bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immunochromatography Test for Rapid Diagnosis of Adenovirus Respiratory Tract Infections: Comparison with Virus Isolation in Tissue Culture
Authors: Tsutsumi Hiroyuki , Ouchi Kazunobu , Ohsaki Masaya , Yamanaka Tatsuru , Kuniya Yoshinori , Takeuchi Yoshinao , Nakai Chiaki , Meguro Hidenori , Chiba Shunzo 
Published: December 2019

ABSTRACT
The sensitivity and the specificity of a new commercial rapid 10-min adenovirus antigen immunochromatography (IC) test were determined by comparison with the sensitivity and specificity of virus isolation. Of 169 pharyngeal swabs from children with suspected adenovirus respiratory tract infections, 95 (56%) were culture positive for adenovirus. The IC test was sensitive (detecting 69 of these 95 infections [72.6%]) and completely specific (identifying 74 of 74 specimens [100%]) when it was compared with cell culture. The test detected adenovirus serotypes 1, 2, 3, 5, and 7 with almost equal sensitivities. This test is not only rapid and easy to perform but also sensitive and specific for adenovirus respiratory tract infections. The test is sufficiently rapid to be used at the bedside or in an outpatient clinic, with the result being available during a patient’s first examination.
Typing of Bovine Viral Diarrhea Viruses Directly from Blood of Persistently Infected Cattle by Multiplex PCR
Authors: Gilbert S. A. , Burton K. M. , Prins S. E. , Deregt D. 
Published: December 2019

ABSTRACT
A nested multiplex PCR was developed for genotyping of bovine viral diarrhea viruses (BVDVs). The assay could detect as little as 3 50% tissue culture infective doses of BVDV per ml and typed 42 out of 42 cell culture isolates. BVDV was also successfully typed, with or without RNA extraction, from all 27 whole-blood samples examined from 22 carriers or probable carriers and 5 experimentally infected cattle.
Oxacillin Susceptibility Testing of Staphylococci Directly from Bactec Plus Blood Cultures by the BBL Crystal MRSA ID System
Authors: Kubina M. , Jaulhac B. , Delabranche X. , Lindenmann C. , Piemont Y. , Monteil H. 
Published: December 2019

ABSTRACT

The BBL Crystal MRSA ID test (Becton Dickinson) was applied directly to blood culture vials containing clusters of gram-positive cocci. The sensitivity and specificity of the test were 84 and 100% and 54 and 100% for vials containing
Staphylococcus aureus
and coagulase-negative staphylococci, respectively. This test is a reliable method for direct detection of methicillin resistance in positive blood culture vials when
S. aureus
is identified in parallel by rapid identification procedures.
Simple Strategy for Direct Identification of Medically Important Yeast Species from Positive Blood Culture Vials
Authors: Sheppard Donald C. , René Pierre , Harris Anthony D. , Miller Mark A. , Laverdière Michel , deSouza Edwige , Robson Hugh G. 
Published: December 2019

ABSTRACT
We compared direct inoculation of the Auxacolor yeast identification system from positive blood culture vials to standard identification with the API 20C AUX (API 20C), using 44 prospectively collected clinical specimens and 25 seeded blood culture vials. Direct inoculation of the Auxacolor system was accurate and more rapid than standard identification with the API 20C.
Enhanced Amplified Mycobacterium Tuberculosis Direct Test for Detection of
Mycobacterium tuberculosis
Complex in Positive BACTEC 12B Broth Cultures of Respiratory Specimens
Authors: Bergmann John S. , Woods Gail L. 
Published: December 2019

ABSTRACT

The reliability of the Gen-Probe enhanced Amplified Mycobacterium Tuberculosis Direct Test (MTD) for identification of
Mycobacterium tuberculosis
complex (MTBC) in BACTEC 12B broth cultures of respiratory specimens was evaluated by testing aliquots from 268 bottles with a growth index of ≥50. MTD results were compared to those obtained by usual laboratory protocol, whereby MTBC was identified by DNA probe (Gen-Probe, Inc.) testing sediment from broth samples or colonies on a solid medium. For the first 134 cultures, from which 68 mycobacterial isolates (including 27 MTBC isolates) were recovered, both fresh and frozen aliquots were tested. MTD results for the frozen aliquots agreed with the identification by usual protocol in all cases, whereas there was one false-negative MTD result with fresh aliquots. For the remaining 134 cultures, only frozen aliquots were tested. Of the total 268 broth cultures (from 210 patients) evaluated, 137 (51.1%) grew mycobacteria, including 60 MTBC isolates. All 60 isolates were MTD positive, as was one additional culture that grew
Mycobacterium gordonae
. The latter culture was from a patient who was diagnosed with tuberculosis a few months earlier and was on therapy; therefore, the MTD result was considered a true positive. Sensitivity, specificity, and positive and negative predictive values of MTD were 100%. The mean times from specimen receipt to identification of MTBC were 15 (±1) days (range, 4 to 27 days) for BACTEC plus MTD and 19 (±1) days (range, 6 to 36 days) for the usual protocol (
P
< 0.001). These data indicate that the MTD is a rapid, reliable method for identification of MTBC in fresh or frozen aliquots of broth from positive BACTEC 12B cultures of respiratory specimens.
Molecular and Epidemiological Characterization of Vaginal
Saccharomyces cerevisiae
Isolates
Authors: Posteraro Brunella , Sanguinetti Maurizio , D’Amore Giuseppina , Masucci Luca , Morace Giulia , Fadda Giovanni 
Published: December 2019

ABSTRACT

Although vaginitis caused by
Saccharomyces cerevisiae
is extremely rare, in recent years we have experienced an increasing frequency of
S. cerevisiae
isolation from the vaginas of fertile-age women. In order to investigate the epidemiology of these vaginal infections, a total of 40 isolates of
S. cerevisiae
derived from symptomatic and asymptomatic women were characterized by two DNA typing approaches, named ribosomal DNA (rDNA) hybridization and Ty917 hybridization, based on the Southern blotting technique. After transfer, the polymorphic DNA restriction fragments were hybridized with the entire repeat of
S. cerevisiae
rDNA for one method and with the entire sequence of the Ty917 retrotransposon for the other. After elaboration with computer-assisted analysis, the results of each method showed that Ty917 hybridization is endowed with a discriminatory power higher than that of rDNA hybridization. With the Ty917 hybridization method, all of the
S. cerevisiae
isolates tested appeared very heterogeneous, with the exception of those collected from individual patients with recurrent vaginitis. This allowed us to exclude a possible common source of infection while the high relatedness among
S. cerevisiae
sequential isolates from recurrent-vaginitis patients could suggest a pattern of relapse rather than frequent reinfection.
Detection of
Helicobacter pylori
DNA in Fecal Samples from Infected Individuals
Authors: Gramley William A. , Asghar Ali , Frierson Henry F. , Powell Steven M. 
Published: December 2019

ABSTRACT

Stool, gastric biopsy, and serum samples were collected from 22 subjects. DNA from stool was extracted, amplified, and hybridized with primers specific for the 16S rRNA gene of
Helicobacter pylori
. DNA from gastric biopsy specimens was analyzed similarly for comparison. Universal primers were used to confirm successful extraction of DNA from samples. Histologic, serologic, and DNA analyses were scored in a blinded fashion. Universal primer amplification verified successful DNA extraction from all stool and gastric tissue specimens. The gastric tissue DNA assay was positive for
H. pylori
in 11 of the 22 subjects, correlating completely with histologic and serologic results. Stool DNA was positive for
H. pylori
by our molecular assay in 8 of these 11
H. pylori
-positive subjects. All subjects who were negative by histologic, serologic, and gastric tissue DNA analyses were also negative by stool DNA analysis. Compared to histology, serology, and gastric tissue DNA analyses, the sensitivity of our stool DNA assay was 73%, with a specificity of 100%.
Detection of Human Papillomavirus Types 6 and 11 in Pubic and Perianal Hair from Patients with Genital Warts
Authors: Boxman Ingeborg L. A. , Hogewoning Arjan , Mulder Linda H. C. , Bavinck Jan Nico Bouwes , ter Schegget Jan 
Published: December 2019

ABSTRACT
Genital human papillomavirus (HPV) types 6 and 11 are of clinical importance due to their role in the development of anogenital warts. A pilot study was performed to investigate whether DNAs from HPV types 6 and 11 are present in hairs plucked from the pubic and perianal regions and eyebrows of patients with genital warts at present and patients with a recent history of genital warts. Genital HPV DNA was detected in 9 of 25 (36%) pubic hair samples and in 11 of 22 (50%) perianal hair samples by the CPI/CPIIg PCR. After sequencing of 17 of 20 samples, HPV type 6 or 11 was detected in 6 of 25 (24%) hair samples from the pubis and 8 of 22 (36%) hair samples from the perianal region. These types were not detected in plucked eyebrow hairs. In contrast, the HPV types associated with epidermodysplasia verruciformis were detected in similar proportions (62%) in both samples of pubic and eyebrow hairs. Moreover, HPV type 6 and 11 DNAs were detected in pubic hairs plucked from two patients who had been successfully treated and who did not show any lesion at the time of hair collection; this finding is an argument that HPV DNA may persist in this region. The presence of genital HPV types in plucked pubic and perianal hair suggests that there is an endogenous reservoir for HPV which may play a role in the recurrences of genital warts.
Detection of Equine Antibodies toBabesia caballiby RecombinantB. caballiRhoptry-Associated Protein 1 in a Competitive-Inhibition Enzyme-Linked Immunosorbent Assay
Authors: Kappmeyer Lowell S. , Perryman Lance E. , Hines Stephen A. , Baszler Timothy V. , Katz Jonathan B. , Hennager Steven G. , Knowles Donald P. 
Published: December 2019

ABSTRACTA competitive-inhibition enzyme-linked immunosorbent assay (cELISA) was developed for detection of equine antibodies specific forBabesia caballi. The assay used recombinantB. caballirhoptry-associated protein 1 (RAP-1) and monoclonal antibody (MAb) 79/17.18.5, which is reactive with a peptide epitope of a native 60-kDaB. caballiantigen. The gene encoding the recombinant antigen was sequenced, and database analysis revealed that the gene product is a rhoptry-associated protein. Cloning and expression of a truncated copy of the gene demonstrated that MAb 79/17.18.5 reacts with the C-terminal repeat region of the protein. The cELISA was used to evaluate 302 equine serum samples previously tested for antibodies toB. caballiby a standardized complement fixation test (CFT). The results of cELISA and CFT were 73% concordant. Seventy-two of the 77 serum samples with discordant results were CFT negative and cELISA positive. Further evaluation of the serum samples with discordant results by indirect immunofluorescence assay (IFA) demonstrated that at a serum dilution of 1:200, 48 of the CFT-negative and cELISA-positive serum samples contained antibodies reactive withB. caballiRAP-1. Four of five CFT-positive and cELISA-negative serum samples contained antibodies reactive withB. caballiwhen they were tested by IFA. These data indicate that following infection withB. caballi, horses consistently produce antibody to the RAP-1 epitope defined by MAb 79/17.18.5, and when used in the cELISA format, recombinant RAP-1 is a useful antigen for the serologic detection of anti-B. caballiantibodies.
Distinct Variants of
Helicobacter pylori cagA
Are Associated with
vacA
Subtypes
Authors: van Doorn Leen-Jan , Figueiredo Céu , Sanna Ricardo , Blaser Martin J. , Quint Wim G. V. 
Published: December 2019

ABSTRACT

The diversity of the cytotoxin-associated gene (
cagA
) of
Helicobacter pylori
was analyzed in 45 isolates obtained from nine countries. We examined variation in the 5′ end of the
cagA
open reading frame as determined by PCR and sequencing. Phylogenetic analysis revealed the existence of at least two distinct types of
cagA
. One variant (
cagA1
) was found exclusively in strains from Europe, the United States, and Australia, whereas a novel variant (
cagA2
) was found in strains from East Asia. The greatest diversity between
cagA1
and
cagA2
was found in the first 20 amino acids of the
cagA
open reading frame, where several consistent insertions or deletions were observed. Additional
cagA
sequence variants that could be classified as separate subtypes were found in two of three Peruvian and in five of seven U.S. strains tested. The calculated isoelectric point of the first 154 amino acids of the
cagA1
variants (7.52 ± 1.54) was significantly higher than that of the first 154 amino acids of the
cagA2
variants (5.61 ± 0.94;
P
< 0.001). Most
cagA2
strains contained
vacA
subtype s1c (
P
< 0.001), and in
vacA
m1 strains
cagA1
was more frequently observed than
cagA2
. These results show the epidemiological relationship between
cagA
and
vacA
at the subtype level and indicate the existence of distinct
H. pylori
lineages that are not uniformly distributed over the globe.
Dissemination of a Chloramphenicol- and Tetracycline-Resistant but Penicillin-Susceptible Invasive Clone of Serotype 5
Streptococcus pneumoniae
in Colombia
Authors: Tamayo Mónica , Sá-Leão Raquel , Sanches Ilda Santos , Castañeda Elizabeth , de Lencastre Hermínia 
Published: December 2019

ABSTRACT

A national surveillance conducted in Colombia between 1994 and 1996 identified serotype 5
Streptococcus pneumoniae
as the second most frequent cause of invasive disease in children younger than 5 years of age. All 43 serotype 5 isolates collected during this period were shown to be susceptible to penicillin, erythromycin, cefotaxime, and vancomycin, but most (38 of 43, or 88%) were highly resistant to chloramphenicol. In order to clarify a possible genetic relatedness among these isolates, additional microbiological and molecular characterizations were performed. Most (40 of 43, or 93%) of the isolates were found to be resistant to tetracycline. Pulsed-field gel electrophoresis (PFGE) patterns of chromosomal DNAs revealed that all the 43 isolates were closely related and that 38 of the 43 isolates were representatives of a “Colombian clone” of
S. pneumoniae
isolates which were recovered throughout the 3-year surveillance period from patients in 13 hospitals located in five Colombian cities. Isolates belonging to this Colombian clone were resistant to chloramphenicol and tetracycline, hybridized with the
cat
and
tetM
DNA probes in the same 340-kb
Sma
I fragment, and had identical PFGE patterns after both
Sma
I and
Apa
I digestions.
Analysis of
vacA
,
cagA
, and IS
605
Genotypes and Those Determined by PCR Amplification of DNA between Repetitive Sequences of
Helicobacter pylori
Strains Isolated from Patients with Nonulcer Dyspepsia or Mucosa-Associated Lymphoid Tissue Lymphoma
Authors: van Doorn Nathalie E. M. , Namavar Ferry , van Doorn Leen-Jan , Durrani Zarmina , Kuipers Ernst J. , Vandenbroucke-Grauls Christina M. J. E. 
Published: December 2019

ABSTRACT

The
vacA
s and m genotypes and the presence of
cagA
and IS
605
were determined in
Helicobacter pylori
strains from patients with mono- and multiple infections. Surprisingly, these genetic markers were not associated with nonulcer dyspepsia or mucosa-associated lymphoid tissue lymphoma. The presence of
cagA
correlated with the presence of the
vacA
s1 allele (
P
< 0.05), whereas the presence of IS
605
was associated with the presence of the s2 allele (
P
< 0.05).
An Untypeable
Shigella flexneri
Strain Associated with an Outbreak in California
Authors: Trevejo Rosalie T. , Abbott Sharon L. , Wolfe Mitchell I. , Meshulam Jerry , Yong David , Flores George R. 
Published: December 2019

ABSTRACT

Eleven
Shigella flexneri
(group B) isolates were recovered from epidemiologically linked patrons and food handlers from a restaurant-associated outbreak of shigellosis. Six isolates available for pulsed-field gel electrophoresis were identical. All strains agglutinated in group B and subgroup factor 6 sera but not in group 1 through group 6 sera.
Distribution of Human Rotavirus G Types Circulating in Paris, France, during the 1997–1998 Epidemic: High Prevalence of Type G4
Authors: Gault Elyanne , Chikhi-Brachet Roxane , Delon Sandrine , Schnepf Nathalie , Albiges Laurence , Grimprel Emmanuel , Girardet Jean-Philippe , Begue Pierre , Garbarg-Chenon Antoine 
Published: December 2019

ABSTRACT
Group A human rotavirus G genotypes were determined by means of reverse transcription-PCR in 170 stool specimens from children with acute diarrhea admitted to a Paris children’s hospital during a 1-year survey (1997 to 1998). The isolates all belonged to types G1 to G4, with type G4 predominating (60%).
PCR and Blood Culture for Detection of
Escherichia coli
Bacteremia in Rats
Authors: Heininger Alexandra , Binder Marlies , Schmidt Sibylle , Unertl Klaus , Botzenhart Konrad , Döring Gerd 
Published: December 2019

ABSTRACT

Critically ill patients often develop symptoms of sepsis and therefore require microbiological tests for bacteremia that use conventional blood culture (BC) techniques. However, since these patients frequently receive early empirical antibiotic therapy before diagnostic procedures are completed, examination by BC can return false-negative results. We therefore hypothesized that PCR could improve the rate of detection of microbial pathogens over that of BC. To test this hypothesis, male Wistar rats were challenged intravenously with 10
6
CFU of
Escherichia coli
. Blood was then taken at several time points for detection of
E. coli
by BC and by PCR with
E. coli
-specific primers derived from the
uidA
gene, encoding β-glucuronidase. In further experiments, cefotaxime (100 or 50 mg/kg of body weight) was administered intravenously to rats 10 min after
E. coli
challenge. Without this chemotherapy, the
E. coli
detection rate decreased at 15 min and at 210 min after challenge from 100% to 62% of the animals with PCR and from 100% to 54% of the animals with BC (
P
, >0.05). Chemotherapy decreased the
E. coli
detection rate at 25 min and at 55 min after challenge from 100% to 50% with PCR and from 100% to 0% with BC (
P
, <0.05). Thus, at clinically relevant serum antibiotic levels, PCR affords a significantly higher detection rate than BC in this rat model. The results suggest that PCR could be a useful adjunct tool supplementing conventional BC techniques in diagnosing bacteremia.
Invasion and Intracellular Development of the Human Granulocytic Ehrlichiosis Agent in Tick Cell Culture
Authors: Munderloh Ulrike G. , Jauron Steven D. , Fingerle Volker , Leitritz Lorenz , Hayes S. Fred , Hautman Joan M. , Nelson Curtis M. , Huberty Brent W. , Kurtti Timothy J. , Ahlstrand Gilbert G. , Greig Barbara , Mellencamp Martha A. , Goodman Jesse L. 
Published: December 2019

ABSTRACT
Human granulocytotropic ehrlichias are tick-borne bacterial pathogens that cause an acute, life-threatening illness, human granulocytic ehrlichiosis (HGE). Ehrlichias within neutrophil granulocytes that invade tick bite sites are likely ingested by the vector, to be transmitted to another mammalian host during the tick’s next blood meal. Thus, the cycle of replication and development in the vector is prerequisite to mammalian infection, and yet these events have not been described. We report tick cell culture isolation of two strains of the HGE agent directly from an infected horse and a dog and have also established a human isolate from HL60 culture in tick cells, proving that the blood stages of the HGE agent are infectious for tick cells, as are those replicating in the human cell line HL60. This required changes to the culture system, including a new tick cell line. In tick cell layers, the HGE agent induced foci of infection that caused necrotic plaques and eventual destruction of the culture. Using the human isolate and electron microscopy, we monitored adhesion, internalization, and replication in vector tick cells. Both electron-lucent and -dense forms adhered to and entered cells by a mechanism reminiscent of phagocytosis. Ehrlichial cell division was initiated soon after, resulting in endosomes filled with numerous ehrlichias. During early development, pale ehrlichias with a tight cell wall dominated, but by day 2, individual bacteria condensed into dark forms with a rippled membrane. These may become compacted into clumps where individual organisms are barely discernible. Whether these are part of an ehrlichia life cycle or are degenerating is unknown.
Performance of the Affymetrix GeneChip HIV PRT 440 Platform for Antiretroviral Drug Resistance Genotyping of Human Immunodeficiency Virus Type 1 Clades and Viral Isolates with Length Polymorphisms
Authors: Vahey Maryanne , Nau Martin E. , Barrick Sandra , Cooley John D. , Sawyer Robert , Sleeker Alex A. , Vickerman Peter , Bloor Stuart , Larder Brendan , Michael Nelson L. , Wegner Scott A. 
Published: December 2019

ABSTRACT

The performance of a silica chip-based resequencing method, the Affymetrix HIV PRT 440 assay (hereafter referred to as the Affymetrix assay), was evaluated on a panel of well-characterized nonclade B viral isolates and on isolates exhibiting length polymorphisms. Sequencing of human immunodeficiency virus type 1 (HIV-1)
pol
cDNAs from clades A, C, D, E, and F resulted in clade-specific regions of base-calling ambiguities in regions not known to be associated with resistance polymorphisms, as well as a small number of spurious resistance polymorphisms. The Affymetrix assay failed to detect the presence of additional serine codons distal to reverse transcriptase (RT) codon 68 that are associated with multinucleoside RT inhibitor resistance. The increasing prevalence of non-clade B HIV-1 strains in the United States and Europe and the identification of clinically relevant
pol
gene length polymorphisms will impact the generalizability of the Affymetrix assay, emphasizing the need to accommodate this expanding pool of
pol
genotypes in future assay versions.
Detection of Phylogenetically Diverse Human Immunodeficiency Virus Type 1 Groups M and O from Plasma by Using Highly Sensitive and Specific Generic Primers
Authors: Yang Chunfu , Pieniazek Danuta , Owen Sherry M. , Fridlund Carol , Nkengasong John , Mastro Timothy D. , Rayfield Mark A. , Downing Robert , Biryawaho Benon , Tanuri Amilcar , Zekeng Leopold , van der Groen Guido , Gao Feng , Lal Renu B. 
Published: December 2019

ABSTRACT

The high degree of genetic diversity within human immunodeficiency virus type 1 (HIV-1), which includes two major groups, M (major) and O (outlier), and various
env
subtypes within group M (subtypes A to J), has made designing assays that will detect all known HIV-1 strains difficult. We have developed a generic primer set based on the conserved immunodominant region of transmembrane protein gp41 that can reliably amplify as few as 10 copies/PCR of viral DNA from near-full-length clones representing group M subtypes A to H (subtypes I and J were not available). The assay is highly sensitive in detecting plasma viral RNA from HIV-1 strains of diverse geographic origins representing different subtypes of HIV-1 group M as well as HIV-1 group O. Of the 253 group M plasma specimens (subtypes A, 68 specimens; B, 71; C, 19; D, 27; E, 23; F, 33; and G, 12), 250 (98.8%) were amplified by using the gp41 M/O primer set. More importantly, all 32 (100%) group O plasma samples were also amplified with these primers. In vitro spiking experiments further revealed that the assay could reliably detect as few as 25 copies/ml of viral RNA and gave positive signals in HIV-1-seropositive specimens with plasma copy numbers below the limits of detection by all commercially available viral load assays. In addition, analysis of five seroconversion panels indicated that the assay is highly sensitive for early detection of plasma viremia during the “window period.” Thus, the highly sensitive assay will be useful for early detection of HIV-1 in clinical specimens from all known HIV-1 infections, regardless of their genotypes and geographic origins.