bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis by Multiplex PCR of the Physical Status of Human Papillomavirus Type 16 DNA in Cervical Cancers
Authors: Yoshinouchi Mitsuo , Hongo Atsushi , Nakamura Keichiro , Kodama Junichi , Itoh Sachio , Sakai Hiroyuki , Kudo Takafumi 
Published: December 2019

ABSTRACT
Integration of human papillomavirus (HPV) DNA occurs early in cancer development and is an important event in malignant transformation of cervical cancer. Integration of HPVs preferentially disrupts or deletes the E2 open reading frame, which results in the loss of its expression. The preferential disruption of the E2 gene causes the absence of the E2 gene sequences in the PCR product following integration. Twenty-two carcinomas positive for HPV type 16 (HPV-16) DNA were first tested for the disruption of the E2 gene by PCR. A specific fragment of the E2 gene was not amplified in 10 cases, suggesting integration of HPV DNA into the host genome. Next, multiplex PCR for the HPV E2 and E6 genes was carried out in the remaining 12 cases. Copy numbers of both genes should be equivalent in episomal forms, while the E2 gene copy number will be smaller than that for E6 following the preferential disruption of the E2 gene in concominant forms. Although relative ratios of HPV E2 to E6 PCR products (E2/E6 ratios) ranged from 1.40 to 2.34 in 10 of 12 cases, multiplex PCR products from 2 cases displayed extremely low ratios of 0.69 and 0.61. Southern blot hybridization with an HPV-16 probe revealed that only in these two cases was both episomal and integrated HPV DNA being carried simultaneously. Thus, multiplex PCR for the E2 and E6 genes of HPV-16 DNA following PCR for the E2 gene can distinguish the pure episomal form from a mixed form of episomal and integrated HPV DNA. Clinical application of this technique will help researchers to understand the implication of the integration of HPV DNA for cervical carcinogenesis and cervical cancer progression.
Evaluation of Protein A Gene Polymorphic Region DNA Sequencing for Typing ofStaphylococcus aureusStrains
Authors: Shopsin B. , Gomez M. , Montgomery S. O. , Smith D. H. , Waddington M. , Dodge D. E. , Bost D. A. , Riehman M. , Naidich S. , Kreiswirth B. N. 
Published: December 2019

ABSTRACTThree hundred and twenty isolates ofStaphylococcus aureuswere typed by DNA sequence analysis of the X region of the protein A gene (spa).spatyping was compared to both phenotypic and molecular techniques for the ability to differentiate and categorizeS. aureusstrains into groups that correlate with epidemiological information. Two previously characterized study populations were examined. A collection of 59 isolates (F. C. Tenover, R. Arbeit, G. Archer, J. Biddle, S. Byrne, R. Goering, G. Hancock, G. A. Hébert, B. Hill, R. Hollis, W. R. Jarvis, B. Kreiswirth, W. Eisner, J. Maslow, L. K. McDougal, J. M. Miller, M. Mulligan, and M. A. Pfaller, J. Clin. Microbiol. 32:407–415, 1994) from the Centers for Disease Control and Prevention (CDC) was used to test for the ability to discriminate outbreak from epidemiologically unrelated strains. A separate collection of 261 isolates form a multicenter study (R. B. Roberts, A. de Lencastre, W. Eisner, E. P. Severina, B. Shopsin, B. N. Kreiswirth, and A. Tomasz, J. Infect. Dis. 178:164–171, 1998) of methicillin-resistantS. aureusin New York City (NYC) was used to compare the ability ofspatyping to group strains along clonal lines to that of the combination of pulsed-field gel electrophoresis and Southern hybridization. In the 320 isolates studied,spatyping identified 24 distinct repeat types and 33 different strain types.spatyping distinguished 27 of 29 related strains and did not provide a unique fingerprint for 4 unrelated strains from the four outbreaks of the CDC collection. In the NYC collection,spatyping provided a clonal assignment for 185 of 195 strains within the five major groups previously described.spasequencing appears to be a highly effective rapid typing tool forS. aureusthat, despite some expense of specificity, has significant advantages in terms of speed, ease of use, ease of interpretation, and standardization among laboratories.
Use of BACTEC MGIT 960 for Recovery of Mycobacteria from Clinical Specimens: Multicenter Study
Authors: Tortoli Enrico , Cichero Paola , Piersimoni Claudio , Simonetti M. Tullia , Gesu Giampietro , Nista Domenico 
Published: December 2019

ABSTRACT

The BACTEC MGIT 960 instrument is a fully automated system that exploits the fluorescence of an oxygen sensor to detect growth of mycobacteria in culture. Its performance was compared to those of the radiometric BACTEC 460 instrument and egg-based Lowenstein-Jensen medium. An identical volume of sample was inoculated in different media, and incubation was carried out for 6 weeks with the automatic systems and for 8 weeks on solid media. A total of 2,567 specimens obtained from 1,631 patients were cultured in parallel. Mycobacteria belonging to nine different taxa were isolated by at least one of the culture systems, with 75% of them being represented by
Mycobacterium tuberculosis
complex. The best yield was obtained with the BACTEC 460 system, with 201 isolates, in comparison with 190 isolates with the BACTEC MGIT 960 system and 168 isolates with Lowenstein-Jensen medium. A similar but not significant difference was obtained when the most-represented organisms, the
M. tuberculosis
complex,
Mycobacterium xenopi
, and the
Mycobacterium avium
complex, were analyzed separately and when combinations of a solid medium with the BACTEC MGIT 960 system and with the BACTEC 460 system were considered. The shortest times to detection were obtained with the BACTEC MGIT 960 system (13.3 days); 1.5 days earlier than that with the BACTEC 460 system (14.8 days) and 12 days earlier than that with Lowenstein-Jensen medium (25.6 days). The BACTEC MGIT 960 system had a contamination rate of 10.0%, intermediate between those of the radiometric system (3.7%) and the egg-based medium (17.0%). We conclude, therefore, that the BACTEC MGIT 960 system is a fully automated, nonradiometric instrument that is suitable for the detection of growth of tuberculous and other mycobacterial species and that is characterized by detection times that are even shorter than that of the “gold standard,” the BACTEC 460 system. The contamination rate was higher than that for the radiometric BACTEC 460 system and needs to be improved.
Identification of
Mycobacterium
Species by PCR-Restriction Fragment Length Polymorphism Analyses Using Fluorescence Capillary Electrophoresis
Authors: Hernandez S. Moises , Morlock Glenn P. , Butler W. Ray , Crawford Jack T. , Cooksey Robert C. 
Published: December 2019

ABSTRACT

We developed a scheme for the rapid identification of
Mycobacterium
species based upon PCR amplification of polymorphic genetic regions with fluorescent primers followed by restriction and analysis by fluorescence capillary electrophoresis.
Mycobacterium
species were identified by restriction enzyme analysis of a 439-bp segment of the 65-kDa heat shock protein gene (labeled [both strands] at the 5′ end with 4,7,2′,7′-tetrachloro-6-carboxyfluorescein) using
Hae
III and
Bst
EII and of a 475-bp hypervariable region of the 16S rRNA gene (labeled [both strands] at the 5′ end with 6-carboxyfluorescein) using
Hae
III and
Cfo
I. Samples were analyzed on an automated fluorescence capillary electrophoresis instrument, and labeled fragments were sized by comparison with an internal standard. DNA templates were prepared with pure cultures of type strains. In all, we analyzed 180 strains, representing 22
Mycobacterium
species, and obtained distinctive restriction fragment length polymorphism (RFLP) patterns for 19 species. Three members of the
Mycobacterium tuberculosis
complex had a common RFLP pattern. A computerized algorithm which eliminates subjectivity from pattern interpretation and which is capable of identifying the species within a sample was developed. The convenience and short preparatory time of this assay make it comparable to conventional methodologies such as high-performance liquid chromatography and hybridization assays for identification of mycobacteria.
Simple and Rapid Identification of the
Mycobacterium tuberculosis
Complex by Immunochromatographic Assay Using Anti-MPB64 Monoclonal Antibodies
Authors: Abe Chiyoji , Hirano Kazue , Tomiyama Tetsuo 
Published: December 2019

ABSTRACT

A newly developed immunochromatographic assay (MPB64-ICA) for identification of the
Mycobacterium tuberculosis
complex was evaluated with 20 reference strains of mycobacterial species and 111 clinical isolates. MPB64-ICA displayed a very strong reaction band with organisms belonging to the
M. tuberculosis
complex but not with mycobacteria other than
M. tuberculosis
(MOTT bacilli), except for one of four
M. marinum
strains tested and one
M. flavescens
strain, both of which gave very weak signals. The effectiveness of MPB64-ICA in combination with two liquid culture systems (MB-REDOX and MGIT) was tested. A total of 108 of 362 sputum specimens processed were positive for acid-fast bacilli. Samples taken from the cultures on the same days when either of the two culture systems became positive for mycobacteria were assayed with MPB64-ICA. Of 108 cultures with mycobacteria, 51 showed a positive signal with the test, in which the presence of the
M. tuberculosis
complex was demonstrated later by the Accuprobe for
M. tuberculosis
complex. In addition, MPB64-ICA could correctly detect the
M. tuberculosis
complex in mixed cultures of the
M. tuberculosis
complex and MOTT bacilli. These results indicate that MPB64-ICA can be easily used for rapid identification of the
M. tuberculosis
complex in combination with culture systems based on liquid media without any technical complexity in clinical laboratories.
Predicting Susceptibility of
Streptococcus pneumoniae
to Ceftriaxone and Cefotaxime by Cefuroxime and Ceftizoxime Disk Diffusion Testing
Authors: Williams-Bouyer Natalie , Hernandez Antonio , Reisner Barbara S. 
Published: December 2019

ABSTRACT

In this study, disk diffusion testing with ceftizoxime and cefuroxime was evaluated for use in predicting the susceptibility of
Streptococcus pneumoniae
to ceftriaxone and cefotaxime. Of the 194 isolates included in this study, 138 were susceptible, 34 were intermediate, and 22 were resistant to cefotaxime by MIC testing; 138 isolates were susceptible, 35 were intermediate, and 21 were resistant to ceftriaxone by MIC testing. A zone of inhibition around the cefuroxime disk of ≥32 mm correctly categorized 101 of 138 isolates as susceptible to cefotaxime and ceftriaxone. A zone of inhibition around the ceftizoxime disk of ≥26 mm correctly categorized 111 of 138 isolates as susceptible to cefotaxime and 114 of 138 as susceptible to ceftriaxone. We conclude that disk diffusion can separate
S. pneumoniae
isolates susceptible to ceftriaxone and cefotaxime from those that are not susceptible. Isolates not falling into the susceptible category by disk diffusion require additional testing to determine the MIC.
A Serotype VIII Strain among Colonizing Group B Streptococcal Isolates in Boston, Massachusetts
Authors: Paoletti Leanne J. , Bradford Jessica , Paoletti Lawrence C. 
Published: December 2019

ABSTRACT

Maternal colonization with group B
Streptococcus
(GBS) is a risk factor for neonatal GBS disease. Whereas serotypes Ia, Ib, II, III, and V are prevalent in the United States, types VI and VIII predominate in Japan. Recently, a serotype VIII strain was detected among 114 clinical GBS isolates from a Boston, Mass., hospital.
Diagnosis of Contagious Bovine Pleuropneumonia by PCR–Laser- Induced Fluorescence and PCR-Restriction Endonuclease Analysis Based on the 16S rRNA Genes of
Mycoplasma mycoides
subsp.
mycoides
SC
Authors: Persson Anja , Pettersson Bertil , Bölske Göran , Johansson Karl-Erik 
Published: December 2019

ABSTRACT

As contagious bovine pleuropneumonia (CBPP) is spreading fast in many African countries, there is an increasing demand for rapid and sensitive diagnostic methods that can be used to confirm the initial diagnosis based on clinical symptoms or pathological findings. Two PCR-based diagnostic systems for identification of the infectious agent,
Mycoplasma mycoides
subsp.
mycoides
SC (
M. mycoides
SC), in various samples are presented. Both systems involve group-specific amplification of the two 16S rRNA genes from mycoplasmas of the
M. mycoides
cluster. The laser-induced fluorescence assay is based on a unique sequence length difference between the two 16S rRNA genes in
M. mycoides
SC. This region was amplified by PCR, and the products were separated by polyacrylamide gel electrophoresis in a DNA sequencer. The resulting electropherogram showed two peaks for strains of
M. mycoides
SC and one peak for all other members of the
M. mycoides
cluster. The second system was based on restriction endonuclease analysis and agarose gel electrophoresis. Restriction of amplicons from a region containing a polymorphism, which is found in
M. mycoides
SC only, resulted in an extra band on the agarose gel because an
Alu
I site is lacking in the
rrnA
operon. Specimens from cows with postmortem signs of CBPP were analyzed with the two PCR systems.
M. mycoides
SC was clearly identified in pleural fluid and lung tissue, and the methods were found to be robust and rapid. The results were in agreement with those obtained by conventional diagnostic techniques.
Multilocus Sequence Typing and Antigen Gene Sequencing in the Investigation of a Meningococcal Disease Outbreak
Authors: Feavers Ian M. , Gray Stephen J. , Urwin Rachel , Russell Joanne E. , Bygraves Jane A. , Kaczmarski Edward B. , Maiden Martin C. J. 
Published: December 2019

ABSTRACT

Multilocus sequence typing and antigen gene sequencing were used to investigate an outbreak of meningococcal disease in a university in the United Kingdom. The data obtained showed that five distinct
Neisseria meningitidis
strains belonging to the ET-37 complex were present in the student population during the outbreak. Three of these strains were not associated with invasive disease, and two distinct strains caused invasive disease, including several fatalities. The initial case of the disease cluster was caused by a strain distinct from that responsible for at least two subsequent cases and two cases remote from the university, which were epidemiologically linked to the outbreak. These observations were consistent with pulsed-field gel electrophoresis data, but the sequence data alone were sufficient to resolve the strains involved in the disease cluster. Interpretation of the nucleotide sequence data was more straightforward than interpretation of the fingerprint patterns, and the sequence data provided information on the genetic differences among the isolates.
Genetic Analysis of
Borrelia garinii
OspA Serotype 4 Strains Associated with Neuroborreliosis: Evidence for Extensive Genetic Homogeneity
Authors: Marconi R. T. , Hohenberger S. , Jauris-Heipke S. , Schulte-Spechtel U. , LaVoie C. P. , Rößler D. , Wilske B. 
Published: December 2019

ABSTRACT

Infection with
Borrelia garinii
outer surface protein (Osp) A serotype 4 strains has been correlated with the development of neuroborreliosis in Lyme borreliosis patients in Europe. OspA serotype 4 isolates have been recovered primarily from human cerebrospinal fluid, suggesting a tropism for this environment. Previous studies with monoclonal antibodies directed against OspA and OspC demonstrated that OspA serotype 4 strains are antigenically closely related. In view of the pronounced antigenic and genetic variability that has been noted in the Osps of other
Borrelia
isolates, we sought to determine if OspA serotype 4 strains represent a recently emerged clonal lineage of
B. garinii
. Toward this goal, a representative group of OspA serotype 4 strains was analyzed for traits that typically exhibit hypervariability among isolates that cause Lyme borreliosis. The following criteria were assessed: (i)
ospC
sequences, (ii) plasmid composition, (iii) genomic restriction fragment length polymorphism (RFLP) patterns, and (iv) the RFLP patterns of the upstream homology box (UHB) element which flanks members of the UHB gene family at their 5′ end. Collectively, these analyses demonstrate genetic homogeneity, suggesting that OspA serotype 4 strains are a recently emerged clonal lineage with an apparent tropism for the central nervous system.
Demonstration of
Bartonella grahamii
DNA in Ocular Fluids of a Patient with Neuroretinitis
Authors: Kerkhoff F. T. , Bergmans A. M. C. , van der Zee A. , Rothova A. 
Published: December 2019

ABSTRACT

We describe the clinical and laboratory features of a 55-year-old human immunodeficiency virus-negative female patient who presented with bilateral intraocular inflammatory disease (neuroretinitis type) and behavioral changes caused by a
Bartonella grahamii
infection. Diagnosis was based on the PCR analysis of DNA extracted from the intraocular fluids. DNA analysis of the PCR product revealed a 100% identity with the 16S rRNA gene sequence of
B. grahamii
. The patient was successfully treated with doxycycline (200 mg/day) and rifampin (600 mg/day) for 4 weeks. This is the first report that demonstrates the presence of a
Bartonella
species in the intraocular fluids of a nonimmunocompromised patient and that indicates that
B. grahamii
is pathogenic for humans.
Quantitative Evaluation of Ehrlichial Burden in Horses after Experimental Transmission of Human Granulocytic Ehrlichia Agent by Intravenous Inoculation with Infected Leukocytes and by Infected Ticks
Authors: Pusterla Nicola , Leutenegger Christian M. , Chae Joon-Seok , Lutz Hans , Kimsey Robert B. , Dumler J. Stephen , Madigan John E. 
Published: December 2019

ABSTRACTThis paper describes the kinetics of the human granulocytic ehrlichiosis agent in the blood of horses experimentally infected by intravenous inoculation with infected leukocytes and by infected ticks as evaluated by using a real-time quantitative PCR assay. The data obtained indicated differences in the period of incubation, duration of rickettsemia, and initial and maximal ehrlichial loads between the two routes of infection.
Comparison of a Nonradiometric Liquid-Medium Method (MB REDOX) with the BACTEC System for Growth and Identification of Mycobacteria in Clinical Specimens
Authors: Liu Yung-Ching , Huang Tsi-Shu , Huang Wen-Kuei 
Published: December 2019

ABSTRACT

Early identification of tuberculosis in the clinical setting is of great importance in order for specific therapy to be swiftly initiated. MB REDOX (Heipha Diagnostika), a growth-based medium without radioactive materials, was evaluated and was compared to the BACTEC system for detection of mycobacteria, including the
Mycobacterium tuberculosis
complex and atypical mycobacteria. MB REDOX consists of a Kirchner medium enriched with growth-promoting additives, antibiotic compounds, and a redox indicator which can be monitored to detect growth of mycobacteria with the naked eye. MB REDOX only detects growth and cannot differentiate the
M. tuberculosis
complex (
M. tuberculosis
,
M. bovis
, and
M. africanum
) from other species of
Mycobacterium
. Therefore, PCR-restriction fragment length polymorphism analysis (PRA) was used in this investigation to identify to the species level organisms showing positive growth with MB REDOX. Our data demonstrate the usefulness of MB REDOX for the detection of mycobacteria in clinical specimens. The rate of detection of
M. tuberculosis
complex with MB REDOX (84.3%) was higher than that with the BACTEC system (68.6%). When combined with PRA for species identification, MB REDOX is easy to perform and is suited to most clinical laboratory settings for the detection and identification of mycobacteria.
Prevalence of the Amylase-Binding Protein A Gene (
abpA
) in Oral Streptococci
Authors: Brown Alan E. , Rogers Jeffrey D. , Haase Elaine M. , Zelasko Peter M. , Scannapieco Frank A. 
Published: December 2019

ABSTRACT

Salivary amylase binds specifically to a number of oral streptococcal species. This interaction may play an important role in dental plaque formation. Recently, a 585-bp gene was cloned and sequenced from
Streptococcus gordonii
Challis encoding a 20.5-kDa amylase-binding protein (AbpA). The goal of this study was to determine if related genes are present in other species of oral streptococci. Biotinylated
abpA
was used in Southern blot analysis to screen genomic DNA from several strains representing eight species of oral streptococci. This probe hybridized with a 4.0-kb
Hin
dIII restriction fragment from all 13 strains of
S. gordonii
tested. The probe did not appear to bind to any restriction fragments from other species of amylase-binding oral streptococci including
Streptococcus mitis
(with the exception of 1 of 14 strains),
Streptococcus crista
(3 strains),
Streptococcus anginosus
(1 strain), and
Streptococcus parasanguinis
(1 strain), or to non-amylase-binding oral streptococci including
Streptococcus sanguinis
(3 strains),
Streptococcus oralis
(4 strains), and
Streptococcus mutans
(1 strain). Primers homologous to sequences within the 3′ and 5′ ends of
abpA
yielded products of 400 bp following PCR of genomic DNA from the Southern blot-positive strains. Several of these PCR products were cloned and sequenced. The levels of similarity of these cloned products to the
abpA
of
S. gordonii
Challis ranged from 91 to 96%. These studies reveal that the
abpA
gene appears to be specific to
S. gordonii
and differs from genes encoding amylase-binding proteins from other species of amylase-binding streptococci.
Evaluation of Three Commercial Serological Tests with Different Methodologies To Assess
Helicobacter pylori
Infection
Authors: van der Ende A. , van der Hulst R. W. M. , Roorda P. , Tytgat G. N. J. , Dankert J. 
Published: December 2019

ABSTRACT

The sera of 142
Helicobacter pylori
-positive and 32
H. pylori
-negative patients were assessed by a desktop test (QuickVue), an enzyme-linked immunosorbent assay (ELISA) (HM-CAP), and a solid-phase, two-step chemiluminescent enzyme immunoassay (Immulite). These tests yielded sensitivities of 97, 97, and 91% and specificities of 97, 94, and 100%, respectively. In conclusion, the desktop test and the ELISA are more sensitive than the chemiluminescent enzyme immunoassay (
P
< 0.05). The chemiluminescent enzyme immunoassay has the advantage that it is fully automated.
Evaluation of a Rapid Assay for Detection of
Chlamydia trachomatis
Infections in Outpatient Clinics in South Kalimantan, Indonesia
Authors: Widjaja Susana , Cohen Surekha , Brady William E. , O'reilly Kevin , Susanto  , Wibowo Ajar , Cahyono  , Graham Robert R. , Porter Kevin R. 
Published: December 2019

ABSTRACT
A multicenter cross-sectional survey was conducted comparing a commercially available chlamydial optical immunoassay (OIA) to the chlamydial ligase chain reaction (LCR). Endocervical samples from 415 outpatients visiting clinics from three hospitals in South Kalimantan, Indonesia, were evaluated. Relative to the LCR, the overall sensitivity and specificity of the OIA were 31.6 and 98.9%, respectively. The sensitivity of the OIA varied among the three hospital laboratories, ranging from 20 to 50%. The OIA performance was slightly lower on samples from patients attending dermatovenereology clinics than on samples from nondermatovenereology clinic patients. The results indicate that the OIA did not perform well compared to LCR.
Identification of
Hafnia alvei
with the MicroScan WalkAway System
Authors: Rodríguez L. A. , Vivas J. , Gallardo C. S. , Acosta F. , Barbeyto L. , Real F. 
Published: December 2019

ABSTRACT

Hafnia alvei
is a gram-negative facultatively anaerobic bacillus that belongs to the family
Enterobacteriaceae
. This organism is a causative agent of intestinal disorders and is found in different environments.
H. alvei
has received increased clinical attention as a cause of different infections in humans. This study was performed to compare the MicroScan WalkAway automated identification system in conjunction with the new MicroScan Combo Negative type 1S panels with conventional biochemical methods for identification of 21
H. alvei
strains. The MicroScan WalkAway system was found capable of correctly identifying 20 of the 21 strains tested.