bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Detection of the
Mycobacterium tuberculosis
Beijing Genotype and Its Ancient and Modern Sublineages by IS
6110
-Based Inverse PCR
Authors: Mokrousov Igor , Jiao Wei Wei , Valcheva Violeta , Vyazovaya Anna , Otten Tatiana , Ly Ho Minh , Lan Nguyen Ngoc , Limeschenko Elena , Markova Nadya , Vyshnevskiy Boris , Shen A Dong , Narvskaya Olga 
Published: August 2006

ABSTRACT

The
Mycobacterium tuberculosis
Beijing genotype strains appear to be hypervirulent and associated with multidrug-resistant tuberculosis. Therefore, the development of a both rapid and simple method to detect the
M. tuberculosis
Beijing genotype is of clinical interest per se. Previously, we described a simple and fast approach to detect the Beijing genotype based on IS
6110
inverse-PCR typing. Here, we evaluated this method against a large, diverse, and recent collection of strains. The study sample included 866
M. tuberculosis
strains representing but not limited to the regions in Russia, Europe, and East Asia where the Beijing genotype is endemic. Based on a spoligotyping method, 408 strains were identified as Beijing genotypes; they were additionally subdivided into ancient and modern sublineages based on the analysis of the NTF locus. All strains were further subjected to the IS
6110
-based inverse PCR. All of the Beijing genotype strains were found to have identical two-band (ancient sublineage) or three-band (modern sublineage) profiles that were easily recognizable and distinct from the profiles of the non-Beijing strains. Therefore, we suggest using IS
6110
-based inverse-PCR typing for the correct identification of the Beijing genotype and its major sublineages. The method is fast and inexpensive and does not require additional experiments but instead is implemented in the routine typing method of
M. tuberculosis
.
Multilocus Sequence Typing of Historical
Burkholderia pseudomallei
Isolates Collected in Southeast Asia from 1964 to 1967 Provides Insight into the Epidemiology of Melioidosis
Authors: McCombie Roberta L. , Finkelstein Richard A. , Woods Donald E. 
Published: August 2006

ABSTRACT

A collection of 207 historically relevant
Burkholderia pseudomallei
isolates was analyzed by multilocus sequence typing (MLST). The strain collection contains environmental isolates obtained from a geographical distribution survey of
B. pseudomallei
isolates in Thailand (1964 to 1967), as well as stock cultures and colony variants from the U.S. Army Medical Research Unit (Malaysia), the Walter Reed Army Institute for Research, and the Pasteur Institute (Vietnam). The 207 isolates of the collection were resolved into 80 sequence types (STs); 56 of these were novel. eBURST diagrams predict that the historical-collection STs segregate into three complexes when analyzed separately. When added to the 760 isolates and 365 STs of the
B. pseudomallei
MLST database, the historical-collection STs cluster significantly within the main complex of the eBURST diagram in an ancestral pattern and alter the
B. pseudomallei
“population snapshot.” Differences in colony morphology among reference isolates were found not to affect the STs assigned, which were consistent with the original isolates. Australian ST84 is likely characteristic of
B. pseudomallei
isolates of Southeast Asia rather than Australia, since multiple environmental isolates from Thailand and Malaysia share this ST with the single Australian clinical isolate in the MLST database. Phylogenetic evidence is also provided suggesting that Australian isolates may not be distinct from those of Thailand, since ST60 is common to environmental isolates from both countries. MLST and eBURST are useful tools for the study of population biology and epidemiology, since they provide methods to elucidate new genetic relationships among bacterial isolates.
Impact of Laboratory Cross-Contamination on Molecular Epidemiology Studies of Tuberculosis
Authors: Martínez Miguel , de Viedma Darío García , Alonso María , Andrés Sandra , Bouza Emilio , Cabezas Teresa , Cabeza Isabel , Reyes Armando , Sánchez-Yebra Waldo , Rodríguez Manuel , Sánchez M. Isabel , Rogado M. Cruz , Fernández Rosa , Peñafiel Teresa , Martínez Juan , Barroso Pilar , Lucerna M. Ángeles , Diez L. Felipe , Gutiérrez Carmelo 
Published: August 2006

ABSTRACT

Laboratory cross-contamination by
Mycobacterium tuberculosis
is known to be responsible for the misdiagnosis of tuberculosis, but its impact on other contexts has not been analyzed. We present the findings of a molecular epidemiology analysis in which the recent transmission events identified by a genotyping reference center were overestimated as a result of unnoticed laboratory cross-contamination in the original diagnostic laboratories.
Epidemiology of Candidemia in Brazil: a Nationwide Sentinel Surveillance of Candidemia in Eleven Medical Centers
Authors: Colombo Arnaldo L. , Nucci Marcio , Park Benjamin J. , Nouér Simone A. , Arthington-Skaggs Beth , da Matta Daniel A. , Warnock David , Morgan Juliette 
Published: August 2006

ABSTRACT

Candidemia studies have documented geographic differences in rates and epidemiology, underscoring the need for surveillance to monitor trends. We conducted prospective candidemia surveillance in Brazil to assess the incidence, species distribution, frequency of antifungal resistance, and risk factors for fluconazole-resistant
Candida
species. Prospective laboratory-based surveillance was conducted from March 2003 to December 2004 in 11 medical centers located in 9 major Brazilian cities. A case of candidemia was defined as the isolation of
Candida
spp. from a blood culture. Incidence rates were calculated per 1,000 admissions and 1,000 patient-days. Antifungal susceptibility tests were performed by using the broth microdilution assay, according to the Clinical and Laboratory Standards Institute guidelines. We detected 712 cases, for an overall incidence of 2.49 cases per 1,000 admissions and 0.37 cases per 1,000 patient-days. The 30-day crude mortality was 54%.
C. albicans
was the most common species (40.9%), followed by
C. tropicalis
(20.9%) and
C. parapsilosis
(20.5%). Overall, decreased susceptibility to fluconazole occurred in 33 (5%) of incident isolates, 6 (1%) of which were resistant. There was a linear correlation between fluconazole and voriconazole MICs (
r
= 0.54 and
P
< 0.001 [Spearman's rho]). This is the largest multicenter candidemia study conducted in Latin America and shows the substantial morbidity and mortality of candidemia in Brazil. Antifungal resistance was rare, but correlation between fluconazole and voriconazole MICs suggests cross-resistance may occur.
Serotype 1-Specific Monoclonal Antibody-Based Antigen Capture Immunoassay for Detection of Circulating Nonstructural Protein NS1: Implications for Early Diagnosis and Serotyping of Dengue Virus Infections
Authors: Xu Hua , Di Biao , Pan Yu-xian , Qiu Li-wen , Wang Ya-di , Hao Wei , He Li-juan , Yuen Kwok-yung , Che Xiao-yan 
Published: August 2006

ABSTRACT

Rapid diagnosis and serotyping of dengue virus (DV) infections are important for timely clinical management and epidemiological control in areas where multiple flaviviruses are endemic. However, the speed and accuracy of diagnosis must be balanced against test cost and availability, especially in developing countries. We developed a specific antigen capture enzyme-linked immunosorbent assay (ELISA) for early detection and serotyping of DV serotype 1 (DV1) by using well-characterized monoclonal antibodies (MAbs) specific to nonstructural protein 1 (NS1) of DV1. With this assay, a total of 462 serum specimens from clinically probable DV1-infected patients during the DV1 epidemic in Guangdong, China, in 2002 and 2003 were analyzed. DV1 NS1 was detectable in blood circulation from the first day up to day 18 after onset of symptoms, with a peak at days 6 to 10. The sensitivity of DV1 NS1 detection in serum specimens with reference to results from reverse transcriptase PCR was 82%, and the specificity was 98.9% with reference to 469 healthy blood donors. No cross-reactions with any of the other three DV serotypes or other closely related members of the genus
Flavivirus
(
Japanese encephalitis virus
and
Yellow fever virus
) were observed when tested with the clinical specimens or virus cultures. These findings suggest that the serotype-specific MAb-based NS1 antigen capture ELISA may be a valuable tool for early diagnosis and serotyping of DV infections, while also providing a standardized assay for the analysis of a great number of clinical samples with convenience and cost-effectiveness.
Molecular Analysis of Fungal Microbiota in Samples from Healthy Human Skin and Psoriatic Lesions
Authors: Paulino Luciana C. , Tseng Chi-Hong , Strober Bruce E. , Blaser Martin J. 
Published: August 2006

ABSTRACTPsoriasis, a common cutaneous disease of unknown etiology, may be triggered by infections, including those due to fungi. Since the fungal community of human skin is poorly characterized, we aimed to analyze the mycological microbiota in healthy skin and psoriatic lesions. Twenty-five skin samples from five healthy subjects (flexor forearm) and three patients with psoriasis were analyzed using broad-range 18S ribosomal DNA (rDNA) and 5.8S rDNA/internal transcribed spacer 2 (ITS2)Malassezia-specific PCR primers. Broad-range PCR analysis indicated that most organisms resembledMalassezia. Malassezia-specific 5.8S/ITS2 analysis of 1,374 clones identified five species and four unknown phylotypes, potentially representing new species. The species distribution appears largely host specific and conserved in different sites of healthy skin. In three subjects, theMalasseziamicrobiota composition appeared relatively stable over time. Samples ofMalasseziamicrobiota from healthy skin and psoriatic lesions were similar in one patient but substantially different in two others. These data indicate the predominance ofMalasseziaorganisms in healthy human skin, host-specific variation, stability over time, and as yet, no consistent patterns differentiating psoriatic skin from healthy skin.
Evaluation of Two New Immunochromatographic Assays (Rapid U Legionella Antigen Test and SD Bioline Legionella Antigen Test) for Detection of
Legionella pneumophila
Serogroup 1 Antigen in Urine
Authors: Diederen Bram M. W. , Peeters Marcel F. 
Published: August 2006

ABSTRACT

We evaluated two new immunochromatographic assays for their abilities to detect
Legionella pneumophila
serogroup 1 antigen in urine. The results were compared with those obtained by the Binax NOW urinary antigen test. The sensitivities and specificities were estimated to be 71.2% and 96.6%, respectively, for the Rapid U test; 31.5% and 98.9%, respectively, for the SD Bioline test; and 91.8% and 100%, respectively, for the Binax NOW test.
Multiple Cases of Familial Transmission of Community-Acquired Methicillin-Resistant
Staphylococcus aureus
Authors: Huijsdens X. W. , van Santen-Verheuvel M. G. , Spalburg E. , Heck M. E. O. C. , Pluister G. N. , Eijkelkamp B. A. , de Neeling A. J. , Wannet W. J. B. 
Published: August 2006

ABSTRACT

The worldwide emergence of community-acquired methicillin-resistant
Staphylococcus aureus
(CA-MRSA) can have severe public health implications. Familial transmissions of CA-MRSA in The Netherlands were investigated. Among the families studied, two clusters of CA-MRSA could be identified. This report demonstrates that family members can serve as reservoirs of CA-MRSA which may become a serious problem in containing the spread of MRSA.
Clinical Evaluation of a Type III Secretion System Real-Time PCR Assay for Diagnosing Melioidosis
Authors: Meumann Ella M. , Novak Ryan T. , Gal Daniel , Kaestli Mirjam E. , Mayo Mark , Hanson Joshua P. , Spencer Emma , Glass Mindy B. , Gee Jay E. , Wilkins Patricia P. , Currie Bart J. 
Published: August 2006

ABSTRACT

A
Burkholderia pseudomallei
type III secretion system real-time PCR assay was evaluated on clinical specimens in a region where melioidosis is endemic. The PCR was positive in 30/33 (91%) patients with culture-confirmed melioidosis. All six patients with melioidosis septic shock were blood PCR positive, suggesting potential for rapid diagnosis and commencement of appropriate therapy.
Ciprofloxacin Treatment of Bacterial Peritonitis Associated with Chronic Ambulatory Peritoneal Dialysis Caused by
Neisseria cinerea
Authors: Taegtmeyer M. , Saxena R. , Corkill J. E. , Anijeet H. , Parry C. M. 
Published: August 2006

ABSTRACT

Bacterial peritonitis is a well-recognized complication of chronic ambulatory peritoneal dialysis (CAPD) in patients with end-stage renal failure. We present a case of peritonitis due to an unusual pathogen,
Neisseria cinerea
, unresponsive to the standard intraperitoneal (i.p.) vancomycin and gentamicin, which responded rapidly to oral ciprofloxacin.
Identification of Genotypes of
Enterocytozoon bieneusi
from Stool Samples from Human Immunodeficiency Virus-Infected Patients in Thailand
Authors: Leelayoova Saovanee , Subrungruang Ittisak , Suputtamongkol Yupin , Worapong Jeerapun , Petmitr Porntip Chavalitshewinkoon , Mungthin Mathirut 
Published: August 2006

ABSTRACT

We identified genotypes of
Enterocytozoon bieneusi
from 33 stool samples of Thai human immunodeficiency virus (HIV)-infected adult patients. Genotype D was identified at the highest frequency (36.4%), while genotype E was the second most common (15.1%). Genotypes O and
Pig
EBITS 7, previously found only in pigs, were observed in Thai HIV-infected patients. Phylogenetic analysis supported a zoonotic nature for
E. bieneusi
.
Measles Virus-Specific Antibody Levels in Individuals in Argentina Who Received a One-Dose Vaccine
Authors: Argüelles Marcelo H. , Orellana Mariana L. , Castello Alejandro A. , Villegas Guillermo A. , Masini Matilde , Belizan Alejandra L. , González Ayala Silvia , Vera Osmar D. , Glikmann Graciela 
Published: August 2006

ABSTRACT

In spite of active measles virus (MV) vaccination strategies, reemergence continues to occur, impairing global eradication programs. The immune status against measles was evaluated in 350 vaccinated healthy Argentine children and teenagers who received a single dose of the MV Schwarz strain Lirugen vaccine (Aventis Pasteur). Sera were assessed for immunoglobulin G (IgG) antibodies by a commercial enzyme immunoassay (EIA) (Enzygnost; Behring), an in-house EIA, and neutralization EIA. Results obtained with these methods showed a marked decline in IgG level with increasing age. At 1 to 4 years of age, 84% of children had IgG antibodies above 200 mIU/ml, conventionally accepted as protective levels, whereas only 32% of older children and teenagers had antibody levels exceeding 200 mIU/ml. Moreover, the MV IgG content in the teenage group was significantly lower than the IgG antibody level of the group of younger children (
P
< 0.0001). In contrast, screening for IgG antibody levels to inactivated tetanus vaccine showed that, on average, 80% of this population was fully protected and that this high level of protection remained through the teenage years. This study suggests that within this population a considerable proportion of individuals had low measles antibody levels that may be insufficient to protect against reinfections or clinical disease.
Identification of
Acinetobacter baumannii
by Detection of the
bla
OXA-51-like
Carbapenemase Gene Intrinsic to This Species
Authors: Turton Jane F. , Woodford Neil , Glover Judith , Yarde Susannah , Kaufmann Mary E. , Pitt Tyrone L. 
Published: August 2006

ABSTRACT

bla
OXA-51-like
was sought in clinical isolates of
Acinetobacter
species in a multiplex PCR, which also detects
bla
OXA-23-like
and class 1 integrase genes. All isolates that gave a band for
bla
OXA-51-like
identified as
A. baumannii
. This gene was detected in each of 141 isolates of
A. baumannii
but not in those of 22 other
Acinetobacter
species.
Widely Distributed and Predominant CTX-M Extended-Spectrum β-Lactamases in Amsterdam, The Netherlands
Authors: al Naiemi N. , Bart A. , de Jong M. D. , Vandenbroucke-Grauls C. M. , Rietra P. J. G. M. , Debets-Ossenkopp Y. J. , Wever P. C. , Spanjaard L. , Bos A. J. , Duim B. 
Published: August 2006

ABSTRACT

Three hundred sixty
Enterobacteriaceae
and nonfermenting gram-negative bacilli, isolated during one week in May 2004 at five hospitals in Amsterdam, The Netherlands, were evaluated for the presence of extended-spectrum beta-lactamases (ESBLs). A prevalence of 7.8% was found, in contrast to the 1% observed in 1997. CTX-M ESBLs dominated, and four types were identified in 18 isolates.
Multitypic Hepatitis C Virus Infection Identified by Real-Time Nucleotide Sequencing of Minority Genotypes
Authors: Buckton Andrew J. , Ngui Siew-Lin , Arnold Catherine , Boast Katie , Kovacs Joanne , Klapper Paul E. , Patel Bharat , Ibrahim Imad , Rangarajan Savita , Ramsay Mary E. , Teo Chong-Gee 
Published: August 2006

ABSTRACTThe prevalence of concurrent multitypic hepatitis C virus (HCV) infection is uncertain. A sensitive and specific approach to identifying minority HCV genotypes in blood is presented. Following serum extraction and reverse transcription PCR to amplify cDNA originating from the viral 5′ noncoding region, the amplified product mixture was treated with genotype-specific restriction endonuclease to digest the dominant genotype. Residual amplicons were subjected to PCR cloning and then to real-time DNA sequencing using a Pyrosequencer to identify the remaining genotypes. Dilution experiments showed that minority genotypes may be detected when they represent 1:10,000 of the total population and in serum specimens with viral loads as low as 1,000 IU/ml. Of 37 patients with bleeding disorders and 44 injecting drug users, infection by more than one HCV genotype was found in 7 (19%) and 4 (9%) patients, respectively. The low rate of detection in people at high risk of repeated HCV infection suggests that multitypic HCV carriage is uncommon.
Clonality and Antimicrobial Resistance Gene Profiles of Multidrug- Resistant
Salmonella enterica
Serovar Infantis Isolates from Four Public Hospitals in Rio de Janeiro, Brazil
Authors: Fonseca E. L. , Mykytczuk O. L. , Asensi M. D. , Reis E. M. F. , Ferraz L. R. , Paula F. L. , Ng L. K. , Rodrigues D. P. 
Published: August 2006

ABSTRACT

In Brazil,
Salmonella enterica
serovar Infantis resistant to various antimicrobials, including cephalosporins, has been identified as an etiological agent of severe gastroenteritis in hospitalized children since 1994. In this study, 35 serovar Infantis strains, isolated from children admitted to four different Rio de Janeiro, Brazil, hospitals between 1996 and 2001, were characterized by pulsed-field gel electrophoresis (PFGE) and antimicrobial susceptibility testing in order to determine their genetic relatedness and antimicrobial resistance profiles. Thirty-four serovar Infantis strains were resistant to at least two antibiotic classes, and all 35 strains were susceptible to fluoroquinolones, cephamycin, and carbapenem. Extended-spectrum beta-lactamase (ESBL) screening by double-disk diffusion indicated that 32 serovar Infantis strains (91.4%) produced beta-lactamases that were inhibited by clavulanic acid. Antimicrobial resistance gene profiles were determined by PCR for a subset of 11 multidrug-resistant serovar Infantis strains, and putative ESBLs were detected by isoelectric focusing. Ten serovar Infantis strains carried
bla
TEM
,
catI
,
ant(3
"
)Ia
and/or
ant(3
"
)Ib
,
sulI
and/or
sulII
, and
tet
(D) genes as well as an integron-associated
aac(6
′
)-Iq
cassette. Eight strains possessed at least four different beta-lactamases with pI profiles that confirmed the presence of both ESBLs and non-ESBLs. Our PFGE profiles indicated that 33 serovar Infantis strains isolated from Rio de Janeiro hospitals came from the same genetic lineage.
False-Positive Results of Enzyme Immunoassays for Human Immunodeficiency Virus in Patients with Uncomplicated Malaria
Authors: Gasasira Anne F. , Dorsey Grant , Kamya Moses R. , Havlir Diane , Kiggundu Moses , Rosenthal Philip J. , Charlebois Edwin D. 
Published: August 2006

ABSTRACT
Malaria may impact upon human immunodeficiency virus (HIV) test results. We evaluated two HIV enzyme immunoassays (EIAs) by testing 1,965 Ugandans with malaria. We found poor positive predictive values (53% and 76%), particularly with younger age. Combining EIAs eliminated false positives but missed 21% of true positives. Performance of HIV EIAs in malaria may be unsatisfactory.
Concurrent Analysis of Nose and Groin Swab Specimens by the IDI-MRSA PCR Assay Is Comparable to Analysis by Individual-Specimen PCR and Routine Culture Assays for Detection of Colonization by Methicillin-Resistant
Staphylococcus aureus
Authors: Bishop Emma J. , Grabsch Elizabeth A. , Ballard Susan A. , Mayall Barrie , Xie Shirley , Martin Rhea , Grayson M. Lindsay 
Published: August 2006

ABSTRACT

The IDI-MRSA assay (Infectio Diagnostic, Inc., Sainte-Foy, Quebec, Canada) with the Smart Cycler II rapid DNA amplification system (Cepheid, Sunnyvale, CA) appears to be sensitive and specific for the rapid detection of nasal colonization by methicillin-resistant
Staphylococcus aureus
(MRSA). We assessed the sensitivity and specificity of this assay under conditions in which both the nose and cutaneous groin specimens were analyzed together and compared the accuracy of this PCR approach to that when these specimens were tested separately and by culture assays in an inpatient population with known high rates (12 to 15%) of MRSA colonization. Of 211 patients screened, 192 had results assessable by all three methods (agar-broth culture, separate nose and groin IDI-MRSA assay, and combined nose-groin IDI-MRSA assay), with MRSA carriage noted in 31/192 (16.1%), 41/192 (21.4%), and 36/192 (18.8%) patients by each method, respectively. Compared to agar culture results, the sensitivity and specificity of the combined nose-groin IDI-MRSA assay were 88.0% and 91.6%, respectively, whereas when each specimen was processed separately, the sensitivities were 90.0% (nose) and 83.3% (groin) and the specificities were 91.7% (nose) and 90.2% (groin). IDI-MRSA assay of a combined nose-groin specimen appears to have an accuracy similar to that of the current recommended PCR protocol, providing results in a clinically useful time frame, and may represent a more cost-effective approach to using this assay for screening for MRSA colonization.