bluuebunny/crossref_metadata_2025_split huggingface dataset:
Beyond Serotypes and Virulence-Associated Factors: Detection of Genetic Diversity among O153:H45 CFA/I Heat-Stable Enterotoxigenic
Escherichia coli
Strains
Authors: Pacheco A. B. F. , Ferreira L. C. S. , Pichel M. G. , Almeida D. F. , Binsztein N. , Viboud G. I. 
Published: July 2002

ABSTRACT

Characterization of enterotoxigenic
Escherichia coli
(ETEC) has been based almost exclusively on the detection of phenotypic traits such as serotypes and virulence-associated factors: heat-labile (LT) and heat-stable (ST) toxins and colonization factors (CFs). In the present work we show that the analysis of band patterns generated by randomly amplified polymorphic DNA (RAPD) analysis and pulsed-field gel electrophoresis (PFGE) of digested chromosomal DNA can be used to detect genetic diversity among ETEC strains expressing identical phenotypic traits. The study included 29 ETEC isolates from Latin America and Spain expressing the phenotype O153:H45 CFA/I ST plus 1 rough derivative, 2 nonmotile derivatives, and 1 O78:H12 CFA/I ST isolate, and a representative of a genetically distinct ETEC group. The results showed that the O153:H45 CFA/I ST ETEC isolates belong to a single clonal cluster whose isolates share on average, 84% of the RAPD bands and 77% of the PFGE restriction fragments, while the O78:H12 isolate shared only 44 and 4% of the RAPD bands and PFGE fragments, respectively, with the isolates of the O153:H45 group. More relevantly, RAPD and PFGE fingerprints disclosed the presence of different clonal lineages among the isolates of the O153:H45 cluster. Some of the genetic variants were isolated from defined geographic areas, while places like São Paulo City in Brazil and the middle-eastern part of Argentina were populated by several genetic variants of related, but not identical, ETEC strains. These results show that molecular biology-based typing methods can disclose strain diversity, which is usually missed in studies restricted to phenotypic typing of ETEC.
Improved Rate of Isolation of
Neisseria meningitidis
by Direct Plating of Pharyngeal Swabs
Authors: Cunningham Richard , Matthews Roger , Lewendon Gill , Harrison Sarah , Stuart James M. 
Published: July 2002

ABSTRACT

Culturing of pharyngeal swabs for
Neisseria meningitidis
is an important clinical and epidemiological tool. Routine methods include direct plating onto solid medium or later plating in the laboratory. A comparison of these methods used with 490 high school students found a significantly higher carriage rate with direct plating (11.8 versus 6.1%;
P
< 0.001).
Reverse Dot Blot Assay (Insertion Site Typing) for Precise Detection of Sites of IS
6110
Insertion in the
Mycobacterium tuberculosis
Genome
Authors: Steinlein Lauren M. , Crawford Jack T. 
Published: July 2002

ABSTRACT

We have developed an amplification-based reverse dot blot assay for the detection of specific sites of insertion of the
Mycobacterium tuberculosis
insertion sequence IS
6110
. In this assay, a set of biotin-labeled amplicons representing the various copies of IS
6110
and their flanking sequences is generated by linker-mediated PCR. The amplicons are then hybridized to immobilized oligonucleotide probes that are specific for known IS
6110
insertion sites. The method was evaluated using an array of oligonucleotide probes corresponding to IS
6110
insertion sites from
M. tuberculosis
strains CDC1551, Erdman, and H37Rv, and multidrug-resistant strain W. A set of 72 DNA samples from 60
M. tuberculosis
clinical isolates was analyzed for the presence or absence of these insertion sites, and the assay was found to be highly reproducible. This method of identifying insertion sites has been named “insite” and can be used for the genotyping of
M. tuberculosis
complex strains based on IS
6110
insertion site profiles.
Biotyping of
Penicillium marneffei
Reveals Concentration-Dependent Growth Inhibition by Galactose
Authors: Wong Samson S. Y. , Ho Timothy Y. C. , Ngan Antonio H. Y. , Woo Patrick C. Y. , Que Tak-Lun , Yuen Kwok-Yung 
Published: July 2002

ABSTRACT

Thirty-two isolates of the dimorphic fungus
Penicillium marneffei
were studied for their biochemical properties. All isolates possessed the enzyme urease and were inhibited by 500 mg of cycloheximide per liter. No strain fermented glucose, and thus no strain fermented any of the other five sugars tested. All assimilated glucose, maltose, and cellobiose; only one of the isolates did not assimilate salicin. Totals of 65.6, 84.4, and 71.9% of the isolates assimilated trehalose, xylose, and nitrate, respectively. Twelve strains possessed the enzyme β-galactosidase. Overall, 17 different biotypes were recognized, but no association was found between the human immunodeficiency virus status of the patients and the biotype. A novel finding of concentration-dependent growth inhibition of
P. marneffei
by galactose is described. Inhibition of growth occurred at a low concentration of galactose (0.015 to 0.25%) when galactose was the sole carbon source in the medium. Morphological changes of the fungal cells were observed in the presence of galactose.
Monitoring the Emergence of Hepatitis B Virus Polymerase Gene Variants during Lamivudine Therapy Using the LightCycler
Authors: Whalley Simon A. , Brown Dave , Teo Chong Gee , Dusheiko Geoffrey M. , Saunders Nicholas A. 
Published: July 2002

ABSTRACT
Treatment of chronic hepatitis B virus (HBV) infection with lamivudine is associated with the appearance in the circulation of HBV variants with mutations in the YMDD (tyrosine, methionine, aspartate, aspartate) motif of the polymerase gene. Fluorometric real-time PCR with the LightCycler assay was used for the detection of resistant variants. Differences in the hybridization melting curve kinetics of probes bound to the sequences encoding the wild-type or the mutant YMDD motifs (YIDD or YVDD in which the methionine residue is altered to an isoleucine or a valine, respectively) distinguished the single-base changes responsible for the resistance phenotype. The LightCycler probe hybridization assay was applied to 40 serum specimens from 19 patients, and the results were correlated with the nucleotide sequences determined for the corresponding PCR products. All three variants could be identified in the specimens. PCR clones obtained from four patients early in the course and prior to lamivudine therapy were investigated for the appearance of YIDD and YVDD variants with the LightCycler assay. In one patient, a transient appearance of the YIDD variant was observed 6 weeks into therapy. Subsequently, after 11 months of lamivudine therapy, the YVDD variant emerged in that patient.
Controlled Comparison of Original Vented Aerobic FAN Medium with New Nonvented BacT/ALERT FA Medium for Culturing Blood
Authors: Mirrett Stanley , Everts Richard J. , Reller L. Barth 
Published: July 2002

ABSTRACT

To evaluate the performance of BacT/ALERT FA (FA) medium, a new aerobic BacT/ALERT FAN (FAN) medium (Organon Teknika Corporation, Durham, N.C.) that does not require the added cost and inconvenience of a venting unit, we inoculated blood specimens from adult patients with suspected sepsis into an original FAN aerobic culture bottle and an FA bottle. Of 7,745 blood culture sets containing both bottles, 5,256 (68%) met the criteria for adequacy of filling. A total of 466 isolates judged to represent the causes of true infections were recovered from 276 patients; 271 isolates were recovered from both bottles, 82 were recovered from the FAN bottle only, and 113 were recovered from the FA bottle only (
P
< 0.05). More
Burkholderia cepacia
isolates (
P
< 0.01),
Candida albicans
isolates (
P
< 0.001),
Cryptococcus neoformans
isolates (
P
< 0.01), yeasts overall (
P
< 0.001), and total microorganisms (
P
< 0.05) were recovered from FA bottles. Of cultures found to be positive within the first 72 h of incubation, the mean times to detection were almost identical for FAN (20.4 h) and FA (20.7 h) bottles. Of 263 isolates that caused monomicrobic episodes of bloodstream infections, 180 were detected in both bottles, 32 were detected in FAN bottles only, and 51 were detected in FA bottles only (
P
< 0.05). Of 186 isolates considered to be contaminants, 63 were detected in both media, 64 were detected in FAN bottles only, and 59 were detected in FA bottles only (
P
was not significant). The number of false-positive results were comparable: 69 (1.3%) in FAN bottles and 56 (1.1%) in FA bottles. However, there were 14 isolates with false-negative results (6 yeasts, 6 nonfermenters, and 1 isolate each of
Propionibacterium acnes
and coagulase-negative staphylococci) in FAN bottles, whereas there were none in FA bottles. On the basis of these results, we conclude that the new nonvented FA bottle is superior to the original vented FAN medium for the recovery of
B. cepacia
and yeasts, especially
C. albicans
and
C. neoformans
, and is comparable to FAN medium for other microorganisms.
Recognition of Two Groups of Methicillin-Resistant
Staphylococcus aureus
Strains Based on Epidemiology, Antimicrobial Susceptibility, Hypervariable-Region Type, and Ribotype in Finland
Authors: Salmenlinna Saara , Vuopio-Varkila Jaana 
Published: July 2002

ABSTRACT

Epidemiological evidence suggests that some methicillin-resistant
Staphylococcus aureus
(MRSA) strains are more prone to dissemination than others. We studied 72 MRSA strains, collected through nationwide MRSA surveillance in 1992 through 1999 and known to be either (i) sporadic, (ii) local outbreak strains spread within one hospital, or (iii) epidemic strains spread among hospitals, by antimicrobial susceptibility testing, hybridization of the
mec
hypervariable region (HVR), and ribotyping. Our results show that two main groups can be identified among these strains. The first group includes mainly nonepidemic, nonmultiresistant MRSA strains showing a specific
mec
HVR hybridization pattern, A, in combination with a variety of ribotypes. The other group includes multiresistant strains with
mec
HVR hybridization pattern B or C in association with closely related ribotype a or b. Sixty-four percent (9 of 14) of Finnish epidemic MRSA strains belong to the latter group. These findings support the existence of differences in epidemic potential among MRSA strains.
Lack of Usefulness of Carbon Utilization Tests for Identification of
Mycobacterium mucogenicum
Authors: Conville Patricia S. , Witebsky Frank G. 
Published: July 2002

ABSTRACT

Carbon utilization tests have proven to be useful for the identification of some species of rapidly growing mycobacteria and have been described as one of the few tests useful for the differentiation of
Mycobacterium mucogenicum
from other rapid growers. We have found the carbon utilization tests to be unreliable for the identification of patient isolates of this species. In this study, using 28 isolates of rapidly growing mycobacteria, we examined several variables which might have an effect on results of citrate, inositol, and mannitol utilization: inoculum concentration, incubation temperature, and medium manufacturer. None of these variables affected results obtained for most species of rapid growers or for ATCC strains of
M. mucogenicum
. Results for patient isolates of
M. mucogenicum
were found to be inconsistent regardless of the methodology employed and resulted in an ambiguous identification of these isolates or an incorrect identification as
Mycobacterium chelonae
. Molecular or cell wall analysis may be the best technique to employ for accurate identification of
M. mucogenicum
.
Detection of Precytopathic Effect of Enteroviruses in Clinical Specimens by Centrifugation-Enhanced Antigen Detection
Authors: Lipson Steven M. , David Kathryn , Shaikh Fatima , Qian Lian 
Published: July 2002

ABSTRACT
Rapid enterovirus detection is important for decisions about antibiotic administration and length of hospital stay. The efficacy of rapid antigen detection-cell culture amplification (Ag-CCA) was evaluated with monoclonal antibodies (MAbs) 5-D8/1 (DAKO) and Pan-Enterovirus clone 2E11 (Chemicon) with 10 poliovirus, echovirus, and coxsackievirus type A and B stock isolates and College of American Pathologists check samples. By using Ag-CCA technology, MAb 2E11 was more sensitive than 5-D8/1 at detecting a greater number of stock isolates at or past tube (cytopathic effect [CPE]) culture (TC) end points. The efficacy of Ag-CCA in the clinical setting was subsequently confirmed with 273 consecutively freshly collected nasopharyngeal aspirate or swab specimens, rectal swab, and cerebrospinal fluid specimens during the 1999 enterovirus season. All specimens were tested by Ag-CCA in parallel with rhesus monkey kidney (RhMk), MRC-5, and A549 conventional TCs. Approximately 60% of field specimens were additionally tested with Hep-2 and HNK conventional TCs. Sixty-two percent of the clinical specimens tested were Ag-CCA positive after 48 h. Among 51 isolates, the mean time to CPE or culture confirmation was 5.5 days (range, 2 to 18 days). After 48 h, Ag-CCA achieved sensitivity, specificity, and positive and negative predictive values of 62, 100, 100, and 93%, respectively. During the same period, TC-CPE displayed test parameters of 12, 100, 100, and 85%, respectively. After 5 days, the sensitivity and specificity of Ag-CCA increased to 92 and 98%, respectively. Within the same period, isolation attained sensitivity and specificity of 52 and 100%, respectively. Although Ag-CCA displayed slightly reduced sensitivity and reduced specificity compared with conventional cell culture after 14 days, the markedly superior 48-h enterovirus Ag-CCA detection rate supports incorporation of this assay into the routine clinical setting.
Detection of
rpoB
Mutations in
Mycobacterium tuberculosis
by Biprobe Analysis
Authors: Edwards K. J. , Metherell L. A. , Yates M. , Saunders N. A. 
Published: July 2002

ABSTRACT

A biprobe assay utilizing LightCycler technology was developed to detect rifampin resistance-associated gene mutations in the
Mycobacterium tuberculosis rpoB
gene. Three biprobes detected all mutations present in the 46 rifampin-resistant isolates. Wild-type sequences were correctly identified in each case. The method was reproducible, accurate, and easy to use.
Immune Reactivity of Human Sera to the Glycoprotein B of Human Herpesvirus 7
Authors: Franti Michael , Aubin Jean-Thierry , De Saint-Maur Guillemette , Kosuge Haruhiko , Yamanishi Koichi , Gautheret-Dejean Agnes , Garbarg-Chenon Antoine , Huraux Jean-Marie , Agut Henri 
Published: July 2002

ABSTRACT

The glycoprotein B (gB) is highly conserved among distinct human herpesvirus 7 (HHV-7) strains. Similarly to other herpesvirus glycoproteins, gB has been assumed to induce a specific human immune response. However, it did not appear as an immunodominant protein in conventional immunoblot assays. Recombinant gB, obtained from either
Escherichia coli
or baculovirus expression systems, did react specifically with HHV-7-seropositive sera, and the main corresponding epitopes were located in its N-terminal part. A 24-amino-acid peptide, corresponding to a predicted hydrophilicity peak and presenting no extensive homology with other betaherpesvirus glycoproteins, was selected in this region at positions 129 to 152 of the gB sequence. When tested by enzyme-linked immunosorbent assay (ELISA), this peptide specifically reacted with HHV-7-seropositive sera. This reactivity was significantly inhibited by the preincubation of sera with the peptide itself, lysates of gB-expressing cells, or lysates of HHV-7-infected cells. The reactivity was not significantly modified when sera were preincubated with lysates of either human cytomegalovirus (HCMV)- or HHV-6-infected cells. In cross-sectional studies including both children and adults, 49 out of 61 serum samples (80%) were found to be positive by HHV-7 ELISA, independent of their reactivity to HCMV. A longitudinal serological study of 17 children during the first 4 years of life showed that the level of ELISA-detected antibodies significantly decreased within a few weeks after birth and then increased in the following months, likely reflecting, respectively, the loss of maternal antibodies and the occurrence of seroconversion. These results demonstrate that gB peptide ELISA might be a useful tool for the serological study of HHV-7 infection.
Staphylococcus
Heterogeneously Resistant to Vancomycin in China and Antimicrobial Activities of Imipenem and Vancomycin in Combination against It
Authors: Benquan Wu , Yingchun Tang , Kouxing Zhang , Tiantuo Zhang , Jiaxing Zhu , Shuqing Tan 
Published: July 2002

ABSTRACT

Of 115 methicillin-resistant
Staphylococcus
strains collected from sputum specimens, 34 strains reduced susceptibility to vancomycin, 9 of which emerged as heterogeneous vancomycin-resistant strains (hetero-VRS), with various degrees of vancomycin resistance at a frequency of 10
−6
or higher. Seventy-six percent (19 of 25) of non-hetero-VRS and 100% (9 of 9) of hetero-VRS were susceptible to synergistic treatment with vancomycin and imipenem. Clinical clearance between 9 hetero-VRS and 25 non-hetero-VRS had an obvious statistical significance (
P
= 0.001). The hetero-VRS may play an important role in vancomycin therapy failure.
Detection of Heat-Stable Antigens of
Campylobacter jejuni
and
C. coli
by Direct Agglutination and Passive Hemagglutination
Authors: Oza A. N. , Thwaites R. T. , Wareing D. R. A. , Bolton F. J. , Frost J. A. 
Published: July 2002

ABSTRACT

The two serotyping schemes for the detection of heat-stable antigens of
Campylobacter jejuni
and
Campylobacter coli
use the same strains for antiserum production but differ in the detection systems used for identifying agglutination. The Penner method uses passive hemagglutination (PHA) while the Laboratory of Enteric Pathogens method uses the same antisera but in a whole-bacterial-cell direct agglutination (DA) protocol.
C. jejuni
produces a polysaccharide capsule, which is antigenic, and is the main component detected by the PHA method. The DA method will detect both capsule antigens and lipopolysaccharide (LPS) or lipooligosaccharide (LOS) surface antigens. Comparison of both methods by using a selection of isolates from human infection has shown a range of variation in agglutination specificity, reflecting the differences in antigens detected by the two methods. While 27.4% of the 416
C. jejuni
isolates reacted with the antisera raised against the same type strains by either method, the majority showed a range of more complex relationships. None of the 37
C. coli
isolates reacted with the same antiserum by both methods. Together the two schemes gave a total of 102 distinct combined serogroups for
C. jejuni
and 16 for
C. coli
. Thus, while some clonally related isolates share the same capsule and LOS or LPS antigens, other strains appear to have a common capsule antigen but differ in their LPS or LOS structures or vice versa.
Development and Application of a New Scheme for Typing
Campylobacter jejuni
and
Campylobacter coli
by PCR-Based Restriction Fragment Length Polymorphism Analysis
Authors: Shi Feng , Chen Yuen Yuen , Wassenaar Trudy M. , Woods Walter H. , Coloe Peter J. , Fry Benjamin N. 
Published: July 2002

ABSTRACT

A molecular typing approach for
Campylobacter jejuni
and
Campylobacter coli
was developed with restriction fragment length polymorphism analysis of a 9.6-kb PCR-amplified portion of the lipopolysaccharide gene cluster. Sixty-one Penner serotype reference strains were analyzed with this new genotyping scheme, and 32 genogroups were found. Eleven additional genogroups were obtained from 87 clinical
C
.
jejuni
strains tested. This molecular typing method shows a correlation with the Penner heat-stable serotyping method, a phenotypic typing method based on lipopolysaccharide structures that is often used as a “gold standard” for subtyping
Campylobacter
spp. This strong correlation suggests that the data obtained can be directly compared with epidemiological data collected in the past by classical serotyping of
C. jejuni
and
C. coli.
In contrast to the high percentage of nontypeability by phenotyping, this molecular typing method results in 100% typeability and provides a superior alternative to serotyping.
Utilization of Nonviral Sequences for Minus-Strand DNA Transfer and Gene Reconstitution during Retroviral Replication
Authors: Cheslock Sara Rasmussen , Anderson Jeffrey A. , Hwang Carey K. , Pathak Vinay K. , Hu Wei-Shau 
Published: July 2002

ABSTRACT
Minus-strand DNA transfer, an essential step in retroviral reverse transcription, is mediated by the two repeat (R) regions in the viral genome. It is unclear whether R simply serves as a homologous sequence to mediate the strand transfer or contains specific sequences to promote strand transfer. To test the hypothesis that the molecular mechanism by which R mediates strand transfer is based on homology rather than specific sequences, we examined whether nonviral sequences can be used to facilitate minus-strand DNA transfer. The green fluorescent protein (GFP) gene was divided into GF and FP fragments, containing the 5′ and 3′ portions of GFP, respectively, with an overlapping F fragment (85 bp). FP and GF were inserted into the 5′ and 3′ long terminal repeats, respectively, of a murine leukemia virus-based vector. Utilization of the F fragment to mediate minus-strand DNA transfer should reconstitute GFP during reverse transcription. Flow cytometry analyses demonstrated that GFP was expressed in 73 to 92% of the infected cells, depending on the structure of the viral construct. This indicated that GFP was reconstituted at a high frequency; molecular characterization further confirmed the accurate reconstitution of GFP. These data indicated that nonviral sequences could be used to efficiently mediate minus-strand DNA transfer. Therefore, placement and homology, not specific sequence context, are the important elements in R for minus-strand DNA transfer. In addition, these experiments demonstrate that minus-strand DNA transfer can be used to efficiently reconstitute genes for gene therapy applications.
Efficient Site-Specific Nonribozyme Opening of Hepatitis Delta Virus Genomic RNA in Infected Livers
Authors: Chang Jinhong , Moraleda Gloria , Gudima Severin , Taylor John 
Published: July 2002

ABSTRACT
Examination of the 1,679-nucleotide (nt) unit-length hepatitis delta virus (HDV) RNAs in the livers of two HDV-infected woodchucks showed that 96% of the antigenomic RNA but only 50% of the genomic RNA was circular. We subsequently found that at least half of the linear unit-length genomic RNA was open at a unique location. Using a modified form of RNA ligation-mediated amplification of cDNA ends, we showed that the 5′ end was located at nt 1212. Like the previously described ribozyme cleavage site at nt 686, the new site produced a 5′-OH. Nevertheless, we showed that this novel site was not produced by activity of the HDV genomic ribozyme. We speculate that the 5′ end at nt 1212 reflects a preferred site of posttranscriptional endonucleolytic cleavage of genomic RNA.