bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonal Distribution of Invasive
Neisseria meningitidis
Isolates from the Norwegian County of Telemark, 1987 to 1995
Authors: Aakre Randi Kersten , Jenkins Andrew , Kristiansen Bjørn-Erik , Frøholm L. Oddvar 
Published: December 2019

ABSTRACT

Forty-two
Neisseria meningitidis
isolates were obtained from patients with meningococcal disease in the Norwegian county of Telemark (January 1987 to March 1995), and all were compared by PCR amplicon restriction endonuclease analysis (PCR-AREA) of the
dhps
gene, chromosomal DNA fingerprinting, and serological analysis. PCR-AREA divided the isolates into 11 classes, of which 4, comprising 15, 8, 6, and 2 isolates, were clonal while the remaining 8 classes were genetically heterogeneous or contained only 1 isolate. Three of the four clonal classes could be tentatively equated with recognized epidemic clones (ET5, ET37, and cluster A4) on the basis of their phenotypic characteristics, while the remaining clone appears to be new. There were significant differences in the geographical distribution of clones, with class 1 (ET5-like) isolates significantly overrepresented in rural parts of Telemark. Class 1 (ET5-like) isolates occurred throughout the study period and were dominant in 1987. Class 2 (ET37-like) isolates occurred from 1988 to 1992, and class 3 isolates (with no recognizable ET affinities) were found only in 1991 and 1992.
Typing of Dengue Viruses in Clinical Specimens and Mosquitoes by Single-Tube Multiplex Reverse Transcriptase PCR
Authors: Harris Eva , Roberts T. Guy , Smith Leila , Selle John , Kramer Laura D. , Valle Sonia , Sandoval Erick , Balmaseda Angel 
Published: December 2019

ABSTRACT
In recent years, dengue viruses (serotypes 1 to 4) have spread throughout tropical regions worldwide. In many places, multiple dengue virus serotypes are circulating concurrently, which may increase the risk for the more severe form of the disease, dengue hemorrhagic fever. For the control and prevention of dengue fever, it is important to rapidly detect and type the virus in clinical samples and mosquitoes. Assays based on reverse transcriptase (RT) PCR (RT-PCR) amplification of dengue viral RNA can offer a rapid, sensitive, and specific approach to the typing of dengue viruses. We have reduced a two-step nested RT-PCR protocol to a single-tube reaction with sensitivity equivalent to that of the two-step protocol (1 to 50 PFU) in order to maximize simplicity and minimize the risk of sample cross-contamination. This assay was also optimized for use with a thermostable RT-polymerase. We designed a plasmid-based internal control that produces a uniquely sized product and can be used to control for both reverse transcription or amplification steps without the risk of generating false-positive results. This single-tube RT-PCR procedure was used to type dengue viruses during the 1995 and 1997-1998 outbreaks in Nicaragua. In addition, an extraction procedure that permits the sensitive detection of viral RNA in pools of up to 50 mosquitoes without PCR inhibition or RNA degradation was developed. This assay should serve as a practical tool for use in countries where dengue fever is endemic, in conjunction with classical methods for surveillance and epidemiology of dengue viruses.
Molecular Analysis by Pulsed-Field Gel Electrophoresis and Antibiogram of
Streptococcus pneumoniae
Serotype 6B Isolates from Selected Areas within the United States
Authors: Rudolph Karen M. , Parkinson Alan J. , Roberts Marilyn C. 
Published: December 2019

ABSTRACT

Fifty-eight clinical isolates of
Streptococcus pneumoniae
serotype 6B, including 16 from Alaska, 14 from Arizona, 11 from Washington, and 17 from seven additional states, were analyzed. The antibiograms of these isolates were assigned to 10 antibiotic profiles based on their susceptibilities to penicillin, erythromycin, tetracycline, and trimethoprim-sulfamethoxazole. Thirty-two (55%) of these isolates were penicillin nonsusceptible, while 21 (36%) were intermediate or resistant to three or more antibiotics. The restriction endonucleases
Apa
I and
Sma
I were used to digest intact chromosomes, and the fragments were resolved by pulsed-field gel electrophoresis (PFGE). The
Apa
I and
Sma
I PFGE patterns were combined, and 13 of the 16 Alaskan isolates showed indistinguishable PFGE patterns. One other isolate exhibited highly related
Apa
I and
Sma
I PFGE patterns, differing by only one band after restriction with
Apa
I. Among the 14 isolates from Arizona, 1 was indistinguishable from the predominant
Apa
I and
Sma
I PFGE patterns seen in the Alaskan isolates; 5 others were highly related (±1 band after cutting with either enzyme) to the Alaskan isolates, suggesting a common ancestral origin. Of the remaining eight isolates, six additional
Apa
I plus
Sma
I PFGE patterns were observed. The 28 isolates from the various contiguous states had 22
Apa
I plus
Sma
I PFGE patterns. No correlations were found between specific PFGE patterns, antibiograms, dates of isolation, or geography. The serotype 6B isolates across the contiguous United States were genetically diverse, while the 6B isolates from Alaska appeared to be much less diverse.
Detection of
Ehrlichia phagocytophila
DNA in
Ixodes ricinus
Ticks from Areas in Switzerland Where Tick-Borne Fever Is Endemic
Authors: Pusterla Nicola , Huder Jon B. , Lutz Hans , Braun Ueli 
Published: December 2019

ABSTRACT

A total of 1,523 adult
Ixodes ricinus
ticks were collected from regions where bovine ehrlichiosis is endemic and were examined for
Ehrlichia phagocytophila
via PCR. Of the ticks from cattle with ehrlichiosis, the ticks from healthy cattle, and the free-living ticks, 26.5% (18 of 68), 4.4% (35 of 802), and 0.8% (5 of 653), respectively, were positive.
Novel Intestinal
Helicobacter
Species Isolated from Cotton-Top Tamarins (
Saguinus oedipus
) with Chronic Colitis
Authors: Saunders Kim E. , Shen Zeli , Dewhirst Floyd E. , Paster Bruce J. , Dangler Charles A. , Fox James G. 
Published: December 2019

ABSTRACT

A disease similar to ulcerative colitis in humans has been identified in cotton-top tamarins (CTTs) in captivity. The clinical signs include weight loss, diarrhea, and rectal bleeding with the pathological features and biochemical abnormalities of ulcerative colitis. Approximately 25 to 40% of these animals develop colon cancer after 2 to 5 years of captivity. An infectious etiology has been proposed; however, no microbial agent to date has been identified.
Helicobacter
spp. have been associated with enterocolitis and inflammatory bowel disease (IBD) in humans and animals. Infection with
Helicobacter pylori
or
Helicobacter mustelae
is associated with an increased risk of gastric adenocarcinoma and lymphoma of the mucosa-associated lymphoid tissue.
Helicobacter hepaticus
causes hepatitis, hepatic adenomas, and hepatocellular carcinomas in susceptible strains of mice. The aim of this study was to assess a colony of CTTs with a high incidence of IBD and colon cancer for the presence of colonic
Helicobacter
spp. A fusiform, gram-negative bacterium with bipolar flagella and periplasmic fibers was isolated from the feces of CTTs. The bacterium grew under microaerobic conditions at 37 and 42°C but not at 25°C, did not hydrolyze urea, was positive for catalase and oxidase, did not reduce nitrate to nitrite, did not hydrolyze indoxyl acetate or alkaline phosphatase, and was resistant to nalidixic acid, cephalothin, and trimethoprim-sulfamethoxazole. On the basis of 16S rRNA gene sequence analysis, the organism was classified as a novel
Helicobacter
species. This is the first
Helicobacter
isolated from CTTs. Further studies are needed to elucidate the role of this novel
Helicobacter
sp. in the pathogenesis of ulcerative colitis and colonic adenocarcinoma in CTTs.
Semiquantitative Species-Specific Detection of
Bartonella henselae
and
Bartonella quintana
by PCR-Enzyme Immunoassay
Authors: Sander Anna , Penno Susanne 
Published: December 2019

ABSTRACT

Bartonella henselae
is the main causative agent of cat-scratch disease, and both
B. henselae
and
Bartonella quintana
cause angioproliferative disorders such as bacillary angiomatosis. To increase the sensitivity of
Bartonella
detection by PCR and to improve the species differentiation, we developed a semiquantitative, species-specific PCR-based enzyme immunoassay (EIA). The 16S rRNA gene was selected as the target sequence. Internal nucleotide sequences derived from the amplified 16S rRNA region were used to develop species-specific oligonucleotide probes for
B. henselae
and
B. quintana
. Biotin-labeled PCR products were immobilized on streptavidin-coated microtiter plates, hybridized to a digoxigenin-labeled probe, and detected with antidigoxigenin peroxidase conjugate. No cross-hybridization with other
Bartonella
or non-
Bartonella
species was observed. This EIA was as sensitive as dot blot hybridization and was 10 times more sensitive than visualization of PCR products on agarose gels. Serial dilutions of
B. henselae
and
B. quintana
suspensions demonstrated that an optical density (OD) of approximately 0.200 was equivalent to 5 CFU in the reaction mixture. By comparing the OD of the bacterial dilutions with that obtained from clinical specimens we could determine that the number of CFU in clinical samples ranged from 10
3
to 10
6
CFU/ml. The PCR-EIA developed in the present study is a rapid, sensitive, and simple method for the diagnosis of
B. henselae
and
B. quintana
infections.
Epidemiological Evidence for Dormant
Cryptococcus neoformans
Infection
Authors: Garcia-Hermoso Dea , Janbon Guilhem , Dromer Françoise 
Published: December 2019

ABSTRACT

To date, the time of acquisition of a
Cryptococcus neoformans
infectious strain has never been studied. We selected a primer, (GACA)
4
, and a probe, CNRE-1, that by randomly amplified polymorphic DNA (RAPD) analysis and restriction fragment length polymorphism (RFLP), respectively, regrouped strains from control samples of
C. neoformans
var.
grubii
environmental isolates according to their geographical origins. The two typing techniques were then used to analyze 103 isolates from 29 patients diagnosed with cryptococcosis in France. Nine of the 29 patients lived in Africa a median of 110 months prior to moving to France; 17 of the patients originated from Europe. Results showed a statistically significant clustering of isolate subtypes from patients originating from Africa compared to those from Europe. We conclude that the patients had acquired the
C. neoformans
infectious strain long before their clinical diagnoses were made.
Usefulness of Seminested Multiplex PCR in Surveillance of Imported Malaria in Spain
Authors: Rubio J. M. , Benito A. , Berzosa P. J. , Roche J. , Puente S. , Subirats M. , López-Vélez R. , García L. , Alvar J. 
Published: December 2019

ABSTRACT

The use of a new PCR-based method for the diagnosis of malaria in the Spanish Malaria Reference Laboratory has promoted an increase in confirmed cases of malaria. From August 1997 to July 1998, a total of 192 whole-blood samples and 71 serum samples from 168 patients were received from the hospitals of the Spanish National Health System. Most of the patients came from west-central African countries (85%). This molecular method showed more sensitivity and specificity than microscopy, detecting 12.4% more positive samples than microscopy and 13% of mixed infections undetectable by Giemsa stain.
Plasmodium falciparum
was the main species detected, with 68% of the total positive malaria cases, followed by
Plasmodium malariae
(29%),
Plasmodium vivax
(14%), and
Plasmodium ovale
(7%), including mixed infections in all cases. This report consists of the first wide, centralized survey of malaria surveillance in Spain. The reference laboratory conducted the analysis of all imported cases in order to detect trends in acquisition. The use of a seminested multiplex PCR permitted confirmation of the origins of the infections and the
Plasmodium
species involved and confirmation of the effectiveness of drug treatments. This PCR also allowed the detection of the presence in Spain of primaquine-tolerant
P. vivax
strains from west-central Africa, as well as the detection of a
P. falciparum
infection induced by transfusion.
Prophage Carriage as a Molecular Epidemiological Marker in
Streptococcus pneumoniae
Authors: Severina Elena , Ramirez Mario , Tomasz Alexander 
Published: December 2019

ABSTRACT

The great majority of clinical isolates of
Streptococcus pneumoniae
carry prophages that may be identified through their hybridization with a DNA probe specific for the pneumococcal
lytA
gene (M. Ramirez, E. Severina, and A. Tomasz, J. Bacteriol. 181:3618–3625, 1999). We now show that the
lytA
hybridization pattern of chromosomal
Sma
I digests is stable for a given strain during extensive serial culturing in the laboratory; the pattern is specific for the strain’s clonal type, as defined by pulsed-field gel electrophoretis (PFGE) pattern, and variations in PFGE subtypes may be explained by changes in the number and chromosomal localization of this prophage(s). These observations indicate that the
lytA
hybridization pattern may be used as a molecular epidemiological marker that offers additional resolution of the genetic background of
S. pneumoniae
strains.
Evaluation of a
vanA
-Specific PCR Assay for Detection of Vancomycin-Resistant
Enterococcus faecium
during a Hospital Outbreak
Authors: Roger Michel , Faucher Marie-Claude , Forest Pierre , St-Antoine Pierre , Coutlée François 
Published: December 2019

ABSTRACT

We investigated the use of PCR as an alternative to culture of fecal samples for detection of
vanA
-containing
Enterococcus faecium
during a recent hospital outbreak. Rectal swabs collected consecutively from 223 patients were analyzed by culture with and without enrichment broth and by
vanA
-specific PCR of enrichment broth samples. Fifty-five specimens were positive for
vanA
-containing
E. faecium
by at least one method. The sensitivities of the
vanA
-specific PCR assay and agar culture with and without enrichment broth were 94.5, 98, and 89%, respectively. All three methods were 100% specific. Final results were obtained much more rapidly by PCR (within 24 to 30 h of specimen submission) than by the culture methods (4 to 5 days). Thus, PCR is an accurate and rapid alternative to culture for detection of vancomycin-resistant enterococci during hospital outbreaks.
Antibiotic Susceptibilities of Group C and Group G Streptococci Isolated from Patients with Invasive Infections: Evidence of Vancomycin Tolerance among Group G Serotypes
Authors: Zaoutis Theoklis , Schneider Barbara , Steele Moore Lynn , Klein Joel D. 
Published: December 2019

ABSTRACT
A retrospective review of medical records for 32 patients with invasive group C streptococcus (GCS) or group G streptococcus (GGS) infections was performed. MICs and minimum bactericidal concentrations (MBCs) of penicillin, erythromycin, and vancomycin for all isolates were obtained. Tolerance of vancomycin, defined as an MBC 32 or more times higher than the MIC, was exhibited by 18 GGS isolates (54%). The identification of tolerance in clinical isolates of GGS and GCS may have clinical implications in treating these seriously ill patients.
Maxillary Sinusitis Caused by Medusoid Form of
Schizophyllum commune
Authors: Sigler Lynne , Bartley James R. , Parr Dinah H. , Morris Arthur J. 
Published: December 2019

ABSTRACT

We present a case of maxillary sinusitis in a diabetic female caused by the basidiomycete fungus
Schizophyllum commune
. Identification of the isolate was hampered by its atypical features. Subcultures formed sterile medusoid structures from nonclamped mycelia until spontaneous dikaryotization resulted in the development of characteristic fan-shaped fruiting bodies. Identification was confirmed by the presence of spicules formed on the hyphae and by vegetative compatibility with known isolates.
Optimizing Culture of
Chlamydia pneumoniae
by Using Multiple Centrifugations
Authors: Pruckler Janet M. , Masse Nirupama , Stevens Valerie A. , Gang Liu , Yang Yonghong , Zell Elizabeth R. , Dowell Scott F. , Fields Barry S. 
Published: December 2019

ABSTRACT

Three methods for the recovery of
Chlamydia pneumoniae
from spiked nasopharyngeal and blood specimens, including extended culture and additional centrifugations, were compared. Additional centrifugations and a 7-day culture time resulted in a 500- to 5,000-fold increase in the number of detectable inclusion-forming units.
Pneumocystis carinii
Carriage in Immunocompetent Patients with Primary Pulmonary Disorders as Detected by Single or Nested PCR
Authors: Sing Andreas , Roggenkamp Andreas , Autenrieth Ingo B. , Heesemann Jürgen 
Published: December 2019

ABSTRACT

Ninety-five bronchoalveolar lavage specimens from 63 immunocompetent adult patients with primary pulmonary disease were analyzed for
Pneumocystis carinii
colonization by primary and nested PCR. Twelve of 63 patients (19%) were PCR positive. None of them developed
P. carinii
pneumonia. These results suggest that
P. carinii
carriage may exist in immunocompetent patients with underlying pulmonary disease.
Comparison of the Quantiplex Version 3.0 Assay and a Sensitized Amplicor Monitor Assay for Measurement of Human Immunodeficiency Virus Type 1 RNA Levels in Plasma Samples
Authors: Highbarger Helene C. , Alvord W. Gregory , Jiang Min Kang , Shah Akram S. , Metcalf Julia A. , Lane H. Clifford , Dewar Robin L. 
Published: December 2019

ABSTRACT

This study evaluated correlation and agreement between version 3 of the Quantiplex human immunodeficiency virus type 1 (HIV-1) RNA assay (v3 branched DNA [bDNA]) and a sensitized Amplicor HIV-1 Monitor assay (reverse transcription [RT]-PCR) for the measurement of HIV RNA. Three hundred eighteen samples from 59 randomly selected, HIV-1-seropositive persons on various drug protocols from the National Institute of Allergy and Infectious Diseases HIV outpatient clinic were studied. The results indicate that v3 bDNA and RT-PCR are highly correlated (
r
= 0.98) and are in good agreement (mean difference in log
10
copies/ml ± 2 standard deviations = 0.072 ± 0.371). The relationship between values obtained by both assays is given by the following equation: log
10
v3 bDNA = −0.0915 + 1.0052 · log
10
RT-PCR. This represents a 1.026-fold difference between log
10
RT-PCR values and log
10
v3 bDNA values.
Comparison of Variant-Specific Hybridization and Single-Strand Conformational Polymorphism Methods for Detection of Mixed Human Papillomavirus Type 16 Variant Infections
Authors: Emeny Rebecca T. , Herron John R. , Xi Long Fu , Koutsky Laura A. , Kiviat Nancy B. , Wheeler Cosette M. 
Published: December 2019

ABSTRACT
PCR-based variant-specific hybridization (VSH) and single-strand conformational polymorphism (SSCP) analyses were compared for their capacities to detect mixed human papillomavirus type 16 (HPV-16) variant infections within clinical specimens. The SSCP assay used in this comparison targets a 682-bp fragment that spans nucleotides 7445 to 222 within the HPV-16 genome. This fragment includes portions of the HPV-16 long control region and the E6 open reading frame and identifies three categories of SSCP patterns: those identical to the patterns of prototype HPV-16 (P), those identical to the patterns of Caski-derived HPV-16 (C), or those that are different from the P and C HPV-16 patterns and that are therefore classified as belonging to novel (N) HPV-16 variants. VSH targets the entire HPV-16 E6-coding region (nucleotides 56 to 640) and distinguishes previously described variant nucleotides at positions 109, 131, 132, 143, 145, 178, 286, 289, 350, 403, and 532. Clinical samples used in VSH and SSCP analyses were subjected to multiple independent amplification reactions. The resultant amplicons were cloned, and 14 to 78 clones per clinical specimen were evaluated by VSH. VSH detected an HPV-16 variant that represented at least 20% of the amplified HPV-16 variant population. In contrast, SSCP analysis detected HPV-16 variants that represented 36% of the amplified HPV-16 population. Comparison studies were conducted with mixed HPV-16 variant laboratory constructs. Again, VSH had a higher sensitivity than SSCP analysis in detecting mixed HPV-16 variant infections in these constructed amplicon targets. Accurate detection of HPV-16 variants may enhance our understanding of the natural history of HPV-16 infections.
Identification of
Candida dubliniensis
Based on Temperature and Utilization of Xylose and α-Methyl-
d
-Glucoside as Determined with the API 20C AUX and Vitek YBC Systems
Authors: Gales A. C. , Pfaller M. A. , Houston A. K. , Joly S. , Sullivan D. J. , Coleman D. C. , Soll D. R. 
Published: December 2019

ABSTRACT

To have a better understanding of the role of
Candida dubliniensis
in clinical infections, it is essential that microbiology laboratories can identify this species rapidly and accurately in clinical specimens.
C. dubliniensis
has been reported to lack the ability to utilize xylose (XYL) and α-methyl-
d
-glucoside (MDG) and to grow poorly or not at all at 45°C, whereas
Candida albicans
isolates utilize XYL and MDG and usually grow well at 45°C. We tested 66 isolates of
C. dubliniensis
and 100 isolates of
C. albicans
with both the API 20C AUX and Vitek YBC systems to evaluate the ability of the XYL and MDG tests contained within each of these systems to distinguish between the two species. The ability to grow at 45°C was also examined. None of the
C. dubliniensis
isolates grew at 45°C, and 23 of 100
C. albicans
isolates (23%) exhibited poor or no growth at 45°C. The XYL and MDG tests contained within the API 20C AUX system were both negative for all 66
C. dubliniensis
isolates and were positive for 98 (XYL) and 56 (MDG) of the 100
C. albicans
isolates. With the Vitek system, 64 of 66
C. dubliniensis
isolates (97.0%) were XYL negative and 63 (95.0%) were MDG negative. Conversely, 96 of 100
C. albicans
isolates (96.0%) were XYL positive and 100 (100.0%) were MDG positive with the Vitek system. Clinical microbiology laboratories could use lack of growth at 45°C and a negative XYL test with either the API 20C AUX or Vitek yeast identification system to provide a presumptive identification of
C. dubliniensis
. A negative MDG test result with either system would also be helpful but may misclassify
C. albicans
as
C. dubliniensis
, especially when the API 20C AUX system is used.
Adenoviruses from Human Immunodeficiency Virus-Infected Individuals, Including Two Strains That Represent New Candidate Serotypes Ad50 and Ad51 of Species B1 and D, Respectively
Authors: De Jong Jan C. , Wermenbol Anton G. , Verweij-Uijterwaal Marja W. , Slaterus Kees W. , Wertheim-Van Dillen Pauline , Van Doornum Gerard J. J. , Khoo Saye H. , Hierholzer John C. 
Published: December 2019

ABSTRACT
Adenovirus (Ad) isolates from a large number of human immunodeficiency virus (HIV)-infected individuals were compared serologically and genetically with Ad isolates from immunocompetent patients. Between 1982 and 1994, stool and urine samples from 137 subjects with AIDS hospitalized in The Netherlands yielded 143 Ad strains. Forty additional Ad strains were obtained from 35 HIV-positive patients in Manchester, United Kingdom, in 1992 and 1993. Of these 183 HIV-associated Ad strains, 84% belonged to species D and 3% belonged to species C. These strains were compared with 2,301 Ad strains collected during general diagnostic examinations in The Netherlands from 1973 to 1992. Of the latter strains, 5% belonged to species D and 49% belonged to species C. Two of the Ads isolated from fecal specimens of AIDS patients represent new serotypes: candidate Ad serotype 50 (prototype strain, Wan) of subspecies B1 and candidate Ad serotype 51 (prototype strain, Bom) of species D. The DNA restriction enzyme patterns of strains Wan and Bom differed from the patterns of all established prototypes.