bluuebunny/crossref_metadata_2025_split huggingface dataset:
Somatic Serogroups, Capsular Types, and Species of Fecal
Klebsiella
in Patients with Ankylosing Spondylitis
Authors: Toivanen Paavo , Hansen Dennis S. , Mestre Francisca , Lehtonen Leena , Vaahtovuo Jussi , Vehma Mari , Möttönen Timo , Saario Riitta , Luukkainen Reijo , Nissilä Martti 
Published: December 2019

ABSTRACT

The purpose of the present study was to find out whether patients with ankylosing spondylitis (AS) carry fecal
Klebsiella
strains that belong to serotypes or species specific for AS. Somatic serotypes (O groups), capsular (K) serotypes, and biochemically identified species were determined for fecal klebsiellae isolated from 187 AS patients and 195 control patients. The controls were patients with fibromyalgia or rheumatoid arthritis. The 638 isolates of
Klebsiella
that were obtained represented 161 strains; 81 from AS patients and 80 from the controls. The average number of
Klebsiella
strains per patient was 1.7 for the AS group and 1.5 for the control group. The most common O group was O1, which was observed for isolates from 23 of 187 AS patients and 24 of 195 control patients. Next in frequency was group O2, which was observed for isolates from 17 AS patients and 15 control patients. Regarding the K serotypes, 59 different types were identified, revealing a heterogeneous representation of
Klebsiella
strains, without a predominance of any serotype. By biochemical identification,
Klebsiella pneumoniae
was the most frequently occurring species, being found in 45 AS patients and 45 control patients. Next in the frequency was
K. oxytoca
, which was observed in 26 AS patients and in 29 control patients.
K. planticola
and
K. terrigena
occurred in only a minority of patients. Altogether, when analyzed either separately or simultaneously according to O groups, K serotypes, and biochemically identified species, no evidence of the existence of AS-specific
Klebsiella
strains was obtained. These findings do not indicate participation of
Klebsiella
in the etiopathogenesis of AS.
Isolation of Rifampin-Resistant Mutants of
Listeria monocytogenes
and Their Characterization by
rpoB
Gene Sequencing, Temperature Sensitivity for Growth, and Interaction with an Epithelial Cell Line
Authors: Morse Robert , O’Hanlon Karen , Virji Mumtaz , Collins Matthew D. 
Published: December 2019

ABSTRACT

The sequence of the
rpoB
gene from
Listeria monocytogenes
was determined. Rifampin-resistant (Rif
r
) mutants arising from
L. monocytogenes
cultures exposed to rifampin were isolated, and by partial sequencing of their
rpoB
genes, seven different point mutations affecting five different amino acids (473Asp→Asn or Gly, 479Gly→Asp, 483His→Tyr or Leu, 528Ile→Phe, and 530Ser→Tyr), which led to MICs of 0.5 to 100 μg/ml for the organisms, were determined. These mutants showed various deficiencies for growth at 42°C, with only one being comparable to the wild-type strain. The interaction of these Rif
r
mutants with human Caco-2 cells was examined by using an immunofluorescence technique. Three mutants failed to interact, while three showed a reduced interaction compared to that of the wild type. It is believed that these pleiotropic phenotypes have arisen as a result of mutations within the DNA-dependent RNA polymerase holoenzyme.
Human Immunodeficiency Virus Type 1 Cloning Vectors for Antiretroviral Resistance Testing
Authors: Martinez-Picado Javier , Sutton Lorraine , De Pasquale Maria Pia , Savara Anu V. , D’Aquila Richard T. 
Published: December 2019

ABSTRACT
Better detection of minority human immunodeficiency virus type 1 (HIV-1) populations containing gene mutations may improve the usefulness of antiretroviral resistance testing for clinical management. Molecular cloning of HIV-1 PCR products which might improve minority detection can be slow and difficult, and commercially available recombinant virus assays test drug susceptibility of virus pools. We describe novel plasmids and simple methods for rapid cloning of HIV-1 PCR products from patient specimens and their application to generate infectious recombinant virus clones for virus phenotyping and genotyping. Eight plasmids with differing deletions of sequences encoding HIV-1 protease, reverse transcriptase, or Gag p7/p1 and Gag p1/p6 cleavage sites were constructed for cloning HIV-1 PCR products. A simple HIV-1 sequence-specific uracil deglycosylase-mediated cloning method with the vectors and primers designed here was more rapid than standard ligase-mediated cloning. Pooled and molecularly cloned infectious recombinant viruses were generated with these vectors. Replicative viral fitness and drug susceptibility phenotypes of cloned infectious viruses containing patient specimen-derived sequences were measured. Clonal resistance genotyping analyses were also performed from virus isolates, plasma HIV-1 RNA, and infected cell DNA. Sequencing of a limited number of molecular clones detected minorities of resistant virus not identified in the pooled population PCR product sequence and linkage of minority mutations.
Outcome of Diagnostic Tests Using Samples from Patients with Culture-Proven Human Monocytic Ehrlichiosis: Implications for Surveillance
Authors: Childs James E. , Sumner John W. , Nicholson William L. , Massung Robert F. , Standaert Steven M. , Paddock Christopher D. 
Published: December 2019

ABSTRACT

We describe the concordance among results from various laboratory tests using samples derived from nine culture-proven cases of human monocytic ehrlichiosis (HME) caused by
Ehrlichia chaffeensis
. A class-specific indirect immunofluorescence assay for immunoglobulin M (IgM) and IgG, using
E. chaffeensis
antigen, identified 44 and 33% of the isolation-confirmed HME patients on the basis of samples obtained at initial clinical presentation, respectively; detection of morulae in blood smears was similarly insensitive (22% positive). PCR amplifications of ehrlichial DNA targeting the 16S rRNA gene, the variable-length PCR target gene, and the
groESL
operon were positive for whole blood specimens obtained from all patients at initial presentation. As most case definitions of HME require a serologic response with compatible illness for a categorization of even probable disease, PCR would have been required to confirm the diagnosis of HME in all nine of these patients without the submission of a convalescent-phase serum sample. These data suggest that many, if not most, cases of HME in patients who present early in the course of the disease may be missed and underscore the limitations of serologically based surveillance systems.
Common Ancestry of
Borrelia burgdorferi
Sensu Lato Strains from North America and Europe
Authors: Postic D. , Ras N. Marti , Lane R. S. , Humair P.-F. , Wittenbrink M. M. , Baranton G. 
Published: December 2019

ABSTRACT

Ten atypical European
Borrelia burgdorferi
sensu lato (
Borrelia
spp.) strains were genetically characterized, and the diversity was compared to that encountered among related
Borrelia
spp. from North America. Phylogenetic analyses of a limited region of the genome and of the whole genome extend existing knowledge about borrelial diversity reported earlier in Europe and the United States. Our results accord with the evidence that North American and European strains may have a common ancestry.
Discrimination of Multidrug-Resistant
Mycobacterium tuberculosis
IS
6110
Fingerprint Subclusters by
rpoB
Gene Mutation Analysis
Authors: Portugal Isabel , Maia Sara , Moniz-Pereira José 
Published: December 2019

ABSTRACT

The
rpoB
gene mutations in a 69-bp region of the gene, resulting in resistance to rifampin, were used to discriminate between
Mycobacterium tuberculosis
IS
6110
fingerprint subclusters. These subclusters exhibited identical IS
6110
fragments or had one or two additional fragments. In the two major subclusters all the analyzed strains have the same variant
rpoB
allele but are different from each other, suggesting the occurrence of independent outbreaks.
Interactions between Methicillin and Vancomycin in Methicillin-Resistant
Staphylococcus aureus
Strains Displaying Different Phenotypes of Vancomycin Susceptibility
Authors: Howe Robin A. , Wootton Mandy , Bennett Peter M. , MacGowan Alasdair P. , Walsh Timothy R. 
Published: December 2019

ABSTRACT

Vancomycin-sensitive, -intermediate, and -heterointermediate methicillin-resistant
Staphylococcus aureus
isolates were tested by using E-tests to explore the interaction of methicillin and vancomycin. For the vancomycin-intermediate and -heterointermediate strains both drugs showed antagonism at concentrations below their MICs but synergy at methicillin concentrations near the MIC. This property could be used to screen for heterointermediate
S. aureus
strains.
Peritonitis Caused by
Haemophilus parainfluenzae
in a Patient Undergoing Continuous Ambulatory Peritoneal Dialysis
Authors: Betriu Carmen , Coronel Francisco , Martin Pilar , Picazo Juan J. 
Published: December 2019

ABSTRACT

We report a case of peritonitis in a patient undergoing continuous ambulatory peritoneal dialysis.
Haemophilus parainfluenzae
biotype III was recovered in pure culture from dialysis fluid.
Multicenter Evaluation of Epidemiological Typing of Methicillin-Resistant
Staphylococcus aureus
Strains by Repetitive-Element PCR Analysis
Authors: Deplano Ariane , Schuermans Annette , Van Eldere Johan , Witte Wolfgang , Meugnier Hèléne , Etienne Jerome , Grundmann Hajo , Jonas Daniel , Noordhoek Gerda T. , Dijkstra Jolanda , van Belkum Alex , van Leeuwen Willem , Tassios Panayotis T. , Legakis Nicholas J. , van der Zee Anneke , Bergmans Anneke , Blanc Dominique S. , Tenover Fred C. , Cookson Barry C. , O'Neil Gael , Struelens Marc J. ,   The European Study Group on Epidemiological Markers of the ESCMID
Published: December 2019

ABSTRACT

Rapid and efficient epidemiologic typing systems would be useful to monitor transmission of methicillin-resistant
Staphylococcus aureus
(MRSA) at both local and interregional levels. To evaluate the intralaboratory performance and interlaboratory reproducibility of three recently developed repeat-element PCR (rep-PCR) methods for the typing of MRSA, 50 MRSA strains characterized by pulsed-field gel electrophoresis (PFGE) (
Sma
I) analysis and epidemiological data were blindly typed by inter-IS
256
, 16S-23S ribosomal DNA (rDNA), and MP3 PCR in 12 laboratories in eight countries using standard reagents and protocols. Performance of typing was defined by reproducibility (
R
), discriminatory power (
D
), and agreement with PFGE analysis. Interlaboratory reproducibility of pattern and type classification was assessed visually and using gel analysis software. Each typing method showed a different performance level in each center. In the center performing best with each method, inter-IS
256
PCR typing achieved
R
= 100% and
D
= 100%; 16S-23S rDNA PCR,
R
= 100% and
D
= 82%; and MP3 PCR,
R
= 80% and
D
= 83%. Concordance between rep-PCR type and PFGE type ranged by center: 70 to 90% for inter-IS
256
PCR, 44 to 57% for 16S-23S rDNA PCR, and 53 to 54% for MP3 PCR analysis. In conclusion, the performance of inter-IS
256
PCR typing was similar to that of PFGE analysis in some but not all centers, whereas other rep-PCR protocols showed lower discrimination and intralaboratory reproducibility. None of these assays, however, was sufficiently reproducible for interlaboratory exchange of data.
Evaluation of the MicroScan Rapid Neg ID3 Panel for Identification of
Enterobacteriaceae
and Some Common Gram-Negative Nonfermenters
Authors: O'Hara Caroline Mohr , Miller J. Michael 
Published: December 2019

ABSTRACT

The MicroScan Rapid Neg ID3 panel (Dade Behring, Inc., West Sacramento, Calif.) is designed for the identification of gram-negative bacilli. We evaluated its ability to accurately identify
Enterobacteriaceae
that are routinely encountered in a clinical laboratory and glucose nonfermenting gram-negative bacilli. Using 511 stock cultures that were maintained at −70°C and passaged three times before use, we inoculated panels according to the manufacturer's instructions and processed them in a Walk/Away instrument using version 22.01 software. The time to identification was 2 h and 30 min. All panel identifications were compared to reference identifications previously determined by conventional tube biochemicals. At the end of the initial 2.5-h incubation period, 405 (79.3%) identifications were correct. An additional 49 (9.6%) isolates were correctly identified after required additional off-line biochemical tests were performed. Thus, at 24 h, 88.8% of the 511 strains tested were correctly identified. Twenty-two (4.3%) were identified to the genus level only. Twenty-six (5.1%) strains were misidentified. Because the system is based on fluorogenics, there are no conventional tests readily available with which to compare possibly incorrect reactions. Of the 28
Salmonella
strains that were tested, 5 were incorrectly reported. The 21 remaining errors were scattered among the genera tested. Testing on nine strains gave a result of “no identification” (very rare biotype). The Rapid Neg ID3 panel in this study approached 89% accuracy for the identification of gram-negative organisms encountered in the hospital laboratory.
Detection of Borreliacidal Antibodies in Dogs after Challenge with
Borrelia burgdorferi
-Infected
Ixodes scapularis
Ticks
Authors: Callister Steven M. , Jobe Dean A. , Schell Ronald F. , Lovrich Steven D. , Onheiber Keysha L. , Korshus Jon B. 
Published: December 2019

ABSTRACT

Detection of borreliacidal antibodies is an accurate serodiagnostic test for confirmation of Lyme disease in humans. In this study, 13 pathogen-free beagles, 12 to 26 weeks old, were infected with
Borrelia burgdorferi
by tick challenge. Dogs were monitored for clinical signs and symptoms of Lyme disease along with borreliacidal antibody production against
B. burgdorferi
sensu stricto isolates 297 and 50772. Ten (77%) dogs developed lameness in one or more legs within 210 days after attachment of
Ixodes scapularis
ticks. Eight (80%) of the lame animals had concurrent fever of ≥38°C. Spirochetes were also recovered from the skin and joints of 12 (92%) dogs, but rarely from other organs. Borreliacidal antibodies against
B. burgdorferi
isolate 297 were detected in only four (31%) dogs, and the levels of killing antibodies remained low for the duration of the infection. In contrast, borreliacidal antibodies against
B. burgdorferi
isolate 50772 were detected in 13 (100%) dogs within 21 days of infection. Furthermore, the borreliacidal antibody levels correlated with the severity of
B. burgdorferi
infection. Detection of borreliacidal antibodies, especially against
B. burgdorferi
isolate 50772, is also a reliable serodiagnostic test for detection of Lyme disease in dogs.
Comparison of Phenotypic and Genotypic Methods for Pyrazinamide Susceptibility Testing with
Mycobacterium tuberculosis
Authors: Davies A. P. , Billington O. J. , McHugh T. D. , Mitchison D. A. , Gillespie S. H. 
Published: December 2019

ABSTRACT

Mycobacterium tuberculosis
converts pyrazinamide to its active form by using the enzyme pyrazinamidase. This enzyme is coded for on the
pncA
gene, and mutations in the
pncA
gene result in absence of active enzyme, conferring resistance to the drug pyrazinamide. We investigated 27 strains of
Mycobacterium tuberculosis
suspected of being multidrug resistant. Each isolate was tested for susceptibility to pyrazinamide by the BACTEC 460TB method, and 19 were pyrazinamide resistant. The presence of active pyrazinamidase enzyme was sought by using the Wayne assay, which was positive in all of the sensitive isolates and four of the resistant isolates. The
pncA
gene was amplified by PCR, and mutations were sought by single-strand conformation polymorphism (SSCP) analysis. We identified four isolates which were phenotypically resistant to pyrazinamide, but which had active pyrazinamide enzyme on the Wayne assay and normal
pncA
gene SSCP. MICs measured by BACTEC 460TB and susceptibility testing at a lower pH of 5.5 confirmed genuine resistance. The
pncA
gene was sequenced in these four isolates and found not to have any mutations. This implies that an alternative mechanism of resistance exists in these strains. We conclude that genotypic assessment of pyrazinamide resistance is unreliable, because it depends on the identification of a single resistance mechanism. Phenotypic methods such as the BACTEC 460TB technique remain the best methods for pyrazinamide susceptibility testing.
PCR Assessment of
Chlamydia trachomatis
Infection of Semen Specimens Processed for Artificial Insemination
Authors: Pannekoek Yvonne , Westenberg Steven M. , de Vries Jan , Repping Sjoerd , Spanjaard Lodewijk , Eijk Paul P. , van der Ende Arie , Dankert Jacob 
Published: December 2019

ABSTRACT

In order to ascertain the microbiological quality of stored semen specimens processed for artificial insemination by a donor (AID), we developed a PCR assay targeting the chlamydial plasmid to detect
Chlamydia trachomatis
in semen. The lower limit of detection of this assay corresponded to 2.5 to 5 elementary bodies per μl of semen. A total of 669 cryopreserved ejaculates from 97 asymptomatic donors were tested for
C. trachomatis
infection. Twelve ejaculates, originating from four donors, were found to be positive, indicating a 4% prevalence of
C. trachomatis
infection among the donor population studied. Cross-contamination between the cryopreserved specimens in the storage container was studied by typing using sequence analysis of PCR-amplified
omp1
genes of the strains. Two donors were infected with serovar E, one was infected with serovar F, and one was infected with serovar K. For two donors, the duration of
C. trachomatis
positivity could be assessed. One donor donated
C. trachomatis
-positive semen for at least 4 successive months, and the other did so for at least 16 months. The occurrence of
C. trachomatis
infection in cryopreserved donor semen indicates that ejaculates from donors not tested for a
C. trachomatis
infection just prior to donation should be tested for infection by a direct test such as the PCR described here. Direct testing of semen specimens will detect not only donors with an active infection but also
C. trachomatis
-infected ejaculates already stored and will thus improve the microbiological quality of AID, since discrepancies in the presence of
C. trachomatis
in urine and semen specimens have been reported.
Rapid and Sensitive Plate Method for Detection of
Aspergillus fumigatus
Authors: Bauters T. G. M. , Nelis H. J. 
Published: December 2019

ABSTRACT

The routine identification of
Aspergillus fumigatus
in clinical samples involves, apart from direct examination, the isolation of the organism on a plate followed by its microscopic characterization. This approach lacks sensitivity, specificity, and speed. A new procedure has been developed combining microcolony formation on a nylon membrane filter at 45°C with the detection of a specific 4-methylumbelliferyl-α-
l
-arabinopyranoside cleaving enzyme activity in digitonin permeabilized cells. The test takes approximately 14 h and has an efficiency of 98.2% and false-positive and -negative rates of 0 and 3.1%, respectively. When applied to 188 clinical samples taken from patients with proven or nonproven presence of
Aspergillus
species, a good agreement with the conventional plate-microscopy method was obtained.
Discrimination between Viable and DeadEncephalitozoon cuniculi(Microsporidian) Spores by Dual Staining with Sytox Green and Calcofluor White M2R
Authors: Green L. C. , LeBlanc P. J. , Didier E. S. 
Published: December 2019

ABSTRACTMicrosporidia are obligate intracellular parasites, recognized as causing chronic diarrhea and systemic disease in AIDS patients, organ transplant recipients, travelers, and malnourished children. Species of microsporidia that infect humans have been detected in drinking-water sources, and methods are needed to ascertain if these microsporidia are viable and capable of causing infections. In this study, Calcofluor White M2R and Sytox Green stains were used in combination to differentiate between live (freshly harvested) and dead (boiled)Encephalitozoon cuniculispores. Calcofluor White M2R binds to chitin in the microsporidian spore wall. Dual-stained live spores appeared as turquoise-blue ovals, while dead spores appeared as white-yellow ovals at an excitation wavelength of 395 to 415 nm used for viewing the Calcofluor stain. Sytox Green, a nuclear stain, is excluded by live spores but penetrates compromised spore membranes. Dual-stained dead spores fluoresced bright yellow-green when viewed at an excitation wavelength of 470 to 490 nm, whereas live spores failed to stain with Sytox Green. After live and dead spores were mixed at various ratios, the number of viably stained spores detected in the dual-staining procedure correlated (P= 0.0025) with the expected numbers of viable spores. Spore mixtures were also assayed for infectivity in a focus-forming assay, and a correlation (P= 0.0002) was measured between the percentage of focus-forming microsporidia and the percentage of expected infectious spores in each mixture. By analysis of variance, no statistically significant differences were measured between the percentage of viably stained microsporidia and the percentage of infectious microsporidia (P= 0.964) in each mixture. These results suggest that Calcofluor White M2R and Sytox Green stains, when used together, may facilitate studies to identify viable microsporidia.
Use of Amplified Fragment Length Polymorphisms for Typing
Corynebacterium diphtheriae
Authors: De Zoysa Aruni , Efstratiou Androulla 
Published: December 2019

ABSTRACT

Amplified fragment length polymorphism (AFLP) was investigated for the differentiation of
Corynebacterium diphtheriae
isolates. Analysis using Taxotron revealed 10 distinct AFLP profiles among 57 isolates. Strains with ribotype patterns D1, D4, and D12 could not be distinguished; however, the technique discriminated isolates of ribotype patterns D3, D6, and D7 further. AFLP was rapid, fairly inexpensive, and reproducible and could be used as an alternative to ribotyping.
Comparison of Six Commercial DNA Extraction Kits for Recovery of Cytomegalovirus DNA from Spiked Human Specimens
Authors: Fahle Gary A. , Fischer Steven H. 
Published: December 2019

ABSTRACT
We evaluated six commercially available DNA extraction kits for their ability to recover DNA from various dilutions of cytomegalovirus (CMV) added to four different specimens: bronchoalveolar lavage, cerebral spinal fluid, plasma, and whole blood. The kits evaluated included the Puregene DNA isolation kit (PG), Generation Capture Column kit, MasterPure DNA purification kit, IsoQuick nucleic acid extraction kit, QIAamp blood kit, and NucliSens isolation kit (NS). All six kits evaluated effectively removed PCR inhibitors from each of the four specimen types and produced consistently positive results down to a spiked concentration of 200 PFU of whole CMV per ml. However, the NS and PG resulted in the most consistently positive results at the lowest concentrations of spiked CMV (4 and 0.4 PFU/ml) and, in this evaluation, offered the most sensitive methods for extracting CMV DNA from the four different spiked specimens. Processing time and cost were also evaluated.
Clinical Comparison of Nonvented Aerobic BacT/Alert Blood Culture Bottle and Standard Aerobic Bottle for Detection of Microorganisms in Blood
Authors: Snyder James W. , Benzing Karen S. , Munier Gina K. , Bostic Grace D. , Bozigar Pamela S. , Hanna Rami , Zervos Marcus J. 
Published: December 2019

ABSTRACT
The current BacT/Alert standard aerobic (VA) blood culture bottle was redesigned and designated a nonvented aerobic (NVA) culture bottle; this bottle does not require venting. A total of 3,873 sets of blood samples for culture were obtained from adult patients with suspected bacteremia or fungemia. The NVA bottle showed performance equivalent to that of the VA bottle for recovery and speed of detection of microorganisms from blood without the need for venting the bottle.