bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Characterization and Drug Resistance Patterns of Strains of
Mycobacterium tuberculosis
Isolated from Patients in an AIDS Counseling Center in Port-au-Prince, Haiti: a 1-Year Study
Authors: Ferdinand Séverine , Sola Christophe , Verdol Béatrice , Legrand Eric , Goh Khye Seng , Berchel Mylène , Aubéry Alexandra , Timothée Maryse , Joseph Patrice , Pape Jean William , Rastogi Nalin 
Published: February 2003

ABSTRACT

Tuberculosis (TB) is one of the most common opportunistic diseases that appear among human immunodeficiency virus (HIV)-positive patients in Haiti. In this context the probable emergence of multidrug-resistant (MDR) strains of
Mycobacterium tuberculosis
is of great epidemiological concern. However, as routine culture of
M. tuberculosis
and drug susceptibility testing are not performed in Haiti, it has not been possible so far to evaluate the rate of drug resistance among
M. tuberculosis
isolates from circulating TB cases. This report describes the first study on the molecular typing and drug resistance of
M. tuberculosis
isolates from patients with culture-positive pulmonary tuberculosis monitored at the GHESKIO Centers in Haiti during the year 2000. Clinical, epidemiological, and drug susceptibility testing results were available for 157 patients with confirmed cases of TB, with a total of 8.9% of patients harboring MDR
M. tuberculosis
. A significant association between the occurrence of resistance and previous TB treatment was observed (
P
< 0.001), suggesting that a previous history of TB treatment was a risk factor associated with MDR TB in Haiti. The DNAs of individual isolates from 106 samples were available and were typed by spoligotyping and determination of the variable number of tandem DNA repeats. Both typing methods provided interpretable results for 96 isolates, and the clusters observed were further confirmed by ligation-mediated PCR to define potential cases of active transmission. Thirty-three (34%) of the isolates were found to be grouped into 11 clusters with two or more identical patterns. However, an assessment of risk factors (sex, HIV positivity, previous treatment, drug resistance) showed that none was significantly associated with the active transmission of TB. These observations suggest that acquired MDR TB is prevalent in Haiti and may be associated with compliance issues during TB treatment since prior TB therapy is the strongest risk factor associated with MDR TB. Prevention of TB transmission in Haiti should target active case investigation, routine detection of drug resistance, and adequate treatment of patients. The use of directly observed short-course therapy should be enforced throughout the country; and relapses, reactivations, or newly acquired infections should be discriminated by genotyping methods.
Clonal Reproduction and Limited Dispersal in an Environmental Population of
Cryptococcus neoformans
var.
gattii
Isolates from Australia
Authors: Halliday C. L. , Carter D. A. 
Published: February 2003

ABSTRACT

Cryptococcus neoformans
var.
gattii
is a causative agent of cryptococcosis and is thought to have a specific ecological association with a number of
Eucalyptus
species in Australia. However, the role that the tree plays in the life cycle of the fungus and the nature of the infectious propagule are not well understood. This study set out to examine whether sexual recombination is occurring in a natural population of
C. neoformans
var.
gattii
and whether the fungus disseminates between colonized trees. Thirty
C. neoformans
var.
gattii
isolates, consisting of both the α and
a
mating types, were collected from 13
Eucalyptus camaldulensis
trees growing along a riverbank in Renmark, South Australia. The genetic diversity within the population was studied by using amplified fragment length polymorphism fingerprinting, and each isolate was assigned a unique multilocus genotype. Population genetic analyses of the multilocus data found no evidence of genetic exchange between members of the population, indicating a clonal population structure. Canonical variate analysis was then used to study the relationship between isolates from different colonized trees. Isolates from individual trees were strongly correlated, and it appeared that dispersal between trees was not occurring to any appreciable extent. These results suggest that the eucalypt may not be the primary niche for
C. neoformans
var.
gattii
but that the decaying wood present in hollows on these trees may provide a favorable substrate for extensive clonal propagation of the yeast cells.
Simple Method for Screening
Candida
Species Isolates for the Presence of Secreted Proteinases: a Tool for the Prediction of Successful Inhibitory Treatment
Authors: Dostál Jií , Hamal Petr , Pavlíčková Libuše , Souček Milan , Ruml Tomáš , Pichová Iva , Hrušková-Heidingsfeldová Olga 
Published: February 2003

ABSTRACT

The yeasts of the genus
Candida
are opportunistic pathogens associated with the rising incidence of life-threatening infections in immunocompromised individuals. Secretion of aspartic proteinases has been determined to be one of the virulence factors of the pathogenic
Candida
species. To analyze the extracellular proteolytic activities of a large number of
Candida
clinical isolates, we developed a screening system based on a solid medium containing hemoglobin as the sole nitrogen source. The cleavage of hemoglobin by the secreted proteinases results in formation of clearance zones. The visibility of such zones was enhanced by addition of an acid-base indicator. Using this system, we assessed 245 clinical isolates of
Candida
from patients in the hospital of the Faculty of Medicine, Palacky University, Olomouc, Czech Republic, for the presence of secreted aspartic proteases (Saps). We also used the test plates for rapid semiquantitative testing of Sap inhibitors. Most of the pepstatin analogs affected the formation of the zones of clearance as well as the growth of
Candida albicans
,
C. tropicalis
, and
C. parapsilosis
colonies. By contrast, the human immunodeficiency virus proteinase inhibitors saquinavir, ritonavir, nelfinavir, and indinavir had no effect on the
Candida
strains tested. These results are in agreement with the inhibition constants obtained for the individual inhibitors with purified Saps. Thus, the plates containing hemoglobin proved to be an appropriate tool for the rapid and reliable assessment of Sap production and inhibition.
Comparison of PCR Assays for Detection of the Agent of Human Granulocytic Ehrlichiosis,
Anaplasma phagocytophilum
Authors: Massung Robert F. , Slater Kimetha G. 
Published: February 2003

ABSTRACT

Human granulocytic ehrlichiosis is an emerging infectious disease in the United States and Europe, and PCR methods have been shown to be effective for the diagnosis of acute infections. Numerous PCR assays and primer sets have been reported in the literature. The analytical sensitivities (limits of detection) of 13 published PCR primer sets were compared using DNA extracted from serial dilutions of
Anaplasma phagocytophilum
-infected HL-60 cells. The specificity of the assays that were able to detect ≤2.5 infected cells was tested by the use of template DNA extracted from
Ehrlichia chaffeensis
,
Rickettsia rickettsii
, and
Bartonella henselae
. The assays with the lowest limits of detection were shown to be a nested assay that amplifies the 16S rRNA gene (primer pairs ge3a-ge10 [primary] and ge9-ge3 [nested]; detects 0.25 infected cell), a direct assay that amplifies the major surface protein gene
msp2
(primer pair msp2-3f-msp2-3r; detects 0.25 infected cell), and a direct assay that amplifies the 16S rRNA gene (primer pair ehr521-ehr790; detects 0.25 infected cell). The specificity and limit of detection of the MSP2 and 16S rRNA direct assays were further tested by use of
A. phagocytophilum
template DNA from both North America and Europe and from human, tick, white-footed mouse, equine, deer, bovine, and wood rat samples and of template DNA from closely related species (
Anaplasma marginale
, the white-tailed deer agent, and additional
E. chaffeensis
-positive samples). Three manufacturers' PCR kits were tested and showed distinct variations in the limit of detection, specificity, and nonspecific background amplification. The importance of these results for the molecular diagnosis of human granulocytic ehrlichiosis is discussed.
Development of a Multilocus Sequence Typing Method for Analysis of
Listeria monocytogenes
Clones
Authors: Salcedo C. , Arreaza L. , Alcalá B. , de la Fuente L. , Vázquez J. A. 
Published: February 2003

ABSTRACT

This study is a first step in the development of multilocus sequence typing (MLST) method for
Listeria monocytogenes.
Nine housekeeping genes were analyzed in a set of 62 strains isolated from different sources and geographic locations in Spain. These strains were previously characterized by pulsed-field gel electrophoresis (PFGE). Because of low diversity, two loci were discarded from the study. The sequence analysis of the seven remaining genes showed 29 different allelic combinations, with 22 of them represented by only one strain. The results of this sequence analysis were generally consistent with those of PFGE. Because MLST allows the easy comparison and exchange of results obtained in different laboratories, the future application of this new molecular method could be a useful tool for the listeriosis surveillance systems that will allow the identification and distribution of analysis of
L. monocytogenes
clones in the environment.
Specimen Processing and Concentration of
Chlamydia trachomatis
Added Can Influence False-Negative Rates in the LCx Assay but Not in the APTIMA Combo 2 Assay When Testing for Inhibitors
Authors: Chong S. , Jang D. , Song X. , Mahony J. , Petrich A. , Barriga P. , Chernesky M. 
Published: February 2003

ABSTRACT

Inhibitors in clinical specimens can be detected by adding the target of nucleic acid amplification to the sample. Introduction of a
Chlamydia trachomatis
L2 434 preparation containing 12 elementary bodies (EBs) into first-void urine (FVU) from 225 nonpregnant women and 190 pregnant women before specimen processing by the assays produced false-negative rates of 0.48% (2 of 415 specimens) and 13% (44 of 338 specimens) by the APTIMA Combo 2 and the Chlamydia LCx tests, respectively. Reducing the amount of
C. trachomatis
added to one EB, a concentration closer to the APTIMA Combo 2 test cutoff, for a subset of 244 FVU specimens increased the number of specimens with false-negative results by the APTIMA Combo 2 assay to 7 (2.9%), suggesting that the strength of the input
C. trachomatis
per specimen has an influence on the number of specimens with false-negative results. Repeat testing after overnight storage and dilution decreased the APTIMA Combo 2 test false-negative rates to 0% (0 of 415 specimens) with the stronger inoculum and 0.8% (2 of 244 specimens) with the weaker inoculum; the false-negative rate of the LCx assay was reduced to 5.4% (18 of 334 specimens). When an additional 70 FVU specimens from women to which 12 EBs were added before specimen processing were tested by the LCx assay, 34 specimens had false-negative results, whereas 21 specimens had false-negative results when the
C. trachomatis
EBs were introduced after processing. Nine of the 21 specimens to which EBs were added after processing and all of the 34 urine specimens to which the target was added before processing remained falsely negative on repeat testing at a 1:2 dilution, suggesting that input
C. trachomatis
DNA was lost during processing by the LCx assay. In contrast, the APTIMA Combo 2 assay appears to have a higher sensitivity and either lost little nucleic acid during processing or demonstrated few problems with inhibitors of transcription-mediated amplification.
Analysis of an IS2404-Based Nested PCR for Diagnosis of Buruli Ulcer Disease in Regions of Ghana Where the Disease Is Endemic
Authors: Stienstra Ymkje , van der Werf Tjip S. , Guarner Jeannette , Raghunathan Pratima L. , Spotts Whitney Ellen A. , van der Graaf Winette T. A. , Asamoa Kwame , Tappero Jordan W. , Ashford David A. , King C. Harold 
Published: February 2003

ABSTRACTMycobacterium ulceranscauses Buruli ulcer disease (BUD), an ulcerative skin disease emerging mainly in West Africa. Laboratory confirmation of BUD is complicated as no “gold standard” for diagnosis exists. A nested primer PCR based on IS2404has shown promise as a diagnostic assay. We evaluated the IS2404-based PCR to detectM. ulceransDNA in tissue specimens from 143 BUD patients diagnosed according to the World Health Organization BUD clinical case definition in Ghana. Comparisons were made with culture and histopathology results. Variables influencing detection rate tested in this PCR protocol included the amount of tissue used and the stage of disease. The nested PCR was repeated on DNA extracted from a different part of the same biopsy specimen of 21 culture-positive samples. Of all 143 specimens, 107 (74.8%; 95% confidence interval, 68 to 82%) showed the presence ofM. ulceransDNA by PCR. Of the 78 histology-confirmed BUD patient samples, 64 (83%) were PCR positive. Detection rates were influenced neither by the amount of tissue processed for PCR nor by the stage of disease (preulcerative or ulcerative). Taken together, the two nested PCR tests on the subset of 21 culture-positive samples were able to detectM. ulceransDNA in all 21 culture-confirmed patients. For future studies, small tissue samples, e.g., punch biopsy samples, might be sufficient for case confirmation.
Rapid Detection of Rifampin Resistance in
Mycobacterium tuberculosis
Isolates by Heteroduplex Analysis and Determination of Rifamycin Cross-Resistance in Rifampin-Resistant Isolates
Authors: Sarıbaş Zeynep , Kocagöz Tanıl , Alp Alpaslan , Günalp Ayfer 
Published: February 2003

ABSTRACT

Direct heteroduplex analysis and a universal heteroduplex generator assay were performed to detect rifampin resistance rapidly in Turkish
Mycobacterium tuberculosis
isolates. Cross-resistance to rifapentine, rifabutin, and rifalazil was investigated. A relationship between specific mutations and resistance patterns, which can guide the choice of an appropriate therapeutic regimen for tuberculosis patients, was identified.
Spread of Integron-Associated VIM-Type Metallo-β-Lactamase Genes among Imipenem-Nonsusceptible
Pseudomonas aeruginosa
Strains in Greek Hospitals
Authors: Giakkoupi P. , Petrikkos G. , Tzouvelekis L. S. , Tsonas S. , Legakis N. J. , Vatopoulos A. C. 
Published: February 2003

ABSTRACT

Fifty-eight imipenem-nonsusceptible (MIC ≥ 8 μg/ml)
Pseudomonas aeruginosa
strains isolated during May 2001 in 15 Greek hospitals were studied. Thirty-six isolates derived from nine hospitals carried VIM-type metallo-β-lactamase genes, as found by PCR. In 34 isolates,
bla
VIM
was associated with class 1 integrons of various sizes. DNA sequencing indicated the presence of
bla
VIM-2
gene cassettes in a variety of integron structures. Random amplified polymorphic DNA typing suggested diversity of the
bla
VIM
-positive strains. Synergy between 2-mercaptoacetic acid and imipenem indicated carbapenemase activity in 26
bla
VIM
-positive strains.
Evaluation of the Specificities of Five DNA Amplification Methods for the Detection of
Neisseria gonorrhoeae
Authors: Palmer H. M. , Mallinson H. , Wood R. L. , Herring A. J. 
Published: February 2003

ABSTRACT

The intragenus specificities of five molecular diagnostic methods for
Neisseria gonorrhoeae
were determined. Three assays were considered suboptimal. Molecular detection of
N. gonorrhoeae
from sites where other
Neisseria
spp. commonly occur or from any site in low-prevalence settings should be confirmed by a test targeting a different genetic locus.
Diagnosis of Enterovirus Infection by Genus-Specific PCR and Enzyme-Linked Immunosorbent Assays
Authors: Craig Maria E. , Robertson Peter , Howard Neville J. , Silink Martin , Rawlinson William D. 
Published: February 2003

ABSTRACT
PCR for the diagnosis of enterovirus infections is resource intensive but is increasingly used due to wide availability. Enzyme-linked immunosorbent assays (ELISAs) that detect heterotypical antibodies against enterovirus immunoglobulin M (IgM), IgA, and IgG were compared with reverse transcription-PCR by using primers specific to the 5′ untranslated regions of 60 enterovirus species. The ELISAs were less sensitive than the PCR, and only the ELISA for IgM was highly specific. When retrospective diagnosis is important or when specimens are unsuitable for PCR, the ELISA has a limited role if PCR is not available.
AFLMP1
Encodes an Antigenic Cell Wall Protein in
Aspergillus flavus
Authors: Woo Patrick C. Y. , Chong Ken T. K. , Leung Andy S. P. , Wong Samson S. Y. , Lau Susanna K. P. , Yuen Kwok-Yung 
Published: February 2003

ABSTRACT

We have previously reported the cloning and characterization of the
MP1
gene in
Penicillium marneffei
and the
AFMP1
gene in
Aspergillus fumigatus
and their use for serodiagnosis of penicilliosis and aspergilloma and invasive aspergillosis, respectively. In this study, we describe the cloning of the
AFLMP1
gene, which encodes the homologous antigenic cell wall protein in
Aspergillus flavus
, the most common
Aspergillus
species associated with human disease in our locality and in other Asian countries and the second most common
Aspergillus
species associated with human disease in Western countries.
AFLMP1
codes for a protein, Aflmp1p, of 273 amino acid residues, with a few sequence features that are present in Mp1p and Afmp1p, the homologous antigenic cell wall proteins in
P. marneffei
and
A. fumigatus
, respectively, as well as several other cell wall proteins of
Saccharomyces cerevisiae
and
Candida albicans
. It contains a serine- and threonine-rich region for O glycosylation, a signal peptide, and a putative glycosylphosphatidylinositol attachment signal sequence. Specific anti-Aflmp1p antibody was generated with recombinant Aflmp1p protein purified from
Escherichia coli
to allow further characterization of Aflmp1p. Indirect immunofluorescence analysis indicated that Aflmp1p is present on the surface of the hyphae of
A. flavus
. Finally, it was observed that patients with aspergilloma and invasive aspergillosis due to
A. flavus
develop a specific antibody response against Aflmp1p. This suggested that the recombinant protein and its antibody may be useful for serodiagnosis in patients with aspergilloma or invasive aspergillosis, and the protein may represent a good cell surface target for host humoral immunity.
Catheter-Related Sepsis Due toRhodotorula glutinis
Authors: Hsueh Po-Ren , Teng Lee-Jene , Ho Shen-Wu , Luh Kwen-Tay 
Published: February 2003

ABSTRACTWe describe a central venous catheter-related (Port-A-Cath; Smiths Industries Medical Systems [SIMS] Deltec, Inc., St. Paul, Minn.) infection caused byRhodotorula glutinisin a 51-year-old man with nasopharyngeal carcinoma. He was treated with fluconazole for 8 weeks and had the catheter removed. Two isolates ofR. glutinisrecovered from blood specimens (one obtained via peripheral veins and one via the catheter) before administration of fluconazole and one recovered from the removed catheter 17 days after initiation of fluconazole therapy exhibited high-level resistance to fluconazole (MICs, >256 μg/ml). These three isolates were found to belong to a single clone on the basis of identical antibiotypes determined by the E test (PDM Epsilometer; AB Biodisk, Solna, Sweden) and biotypes determined by API ID32 C (bioMerieux, Marcy I'Etoile, France) and their identical random amplified polymorphic DNA patterns.
Development of a 5′ Fluorogenic Nuclease-Based Real-Time PCR Assay for Quantitative Detection of
Actinobacillus actinomycetemcomitans
and
Porphyromonas gingivalis
Authors: Yoshida Akihiro , Suzuki Nao , Nakano Yoshio , Oho Takahiko , Kawada Miki , Koga Toshihiko 
Published: February 2003

ABSTRACT

A 5′ nuclease TaqMan PCR was developed for the quantitative detection of the periodontopathic bacteria
Actinobacillus actinomycetemcomitans
and
Porphyromonas gingivalis
. The relative numbers of bacteria were measured by the comparative threshold cycle method. This simplified method is a way of obtaining the relative quantities of these organisms from specimens and of monitoring the effect of therapy.
Rapid Identification of the Genus
Fonsecaea
by PCR with Specific Oligonucleotide Primers
Authors: Abliz Paride , Fukushima Kazutaka , Takizawa Kayoko , Nieda Norikazu , Miyaji Makoto , Nishimura Kazuko 
Published: February 2003

ABSTRACT

An oligonucleotide primer set based on internal transcribed spacer regions of ribosomal DNA for PCR which gives the amplicon for only the DNA from
Fonsecaea
species was designed. This set yielded an amplicon with 333 bp for all strains of
Fonsecaea pedrosoi
and
Fonsecaea compacta
examined but no amplicons for related dematiaceous fungi and pathogenic yeasts. PCR using this primer set was considered to be a useful method for the rapid identification of the genus
Fonsecaea
.
Ubiquity of Putative Type III Secretion Genes among Clinical and Environmental
Burkholderia pseudomallei
Isolates in Northern Australia
Authors: Smith-Vaughan H. C. , Gal D. , Lawrie P. M. , Winstanley C. , Sriprakash K. S. , Currie B. J. 
Published: February 2003

ABSTRACT

Horseradish peroxidase-like type III secretion (TTS1) genes were present in all 116 Northern Australian
Burkholderia pseudomallei
isolates tested but were not detected in other common environmental
Burkholderia
species. PCR of TTS1 genes may prove valuable as a diagnostic test.
Direct Identification of
Staphylococcus aureus
from Positive Blood Culture Bottles
Authors: Oliveira Kenneth , Brecher Stephen M. , Durbin Annette , Shapiro Daniel S. , Schwartz Donald R. , De Girolami Paola C. , Dakos Joanna , Procop Gary W. , Wilson Deborah , Hanna Chad S. , Haase Gerhard , Peltroche-Llacsahuanga Heidrun , Chapin Kimberle C. , Musgnug Michael C. , Levi Michael H. , Shoemaker Cynthia , Stender Henrik 
Published: February 2003

ABSTRACT

Fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes targeting
Staphylococcus aureus
16S rRNA is a novel method for direct identification of
S. aureus
from positive blood culture bottles. The test (S. aureus PNA FISH) is performed on smears made directly from positive blood culture bottles with gram-positive cocci in clusters (GPCC) and provides results within 2.5 h. A blinded comparison of
S. aureus
PNA FISH with standard identification methods was performed in collaboration with eight clinical microbiology laboratories. A total of 564 routine blood culture bottles positive for GPCC recovered from both aerobic and anaerobic media from three different manufacturers (ESP, BACTEC, and BacT/Alert) were included in the study. The sensitivity and specificity of
S. aureus
PNA FISH were 100% (57 of 57) and 99.2% (116 of 117), respectively, with 174 GPCC-positive ESP blood culture bottles, 98.5% (67 of 68) and 98.5% (129 of 131), respectively, with 200 GPCC-positive BACTEC blood culture bottles, and 100% (74 of 74) and 99.1% (115 of 116), respectively, with 190 GPCC-positive BacT/Alert blood culture bottles. It is concluded that
S. aureus
PNA FISH performs well with commonly used continuously monitoring blood culture systems.
PCR Assay To Detect
Bacillus anthracis
Spores in Heat-Treated Specimens
Authors: Fasanella A. , Losito S. , Adone R. , Ciuchini F. , Trotta T. , Altamura S. A. , Chiocco D. , Ippolito G. 
Published: February 2003

ABSTRACT

Recent interest in anthrax is due to its potential use in bioterrorism and as a biowarfare agent against civilian populations. The development of rapid and sensitive techniques to detect anthrax spores in suspicious specimens is the most important aim for public health. With a view to preventing exposure of laboratory workers to viable
Bacillus anthracis
spores, this study evaluated the suitability of PCR assays for detecting anthrax spores previously inactivated at 121°C for 45 min. The results indicate that heat treatment ensures the complete inactivation of
B. anthracis
spores without significantly affecting the efficiency of PCR assays.