bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and Function of Plasmid pColD157 of Enterohemorrhagic
Escherichia coli
O157 and Its Distribution among Strains from Patients with Diarrhea and Hemolytic-Uremic Syndrome
Authors: Hofinger Clemens , Karch Helge , Schmidt Herbert 
Published: December 2019

ABSTRACT

In this study, pColD157, a 6.7-kb colicinogenic plasmid of enterohemorrhagic
Escherichia coli
(EHEC) O157:H7 strain CL40cu, was characterized by restriction mapping and determination of its complete nucleotide sequence. The sequence consists of 6,675 bp and shows a high degree of similarity to the nucleotide sequence of colicinogenic plasmids pColD-CA23 and pColK. Seven potential genes were located on pColD157, three of which were closely related (>97.9%) to the colicin D structural gene and the corresponding immunity and lysis genes of plasmid pColD-CA23, and these were therefore designated
cda
,
cdi
, and
cdl
, respectively, using the reference extension -CL40 for differentiation. The adjacent 3′ region is related to the origin of replication of pColD-CA23. In contrast, the remaining part of the plasmid harbors a cluster of genes, closely related to the mobilization genes of pColK, which is followed by a 0.3-kb stretch homologous to the pColK resolution function. These determinants were designated
mbdA
,
mbdB
,
mbdC
, and
mbdD
and
cdr
, respectively. Southern blot analysis was performed with a probe specific for the
cda
gene of pColD157 and two groups of EHEC O157:H7 isolates from patients with diarrhea or hemolytic-uremic syndrome resident in Germany. Whereas 16 of 46
E. coli
O157 strains isolated between 1987 and 1991 harbored plasmid pColD157, only 1 of 50 strains isolated during 1996 carried this plasmid. In addition, all strains harboring plasmid pColD157 were shown to have colicinogenic activity.
Development of an Immunomagnetic Method for Selective Isolation of
Actinobacillus pleuropneumoniae
Serotype 1 from Tonsils
Authors: Gagné Annie , Lacouture Sonia , Broes André , D’Allaire Sylvie , Gottschalk Marcelo 
Published: December 2019

ABSTRACT

An immunomagnetic separation technique (IMS) for the selective isolation of
Actinobacillus pleuropneumoniae
serotype 1 was developed. Superparamagnetic polystyrene beads (immunomagnetic beads [IMBs]) were coated with purified rabbit immunoglobulin G specific for
A. pleuropneumoniae
serotype 1. The antibody concentration, the number of IMBs, the incubation time, and the temperature of incubation influenced the recovery of the target bacteria. The sensitivity of the IMS technique was 1,000-fold higher than that of direct culture. When tonsils from animals from infected herds were tested, significantly more positive tonsils were detected by the IMS technique (68%) than by the standard procedures (22%). The method represents an innovative and highly sensitive approach for the isolation of
A. pleuropneumoniae
from carrier animals.
Isolation of
Serpulina pilosicoli
from Rectal Biopsy Specimens Showing Evidence of Intestinal Spirochetosis
Authors: Trivett-Moore Nicolle L. , Gilbert Gwendolyn L. , Law Carmella L. H. , Trott Darren J. , Hampson David J. 
Published: December 2019

ABSTRACT

Histologic evidence of intestinal spirochetosis (IS) was found in 22 of 41 (53.7%) rectal biopsy specimens from homosexual men attending a sexually transmitted diseases clinic.
Serpulina pilosicoli
was cultured from 11 of the IS-positive biopsy specimens (50%) and from 2 specimens (10.5%) in which spirochetes were not observed. The association between seeing spirochetes in biopsy specimens and isolating
S. pilosicoli
was statistically significant, clearly indicating that this spirochete is the agent of IS.
Species-Specific Plasmid Sequences for PCR Identification of the Three Species of
Borrelia burgdorferi
Sensu Lato Involved in Lyme Disease
Authors: Misonne Marie-Christine , Hoet Philippe Pierre 
Published: December 2019

ABSTRACT

Species-specific sequences were shown to be carried by plasmids of the three main species of
Borrelia burgdorferi
sensu lato involved in Lyme disease. Libraries of the 16-, 33-, and 25-kb plasmids of
B. burgdorferi
sensu stricto,
Borrelia garinii
, and
Borrelia afzelii
, respectively, were then built and used to isolate species-specific sequences. After sequencing of the cloned inserts, three sets of primers were designed. They were shown to determine species-specific PCR amplification products. The sensitivities of the PCR assay with these primers were 100 spirochetes for
B. burgdorferi
sensu stricto and 1,000 spirochetes for
B. garinii
and
B. afzelii
. The usefulness of these primers for the identification of species in biological samples (tick, serum, and cerebrospinal fluid samples) was ascertained.
Premarket Evaluation of a Commercial Glycoprotein G-Based Enzyme Immunoassay for Herpes Simplex Virus Type-Specific Antibodies
Authors: Ashley Rhoda L. , Wu Linxian , Pickering Jerry W. , Tu Ming-Chieh , Schnorenberg Laura 
Published: December 2019

ABSTRACT
A new commercial glycoprotein G-based enzyme immunoassay (gG-EIA) was compared with Western blotting (WB) for detection of herpes simplex virus type 1 (HSV-1) or HSV-2 type-specific antibodies in 193 serum samples. Sensitivity for HSV-1 was 95%; specificity was 96%. Sensitivity for HSV-2 was 98%; specificity was 97%. Twelve of 13 serum samples with equivocal gG-EIA results were serotyped by WB.
Evaluation of the BIOMIC Video Reader System for Determining Interpretive Categories of Isolates on the Basis of Disk Diffusion Susceptibility Results
Authors: Korgenski E. Kent , Daly Judy A. 
Published: December 2019

ABSTRACT
The BIOMIC System (Giles Scientific, New York, N.Y.) includes software and a video-assisted plate reader that functions with a personal computer to automate, speed read, and interpret standard antibiotic disk diffusion test plates. The video reader helps standardize endpoints, speeds quantitative measurements by 40 to 90%, and reduces fatigue and transcription and interpretation errors (H. Wei-Fang, Am. Clin. Lab. 13:28–29, 1994). Organisms tested were isolated from patient specimens collected at Primary Children’s Medical Center and included rapidly growing gram-positive and gram-negative strains that fulfill the National Committee for Clinical Laboratory Standards guidelines for disk diffusion susceptibility testing. A comparison of the plate reader-determined zones and visually measured zones for 3,339 organism-antimicrobial agent combinations was performed. The results demonstrated 0.1% (4 of 3,339) false-susceptible reads and 0.2% (6 of 3,339) false-resistant reads by the video reader compared with visual reads. Minor discrepancies (4.7% [156 of 3339]), resulting in category interpretation changes of intermediate to resistant or susceptible or changes of resistant or susceptible to intermediate, were also encountered. Of the discrepant results, 80.8% (139 of 172) resulted from a 3-mm or less zone diameter difference between the two different techniques. We conclude that the video-assisted plate reader is a reliable system for determining interpretative categories from zone diameters of standard antibiotic disk diffusion test plates.
Absolute Copy Number and Relative Change in Determinations of Human Immunodeficiency Virus Type 1 RNA in Plasma: Effect of an External Standard on Kit Comparisons
Authors: Brambilla Donald , Leung Sheila , Lew Judy , Todd John , Herman Steven , Cronin Mike , Shapiro David E. , Bremer James , Hanson Celine , Hillyer George V. , McSherry George D. , Sperling Rhoda S. , Coombs Robert W. , Reichelderfer Patricia S. 
Published: December 2019

ABSTRACT
Use of a common set of human immunodeficiency virus type 1 (HIV-1) RNA standards eliminated differences among absolute HIV-1 RNA copy number estimates made with three commercially available assays. The relative changes in the viral RNA levels determined by the commercial assays were similar and were unaffected by the use of a common set of standards.
Evaluation of a New Method for Rapid Drug Susceptibility Testing of
Mycobacterium avium
Complex Isolates by Using the Mycobacteria Growth Indicator Tube
Authors: Piersimoni Claudio , Nista Domenico , Bornigia Stefano , De Sio Giuseppina 
Published: December 2019

ABSTRACT

The reliability of the Mycobacteria Growth Indicator Tube (MGIT [BBL]) for rapid drug susceptibility testing of
Mycobacterium avium
complex (MAC) isolates was evaluated. MICs of amikacin, clarithromycin, clofazimine, ethambutol, and rifabutin were determined by the MGIT system for 16 MAC strains. The results were compared with those obtained by the BACTEC broth macrodilution method. The turnaround times were 6 to 8 days (median, 7 days) for the MGIT and 5 to 7 days (median, 6 days) for the BACTEC system. Agreements with BACTEC system-determined MICs, within ±1 log
2
dilution, were 100, 100, 88, 63, and 44% for amikacin, clofazimine, rifabutin, clarithromycin, and ethambutol, respectively. Within ±2 log
2
dilutions, agreement with BACTEC system-determined MICs increased to 100% for all the tested drugs. In addition, if MGIT-determined MICs were evaluated according to the thresholds adopted for the interpretation of BACTEC system-determined ones, ethambutol was the only drug for which susceptible strains were frequently misclassified as resistant. It is concluded that the MGIT system is a promising, nonradiometric alternative to the BACTEC method for rapid susceptibility testing of MAC isolates; however, additional studies are required to confirm our results and to determine the optimal criteria for the interpretation of ethambutol MICs.
Molecular Epidemiology of Recent Belgian Isolates of
Neisseria meningitidis
Serogroup B
Authors: Van Looveren M. , Vandamme P. , Hauchecorne M. , Wijdooghe M. , Carion F. , Caugant D. A. , Goossens H. 
Published: December 2019

ABSTRACT

In Belgium an increase in the incidence of meningococcal disease has been noted since the early 1990s. Four hundred twenty clinical strains isolated during the period from 1990 to 1995, along with a set of 30 European reference strains, and 20 Dutch isolates were examined by random-primer and repetitive-motif-based PCR. A subset was investigated by multilocus enzyme electrophoresis and pulsed-field gel electrophoresis. The data were compared with results obtained by serotyping (M. Van Looveren, F. Carion, P. Vandamme, and H. Goossens, Clin. Microbiol. Infect. 4:224–228, 1998). Both phenotypic and molecular epidemiological data suggest that the lineage III of
Neisseria meningitidis
, first encountered in The Netherlands in about 1980, has been introduced in Belgium. The epidemic clone, as defined by oligonucleotide D8635-primed PCR, encompasses mainly phenotypes B:4:P1.4 and B:nontypeable:P1.4, but strains with several other phenotypes were also encountered. Therefore, serotyping alone would underestimate the prevalence of the epidemic clone.
Prevalence of
Candida dubliniensis
Isolates in a Yeast Stock Collection
Authors: Odds Frank C. , Van Nuffel Luc , Dams Géry 
Published: December 2019

ABSTRACT

To establish the historical prevalence of the novel yeast species
Candida dubliniensis
, a survey of 2,589 yeasts originally identified as
Candida albicans
and maintained in a stock collection dating back to the early 1970s was undertaken. A total of 590 yeasts, including 93 (18.5%) β-glucosidase-negative isolates among 502 isolates that showed abnormal colony colors on a differential chromogenic agar and 497 other isolates, were subjected to DNA fingerprinting with the moderately repetitive sequence Ca3. On this basis, 53 yeasts were reidentified as
C. dubliniensis
(including the
C. dubliniensis
type strain, included as a blind control in the panel of yeasts). The 52 newly found isolates came from 36 different persons, and a further 3
C. dubliniensis
isolates were detected by DNA fingerprinting of previously untested isolates from one of these individuals. The prevalence of
C. dubliniensis
among yeasts in oral and fecal samples was significantly higher than that among yeasts from other anatomical sites and was significantly higher among human immunodeficiency virus (HIV)-infected individuals than among known or presumed HIV-negative individuals. However, a single vaginal isolate and two oral isolates from healthy volunteers confirmed that the species is restricted neither to gastrointestinal sites nor to patients with overt disease. The oldest examples of
C. dubliniensis
were from oral samples of three patients in the United Kingdom in 1973 and 1975. In comparison with age-matched control isolates of
C. albicans
, the
C. dubliniensis
isolates showed slightly higher levels of susceptibility in vitro to amphotericin B and flucytosine and slightly lower levels of susceptibility to three azole antifungal agents.
Fluconazole Susceptibility Testing of
Cryptococcus neoformans
: Comparison of Two Broth Microdilution Methods and Clinical Correlates among Isolates from Ugandan AIDS Patients
Authors: Jessup C. J. , Pfaller M. A. , Messer S. A. , Zhang J. , Tumberland M. , Mbidde E. K. , Ghannoum M. A. 
Published: December 2019

ABSTRACT

We compared the yeast nitrogen base (YNB) broth microdilution method with the National Committee for Clinical Laboratory Standards (NCCLS) M27-A microdilution reference method for measuring the in vitro susceptibility of
Cryptococcus neoformans
isolates to fluconazole. A total of 149 isolates of
C. neoformans
var.
neoformans
from Ugandan AIDS patients was tested by both methods. An overall agreement of 88% between the two microdilution methods was observed. All isolates grew well in both RPMI 1640 and YNB media, and MICs could be read after 48 h of incubation by both methods. The range of fluconazole MICs obtained with the YNB method was broader than that obtained with the NCCLS method. The extended range of MICs provided by the YNB method may be of clinical value, as it appears that the clinical outcome may be better among patients infected with strains inhibited by lower concentrations of fluconazole as determined by the YNB method. The YNB method appears to be a viable option for testing
C. neoformans
against fluconazole.
Comparison of In Vitro Activities of the New Triazole SCH56592 and the Echinocandins MK-0991 (L-743,872) and LY303366 against Opportunistic Filamentous and Dimorphic Fungi and Yeasts
Authors: Espinel-Ingroff Ana 
Published: December 2019

ABSTRACT

The in vitro antifungal activities of SCH56592, MK-0991, and LY303366 against 83 isolates of
Acremonium strictum
,
Aspergillus flavus
,
Aspergillus fumigatus
,
Aspergillus terreus
,
Bipolaris
spp.,
Blastomyces dermatitidis
,
Cladophialophora bantiana
,
Fusarium oxysporum
,
Fusarium solani
,
Histoplasma capsulatum
,
Phialophora
spp.,
Pseudallescheria boydii
,
Rhizopus arrhizus
,
Scedosporium prolificans
, and
Sporothrix schenckii
were compared. The in vitro activities of these agents against 104 isolates of yeast pathogens of
Candida
spp.,
Cryptococcus neoformans
, and
Trichosporon beigelii
were also compared. MICs were determined by following a procedure under evaluation by the National Committee for Clinical Laboratory Standards (NCCLS) for broth microdilution testing of the filamentous fungi (visual MICs) and the NCCLS M27-A broth microdilution method for yeasts (both visual and turbidimetric MICs). The in vitro fungicidal activity of SCH56592 was superior (minimum fungicidal concentrations [MFCs], 0.25 to 4 μg/ml for 7 of 18 species tested) to those of MK-0991 and LY303366 (MFCs, 8 to >16 μg/ml for all species tested) for the molds tested, but the echinocandins had a broader spectrum of fungicidal activity (MFCs at which 90% of strains are inhibited [MFC
90
s], 0.5 to 4 μg/ml for 6 of 9 species tested) than SCH56592 (MFC
90
s, 0.25 to 8 μg/ml for 4 of 9 species tested) against most of the yeasts tested. Neither echinocandin had in vitro activity (MICs, >16 μg/ml) against
C. neoformans
and
T. beigelii
, while the SCH56592 MICs ranged from 0.12 to 1.0 μg/ml for these two species. The MICs of the three agents for the other species ranged from <0.03 to 4 μg/ml. These results suggest that these new agents have broad-spectrum activities in vitro; their effectiveness in the treatment of human mycoses is to be determined.
Comparison of Different DNA Fingerprinting Techniques for Molecular Typing of
Bartonella henselae
Isolates
Authors: Sander Anna , Ruess Michael , Bereswill Stefan , Schuppler Markus , Steinbrueckner Bernhard 
Published: December 2019

ABSTRACT

Seventeen isolates of
Bartonella henselae
from the region of Freiburg, Germany, obtained from blood cultures of domestic cats, were examined for their genetic heterogeneity. On the basis of different DNA fingerprinting methods, including pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus (ERIC)-PCR, repetitive extragenic palindromic (REP) PCR, and arbitrarily primed (AP)-PCR, three different variants were identified among the isolates (variants I to III). Variant I included 6 strains, variant II included 10 strains, and variant III included only one strain. By all methods used, the isolates could be clearly distinguished from the type strain, Houston-1, which was designated variant IV. A previously published type-specific amplification of 16S rDNA differentiated two types of the
B. henselae
isolates (16S rRNA types 1 and 2). The majority of the isolates (16 of 17), including all variants I and II, were 16S rRNA type 2. Only one isolate (variant III) and the Houston-1 strain (variant IV) comprised the 16S rRNA type 1. Comparison of the 16S rDNA sequences from one representative strain from each of the three variants (I to III) confirmed the results obtained by 16S rRNA type-specific PCR. The sequences from variant I and variant II were identical, whereas the sequence of variant III differed in three positions. All methods applied in this study allowed subtyping of the isolates. PFGE and ERIC-PCR provided the highest discriminatory potential for subtyping
B. henselae
strains, whereas AP-PCR with the M13 primer showed a very clear differentiation between the four variants. Our results suggest that the genetic heterogeneity of
B. henselae
strains is high. The methods applied were found useful for typing
B. henselae
isolates, providing tools for epidemiological and clinical follow-up studies.
Plaque Formation by and Plaque Cloning of
Chlamydia trachomatis
Biovar Trachoma
Authors: Matsumoto Akira , Izutsu Hiroshi , Miyashita Naoyuki , Ohuchi Masanobu 
Published: December 2019

ABSTRACT

A new technique for the induction of plaque formation by
Chlamydia trachomatis
biovar trachoma applicable to the titration of infectivity and cloning of biovar trachoma was established. Three novel strains were cloned and confirmed to be free of glycogen inclusions. The lack of glycogen accumulation correlated with the absence of a 7.5-kb plasmid, which is highly conserved in other strains of
C. trachomatis
. Although the growth efficiency of these plasmid-free strains was slightly lower than that of plasmid-positive strains, possession of the plasmid and glycogen accumulation were not essential for the survival of
C. trachomatis
.
Genotyping of 27 Human Papillomavirus Types by Using L1 Consensus PCR Products by a Single-Hybridization, Reverse Line Blot Detection Method
Authors: Gravitt P. E. , Peyton C. L. , Apple R. J. , Wheeler C. M. 
Published: December 2019

ABSTRACT

Amplification of human papillomavirus (HPV) DNA by L1 consensus primer systems (e.g., MY09/11 or GP5
+
/6
+
) can detect as few as 10 to 100 molecules of HPV targets from a genital sample. However, genotype determination by dot blot hybridization is laborious and requires at least 27 separate hybridizations for substantive HPV-type discrimination. A reverse blot method was developed which employs a biotin-labeled PCR product hybridized to an array of immobilized oligonucleotide probes. By the reverse blot strip analysis, genotype discrimination of multiple HPV types can be accomplished in a single hybridization and wash cycle. Twenty-seven HPV probe mixes, two control probe concentrations, and a single reference line were immobilized to 75- by 6-mm nylon strips. Each individual probe line contained a mixture of two bovine serum albumin-conjugated oligonucleotide probes specific to a unique HPV genotype. The genotype spectrum discriminated on this strip includes the high-risk, or cancer-associated, HPV genotypes 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 55, 56, 58, 59, 68 (ME180), MM4 (W13B), MM7 (P291), and MM9 (P238A) and the low-risk, or non-cancer-associated, genotypes 6, 11, 40, 42, 53, 54, 57, 66, and MM8 (P155). In addition, two concentrations of β-globin probes allowed for assessment of individual specimen adequacy following amplification. We have evaluated the performance of the strip method relative to that of a previously reported dot blot format (H. M. Bauer et al., p. 132–152,
in
C. S. Herrington and J. O. D. McGee (ed.),
Diagnostic Molecular Pathology: a Practical Approach
, (1992), by testing 328 cervical swab samples collected in Digene specimen transport medium (Digene Diagnostics, Silver Spring, Md.). We show excellent agreement between the two detection formats, with 92% concordance for HPV positivity (kappa = 0.78,
P
< 0.001). Nearly all of the discrepant HPV-positive samples resulted from weak signals and can be attributed to sampling error from specimens with low concentrations (<1 copy/μl) of HPV DNA. The primary advantage of the strip-based detection system is the ability to rapidly genotype HPVs present in genital samples with high sensitivity and specificity, minimizing the likelihood of misclassification.
IS
1245
Restriction Fragment Length Polymorphism Typing of
Mycobacterium avium
Isolates: Proposal for Standardization
Authors: van Soolingen Dick , Bauer Jeanett , Ritacco Viviana , Leão Sylvia Cardoso , Pavlik Ivo , Vincent Veronique , Rastogi Nalin , Gori Andrea , Bodmer Thomas , Garzelli Carlo , Garcia Maria J. 
Published: December 2019

ABSTRACT

Mycobacterium avium
has become a major human pathogen, primarily due to the emergence of the AIDS epidemic. Restriction fragment length polymorphism (RFLP) typing, using insertion sequence IS
1245
as a probe, provides a powerful tool in the molecular epidemiology of
M. avium
-related infections and will facilitate well-founded studies into the sources of
M. avium
infections in animal and environmental reservoirs. The standardization of this technique allows computerization of IS
1245
RFLP patterns for comparison on a local level and the establishment of
M. avium
DNA fingerprint databases for interlaboratory comparison. Moreover, by combining international DNA typing results of
M. avium
complex isolates from a broad spectrum of sources, long-lasting questions on the epidemiology of this major agent of mycobacterial infections will be answered.
Staphylococcal Scalded-Skin Syndrome Complicating Wound Infection in a Preterm Infant with Postoperative Chylothorax
Authors: Peters Bjoern , Hentschel Juliane , Mau Harald , Halle Elke , Witte Wolfgang , Obladen Michael 
Published: December 2019

ABSTRACT

The course of infection in a 3-week-old premature newborn suffering from extensive dermatitis with flaccid blisters is described.
Staphylococcus aureus
was recovered from a local wound infection around a chest tube inserted to drain a postoperative chylothorax. The strain isolated tested positive for the
eta
gene for exfoliative toxin A, the causative agent of staphylococcal scalded-skin syndrome (SSSS). In this case, prematurity and loss of chylus with consecutive lymphopenia may have contributed to development of SSSS.
Genotyping of
Chlamydia trachomatis
in Urine Specimens Will Facilitate Large Epidemiological Studies
Authors: Morré Servaas A. , Moes Robert , Van Valkengoed Irene , Boeke Joan P. , van Eijk Jacques T. M. , Meijer Chris J. L. M. , Van den Brule Adriaan J. C. 
Published: December 2019

ABSTRACT

The serovars of
Chlamydia trachomatis
-positive urine specimens (
n
= 81; as detected by PCR and ligase chain reaction) were successfully analyzed in 94% of cases by
omp1
PCR-based RFLP analysis. The use of urine specimens and this simple and sensitive typing method will greatly facilitate epidemiological studies of
C. trachomatis
serovar distribution in asymptomatic
C. trachomatis
infections in both females and males.