bluuebunny/crossref_metadata_2025_split huggingface dataset:
Presence of Multiple “
Helicobacter heilmannii
” Strains in an Individual Suffering from Ulcers and in His Two Cats
Authors: Dieterich Christine , Wiesel Paul , Neiger Reto , Blum André , Corthésy-Theulaz Irène 
Published: December 2019

ABSTRACT

Circumstantial evidence suggests that “
Helicobacter heilmannii
” infection is an example of zoonosis. The presence of “
H. heilmannii
” strains in a human subject with acute gastric erosions, in his two cats, and in two unrelated cats was analyzed, and the genetic relatedness of the human and feline strains was assessed. A 580-bp, PCR-amplified sequence of “
H. heilmannii
” urease B gene (
ureB
) obtained from biopsies from the human subject and his two cats was restricted with
Alu
I and cloned for sequencing. Analysis of the restriction fragment length polymorphism of the
ureB
-amplified product suggested the presence of different individual “
H. heilmannii
” strains in the cats and of three distinct strains in the human subject. One of the “
H. heilmannii
”
ureB
sequences amplified from the human subject’s biopsies was identical to that derived from one of his cats. The degree of similarity between the other “
H. heilmannii
” human and feline nucleotide sequences was higher than 97%. Most of the base substitutions were conservative. We conclude that human and animal “
H. heilmannii
” strains are closely related and that humans can be infected by more than one “
H. heilmannii
” strain, as has been observed for
Helicobacter pylori.
Molecular Epidemiology of Oral Treponemes Associated with Periodontal Disease
Authors: Moter Annette , Hoenig Carina , Choi Bong-Kyu , Riep Birgit , Göbel Ulf B. 
Published: December 2019

ABSTRACT

Periodontitis, a disease responsible for tooth loss worldwide, is characterized by chronic inflammation of the periodontium, eventually leading to destruction of periodontal ligaments and supporting alveolar bone. Spirochetes, identified by dark-field microscopy as being the most predominant bacteria in advanced lesions, are thought to play a causative role. Various spirochetal morphotypes were observed, but most of these morphotypes are as yet uncultivable. To assess the role of these organisms we designed oligonucleotide probes for the identification of both cultivable and so far uncultivable spirochetes in periodontitis patients. Subgingival plaque specimens taken from diseased sites (
n
= 200) and healthy control sites (
n
= 44) from 53 patients with rapidly progressive periodontitis (RPP) were submitted to direct in situ hybridization or dot blot hybridization after prior amplification with eubacterial primers. Spirochetes were found in all patients, but their distributions varied considerably. Parallel use of oligonucleotide probes specific for cultivable or so far uncultivable treponemes suggested the presence of novel yet unknown organisms at a high frequency. These uncultivable treponemes were visualized by fluorescence in situ hybridization, and their morphologies, sizes, and numbers could be estimated. All RPP patients included in this study harbored oral treponemes that represent either novel species, e.g.,
Treponema maltophilum
, or uncultivable phylotypes. Therefore, it is necessary to include these organisms in etiologic considerations and to strengthen efforts to cultivate these as yet uncultivable treponemes.
Novel Enzyme-Linked Immunoassay To Determine Nanogram Levels of Pneumocandins in Human Plasma
Authors: Karkhanis Y. D. , Schmatz D. M. 
Published: December 2019

ABSTRACT
A binding enzyme-linked immunosorbent assay (ELISA) has been developed for measuring nanogram concentrations of semisynthetic pneumocandin antifungal agents in human plasma. Semisynthetic pneumocandin L-733,560 was conjugated to succinylated hemocyanin by water-soluble carbodiimide and was used as an immunogen to produce polyclonal antibodies in rabbits. Pneumocandins were used to directly coat the wells of a microtiter plate, and quantitation was achieved by using rabbit polyclonal antibodies to pneumocandin L-733,560 and goat anti-rabbit immunoglobulin G conjugated to either alkaline phosphatase or horseradish peroxidase. Maximum binding of L-733,560 and most related analogs to the wells of the microtiter plate was found to occur in the first 5 min of incubation at 4°C. Once bound to the plate, these pneumocandins could not be removed from the plate, either by treatment with 4.0 to 6.0 M urea or by treatment with 4.0 to 6.0 M guanidine hydrochloride for 24 h at 4°C. The binding ELISA is linear with drug concentration and can detect levels of L-733,560 as low as 5 ng/ml in human plasma. The assay is also useful for quantitating plasma levels of related semisynthetic pneumocandins including clinical candidate MK-0991.
Routine Use of PCR–Reverse Cross-Blot Hybridization Assay for Rapid Identification of
Mycobacterium
Species Growing in Liquid Media
Authors: Sanguinetti M. , Posteraro B. , Ardito F. , Zanetti S. , Cingolani A. , Sechi L. , De Luca A. , Ortona L. , Fadda G. 
Published: December 2019

ABSTRACT

A PCR–reverse cross-blot hybridization assay procedure that is able to rapidly identify 13 species of clinically relevant mycobacteria was evaluated for routine use in the identification of acid-fast isolates growing in BACTEC 460 TB (12B and 13A) and BACTEC 9000 MB (Myco/F) liquid media. Eight of the probes used were already described by Kox et al. (L. F. F. Kox et al., J. Clin. Microbiol. 33:3225–3233, 1995). In addition, we used six other probes specific for
M. chelonae
,
M. malmoense
or
M. szulgai
,
M. genavense
,
M. gordonae
,
M. terrae
, and
M. marinum/M. ulcerans
that we designed ourselves. This procedure allowed us to identify 459 mycobacterial species directly from broth cultures of 5,466 clinical samples collected over 1 year and processed with the radiometric or nonradiometric BACTEC system. Our results were in agreement with those obtained by conventional identification methods and also with those obtained by mycolic acid analysis by high-performance liquid chromatography. This assay seems to be a reliable procedure for the routine identification of mycobacteria, providing an accurate identification of mycobacterial isolates more rapidly than conventional tests, with remarkable implications for an efficacious specific antimycobacterial therapy.
Suitability of Repetitive-DNA-Sequence-Based PCR Fingerprinting for Characterizing Epidemic Isolates of
Salmonella enterica
Serovar Saintpaul
Authors: Beyer W. , Mukendi F. M. , Kimmig P. , Böhm R. 
Published: December 2019

ABSTRACT

Three molecular typing methods, repetitive-sequence-based PCR (rep-PCR) fingerprinting, plasmid profiling, and arbitrarily primed PCR fingerprinting, were used to characterize isolates of
Salmonella enterica
serovar Saintpaul. Most of the isolates were obtained from epidemic human cases of food-borne salmonellosis, together with some from the food material suspected to be the source of infection, and a few were obtained from other cases apparently not related to the epidemic. All three methods adequately discriminated the epidemic strain from other strains of the serovar. In addition several isolates from human cases which are not identical to the epidemic strain were found. These isolates therefore must have been responsible for some sporadic infections, which were only temporally related to the epidemic. These strains showed a high degree of similarity to a strain isolated from a turkey. rep-PCR fingerprinting with REP-Dt primers and primer ERIC1R, applicable even to crude cell lysates, offers an attractive choice as a primary method for the discrimination of various
Salmonella
serotypes as well as isolates within serotype Saintpaul.
Flow Cytometric Testing of Susceptibilities of
Mycobacterium tuberculosis
Isolates to Ethambutol, Isoniazid, and Rifampin in 24 Hours
Authors: Kirk Scott M. , Schell Ronald F. , Moore Andrea V. , Callister Steven M. , Mazurek Gerald H. 
Published: December 2019

ABSTRACT

Susceptibility testing of
Mycobacterium tuberculosis
is seriously limited by the time required to obtain results. We show that susceptibility testing of clinical isolates of
M. tuberculosis
can be accomplished rapidly with acceptable accuracy by using flow cytometry. The susceptibilities of 35 clinical isolates of
M. tuberculosis
to various concentrations of isoniazid, rifampin, and ethambutol were tested by the agar proportion method and by flow cytometry. Agreement between the results from the two methods was 95, 92, and 83% for isoniazid, ethambutol, and rifampin, respectively. Only 11 discrepancies were detected among 155 total tests. The results of flow cytometric susceptibility tests were available within 24 h of inoculation of drug-containing medium, while the proportion method required 3 weeks to complete. The flow cytometric method is also simple to perform.
Mapping and Serodiagnostic Application of a Dominant Epitope within the Human Herpesvirus 8 ORF 65-Encoded Protein
Authors: Pau Chou-Pong , Lam Lee L. , Spira Thomas J. , Black Jodi B. , Stewart John A. , Pellett Philip E. , Respess Richard A. 
Published: December 2019

ABSTRACT
A dominant epitope within the human herpesvirus 8 (HHV8) ORF 65-encoded protein was mapped to an 8-amino-acid (aa) sequence (RKPPSGKK [aa 162 to 169]) by an amino acid replacement method. Using a 14-aa peptide (P4) encompassing this epitope as the antigen, we developed an enzyme immunoassay for HHV8 antibodies. The presence of P4 antibodies in a panel of 61 human serum specimens was highly correlated with biopsy-confirmed Kaposi’s sarcoma. The homologous Epstein-Barr virus peptide derived from BFBR3-encoded protein did not interfere with the assay, suggesting that P4 is specific for HHV8.
“
Flexispira rappini
” Bacteremia in a Child with Pneumonia
Authors: Tee Wee , Leder Karin , Karroum Elena , Dyall-Smith Michael 
Published: December 2019

ABSTRACT

We describe a case of “
Flexispira rappini
” bacteremia from a 9-year-old girl who presented with a 5-day history of fever, productive cough, and malaise. A chest X-ray result was compatible with right middle lobe pneumonia. Blood culture grew a gram-negative spiral fusiform bacterium 2 days after the inoculation. Biochemical tests showed the organism to be catalase negative, oxidase positive, sodium hippurate hydrolysis negative, and urea hydrolysis negative. 16S rRNA gene sequencing identified this organism as “
F. rappini
,” showing a six-base substitution from the type strain. This is the first report of “
F. rappini
” bacteremia in a human, suggesting that this organism has the potential of causing invasive infection, but its role in pneumonia is uncertain and could be unrelated to the bacteremia.
Hepatitis C Virus Infections in Dialysis Centers in The Netherlands: a National Survey by Serological and Molecular Methods
Authors: Schneeberger Peter M. , Keur Ingrid , van der Vliet Walter , van Hoek Kitty , Boswijk Henk , van Loon Anton M. , van Dijk Willemien C. , Kauffmann Robert H. , Quint Wim , van Doorn Leen-Jan 
Published: December 2019

ABSTRACT
A national survey of hepatitis C virus (HCV) infections among dialysis patients in The Netherlands was performed. The study involved 2,653 patients (2,108 hemodialysis patients and 545 chronic ambulatory peritoneal dialysis [CAPD] patients) from 39 of the 49 dialysis centers in the country. Patient sera were analyzed by both serological and molecular methods. Screening by a third-generation enzyme immunoassay (EIA) yielded 79 reactive sera. The presence of anti-HCV antibodies was confirmed in 70 patients by a line immunoassay. All seropositive samples were tested by reverse transcriptase PCR, and 57 samples were found to contain HCV RNA. Of the nine EIA-positive and line immunoassay-negative or indeterminate samples, four were HCV RNA positive. All seronegative samples were screened for the presence of HCV RNA in pools of five sera. Of 2,576 antibody-negative samples, 6 contained HCV RNA. All antibody-positive and RNA-positive samples were also tested by a second serological assay. The prevalence of HCV infections among Dutch dialysis patients as determined by serology or the presence of HCV RNA was 3% (80 of 2,653), i.e., 3.5% (73 of 2,108) in patients treated on hemodialysis and 1.3% (7 of 545) in patients on CAPD. Of these 80 HCV-infected dialysis patients, 67 (84%) were HCV RNA positive. Serological screening alone would have diagnosed only 70 infected patients. Therefore, antibody screening combined with detection of HCV RNA should be considered as the “gold standard” for diagnosing HCV infection in dialysis patients. The prevalence of HCV-infected patients in Dutch dialysis centers ranged from 0 to 8%, suggesting the existence of local risk factors for acquiring HCV infection. Genotyping analysis by reverse hybridization line probe assay revealed the presence of genotypes 1a (23%), 1b (46%), 2 (3%), 2a (13%), 2b (1%), 3a (7%), and 4a (4%). In four (6%) samples multiple genotypes were detected. The genotype distribution of HCV isolates among Dutch dialysis patients was similar to the distribution among nondialysis patients from the Benelux, except for subtype 1a, which was significantly more prevalent among dialysis patients. In only one center, a high prevalence of an uncommon genotype was suggestive of infection from a common source.
Isolation of
Lautropia mirabilis
from Oral Cavities of Human Immunodeficiency Virus-Infected Children
Authors: Rossmann Susan Norton , Wilson Patricia H. , Hicks John , Carter Bruce , Cron Stanley G. , Simon Cara , Flaitz Catherine M. , Demmler Gail J. , Shearer William T. , Kline Mark W. 
Published: December 2019

ABSTRACT

Lautropia mirabilis
, a pleomorphic, motile, gram-negative coccus, has been isolated from the oral cavities of 32 of 60 (53.3%) children infected with human immunodeficiency virus (HIV) and 3 of 25 (12.0%) HIV-uninfected controls; the association of
L. mirabilis
isolation with HIV infection is significant (
P
< 0.001). All children in the study, both HIV-infected children and controls, were born to HIV-infected mothers. The presence of this bacterium was not associated with clinical disease in these children. The HIV-infected children with
L. mirabilis
did not differ from the HIV-infected children without
L. mirabilis
in immunological status, clinical status, or systemic medications. The role of HIV infection itself or concomitant factors in the establishment of
L. mirabilis
in the oral cavity remains to be elucidated.
Peritonitis Associated with Vancomycin-Resistant
Lactobacillus rhamnosus
in a Continuous Ambulatory Peritoneal Dialysis Patient: Organism Identification, Antibiotic Therapy, and Case Report
Authors: Klein Günter , Zill Edith , Schindler Ralf , Louwers Jacobus 
Published: December 2019

ABSTRACT

A case of
Lactobacillus rhamnosus
-associated peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis is reported. The patient was treated with vancomycin after isolation of glycopeptide-susceptible coagulase-negative staphylococci. After a skin rash developed, vancomycin was discontinued and replaced with teicoplanin. Seven weeks after the glycopeptide therapy was discontinued, a
Lactobacillus
strain was isolated in pure cultures. The isolate was identified first incorrectly as
L. acidophilus
but later correctly as
L. rhamnosus
. Antibiotic susceptibility testing showed that the isolate was resistant to glycopeptides but susceptible to several other antibiotics. The antibiotic treatment was then switched to imipenem and was successful.
High Human Herpesvirus 8 Seroprevalence in the Homosexual Population in Switzerland
Authors: Regamey Nicolas , Cathomas Gieri , Schwager Martine , Wernli Marion , Harr Thomas , Erb Peter 
Published: December 2019

ABSTRACT
The seroprevalence of human herpesvirus 8 (HHV-8) in the Swiss population was investigated. By enzyme-linked immunosorbent assay, sera reactive to the recombinant HHV-8 antigen orf 65.2 were found in 24% of human immunodeficiency virus (HIV)-positive patients without and in 92% of HIV-positive patients with Kaposi’s sarcoma. Surprisingly, 20% of homosexual HIV-negative men, versus only 7% of heterosexual HIV-negative individuals and 5% of blood donors, had antibodies to HHV-8.
Reverse Transcriptase PCR Amplification of
Rickettsia typhi
from Infected Mammalian Cells and Insect Vectors
Authors: Higgins James A. , Radulovic Suzana , Noden Bruce H. , Troyer Jill M. , Azad Abdu F. 
Published: December 2019

ABSTRACT

We developed a reverse transcriptase PCR assay to detect expression of 120- and 17-kDa antigen genes in
Rickettsia typhi
. Infected Vero cell and flea RNAs were reverse transcribed by using random hexamers. The cDNA was amplified by using high concentrations of primer and template in an inexpensive, nonradioactive assay.
Characterization of IS
1245
for Strain Typing of
Mycobacterium avium
Authors: Pestel-Caron Martine , Arbeit Robert D. 
Published: December 2019

ABSTRACT

IS
1245
is an insertion element widely prevalent among isolates of
Mycobacterium avium
. We used
Pvu
II Southern blots to analyze IS
1245
polymorphisms among 159
M. avium
isolates (141 clinical isolates from 40 human immunodeficiency virus-infected patients plus 18 epidemiologically related environmental isolates) that represented 40 distinct
M. avium
strains, as resolved by previous studies by pulsed-field gel electrophoresis (PFGE). All 40 strains carried DNA homologous to IS
1245
and thus were typeable. Twenty-five (63%) strains had ≥10 copies of the element, 6 (15%) had 4 to 9 copies, and 9 (23%) had only 1 to 3 copies. Among the last group of nine strains (each of which was distinct by PFGE analysis), IS
1245
typing resolved only four patterns and thus provided poor discriminatory power. To evaluate the in vivo stability of IS
1245
, we analyzed 32 strains for which sets of 2 to 19 epidemiologically related isolates were available. For 19 (59%) of these sets, all isolates representing the same strain had indistinguishable IS
1245
patterns. Within eight (25%) sets, one or more isolates had IS
1245
patterns that differed by one or two fragments from the modal pattern for the isolates of that strain. Five (16%) sets included isolates whose patterns differed by three or more fragments; on the basis of IS
1245
typing those isolates would have been designated distinct strains. IS
1245
was stable during in vitro passage, suggesting that the variations observed represented natural translocations of the element. IS
1245
provides a useful tool for molecular strain typing of
M. avium
but may have limitations for analyzing strains with low copy numbers or for resolving extended epidemiologic relationships.
Use of Multiple Competitors for Quantification of Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Vener Tanya , Nygren Malin , Andersson AnnaLena , Uhlén Mathias , Albert Jan , Lundeberg Joakim 
Published: December 2019

ABSTRACT
Quantification of human immunodeficiency virus type 1 (HIV-1) RNA in plasma has rapidly become an important tool in basic HIV research and in the clinical care of infected individuals. Here, a quantitative HIV assay based on competitive reverse transcription-PCR with multiple competitors was developed. Four RNA competitors containing identical PCR primer binding sequences as the viral HIV-1 RNA target were constructed. One of the PCR primers was fluorescently labeled, which facilitated discrimination between the viral RNA and competitor amplicons by fragment analysis with conventional automated sequencers. The coamplification of known amounts of the RNA competitors provided the means to establish internal calibration curves for the individual reactions resulting in exclusion of tube-to-tube variations. Calibration curves were created from the peak areas, which were proportional to the starting amount of each competitor. The fluorescence detection format was expanded to provide a dynamic range of more than 5 log units. This quantitative assay allowed for reproducible analysis of samples containing as few as 40 viral copies of HIV-1 RNA per reaction. The within- and between-run coefficients of variation were <24% (range, 10 to 24) and <36% (range, 27 to 36), respectively. The high reproducibility (standard deviation, <0.13 log) of the overall procedure for quantification of HIV-1 RNA in plasma, including sample preparation, amplification, and detection variations, allowed reliable detection of a 0.5-log change in RNA viral load. The assay could be a useful tool for monitoring HIV-1 disease progression and antiviral treatment and can easily be adapted to the quantification of other pathogens.
Algorithmic Approach to High-Throughput Molecular Screening for Alpha Interferon-Resistant Genotypes in Hepatitis C Patients
Authors: Sreevatsan Srinand , Bookout Jack B. , Ringpis Fidel M. , Pottathil Mridula R. , Marshall David J. , De Arruda Monika , Murvine Christopher , Fors Lance , Pottathil Raveendran M. , Barathur Raj R. 
Published: December 2019

ABSTRACT
This study was designed to analyze the feasibility and validity of using Cleavase Fragment Length Polymorphism (CFLP) analysis as an alternative to DNA sequencing for high-throughput screening of hepatitis C virus (HCV) genotypes in a high-volume molecular pathology laboratory setting. By using a 244-bp amplicon from the 5′ untranslated region of the HCV genome, 61 clinical samples received for HCV reverse transcription-PCR (RT-PCR) were genotyped by this method. The genotype frequencies assigned by the CFLP method were 44.3% for type 1a, 26.2% for 1b, 13.1% for type 2b, and 5% type 3a. The results obtained by nucleotide sequence analysis provided 100% concordance with those obtained by CFLP analysis at the major genotype level, with resolvable differences as to subtype designations for five samples. CFLP analysis-derived HCV genotype frequencies also concurred with the national estimates (N. N. Zein et al., Ann. Intern. Med. 125:634–639, 1996). Reanalysis of 42 of these samples in parallel in a different research laboratory reproduced the CFLP fingerprints for 100% of the samples. Similarly, the major subtype designations for 19 samples subjected to different incubation temperature-time conditions were also 100% reproducible. Comparative cost analysis for genotyping of HCV by line probe assay, CFLP analysis, and automated DNA sequencing indicated that the average cost per amplicon was lowest for CFLP analysis, at $20 (direct costs). On the basis of these findings we propose that CFLP analysis is a robust, sensitive, specific, and an economical method for large-scale screening of HCV-infected patients for alpha interferon-resistant HCV genotypes. The paper describes an algorithm that uses as a reflex test the RT-PCR-based qualitative screening of samples for HCV detection and also addresses genotypes that are ambiguous.