may be useful in this setting because it is easy to perform and is able to distinguish closely related species and subspecies. This level of discrimination may have significant clinical ramifications, as closely related organisms may have different antibiotic susceptibility patterns.
A Combination of Two Genetic Markers Is Sufficient for Restriction Fragment Length Polymorphism Typing of
Mycobacterium tuberculosis
Complex in Areas with a High Incidence of Tuberculosis
Authors: Rasolofo-Razanamparany Voahangy , Ramarokoto Herimanana , Aurégan Guy , Gicquel Brigitte , Chanteau Suzanne 
Published: July 2002

ABSTRACT

The incidence of tuberculosis (TB) in Madagascar is 150 cases per 100,000 people. Because of this endemicity, we studied the genetic diversity of
Mycobacterium tuberculosis
strains isolated in four big cities in 1994 to 1995 with the aim of monitoring TB transmission. Isolates from 316 cases of pulmonary TB (PTM
+
) were typed by Southern hybridization with genetic markers IS
6110
and DR. Of the 316 PTM
+
strains, 66 (20.8%) had a single IS
6110
band and were differentiated by the DR marker into 33 profiles. Using both markers, 37.7% (119) of the patients were clustered, a proportion similar to that in countries with a high prevalence of TB. There was no significant difference between clustered and nonclustered patients in age, sex,
Mycobacterium bovis
BCG status, and drug susceptibility of strains. Clustering was significantly greater in the capital, Antananarivo, than in the other cities, suggesting a higher rate of transmission. However, most of the patients in clusters were living in different areas, and, within a distance of 0.7 km, we did not find epidemiologically unrelated strains with the same restriction fragment length polymorphism profile. Despite an apparently low polymorphism, genetic markers such as IS
6110
are potentially valuable for monitoring TB transmission. However, the high proportion of Malagasy isolates with a single IS
6110
copy makes this marker alone unsuitable for typing. Additional markers such as DR are necessary for the differentiation of the isolates and for epidemiological surveys.
Random Amplified Polymorphic DNA Assay as a Rapid Tool in Screening for
Neisseria meningitidis
Serogroup C Isolates of Electrophoretic Type 24
Authors: Schmink Susanna , Reeves Michael W. , Plikaytis Brian , Popovic Tanja 
Published: July 2002

ABSTRACT

Neisseria meningitidis
serogroup C (NMSC) isolates of electrophoretic type 24 (ET-24), as identified by multilocus enzyme electrophoresis, are the main cause of serogroup C meningococcal disease outbreaks and sporadic meningococcal disease in the United States. We evaluated a random amplified polymorphic DNA assay as a rapid tool to screen for isolates of ET-24 by testing 199 NMSC isolates of 51 different ETs. A sensitivity of 88% and a specificity of 87% was achieved in identification of ET-24 isolates when the patterns obtained by two primers, P1 and P5, were analyzed together.
PCR-Hybridization Assay for
Mycobacterium avium
Complex: Optimization of Detection in Peripheral Blood from Humans
Authors: Ferrario Giulio , Gori Andrea , Rossi Agostino , Catozzi Lidia , Molteni Chiara , Marchetti Giulia , Bandera Alessandra , Rossi Maria Cristina , Esposti Anna Degli , Franzetti Fabio 
Published: July 2002

ABSTRACT

We evaluated the sensitivity of a DNA amplification test for the detection of
Mycobacterium avium
in blood samples using different blood components and different DNA extraction methods.
M. avium
-inoculated blood samples were processed to obtain separate blood components: peripheral blood mononuclear cells (PBMCs), polymorphonuclear cells (PMNCs), and whole-blood sodium dodecyl sulfate (SDS)-lysate pellets. The sensitivity for the detection of the lowest mycobacterial load (1 CFU/ml) was significantly greater (
P
< 0.01) with DNA extracted from SDS-lysate pellets than with DNA extracted from PBMCs or PMNCs. Subsequently, DNA extraction methods based on guanidine NaOH, and proteinase were compared. The sensitivity of the guanidine-based method was significantly greater (
P
< 0.01) than those of the others.
One-Step Purification of
Enterocytozoon bieneusi
Spores from Human Stools by Immunoaffinity Expanded-Bed Adsorption
Authors: Accoceberry Isabelle , Thellier Marc , Datry Annick , Desportes-Livage Isabelle , Biligui Sylvestre , Danis Martin , Santarelli Xavier 
Published: July 2002

ABSTRACT

An original, reliable, and reproducible method for the purification of
Enterocytozoon bieneusi
spores from human stools is described. We recently reported the production of a species-specific monoclonal antibody (MAb) 6E52D9 immunoglobulin G2a (IgG2a) raised against the exospore of
E. bieneusi
spore walls. The MAb was used as a ligand to develop an immunoaffinity matrix. The mouse IgG2a MAb was bound directly to a Streamline rProtein A adsorbent, used for expanded-bed adsorption of immunoglobulins, for optimal spatial orientation of the antibody and maximum binding efficiency of the antigen. The complex was then cross-linked covalently using dimethyl pimelimidate dihydrochloride. After incubation of the immunoaffinity matrix with filtered stool samples containing numerous
E. bieneusi
spores and before elution with 6 M guanidine HCl, the expansion of the adsorbent bed eliminated all the fecal contaminants. The presence of spores in the elution fractions was determined by an indirect immunofluorescence antibody test (IFAT).
E. bieneusi
spores were found in the elution fraction in all four experiments and were still highly antigenic as indicated by IFAT. Smears examined by light microscopy contained very clean spores with no fecal debris or background bacterial and fungal contaminants. However, spore recovery rates were relatively low: an average of 10
7
spores were purified per run. This technique for isolating
E. bieneusi
spores directly from human stool samples with a high degree of purity opens up new approaches for studying this parasite.
Development of an
env
gp41-Based Heteroduplex Mobility Assay for Rapid Human Immunodeficiency Virus Type 1 Subtyping
Authors: Agwale S. M. , Robbins K. E. , Odama L. , Saekhou A. , Zeh C. , Edubio A. , Njoku O. M. , Sani-Gwarzo N. , Gboun M. F. , Gao F. , Reitz M. , Hone D. , Folks T. M. , Pieniazek D. , Wambebe C. , Kalish M. L. 
Published: July 2002

ABSTRACT

The gp120 region of the human immunodeficiency virus type 1 (HIV-1) envelope (
env
) gene exhibits a high level of genetic heterogeneity across the group M subtypes. The heteroduplex mobility assay (HMA) has successfully been used to assign subtype classifications, but C2V5 primers often fail to amplify African strains. We developed an
env
gp41-based HMA for which the target sequence is amplified with highly conserved gp41 primers, known to efficiently amplify nucleic acids from HIV-1 group M, N, and O viruses. By using gp41 from a new panel of reference strains, the subtype assignments made by our modified HMA were concordant with those obtained by sequencing and phylogenetic analysis of 34 field strains from 10 countries representing subtypes A to G. Testing of field strains from Nigeria further demonstrated the utility of this modified assay. Of 28 samples, all could be amplified with gp41 primers but only 17 (60.7%) could be amplified with the standard C2V5 primers. Therefore, gp41-based HMA can be a useful tool for the rapid monitoring of prevalent subtypes in countries with divergent strains of circulating HIV-1.
Amplified Fragment Length Polymorphism Fingerprinting for Identification of a Core Group of
Neisseria gonorrhoeae
Transmitters in the Population Attending a Clinic for Treatment of Sexually Transmitted Diseases in Amsterdam, The Netherlands
Authors: Spaargaren Joke , Stoof Jeroen , Fennema Han , Coutinho Roel , Savelkoul Paul 
Published: July 2002

ABSTRACT

Amplified fragment length polymorphism analysis seems well suited for studying the epidemiology of isolates of
Neisseria gonorrhoeae
obtained from patients attending the Sexually Transmitted Disease Outpatient Clinic in Amsterdam, The Netherlands. It shows potential to identify the core group of transmitters.
Genetic Diversity and Biochemical Characteristics of
Trichosporon asahii
Isolated from Clinical Specimens, Houses of Patients with Summer-Type-Hypersensitivity Pneumonitis, and Environmental Materials
Authors: Sugita Takashi , Ichikawa Tomoe , Matsukura Manami , Sueda Mika , Takashima Masako , Ikeda Reiko , Nishikawa Akemi , Shinoda Takako 
Published: July 2002

ABSTRACT

Trichosporon asahii
, which is distributed in the environment, is the major causative agent of the opportunistic infection trichosporonosis, and it also causes summer-type hypersensitivity pneumonitis (SHP). Random amplification of polymorphic DNA analysis was used to determine the intraspecies diversity of 39
T. asahii
isolates from clinical specimens, SHP patients' houses, and environmental materials. The three primers used revealed 46 polymorphic bands. A phenogram was generated by the unweighted pair-group method with arithmetic mean. Clinical isolates formed a cluster, characterized by a 90% matching coefficient, but they did not cluster with strains isolated from SHP patients' houses or environmental sources. In addition, the biochemical characteristics of 86 strains from three sources were examined with 31 compounds using an ID32C kit, and a phenogram was constructed. The phenogram consisted of three major clusters. Cluster I included most of the clinical SHP isolates, and cluster II included most of the environmental isolates. Cluster III contained only one strain. A remarkable difference was found in the abilities of the strains belonging to clusters I and II to utilize six compounds. These results suggest that the genetic diversity and biochemical characteristics of
T. asahii
seem to be related to the source of the isolate. We also found a specific DNA fragment for the clinical isolates and strains isolated from SHP patients' houses.
Utility of 2,3-Bis(2-Methoxy-4-Nitro-5-Sulfophenyl)-5-[(Phenyl-Amino)Carbonyl]-2
H
-Tetrazolium Hydroxide (XTT) and Minimum Effective Concentration Assays in the Determination of Antifungal Susceptibility of
Aspergillus fumigatus
to the Lipopeptide Class of Compounds
Authors: Hawser S. P. , Jessup C. , Vitullo J. , Ghannoum M. A. 
Published: July 2002

ABSTRACT

The susceptibility of
Aspergillus fumigatus
to mulundocandin, an echinocandin-like compound, and other antifungal agents was assessed by the National Committee for Clinical Laboratory Standards (NCCLS) M38-P method, a 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-5-[(phenyl-amino)carbonyl]-2
H
-tetrazolium hydroxide (XTT)-based colorimetric assay, and determination of morphologic alterations by microscopy. In contrast to the NCCLS M38-P method, which does not predict the activity in vivo, the XTT-based assay showed that
A. fumigatus
is susceptible to mulundocandin. Thus, the XTT-based assay might be useful for determination of the susceptibilities of molds to echinocandins. Further evaluation is warranted.
First Report of Human Infection Due to the Fungus
Triadelphia pulvinata
Authors: Al-Hedaithy Saleh S. A. 
Published: July 2002

ABSTRACT

Triadelphia pulvinata
, a soil hyphomycete, was found to be the cause of eczematoid, scaly, grey lesions on the skin of both eyelids of a 30-year-old Indian male living in Saudi Arabia. Repeated KOH preparations of the skin scrapings showed presence of sclerotic, branched, septate hyphae. When cultured, skin scrapings from the lesion grew the dematiaceous fungus
T. pulvinata
. Treatment with topical clotrimazole cured the infection, and no recurrence of the infection was noted in a 5-year follow-up.
Phylogenetic Origin of Hepatitis B Virus Strains with Precore C-1858 Variant
Authors: Alestig Erik , Hannoun Charles , Horal Peter , Lindh Magnus 
Published: July 2002

ABSTRACT
Mutations that prevent the expression of the hepatitis B e antigen frequently emerge in the immunoreactive phase of infection. The predominant mutation, the precore G→A-1896 mutation, is restricted by the variability at position 1858 and is rare in strains with cytosine at nucleotide 1858. The C-1858 variant is characteristic of genotype A. It also occurs in genotypes C and F, but not in B, D, or E, explaining the geographical variation in the prevalence of precore mutants. C-1858 strains have been frequently observed in southeast Asia, but have not been phylogenetically characterized. By sequencing eight complete hepatitis B virus genomes, C-1858 variants of east Asian origin were found to constitute a phylogenetic entity within genotype C that probably diverged several hundred years ago. Further study of the distribution of this variant is warranted.
Performance Characteristics of the COBAS Amplicor Hepatitis C Virus (HCV) Monitor, Version 2.0, International Unit Assay and the National Genetics Institute HCV Superquant Assay
Authors: Konnick Eric Q. , Erali Maria , Ashwood Edward R. , Hillyard David R. 
Published: July 2002

ABSTRACT

The COBAS Amplicor Hepatitis C Virus (HCV) Monitor assay, version 2.0, which reports in international units per milliliter, was compared to the assay reported in copies per milliliter by analyzing dilution series and clinical plasma samples by both methods. In addition, the Amplicor international unit assay was compared to the National Genetics Institute HCV Superquant assay. The dilution series ranged from <100 to 5,000,000 HCV RNA copies/ml and consisted of 32 points, assayed in triplicate in each assay. Thirty clinical samples ranging from 1,000 to 1,000,000 HCV RNA copies/ml were assayed in duplicate. Deming regression analysis comparing the Amplicor HCV RNA international units-per-milliliter and copies-per-milliliter assays was calculated as follows: (Amplicor international units per milliliter) = 1.030(Amplicor copies per milliliter) − 0.392;
R
2
= 0.981;
n
= 28;

S
y/x

(standard error of the estimate) = 0.129. The linearity of the Amplicor international units-per-milliliter assay was as follows: observed = 0.886(expected) + 0.437;
R
2
= 0.983;
n
= 30. The linearity of the Superquant assay was as follows: observed= 0.918 (expected) + 0.436;
R
2
= 0.986;
n
= 32. Deming regression analysis comparing the Amplicor and Superquant assays was calculated as follows: Superquant = 1.066(Amplicor) − 0.0197;
R
2
= 0.908;

S
y/x

= 0.308;
n
= 28. The Amplicor and Superquant assays were linear through the range of 600 to 600,000 IU of HCV RNA/ml and ∼300 to 5,000,000 HCV RNA copies/ml, respectively. The narrow range of the Amplicor assay means that some samples will require dilution and retesting for accurate quantification above 600,000 IU of HCV RNA/ml. The Amplicor and Superquant assays agreed well within the range of 600 to 600,000 IU of HCV RNA/ml (∼1,000 to ∼1,000,000 HCV RNA copies/ml). Overall, the Amplicor and Superquant assays agree well, and results obtained in one assay could be expected to compare well with results from the other when reported in copies per milliliter.
Detection of Neutralizing Antibodies against Human Papillomaviruses (HPV) by Inhibition of Gene Transfer Mediated by HPV Pseudovirions
Authors: Bousarghin Latifa , Combita-Rojas Alba-Lucia , Touzé Antoine , El Mehdaoui Slimane , Sizaret Pierre-Yves , Bravo Maria-Mercedes , Coursaget Pierre 
Published: July 2002

ABSTRACT
The goal of this study was to develop a human papillomavirus (HPV) neutralization assay using HPV pseudovirions generated in vitro. For this purpose, gene transfer efficiency of HPV virus-like particles (VLPs) was improved by using direct interaction between a reporter plasmid and the VLPs. Electron microscopic observation of the interaction between DNA molecules and VLPs revealed that VLPs always interact with a single DNA molecule and that VLPs bind to the end of linearized DNA molecules. An 100-fold improvement in the gene transfer was obtained by simple interaction between a linearized DNA molecule and VLPs. Moreover, direct interaction methods offer the possibility of transferring plasmids a size higher than that of the papillomavirus genome. The approach that we developed to generate HPV-16 and HPV-31 pseudovirions proved to be suitable for testing neutralizing antibodies in human sera both after immunization and after natural infection.