bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of Pulmonary Tuberculosis in Belgrade, Central Serbia
Authors: Vuković Dragana , Rüsch-Gerdes Sabine , Savić Branislava , Niemann Stefan 
Published: September 2003

ABSTRACT

In order to gain precise data on the actual epidemiology of tuberculosis (TB) in Belgrade, central Serbia, we conducted the molecular epidemiological investigation described herein. IS
6110
restriction fragment length polymorphism (RFLP) typing of 176
Mycobacterium tuberculosis
isolates was performed. These strains were obtained from 48.4% of all patients diagnosed with culture-proven pulmonary TB from April through September 1998 and from May through October 1999. Clusters containing strains with identical RFLP IS
6110
patterns were assumed to have arisen from recent transmission. Of the 176 cases, 55 (31.2%) were grouped into 23 clusters ranging in size from two to six patients. Nearly 80% of clustered patients were directly interviewed, and transmission between family-unrelated contacts was found to be predominant in the study population. Classical contact investigation identified only 2 (3.6%) of the 55 clustered patients. The clustering of TB patients was not associated with any demographic or clinical characteristic other than infection with multidrug-resistant (MDR)
M. tuberculosis
strains. Nearly 70% of MDR strains were clustered, which indicates active transmission of MDR TB in Belgrade. However, this was not observed by conventional epidemiologic surveillance. In conclusion, the first molecular epidemiologic analysis of TB in the region revealed frequent recent transmission of TB and pointed out significant shortcomings of the current concept for conventional contact tracing. The results presented also demonstrate that transmission of MDR TB in Belgrade is not optimally controlled, and they provide support for the development of improved control strategies, including application of molecular methods.
Applicability of a Real-Time Quantitative PCR Assay for Diagnosis of Respiratory Syncytial Virus Infection in Immunocompromised Adults
Authors: van Elden L. J. R. , van Loon A. M. , van der Beek A. , Hendriksen K. A. W. , Hoepelman A. I. M. , van Kraaij M. G. J. , Schipper P. , Nijhuis M. 
Published: September 2003

ABSTRACT
Respiratory syncytial virus (RSV) accounts for the majority of respiratory virus infections, producing high mortality rates in immunocompromised patients with hematologic malignancies. The available methods for the rapid detection of RSV by antigen detection or PCR either lack sensitivity, require complex laboratory manipulation, or have not been evaluated in this patient population. To assess the applicability of a TaqMan-based real-time PCR technique for the detection of RSV A and B in immunocompromised adults, we developed a rapid, sensitive detection method that simultaneously detects RSV A and B and can be applied in routine diagnostics. The specificity of the assay was assessed using a panel of reference strains of other respiratory viruses and RSV. Electron microscopy-counted stocks of RSV A and B were used to develop a quantitative PCR format. Eleven copies of viral RNA could be detected for RSV A strain Long, and 14 copies could be detected for RSV B strain 9320, corresponding to 50% tissue culture infective doses of 0.86 and 0.34, respectively. The assay was evaluated on 411 combined nose and throat swabs derived from immunocompromised adults with or without signs of respiratory tract infection. The diagnostic efficacy of the TaqMan PCR determined on the clinical samples showed that this real-time PCR technique was substantially more sensitive than the combination of conventional viral culture and shell vial culture. None of the clinical specimens derived from patients without signs of respiratory illness were found to be positive for RSV by real-time TaqMan PCR.
Real-Time PCR Assay Compared to Nested PCR and Antigenemia Assays for Detecting Cytomegalovirus Reactivation in Adult T-Cell Leukemia-Lymphoma Patients
Authors: Ikewaki Junji , Ohtsuka Eiichi , Kawano Rie , Ogata Masao , Kikuchi Hiroshi , Nasu Masaru 
Published: September 2003

ABSTRACT
We analyzed the efficiency of the quantitative real-time PCR assay for cytomegalovirus (CMV) reactivation in adult T-cell leukemia-lymphoma (ATL) patients and compared the results with those obtained with qualitative nested PCR and antigenemia assays. The viral load obtained by the real-time PCR assay closely paralleled the number of antigen-positive cells obtained with the antigenemia assay. Real-time PCR revealed that a large number of DNA copies could be present even in samples assessed as negative or low in antigen-positive cells (0 to 10 antigen-positive cells/50,000 cells) by antigenemia assay. CMV copy numbers did not differ between the negative and low-antigen-positive groups. When the input concentration for real-time PCR assay was 2,500 to 5,000 copies/ml, the positivity rate for the nested PCR assay was 47.3%, while the positivity rate was more than 90% at an input concentration of ≥50,000 copies/ml. Real-time PCR is more sensitive than the antigenemia and nested PCR assays. Moreover, real-time PCR was able to detect CMV reactivation earlier than the antigenemia and nested PCR assays through the use of longitudinal analysis in four ATL patients with CMV pneumonia. In longitudinal assessments, analysis of the results suggested that a cutoff level of 5,000 copies/ml might be used to initiate treatment. Real-time PCR is more suitable for monitoring CMV reactivation in ATL patients than the antigenemia and nested PCR assays. CMV viral loads of 5,000 copies/ml are proposed as the cutoff for initiating antiviral therapy in ATL patients.
Molecular Typing of
Salmonella enterica
Serovar Typhi Isolates from Various Countries in Asia by a Multiplex PCR Assay on Variable-Number Tandem Repeats
Authors: Liu Yichun , Lee May-Ann , Ooi Eng-Eong , Mavis Yeo , Tan Ai-Ling , Quek Hung-Hiang 
Published: September 2003

ABSTRACT

A multiplex PCR method incorporating primers flanking three variable-number tandem repeat (VNTR) loci (arbitrarily labeled TR1, TR2, and TR3) in the CT18 strain of
Salmonella enterica
serovar Typhi has been developed for molecular typing of
S. enterica
serovar Typhi clinical isolates from several Asian countries, including Singapore, Indonesia, India, Bangladesh, Malaysia, and Nepal. We have demonstrated that the multiplex PCR could be performed on crude cell lysates and that the VNTR banding profiles produced could be easily analyzed by visual inspection after conventional agarose gel electrophoresis. The assay was highly discriminative in identifying 49 distinct VNTR profiles among 59 individual isolates. A high level of VNTR profile heterogeneity was observed in isolates from within the same country and among countries. These VNTR profiles remained stable after the strains were passaged extensively under routine laboratory culture conditions. In contrast to the
S. enterica
serovar Typhi isolates, an absence of TR3 amplicons and a lack of length polymorphisms in TR1 and TR2 amplicons were observed for other
S. enterica
serovars, such as
Salmonella enterica
serovar Typhimurium,
Salmonella enterica
serovar Enteritidis, and
Salmonella enterica
serovar Paratyphi A, B, and C. DNA sequencing of the amplified VNTR regions substantiated these results, suggesting the high stability of the multiplex PCR assay. The multiplex-PCR-based VNTR profiling developed in this study provides a simple, rapid, reproducible, and high-resolution molecular tool for the epidemiological analysis of
S. enterica
serovar Typhi strains.
Comparing First-Void Urine Specimens, Self-Collected Vaginal Swabs, and Endocervical Specimens To DetectChlamydia trachomatisandNeisseria gonorrhoeaeby a Nucleic Acid Amplification Test
Authors: Shafer Mary-Ann , Moncada Jeanne , Boyer Cherrie B. , Betsinger Kelli , Flinn Scott D. , Schachter Julius 
Published: September 2003

ABSTRACTWe set out to determine the prevalences ofChlamydia trachomatisandNeisseria gonorrhoeaeby ligase chain reaction as well as to determine the prevalence ofTrichomonas vaginalisby culture in a large and diverse national sample of non-health-care-seeking young women entering the military; we also sought to compare the abilities of three different techniques of collecting specimens (first-void urine, self-collected vaginal swab, and clinician-collected endocervical swab) to identify a positive specimen. A cross-sectional sample of young women was voluntarily recruited; as a part of their routine entry pelvic examination visit, they completed a self-administered reproductive health questionnaire and provided first-void urine (used to detectC. trachomatisandN. gonorrhoeae) and self-collected vaginal swabs (used to detectC. trachomatis,N. gonorrhoeae, andT. vaginalis). The number of positive tests divided by the number of sexually active women screened by each sampling method determined the rates of prevalence. The rate of infection with any of the three sexually transmitted diseases (STDs) tested was 14.1%. The total positive rates for each STD (identified by ≥1 specimen) were the following: forC. trachomatis, 11.6%;N. gonorrhoeae, 2.4%; andT. vaginalis, 1.7%. The proportions of positives identified by specimen type were, forC. trachomatisandN. gonorrhoeae, respectively, endocervix, 65 and 40%; urine, 72 and 24%; and vagina, 81 and 72%. The proportions of positives when specimen results were combined were, forC. trachomatisandN. gonorrhoeae, respectively, cervix plus urine, 86 and 49%; cervix plus vagina, 91 and 93%; and vagina plus urine, 94 and 79%. We concluded that STDs were epidemic in this population. Self-collected vaginal swabs identified the highest number of positive test results among single specimens, with the combined cervix-vagina results identifying the highest number of positive results. Self-collected vaginal swab collections are a feasible alternative to cervical specimen collections in this population, and the use of multiple types of specimens increases the positive yield markedly.
Unexpected Detection of Animal VP7 Genes among Common Rotavirus Strains Isolated from Children in Mexico
Authors: Laird A. R. , Ibarra V. , Ruiz-Palacios G. , Guerrero M. L. , Glass R. I. , Gentsch J. R. 
Published: September 2003

ABSTRACT
In the course of characterizing 103 rotaviruses from children in Mexico, we found that the majority of strains were globally common types (55.4% of total), while uncommon types represented 5.7%, mixed infections with common types represented 14.8%, and partially or fully nontypeable isolates represented about 24%. Serotype G9 was detected for the first time in Mexico. We sequenced a subset of strains that were G nontypeable by reverse transcriptase PCR and found surprisingly that two strains having common human rotavirus P genotypes (8 and 6) had serotype G3 and G4 VP7 gene sequences that shared closer homology with canine and porcine strains, respectively, than with human strains, suggesting that these isolates represented reassortants between human and animal rotaviruses.
Screening of Volunteer Students in Yaounde (Cameroon, Central Africa) forChlamydia trachomatisInfection and Genotyping of IsolatedC. trachomatisStrains
Authors: Ngandjio Antoinette , Clerc Maithe , Fonkoua Marie Christine , Thonnon Jocelyn , Njock Friede , Pouillot Regis , Lunel Françoise , Bebear Christiane , de Barbeyrac Bertille , Bianchi Anne 
Published: September 2003

ABSTRACTThe prevalence ofChlamydia trachomatisinfection was 3.78% out of 1,277 volunteer students screened by direct fluorescence assay and Cobas Amplicor PCR. The infection was associated with the nonuse or inconsistent use of condoms in women (P= 0.026) and a previous sexually transmitted infection in men (P= 0.023). The most frequent genotypes determined by sequencing theomp1genes of 25 clinical isolates were E (44%) and F (20%), and some strains harbored mutations, but E genotype strains did not.
Chemically Defined Media for Growth of
Haemophilus influenzae
Strains
Authors: Coleman Hannah N. , Daines Dayle A. , Jarisch Justin , Smith Arnold L. 
Published: September 2003

ABSTRACT

A chemically defined medium that supports the growth of both encapsulated and nontypeable
Haemophilus influenzae
strains in broth to densities that are ≥ 10
9
CFU/ml or on agar plates is described. The mean generation time of a panel of clinical isolates was comparable to that in rich, chemically undefined media (brain-heart infusion broth supplemented with heme and β-NAD).
Outbreak of Serogroup C Meningococcal Disease Caused by a Variant of
Neisseria meningitidis
Serotype 2a ET-15 in a Community of Men Who Have Sex with Men
Authors: Tsang Raymond S.W. , Kiefer Lori , Law Dennis K. S. , Stoltz Jan , Shahin Rita , Brown Shirley , Jamieson Frances 
Published: September 2003

ABSTRACT

We describe an outbreak, in a community of men who have sex with men, of serogroup C meningococcal disease caused by a genetic variant of the serotype 2a ET-15
Neisseria meningitidis
characterized by a point mutation in the gene coding for the serotype 2a antigen. A microbiological characterization of the outbreak strain is presented in this report.
Confirmation of Nontypeable
Streptococcus pneumoniae-
Like Organisms Isolated from Outbreaks of Epidemic Conjunctivitis as
Streptococcus pneumoniae
Authors: Carvalho Maria Gloria S. , Steigerwalt Arnold G. , Thompson Terry , Jackson Delois , Facklam Richard R. 
Published: September 2003

ABSTRACT

Eleven isolates representing five distinct outbreaks of pneumococcal conjunctivitis were examined for phenotypic and genetic characteristics. None of the strains possessed capsules, and all strains were susceptible to optochin, bile soluble, and Gen-Probe AccuProbe test positive. All 11 isolates were confirmed as
Streptococcus pneumoniae
by DNA-DNA reassociation experiments.
Evaluation of INNO-LiPA MYCOBACTERIA v2: Improved Reverse Hybridization Multiple DNA Probe Assay for Mycobacterial Identification
Authors: Tortoli Enrico , Mariottini Alessandro , Mazzarelli Gianna 
Published: September 2003

ABSTRACTINNO-LiPA MYCOBACTERIA (Innogenetics, Ghent, Belgium) is a reverse hybridization DNA probe assay that has been recently improved by increasing the number of identifiable mycobacterial species to 16. Our assessment, performed with 197 mycobacteria belonging to 81 taxa, revealed 100% specificity and sensitivity for 20 out of 23 probes. The probes specific forMycobacterium fortuitumcomplex, for theMycobacterium avium-intracellulare-scrofulaceumgroup, and forMycobacterium intracellularetype 2 cross-reacted with several mycobacteria rarely isolated from clinical specimens. The overall sensitivity was 100%, and the overall specificity was 94.4%.
Role of Baseline Human Immunodeficiency Virus Genotype as a Predictor of Viral Response to Tenofovir in Heavily Pretreated Patients
Authors: Barrios Ana , de Mendoza Carmen , Martín-Carbonero Luz , Ribera Esteve , Domingo Pere , Galindo María José , Gálvez Juan , Estrada Vicente , Dalmau David , Asensi Víctor , Soriano Vincent 
Published: September 2003

ABSTRACT

Human immunodeficiency virus (HIV)-infected patients (
n
= 153) failing antiretroviral therapy after exposure to compounds from all three drug families were monitored for 6 months after beginning a rescue intervention program including tenofovir (TDF). At 3 months, levels of HIV RNA in plasma dropped by a mean of 0.9 log
10
and the mean CD4 count increased by 52 cells/μl. At 6 months, HIV RNA levels had dropped by a mean of 1.06 log
10
and the mean CD4 count had increased by 49 cells/μl. Only five (3.7%) patients discontinued TDF use due to adverse events. In the multivariate analysis, the presence of M41L and/or L210W at baseline was the only viral determinant of a lower response to TDF.
Population Dynamics of Persistent
Staphylococcus aureus
Isolated from the Airways of Cystic Fibrosis Patients during a 6-Year Prospective Study
Authors: Kahl Barbara C. , Duebbers Angelika , Lubritz Gabriele , Haeberle Johannes , Koch Hans G. , Ritzerfeld Barbara , Reilly Marion , Harms Erik , Proctor Richard A. , Herrmann Mathias , Peters Georg 
Published: September 2003

ABSTRACT

Molecular typing of normal (
n
= 456) and small-colony-variant (SCV;
n
= 239)
Staphylococcus aureus
isolates cultured from the airways of 52 of 72 cystic fibrosis (CF) patients (72.2%) during a 6-year prospective study revealed a median long-term persistence of 37 months (range, 6 to 70). SCV persisted longer in the airways than the normal
S. aureus
(statistically not significant). Pulsed-field gel electrophoresis identified six prevalent clonal lineages, which were cultured from more than one patient (3 to 12 patients), and 39 individual clones, which were isolated only from single patients. The SCV phenotype was not restricted to a distinct clonal lineage but occurred in many different clones. Most patients (33 of 52, 63.46%) harbored single clones. This study provides a basis for improved understanding of
S. aureus
colonization and infection dynamics in CF patients.
Prevalence of Fragilysin Gene in
Bacteroides fragilis
Isolates from Blood and Other Extraintestinal Samples
Authors: Foulon Ina , Piérard Denis , Muyldermans Gaëtan , Vandoorslaer Kristof , Soetens Oriane , Rosseel Paul , Lauwers Sabine 
Published: September 2003

ABSTRACT

Of 166
Bacteroides fragilis
isolates, 26.2% of 103 isolates from blood and 20.6% of 63 extraintestinal isolates harbored the fragilysin gene (difference not statistically significant). Clinical characteristics and evolution were comparable in patients with
B. fragilis
bacteremia with or without this enterotoxin. Fragilysin seems not to be an important virulence factor in
B. fragilis
disease.
Highly Sensitive PCR Assay for Routine Diagnosis of African Swine Fever Virus in Clinical Samples
Authors: Agüero M. , Fernández J. , Romero L. , Sánchez Mascaraque C. , Arias M. , Sánchez-Vizcaíno J. M. 
Published: September 2003

ABSTRACT
This work provides a novel, highly sensitive, hot start PCR method for rapid and specific detection of African swine fever virus (ASFV) that can be used as a routine diagnostic test for ASFV in surveillance, control, and eradication programs. A confirmatory test of the specificity of this method based on restriction endonuclease analysis was also developed.
Streptococcus pneumoniae
Endocarditis: Persistence of DNA on Heart Valve Material 7 Years after Infectious Episode
Authors: Branger S. , Casalta J. P. , Habib G. , Collard F. , Raoult D. 
Published: September 2003

ABSTRACT

We amplified by PCR and sequenced
Streptococcus pneumoniae rpoB
from DNA of the cardiac valve of a man who had presented with pneumococcal endocarditis 7 years earlier. Histopathologically, the valve did not show evidence of endocarditis. This case raises the question of persistence of DNA without any evidence of infection.
Development of a 5′ Nuclease-Based Real-Time PCR Assay for Quantitative Detection of Cariogenic Dental Pathogens
Streptococcus mutans
and
Streptococcus sobrinus
Authors: Yoshida Akihiro , Suzuki Nao , Nakano Yoshio , Kawada Miki , Oho Takahiko , Koga Toshihiko 
Published: September 2003

ABSTRACT

A 5′ nuclease TaqMan PCR assay was developed for the quantitative detection of the major cariogenic bacteria
Streptococcus mutans
and
Streptococcus sobrinus
. The absolute and relative numbers of bacteria were measured by this method. This assay will be useful for quantifying these organisms in oral specimens and for analyzing biofilm formation.
Emergence of Invasive Serotype VIII Group B Streptococcal Infections in Denmark
Authors: Ekelund Kim , Slotved Hans-Christian , Nielsen Hans Ulrik , Kaltoft Margit S. , Konradsen Helle B. 
Published: September 2003

ABSTRACT
Serotype VIII group B streptococcus has only rarely been described outside Japan. The Streptococcus Unit, Statens Serum Institut, performed national surveillance of invasive group B streptococcal (GBS) diseases in Denmark in 1999 to 2002 and identified seven clinical GBS isolates of serotype VIII in blood from seven patients admitted to different hospitals.
Latex Assay for Serotyping of Group B
Streptococcus
Isolates
Authors: Slotved H.-C. , Elliott J. , Thompson T. , Konradsen H. B. 
Published: September 2003

ABSTRACT
We developed a group B streptococcus (GBS) latex serotyping kit that reduces the numbers of GBS nontypeable isolates by nearly 50%. A total of 232 isolates were tested, and 203 isolates were serotyped by the GBS latex test, while the capillary precipitation test serotyped 184 isolates.
Detection of
Mycoplasma pneumoniae
by Real-Time Nucleic Acid Sequence-Based Amplification
Authors: Loens K. , Ieven M. , Ursi D. , Beck T. , Overdijk M. , Sillekens P. , Goossens H. 
Published: September 2003

ABSTRACT

Real-time isothermal nucleic acid sequence-based amplification (RT-NASBA) was applied to the detection of
Mycoplasma pneumoniae
. In vitro-generated
M. pneumoniae
RNA was used to assess the sensitivity of the assay. The 95% hit rate was 148 molecules of
M. pneumoniae
RNA in the amplification and 10
4
molecules of in vitro-generated RNA after nucleic acid extraction. The sensitivity of the RT-NASBA and the conventional NASBA assays corresponded to 5 color-changing units (CCU) of
M. pneumoniae
. In spiked throat swabs, nasopharyngeal aspirates, bronchoalveolar lavages, and sputum, the sensitivity of both NASBA assays corresponded to 5 to 50 CCU of
M. pneumoniae
. A total of 17 clinical specimens positive for
M. pneumoniae
by PCR were also positive by conventional NASBA, but one specimen was negative by RT-NASBA. These results indicate that the sensitivity of detection of
M. pneumoniae
by RT-NASBA in respiratory samples might be slightly reduced compared to that by conventional NASBA. However, the real-time assay is superior in speed and ease of handling.
Genital Human Papillomavirus Genotypes in Northwestern Tanzania
Authors: Mayaud Philippe , Weiss Helen A. , Lacey Charles J. N. , Gill Dilbinder K. , Mabey David C. W. 
Published: September 2003

ABSTRACT
Using MY09-MY11 PCR and human papillomavirus (HPV) typing by reverse blot hybridization, we found a 34% cervical HPV prevalence among 561 pregnant women in Tanzania. One hundred three of 123 women (84%) with typeable samples harbored high-risk oncogenic strains. HPV type 16 (HPV-16) was the most prevalent subtype (18%) among HPV-infected women and among women with cervical neoplasia (3 of 19). A multivalent vaccine for HPV-16, -18, -31, -33, and -35 would be necessary to prevent 50% of the neoplasia in this population.
Direct Detection of Multidrug-Resistant
Mycobacterium tuberculosis
in Clinical Specimens in Low- and High-Incidence Countries by Line Probe Assay
Authors: Johansen Isik Somuncu , Lundgren Bettina , Sosnovskaja Anaida , Thomsen Vibeke Østergaard 
Published: September 2003

ABSTRACT

The INNO-LiPA Rif.TB assay is designed for the detection of
rpoΒ
gene mutations causing rifampin resistance in isolates. We applied the method directly to 60 Lithuanian and Danish clinical specimens to detect rifampin resistance rapidly. Results were obtained in 78.3% of clinical specimens, and all were concordant with those obtained by BACTEC 460. The assay could have major impact on the management of multidrug-resistant tuberculosis.
Difference in
FKS1
Gene Sequences between Serotypes A and D of
Cryptococcus neoformans
Authors: Tanaka Reiko , Imanishi Yumi , Nishimura Kazuko 
Published: September 2003

ABSTRACT

We compared sequences of the glucan synthase (
FKS1
) gene in serotypes A and D of
Cryptococcus neoformans
. Four introns were present in serotype D but not serotype A. PCR with primers that flank these introns permits simple differentiation of serotypes A and D.
Shell Vial Culture as a Tool for Isolation of
Brucella melitensis
in Chronic Hepatic Abscess
Authors: Rovery Clarisse , Rolain Jean Marc , Raoult Didier , Brouqui Philippe 
Published: September 2003

ABSTRACT

A 50-year-old man was admitted with a liver abscess and positive serology for
Brucella
spp. Liver pus and blood cultures remained sterile on conventional culture. Inoculation of liver pus onto eukaryotic cells by the centrifugation-shell vial technique yielded
Brucella melitensis
, identified by 16S rRNA gene amplification and sequencing.