bluuebunny/crossref_metadata_2025_split huggingface dataset:
Typing of Human
Mycobacterium avium
Isolates in Italy by IS
1245
-Based Restriction Fragment Length Polymorphism Analysis
Authors: Lari Nicoletta , Cavallini Michela , Rindi Laura , Iona Elisabetta , Fattorini Lanfranco , Garzelli Carlo 
Published: December 2019

ABSTRACT

All but 2 of 63
Mycobacterium avium
isolates from distinct geographic areas of Italy exhibited markedly polymorphic, multibanded IS
1245
restriction fragment length polymorphism (RFLP) patterns; 2 isolates showed the low-number banding pattern typical of bird isolates. By computer analysis, 41 distinct IS
1245
patterns and 10 clusters of essentially identical strains were detected; 40% of the 63 isolates showed genetic relatedness, suggesting the existence of a predominant AIDS-associated IS
1245
RFLP pattern.
Multicenter Evaluation of a Modified Protocol for the RAPIDEC Staph System for Direct Identification of
Staphylococcus aureus
in Blood Cultures
Authors: van Griethuysen Arjanne , Buiting Anton , Goessens Wil , van Keulen Peter , Wintermans Rob , Kluytmans Jan 
Published: December 2019

ABSTRACT

A modified protocol for the RAPIDEC Staph system (bioMérieux, Marcy-l’Etoile, France) for direct identification of
Staphylococcus aureus
in blood cultures was evaluated in a multicenter study. A total of 129 blood cultures (BACTEC 9000 Blood Culture System; Becton Dickinson Diagnostic Instrument Systems, Sparks, Md.) containing gram-positive cocci in clusters were analyzed by conventional methods and by RAPIDEC Staph in accordance with the manufacturer’s protocol and in accordance with a modified protocol. The sensitivity, specificity, and positive and negative predictive values obtained with the manufacturer’s protocol were 90.5, 97.7, 95.0, and 95.5%, respectively, and those obtained with the modified protocol were 100, 96.6, 93.3, and 100%, respectively. The modified protocol for the RAPIDEC Staph is easier to perform than the manufacturer’s protocol and is very reliable.
Development of a Scheme for Genotyping
Helicobacter pylori
Based on Allelic Variation in Urease Subunit Genes
Authors: Owen Robert J. , Slater Eleanor R. , Xerry Jacqueline , Peters Tansy M. , Teare E. Louise , Grant Andrew 
Published: December 2019

ABSTRACT

Helicobacter pylori
urease subunit genes in 383 isolates from 10 countries were investigated by PCR-restriction fragment length polymorphism (
Hae
III) analysis. Eighty-two different
ureAB
profiles were documented by reference to known sequences. Variation among 51% of strains was accounted for by 10 predominant patterns, which provided a unique framework for categorizing isolates with geographically diverse origins.
Rapid Differentiation of Closely Related
Candida
Species and Strains by Pyrolysis-Mass Spectrometry and Fourier Transform-Infrared Spectroscopy
Authors: Timmins Éadaoin M. , Howell Susan A. , Alsberg Bjørn K. , Noble William C. , Goodacre Royston 
Published: December 2019

ABSTRACT

Two rapid spectroscopic approaches for whole-organism fingerprinting of pyrolysis-mass spectrometry (PyMS) and Fourier transform-infrared spectroscopy (FT-IR) were used to analyze a group of 29 clinical and reference
Candida
isolates. These strains had been identified by conventional means as belonging to one of the three species
Candida albicans
,
C. dubliniensis
(previously reported as atypical
C. albicans
), and
C. stellatoidea
(which is also closely related to
C. albicans
). To observe the relationships of the 29 isolates as judged by PyMS and FT-IR, the spectral data were clustered by discriminant analysis. On visual inspection of the cluster analyses from both methods, three distinct clusters, which were discrete for each of the
Candida
species, could be seen. Moreover, these phenetic classifications were found to be very similar to those obtained by genotypic studies which examined the
Hin
fI restriction enzyme digestion patterns of genomic DNA and by use of the 27A
C. albicans
-specific probe. Both spectroscopic techniques are rapid (typically, 2 min for PyMS and 10 s for FT-IR) and were shown to be capable of successfully discriminating between closely related isolates of
C. albicans
,
C. dubliniensis
, and
C. stellatoidea
. We believe that these whole-organism fingerprinting methods could provide opportunities for automation in clinical microbial laboratories, improving turnaround times and the use of resources.
Comparison of PCR, Isoenzyme Analysis, and Antigen Detection for Diagnosis of
Entamoeba histolytica
Infection
Authors: Haque Rashidul , Ali I. K. M. , Akther S. , Petri William A. 
Published: December 2019

ABSTRACT

The diagnosis of amebiasis by microscopic identification of the parasite in stool is insensitive and unable to distinguish the invasive parasite
Entamoeba histolytica
from the commensal parasite
E. dispar
. In this study, we have tested a PCR technique for the detection of
E. histolytica
and compared it with isoenzyme analysis and the TechLab
E. histolytica
-specific antigen detection test. The nested-PCR test we used is based on amplification of the small subunit rRNA gene of
E. histolytica
and
E. dispar
followed by restriction digest analysis of the PCR product. Single stool samples were obtained from 98 patients from Dhaka, Bangladesh, with diarrhea: 88 patients diagnosed by microscopy and/or culture with
E. histolytica
and/or
E. dispar
infection and 10 patients without infection. Isoenzyme analysis identified 53 of the infections as
E. histolytica
and 28 as
E. dispar
. PCR and isoenzyme identification of
E. histolytica
agreed in 96% (51 of 53) of amebic cultures. PCR for
E. histolytica
was negative in all 10 samples that were negative for
E. histolytica
by isoenzyme and antigen detection. PCR and antigen detection had comparable sensitivities when performed directly on fresh stool specimens, identifying 87% (46 of 53) and 85% (45 of 53), respectively, of
E. histolytica
infections identified by isoenzyme analysis. The correlation of results by antigen detection and PCR for identification of
E. histolytica
in stool was 93% (45 of 48 cases). Mixed infections with
E. histolytica
and
E. dispar
were detected by PCR in 14% (12 of 88) of cases. In conclusion, all three techniques for specific identification of
E. histolytica
in fresh stool showed excellent correlation. Only the TechLab
E. histolytica
antigen detection test was both rapid and technically simple.
Antibodies against Early Proteins of Human Papillomaviruses as Diagnostic Markers for Invasive Cervical Cancer
Authors: Meschede Wolfgang , Zumbach Klaus , Braspenning Joris , Scheffner Martin , Benitez-Bribiesca Luis , Luande Jeff , Gissmann Lutz , Pawlita Michael 
Published: December 2019

ABSTRACT
Cervical cancer is the most prevalent tumor in developing countries and the second most frequent cancer among females worldwide. Specific human papillomaviruses (HPVs) and, most notably, HPV types 16 and 18 are recognized as being causally associated with this malignancy. Antibodies against early HPV proteins E6 and E7 have been found more often in patients with tumors than in controls. Existing peptide enzyme-linked immunosorbent assays (ELISAs) for the detection of anti-E6 and anti-E7 antibodies in human sera have low levels of sensitivity and specificity and thus are not suitable for use as diagnostic tools. Based on highly purified recombinant native proteins, we developed four sandwich ELISAs for the detection of antibodies against HPV type 16 and 18 E6 and E7 proteins. We demonstrate their sensitivities and high degrees of specificity for cervical cancer. Among a total of 501 serum specimens from unselected patients with invasive cervical cancer, 52.9% reacted positively in at least one of the four assays. In contrast, among 244 serum specimens from control subjects without cervical cancer, only 2 reactive serum specimens (0.8%) were found. For 19 of 19 antibody-positive patients, the HPV type indicated by seroreactivity was identical to the HPV DNA type found in the tumor, which also indicates a high degree of specificity for antibody detection with respect to HPV type. In a direct comparison of 72 serum specimens from patients with cervical cancer, 56% of the specimens reacted in at least one of the four protein ELISAs, whereas 40% reacted in at least one of seven peptide ELISAs covering the four antigens. These assays could be of value for the detection of invasive cervical cancer in settings in which cytology-based early tumor screening is not available, for the clinical management of patients diagnosed with cervical cancer, and for the immunological monitoring of E6 and E7 vaccination trials.
Molecular Fingerprinting of
Mycobacterium tuberculosis
and Risk Factors for Tuberculosis Transmission in Paris, France, and Surrounding Area
Authors: Gutiérrez M. C. , Vincent V. , Aubert D. , Bizet J. , Gaillot O. , Lebrun L. , Le Pendeven C. , Le Pennec M. P. , Mathieu D. , Offredo C. , Pangon B. , Pierre-Audigier C. 
Published: December 2019

ABSTRACT

Forty-three percent of the tuberculosis cases reported in France are from the Ile de France region. The incidence of tuberculosis in this region is 33 cases per 100,000 inhabitants, twice the national average. A restriction fragment length polymorphism (RFLP) analysis was performed with clinical isolates of
Mycobacterium tuberculosis
isolated during 1995 in 10 hospitals in Paris and surrounding areas to detect tuberculosis transmission and define the factors associated with clustering in this population. The molecular markers used were the insertion sequence IS
6110
and the direct repeat (DR) sequence. Social, demographic, and clinical data were collected from the patients’ medical files. Ten patients with isolates with a single copy of IS
6110
were excluded from further analysis. Twenty-four patients with false-positive cultures due to laboratory contamination (based on RFLP analysis with IS
6110
and examination of patient data) were also excluded. The study was then conducted with 272 strains isolated from 272 patients. Further fingerprinting was performed by using the DR element with strains with patterns by RFLP analysis with IS
6110
that differed by one band only and strains with identical patterns by RFLP analysis with IS
6110
and with low numbers of copies of IS
6110
. The combined use of both markers identified unique patterns for 177 strains and clustered 95 (35.7%) strains in 26 groups, each containing isolates from 2 to 12 patients. The clustering was strongly associated with homelessness and the male sex. It was not associated with age, birth in a foreign country, human immunodeficiency virus positivity, or residence in hostels or prison. Isolates from homeless people were often included in large clusters, and homeless people could be the source of tuberculosis transmission for more than 50% of the clustered patients. These results suggest that homeless people play a key role in the spread of
M. tuberculosis
in the community and that poor socioeconomic conditions are the main risk factors associated with active tuberculosis transmission.
Viruses and Bacteria in the Etiology of the Common Cold
Authors: Mäkelä Mika J. , Puhakka Tuomo , Ruuskanen Olli , Leinonen Maija , Saikku Pekka , Kimpimäki Marko , Blomqvist Soile , Hyypiä Timo , Arstila Pertti 
Published: December 2019

ABSTRACT

Two hundred young adults with common colds were studied during a 10-month period. Virus culture, antigen detection, PCR, and serology with paired samples were used to identify the infection. Viral etiology was established for 138 of the 200 patients (69%). Rhinoviruses were detected in 105 patients, coronavirus OC43 or 229E infection was detected in 17, influenza A or B virus was detected in 12, and single infections with parainfluenza virus, respiratory syncytial virus, adenovirus, and enterovirus were found in 14 patients. Evidence for bacterial infection was found in seven patients. Four patients had a rise in antibodies against
Chlamydia pneumoniae
, one had a rise in antibodies against
Haemophilus influenzae
, one had a rise in antibodies against
Streptococcus pneumoniae
, and one had immunoglobulin M antibodies against
Mycoplasma pneumoniae
. The results show that although approximately 50% of episodes of the common cold were caused by rhinoviruses, the etiology can vary depending on the epidemiological situation with regard to circulating viruses. Bacterial infections were rare, supporting the concept that the common cold is almost exclusively a viral disease.
Use of Gas Chromatographic Fatty Acid and Mycolic Acid Cleavage Product Determination To Differentiate among
Mycobacterium genavense
,
Mycobacterium fortuitum
,
Mycobacterium simiae
, and
Mycobacterium tuberculosis
Authors: Chou S. , Chedore P. , Kasatiya S. 
Published: December 2019

ABSTRACT

Three
Mycobacterium genavense
strains and three American Type Culture Collection reference strains each of
Mycobacterium fortuitum
,
Mycobacterium simiae
, and
Mycobacterium tuberculosis
were subcultured onto Mycobacteria 7H11 agar (Difco Laboratories, Detroit, Mich.) supplemented with mycobactin J (Allied Laboratories, Fayette, Mo.). After 4 weeks of incubation at 37°C in 10% CO
2
, the cultures were analyzed by gas-liquid chromatography (GLC) for their fatty acids and mycolic acid cleavage products.
M. fortuitum
was clearly differentiated from
M. genavense
by the presence of the specific marker 2-methyloctadecenoic acid in
M. fortuitum
and by the ratio of tetracosanoic acid to hexacosanoic acid. This ratio was <1 for
M. genavense
and >3 for
M. fortuitum. M. fortuitum
also contained docosanoic acid, which was not detected in
M. genavense. M. genavense
,
M. simiae
, and
M. tuberculosis
, which have similar GLC profiles, were also differentiated from each other by the presence of either
cis
-10-hexadecenoic acid or
cis
-11-hexadecenoic acid and by tetradecanoic acid content.
Comparison of Use of Cerebrospinal Fluid, Serum, and Throat Swab Specimens in Diagnosis of Enteroviral Acute Neurological Infection by a Rapid RNA Detection PCR Assay
Authors: Andréoletti Laurent , Blassel-Damman Nathalie , Dewilde Anny , Vallée Louis , Cremer Robin , Hober Didier , Wattré Pierre 
Published: December 2019

ABSTRACT
A PCR assay for detection of enterovirus RNA in multiple specimen types from patients with neurological infections was evaluated. Combined PCR assay of cerebrospinal fluid and serum (systemic specimens) was more sensitive than assaying either specimen alone in children but not in adults. Compared with PCR in systemic specimens, detection of enterovirus RNA in throat swabs showed a sensitivity of 62.5% and a specificity of 75.6%.
Comparative Study of Different Standardization Concepts in Quantitative Competitive Reverse Transcription-PCR Assays
Authors: Haberhausen Gerd , Pinsl Judith , Kuhn Carl-Christoph , Markert-Hahn Christine 
Published: December 2019

ABSTRACT
Four different standardization approaches based on a competitive reverse transcription (RT)-PCR assay were compared with a noncompetitive assay based on an external standard curve. Criteria for assessment were accuracy in quantitation, correctness of recovery, sensitivity, dynamic range, reproducibility, throughput, and convenience of sample handling. As a model system, we used the 5′-noncoding region of hepatitis C virus (HCV) for amplification in all quantitative RT-PCRs. A computer program that allowed parallel data processing was developed. Surprisingly, all methods were found suitable for accurate quantitation and comparable with respect to the criterion correctness of recovery. All results differed only by a factor of about 2. The reason for this finding might be that all of our mimics, as well as the wild-type genome of HCV, exhibited exactly the same amplification and hybridization efficacy. Moreover, minimal competition occurred in our experiments over a 5-log dynamic range. A further topic of our investigation was the comparison of two different competitive RNA fragments, mimics, with regard to their suitability as internal standards. One was a heterologous mimic, in which only the primer binding sites were identical to the wild type. The second one was a homologous mimic identical to the wild type except for a small region used for differential hybridization, which was replaced by a permutated sequence of the same length. Both the homologous and heterologous internal mimics were found appropriate for an accurate competitive RT-PCR assay, provided that amplification efficacy, as well as capture efficacy, is proven identical for both analyte and mimic.
Detection and Prevalence of
Helicobacter
Infection in Pet Cats
Authors: Neiger R. , Dieterich C. , Burnens A. , Waldvogel A. , Corthésy-Theulaz I. , Halter F. , Lauterburg B. , Schmassmann A. 
Published: December 2019

ABSTRACT

The presence of spiral bacteria in the feline stomach has been recognized for over a century, but the identities and degrees of prevalence of such organisms in privately owned cats are still poorly documented. The aims of this study were (i) to adapt different diagnostic tools and evaluate their practicality for diagnosing feline gastric
Helicobacter
colonization, (ii) to determine the prevalence of gastric
Helicobacter
-like organisms in pet cats, (iii) to identify the feline species, and (iv) to correlate the presence of a
Helicobacter
infection with gastritis. Biopsy samples were taken gastroscopically from the antra and the corpora of clinically healthy pet cats.
Helicobacter
-like organisms were detected by Gram staining, Warthin-Starry staining, and rapid urease testing in biopsy specimens and by [
13
C]urea breath testing in 79, 77, 78, and 85% of cases, respectively. PCR analysis revealed that 78% of the cats (38 of 49) were infected by
Helicobacter heilmannii
; however, none of them was harboring
Helicobacter pylori
or
Helicobacter felis
. Culture was positive for one cat; the organism was identified as
Helicobacter pametensis
by dot blot DNA hybridization. By a combination of the detection methods, 91% of the pet cats were found to be
Helicobacter
positive. For 46 cats (79%) diagnostic tests were concordant. All cats showed mild to moderate gastritis in either the antrum or the corpus, regardless of the presence or density of gastric bacteria. In summary, pet cats are frequently colonized by
H. heilmannii
without a significant correlation between infection and degree of gastritis.
Serologic Evidence of Infection with
Ehrlichia
spp. in Wild Rodents (Muridae: Sigmodontinae) in the United States
Authors: Nicholson William L. , Muir Susie , Sumner John W. , Childs James E. 
Published: December 2019

ABSTRACT

Rodent (Muridae: Sigmodontinae) blood and sera collected from 14 states were tested for seroreactivity to a cultured isolate of the human granulocytic ehrlichiosis (HGE) agent by using an indirect immunofluorescence assay. Of the 1,240 samples tested, 136 (11%) were found to be reactive at titers of ≥32. Rodents with HGE agent-specific antibodies were found in New York (23% of 491 samples; geometric mean endpoint titer [GMT] = 441), Connecticut (11% of 100 samples; GMT = 481), California (9% of 32 samples; GMT = 323), Colorado (2% of 212 samples; GMT = 256), Florida (7% of 27 samples; GMT = 362), Maryland (7% of 15 samples; titer = 64), New Jersey (4% of 76 samples; titer = 256), and Wisconsin (13% of 8 samples; titer = 128). Samples from Georgia (
n
= 16), Illinois (
n
= 27), Nevada (
n
= 27), North Carolina (
n
= 52), Ohio (
n
= 57), and Utah (
n
= 100) were not reactive. The earliest seroreactive sample was from a
Peromyscus leucopus
mouse collected in June 1986 in Connecticut, and the majority of the seroreactive samples (68%) were from this species. Samples from other
Peromyscus
species (
P. boylii
,
P. maniculatus
, and
P. gossypinus
) were also found to be reactive, with a GMT for the genus of 410. Several species of
Neotoma
woodrats (
N. fuscipes
,
N. lepida
,
N. albigula
, and
N. mexicana
) from California and Colorado had antibodies that reacted with the HGE agent (genus GMT = 194), suggesting that enzootic cycles of
Ehrlichia
spp. exist outside of the areas of confirmed human disease. Attempts to amplify and detect ehrlichial DNA from the limited tissues available (
n
= 40 animals) were unsuccessful. Further studies are needed to determine the identity of the organisms inducing antibody production in these rodent species and to elucidate the epidemiology and public health importance of these agents.
Lyme Disease in Taiwan: First Human Patient with Characteristic Erythema Chronicum Migrans Skin Lesion
Authors: Shih Chien-Ming , Wang Jin-Choung , Chao Li-Lian , Wu Trong-Neng 
Published: December 2019

ABSTRACT

We report herein the first laboratory-diagnosed case of Lyme disease in a human in Taiwan. A 45-year-old Taiwanese man living in Taipei, in northern Taiwan, had an expanding skin lesion (measuring 23 by 15 cm) on his abdomen for 2 to 3 weeks and recurrent attacks of pain and swelling of the knee joint. Serologic tests indicated a significantly elevated titer of antibody to
Borrelia burgdorferi
. After appropriate antibiotic treatment for 3 weeks, the skin lesion was cured and the joint swelling was improved. Although several strains of
Borrelia
spirochetes had been isolated from rodents (
Rattus losea
) in Taiwan, the tick vector responsible for the transmission remains to be identified.
Epidemiologic Evaluation of Antimicrobial Resistance in Community-Acquired Enterococci
Authors: Silverman J. , Thal L. A. , Perri M. B. , Bostic G. , Zervos M. J. 
Published: December 2019

ABSTRACT

Fecal samples from 200 consecutive patients admitted to a community hospital yielded 107 enterococci. High-level gentamicin resistance occurred in 10 (14%) of the
Enterococcus faecalis
isolates. Ampicillin resistance occurred in two (3%) of the
E. faecalis
isolates and six (23%) of the
Enterococcus faecium
isolates. There were no vancomycin-resistant enterococci. Risk factors for enterococci with high-level aminoglycoside (gentamicin) or ampicillin resistance included prior hospitalization and previous antibiotic use.
Intra-Assay Performance Characteristics of Five Assays for Quantification of Human Immunodeficiency Virus Type 1 RNA in Plasma
Authors: Lin Hsiang Ju , Pedneault Louise , Hollinger F. Blaine 
Published: December 2019

ABSTRACT
Three kits (Roche AMPLICOR human immunodeficiency virus type 1 [HIV-1] Monitor, Chiron enhanced-sensitivity bDNA, and Organon Teknika NASBA HIV-1 QT) and two in-house assays (from National Genetics Institute and Baylor College of Medicine) were compared with a blinded panel. The results were evaluated as to intra-assay sensitivity, precision, and ability to detect differences in a dilution series.
Detection and Direct Typing of Herpes Simplex Virus in Perianal Ulcers of Patients with AIDS by PCR
Authors: do Nascimento Maria C. , Sumita Laura M. , de Souza Vanda A. U. F. , Pannuti Cláudio S. 
Published: December 2019

ABSTRACT
The presence of herpes simplex virus type 1 (HSV-1) and HSV-2 in perianal ulcerations of 41 AIDS patients was assessed by virus culture and a type-specific PCR-based assay. HSV was isolated from the lesion site in 24 of 41 (58.5%) patients, and HSV DNA was detected by PCR in all 24 (100%) of these specimens. Additionally, PCR was used to detect HSV DNA in 12 of 17 (70.5%) HSV culture-negative samples. Thus, HSV genomic sequences could be demonstrated in 36 of 41 (87.8%) perianal ulcers in this series. Full agreement in HSV typing by either immunodot assay or PCR was seen in 24 samples that were positive by both virus culture and PCR. HSV-2 was demonstrated in 35 of 36 (97.2%) HSV-positive samples.