bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosis of Extrapulmonary Tuberculosis by Smear, Culture, and PCR Using Universal Sample Processing Technology
Authors: Chakravorty Soumitesh , Sen Manas Kamal , Tyagi Jaya Sivaswami 
Published: September 2005

ABSTRACTDefinitive and rapid diagnosis of extrapulmonary tuberculosis is challenging since conventional techniques have limitations. We have developed a universal sample processing (USP) technology for detecting mycobacteria in clinical specimens. In this study, this technology was evaluated blindly on 99 extrapulmonary specimens collected from 87 patients. USP-processed specimens were submitted to smear microscopy for detection of acid-fast bacilli (AFB), culture, and two PCR tests targetingdevR(Rv3133c) and IS6110gene sequences. On the basis of clinical characteristics, histology and cytology, conventional microbiology results, and response to antitubercular therapy, 68 patients were diagnosed with tuberculosis. Although USP smear and culture were significantly superior to conventional microbiology, which was not optimized (P< 0.0001), these approaches fell short of PCR tests (P< 0.0001). The low yields by smear and culture are attributed to the paucibacillary load in the specimens. The highest sensitivity in PCR was achieved whendevRand IS6110test results were combined; the sensitivity and specificity values were 83 and 93.8%, 87.5 and 100%, and 66.7 and 75%, respectively, in pleural fluid, needle-biopsied pleural tissue, and lymph node specimens. In conclusion, the application of USP technology, together with clinicopathological characteristics, promises to improve the accuracy and confidence of extrapulmonary tuberculosis diagnosis.
Widespread Distribution of Disinfectant Resistance Genes among Staphylococci of Bovine and Caprine Origin in Norway
Authors: Bjorland Jostein , Steinum Terje , Kvitle Bjørg , Waage Steinar , Sunde Marianne , Heir Even 
Published: September 2005

ABSTRACTWe demonstrate here a widespread distribution of genes mediating efflux-based resistance to quaternary ammonium compounds (QACs) in staphylococci from unpasteurized milk from 127 dairy cattle herds and 70 dairy goat herds. QAC resistance genes were identified in 21% of the cattle herds (qacA/B,smr,qacG, andqacJ) and in 10% of the goat herds (qacA/Bandsmr). Further examination of 42 QAC-resistant bovine and caprine isolates revealed the following genes:qacA/B(12 isolates) was present in four different species of coagulase-negative staphylococci (CoNS),smr(27 isolates) was detected in eight different CoNS species and inStaphylococcus aureuson a previously reported plasmid (pNVH99),qacG(two isolates) was detected on two plasmids (pST94-like) inStaphylococcus cohniiandStaphylococcus warneri, andqacJ(two isolates) was found inStaphylococcus hominisandStaphylococcus delphinion a plasmid (pNVH01) previously found in equine staphylococci. Isolation of indistinguishable pulsed-field gel electrophoresis (PFGE) CoNS types from tank milk and mammary quarter milk samples in a dairy cattle herd suggested that these QAC-resistant staphylococci were of intramammary origin. Indistinguishable or closely related PFGE types of bovine QAC-resistant CoNS were observed in different herds. One particular bovineS. warneriPFGE type was isolated repeatedly from samples collected during a 30-month period in a herd, showing long-term persistence. In conclusion, it seems that the widespread distribution of staphylococci carrying QAC resistance genes in Norwegian dairy cattle and goat herds is the result of both the intra- and interspecies spread of QAC resistance plasmids and the clonal spread of QAC-resistant strains.
M Protein Gene (
emm
Type) Analysis of Group A Beta-Hemolytic Streptococci from Ethiopia Reveals Unique Patterns
Authors: Tewodros Wezenet , Kronvall Göran 
Published: September 2005

ABSTRACT

The genetic diversity of group A streptococcal (GAS) isolates obtained in 1990 from Ethiopian children with various streptococcal diseases was studied by using
emm
gene sequence analysis. A total of 217 GAS isolates were included: 155 and 62 isolates from throat and skin, respectively. A total of 78 different
emm/st
types were detected among the 217 isolates. Of these, 166 (76.5%) belonged to 52 validated reference
emm
types, 26 (11.9%) belonged to 16 already recognized sequence types (
st
types) and 25 (11.5%) belonged to 10 undocumented new sequence types. Resistance to tetracycline (148 of 217) was not correlated to
emm
type. Isolation rate of the classical rheumatogenic and nephritogenic strains was low from cases of acute rheumatic fever (ARF) and acute glomerulonephritis (AGN), respectively. Instead, the recently discovered
st
types were overrepresented among isolates from patients with ARF (3 of 7) and AGN (9 of 16) (
P
< 0.01) compared to isolates from subjects with tonsillitis and from healthy carriers (10 of 57 and 16 of 90, respectively). In contrast to rheumatogenic strains from the temperate regions, more than half of the isolates from ARF (four of seven) carried the genetic marker for skin preference,
emm
pattern D, although most of them (six of seven) were isolated from throat. Of 57 tonsillitis-associated isolates, 16 (28%) belonged to
emm
pattern D compared to <1% in temperate regions. As in other reports
emm
patterns A to C were strongly associated with throat, whereas
emm
pattern D did not correlate to skin. This first large-scale
emm
typing report from Africa has demonstrated a heterogeneous GAS population and contrasting nature of GAS epidemiology in the region.
Development of a Multilocus Sequence Typing Scheme for Characterization of Clinical Isolates of
Acinetobacter baumannii
Authors: Bartual Sergio G. , Seifert Harald , Hippler Corinna , Luzon M. Angeles Domínguez , Wisplinghoff Hilmar , Rodríguez-Valera Francisco 
Published: September 2005

ABSTRACT

In this study a multilocus sequence typing (MLST) scheme for
Acinetobacter baumannii
was developed and evaluated by using 40 clinical
A. baumannii
isolates recovered from outbreaks in Spanish and German hospitals during the years 1990 to 2001, as well as isolates from other European hospitals and two DSMZ reference strains of
A. baumannii
. For comparison, two isolates of
Acinetobacter
species 13 (sensu Tjernberg and Ursing), two clinical isolates, and three DSMZ strains of
A. calcoaceticus
(both belonging to the
A. calcoaceticus
-
A. baumannii
complex) were also investigated. Primers were designed for conserved regions of housekeeping genes, and 305- to 513-bp internal fragments of seven such genes—
gltA
,
gyrB
,
gdhB
,
recA
,
cpn60
,
gpi
, and
rpoD
—were sequenced for all strains. The number of alleles at individual loci ranged from 6 to 12, and a total of 20 allelic profiles or sequence types were distinguished among the investigated
A. baumannii
strains. The MLST data were in high concordance with the epidemiologic typing results generated by pulsed-field gel electrophoresis and amplified fragment length polymorphism fingerprinting. The MLST scheme provides a high level of resolution and an excellent tool for studying the population structure and long-term epidemiology of
A. baumannii
.
Detection of Antibodies against Adenovirus Protein IX, Fiber, and Hexon in Human Sera by Immunoblot Assay
Authors: Bauer Ulrike , Flunker Gisela , Bruss Kornelia , Kallwellis Knut , Liebermann Herbert , Luettich Tanja , Motz Manfred , Seidel Werner 
Published: September 2005

ABSTRACT

The 51 serotypes of human adenoviruses (HAdVs) of the genus
Mastadenovirus
are classified into the six species HAdV-A to HAdV-F. For the detection of genus- and species-specific antibodies in human sera an immunoblot assay was developed. The recombinant long fiber of HAdV-41[F] (Ad41Fi) and the native hexon of HAdV-5[C] were used as genus-specific antigens. The recombinant capsid protein IX (pIX) of HAdV-2 (Ad2pIX[C]) and HAdV-41 (Ad41pIX[F]), the C-terminal pIX part of HAdV-3 (Ad3pIXC[B]), and the fiber knob of HAdV-8 (Ad8FiKn[D]) were evaluated as representative species-specific antigens. Hence, the pIX amino acid sequences of numerous serotypes of all HAdV species were compared, and the cross-reactivities of pIX antigens with rabbit hyperimmune sera among HAdV-A to -F were analyzed. In an epidemiological study, 667 human patient sera, not selected for viral infection, were screened for adenovirus seroprevalence. The genus-specific antibody prevalences directed against the Ad41Fi and HAdV-5 hexon were 82.8 and 98.8%, respectively. The species-specific antibody prevalence of 44.7% against Ad2pIX[C], 36.6% against Ad41pIX[F], 26.4% against Ad8FiKn[D], and 18% against Ad3pIXC[B] showed an age-dependent distribution and correlated well with the frequency of isolated serotypes of the respective species in earlier studies (except HAdV-D). In conclusion, the immunoblot assay using pIX, fiber, and hexon antigens represents a valuable and new serological tool for refined adenovirus diagnosis as shown in an epidemiological study.
Multilocus Sequence Typing of Methicillin-Resistant
Staphylococcus aureus
from an Area of Low Endemicity by Real-Time PCR
Authors: Berglund Carolina , Mölling Paula , Sjöberg Lennart , Söderquist Bo 
Published: September 2005

ABSTRACT

A protocol for multilocus sequence typing (MLST) of methicillin-resistant
Staphylococcus aureus
(MRSA) was adapted to real-time LightCycler System PCR for efficient and rapid amplification of seven housekeeping genes in the same PCR run and real-time detection of the products. The method was evaluated on a representative and well-characterized collection of clinical MRSA isolates (
n
= 57) obtained from an area of low endemicity. Twenty sequence types (STs) and nine clonal complexes were identified. Combining STs and the staphylococcal cassette chromosome
mec
(SCC
mec
) type identified 27 different genotypes, and type IV SCC
mec
was present in 11 different STs. The presence of the Panton Valentine leukocidin (PVL) genes was found in isolates of four different STs. Eleven different STs were found among the community-acquired as well as among the hospital-acquired MRSA. The genetic heterogeneity was also denoted by pulsed-field gel electrophoresis analysis that showed 24 different pulsotypes among the 57 MRSA isolates. The presence of more than one different type of SCC
mec
in the same ST indicates that the MRSA clones have arisen at several occasions in the same genetic background by independent acquisition of SCC
mec
into methicillin-sensitive strains. This circumstance shows the importance of combining MLST data with SCC
mec
-typing results when investigating the origins of MRSA.
Detection and Characterization of Human Group C Rotaviruses in Bangladesh
Authors: Rahman Mustafizur , Banik Sukalyani , Faruque Abu S. G. , Taniguchi Koki , Sack David A. , Van Ranst Marc , Azim Tasnim 
Published: September 2005

ABSTRACT
Group C rotaviruses were detected by reverse transcription-PCR in 14 (2.3%) of 611 group A rotavirus-negative stool specimens from the patients admitted to the International Centre for Diarrhoeal Disease Research, Bangladesh hospital, Dhaka, Bangladesh, during July to December 2003. The low rate of detection suggested that infection with group C rotaviruses was an uncommon cause of hospitalization due to gastroenteritis. In addition, coinfections with pathogenic enteric bacteria were frequently observed in group C rotavirus-infected patients. Nucleotide sequence comparison of the VP4, VP6, and VP7 genes revealed that the Bangladeshi group C rotaviruses were most similar to Nigerian group C rotavirus strains. Phylogenetic analysis suggested that all human group C rotaviruses, including the strains isolated in our study, clustered in a monophyletic branch, which was distantly related to the branch comprised of animal group C rotaviruses.
Breakpoints for Predicting
Pseudomonas aeruginosa
Susceptibility to Inhaled Tobramycin in Cystic Fibrosis Patients: Use of High-Range Etest Strips
Authors: Morosini María I. , García-Castillo María , Loza Elena , Pérez-Vázquez María , Baquero Fernando , Cantón Rafael 
Published: September 2005

ABSTRACT

Inhaled administration of tobramycin assures high concentrations in cystic fibrotic lungs, improving the therapeutic ratio over that of parenteral tobramycin levels, particularly against
Pseudomonas aeruginosa
. Conventional Clinical and Laboratory Standards Institute (CLSI; formerly National Committee for Clinical Laboratory Standards) breakpoints only consider parenteral levels and do not take into account these high antimicrobial concentrations. The Spanish Antibiogram Committee (The MENSURA Group) has tentatively defined specific breakpoint values for inhaled tobramycin when testing
P. aeruginosa
isolates from cystic fibrosis (CF) patients (susceptible, ≤64 μg/ml; resistant, ≥128 μg/ml). The antimicrobial susceptibilities of 206 prospectively collected CF
P. aeruginosa
isolates were determined by the reference agar dilution method. For tobramycin, the performance of high range tobramycin Etest strips (AB Biodisk, Solna, Sweden) and conventional tobramycin disks were assessed with the same collection. Applying MENSURA proposed breakpoints, 95.1% of the strains were categorized as susceptible to tobramycin, either using agar dilution or Etest high-range strips (99% categorical agreement between both methods). With CLSI breakpoints, susceptibility rates decreased to 79.1 and 81.1% for agar dilution and Etest strips, respectively (83.5% categorical agreement). Minor, major, and very major errors for Etest strips (CLSI criteria) were 13.6, 1.2, and 14.8%, respectively. Upon applying the new proposed criteria for inhaled tobramycin, only one major and one very major error were observed with Etest strips. Whenever inhaled tobramycin is considered for therapy, we suggest that
P. aeruginosa
strains from CF patients categorized as intermediate or resistant to tobramycin according to the CLSI criteria should be retested with high-range Etest strips and recategorized using MENSURA interpretive criteria. CLSI breakpoints should still be followed when intravenous tobramycin is used in CF patients, particularly during the course of exacerbations.
Microbiologic Response to Treatment of Bacterial Vaginosis with Topical Clindamycin or Metronidazole
Authors: Austin M. N. , Beigi R. H. , Meyn L. A. , Hillier S. L. 
Published: September 2005

ABSTRACT

To compare the frequencies, concentrations, and antimicrobial susceptibilities of vaginal microbes isolated from women with bacterial vaginosis (BV) before and after therapy, 119 nonpregnant women aged 18 to 45 with clinical and Gram stain evidence of BV were randomized to receive intravaginal clindamycin or metronidazole. Vaginal swabs were collected at baseline and 7 to 12 days, 35 to 45 days, and 70 to 90 days following therapy for quantitative vaginal culture. For the 99 women completing all four visits, statistical analyses were performed comparing differences in vaginal microflora between the two treatment arms and between visits in the same treatment group. Antimicrobial susceptibility testing using the agar dilution method was performed for anaerobic gram-negative rods. Although both therapies resulted in decreased colonization by
Gardnerella vaginalis
and
Mycoplasma hominis
, only metronidazole treatment resulted in a significant decrease in the frequency and concentration of
Prevotella bivia
and black-pigmented
Prevotella
species. Of the 865 anaerobic gram-negative rods evaluated for susceptibility, only 3 (0.3%) were resistant to metronidazole, whereas clindamycin resistance increased significantly for
P. bivia
and black-pigmented anaerobic gram-negative rods persisting following clindamycin therapy. Clindamycin-resistant subpopulations of
P. bivia
and black-pigmented
Prevotella
species emerged 7 to 12 days after therapy even among women colonized initially by clindamycin-susceptible strains. These resistant subpopulations persisted at high frequencies (42 to 50%) 70 to 90 days following therapy. The two topical agents for treatment of BV have differing microbiologic effects on the vaginal microflora. The emergence of clindamycin-resistant anaerobic gram-negative rods following therapy is of concern.
Use of rMPB70 Protein and ESAT-6 Peptide as Antigens for Comparison of the Enzyme-Linked Immunosorbent, Immunochromatographic, and Latex Bead Agglutination Assays for Serodiagnosis of Bovine Tuberculosis
Authors: Koo Hye Cheong , Park Yong Ho , Ahn Jongsam , Waters W. Ray , Palmer Mitch V. , Hamilton Mary Jo , Barrington George , Mosaad Abdelaziz A. , Park Kun Taek , Jung Woo Kyung , Hwang In Yeong , Cho Sang-Nae , Shin Sang Jae , Davis William C. 
Published: September 2005

ABSTRACTCurrent assays used to detectMycobacterium bovisinfection lack accuracy, especially for recently infected animals, or are impractical for rapid field diagnostic applications. To overcome these limitations with serological assays, a synthetic peptide derived from early secretory antigenic target 6 (ESAT6-p) and a recombinant major secreted immunogenic protein (rMPB70) ofM. boviswere used in an enzyme-linked immunosorbent assay (EIA), an immunochromatographic assay (ICGA), and a latex bead agglutination assay (LBAA). Sera from noninfected,M. bovis-infected, orM. aviumsubsp.paratuberculosis-infected (by natural and experimental routes) animals were evaluated. Receiver operating characteristic analysis comparing optical density values from the EIA with results of bacterial culture or skin test, the reference test, established suitable cutoff values for assessing sensitivity and specificity. The EIA and LBAA, respectively, had sensitivities of 98.6 and 94.8%, specificities of 98.5 and 92.6%, and kappa values of 0.97 and 0.88 with ESAT6-p. The EIA, ICGA, and LBAA, respectively, had sensitivities of 96.8, 83.0, and 86.7%, specificities of 90.1, 99.4, and 97.8%, and kappa values of 0.87, 0.85, and 0.83 with rMPB70. Examination of serial samples of sera collected from experimentallyM. bovis-infected cattle and deer revealed that ESAT6-p-specific responses developed early after infection whereas responses to rMPB70 developed later in the course of disease. The advantage of the LBAA and ICGA as initial tests for multiple species is a rapid reaction obtained in 2 to 3 h by LBAA or 20 min by ICGA without species-specific secondary antibodies under field conditions, thus allowing immediate segregation of suspect animals for further testing before culling.
Rapid Identification of
Candida
Species and Other Clinically Important Yeast Species by Flow Cytometry
Authors: Page Brent T. , Kurtzman Cletus P. 
Published: September 2005

ABSTRACT

Two rapid diagnostic assays, utilizing two different Luminex flow cytometry methods, were developed for identification of clinically important ascomycetous yeast species. Direct hybridization and allele-specific primer extension methods were both successful in establishing a DNA-based assay that can rapidly and accurately identify
Candida albicans
,
Candida krusei
,
Candida parapsilosis
,
Candida glabrata
, and
Candida tropicalis
as well as other clinical species. The direct hybridization assay was designed to identify a total of 19 ascomycetous yeast species, and the allele-specific primer extension assay was designed to identify a total of 34 species. Probes were validated against 438 strains representing 303 species. From culture to identification, the allele-specific primer extension method takes 8 h and the direct hybridization method takes less than 5 h to complete. These assays represent comprehensive, rapid tests that are well suited for the clinical laboratory.
Evaluation of tRNA Gene PCR for Identification of
Mollicutes
Authors: Stakenborg Tim , Vicca Jo , Verhelst Rita , Butaye Patrick , Maes Dominiek , Naessens Anne , Claeys Geert , De Ganck Catharine , Haesebrouck Freddy , Vaneechoutte Mario 
Published: September 2005

ABSTRACT

We evaluated the applicability of tRNA gene PCR in combination with fluorescent capillary electrophoresis with an ABI310 genetic analyzer (Applied Biosystems, Calif.) for the identification of different mollicute species. A total of 103 strains and DNA extracts of 30 different species belonging to the genera
Acholeplasma
,
Mycoplasma
, and
Ureaplasma
were studied. Reproducible peak profiles were generated for all samples, except for one
M. genitalium
isolate, the three
M. gallisepticum
isolates, and 8 of the 24
Ureaplasma
cultures, where no amplification could be obtained. Clustering revealed numerous discrepancies compared to the identifications that had been previously obtained by means of biochemical and serological tests. Final identification was obtained by 16S rRNA gene amplification followed by sequence analysis and/or restriction digestion. This confirmed the identification obtained by tRNA gene PCR in all cases. Seven samples yielded an unexpected tRNA gene PCR profile. Sequence analysis of the 16S rRNA genes showed that six of these samples were mixed and that one had a unique sequence that did not match any of the published sequences, pointing to the existence of a not-yet-described species. In conclusion, we found tRNA gene PCR to be a rapid and discriminatory method to correctly identify a large collection of different species of the class of
Mollicutes
and to recognize not-yet-described groups.
Microsatellite Marker Analysis as a Typing System for
Candida glabrata
Authors: Foulet F. , Nicolas N. , Eloy O. , Botterel F. , Gantier J.-C. , Costa J.-M. , Bretagne S. 
Published: September 2005

ABSTRACT

Candida glabrata
is one of the most important causes of nosocomial fungal infection. We investigated, using a multiplex PCR, three polymorphic microsatellite markers,
RPM2
,
MTI
, and
ERG3
, in order to obtain a rapid genotyping method for
C. glabrata
. One set of primers was designed for each locus, and one primer of each set was dye labeled to read PCR signals using an automatic sequencer. Eight reference strains including other
Candida
species and 138 independent
C. glabrata
clinical isolates were tested. The clinical isolates were collected from different anatomical sites of adult patients either hospitalized in different wards of two different hospitals or not hospitalized. Since
C. glabrata
is haploid, one single PCR product for each PCR set was obtained and assigned to an allele. The numbers of different alleles were 5, 7, and 15 for the
RPM2
,
MTI
, and
ERG3
loci, respectively. The number of allelic associations was 21, leading to a discriminatory power of 0.84. The markers were stable after 25 subcultures, and the amplifications were specific for
C. glabrata
. A factorial correspondence analysis did not indicate any correlation between the 21 multilocus genotypes and the clinical data (source, sex, ward, anatomical sites). Microsatellite marker analysis is a rapid and reliable technique to investigate clinical issues concerning
C. glabrata
. However, its discriminatory power should be improved by testing other polymorphic microsatellite loci.