bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of Resolution and Intercenter Reproducibility of Results of Genotyping
Staphylococcus aureus
by Pulsed-Field Gel Electrophoresis of
Sma
I Macrorestriction Fragments: a Multicenter Study
Authors: van Belkum Alex , van Leeuwen Willem , Kaufmann Mary Elizabeth , Cookson Barry , Forey Françoise , Etienne Jerome , Goering Richard , Tenover Fred , Steward Christine , O’Brien Frances , Grubb Warren , Tassios Panayotis , Legakis Nicholas , Morvan Anne , El Solh Névine , de Ryck Raf , Struelens Marc , Salmenlinna Saara , Vuopio-Varkila Jaana , Kooistra Mirjam , Talens Adriaan , Witte Wolfgang , Verbrugh Henri 
Published: December 2019

ABSTRACT

Twenty well-characterized isolates of methicillin-resistant
Staphylococcus aureus
were used to study the optimal resolution and interlaboratory reproducibility of pulsed-field gel electrophoresis (PFGE) of DNA macrorestriction fragments. Five identical isolates (one PFGE type), 5 isolates that produced related PFGE subtypes, and 10 isolates with unique PFGE patterns were analyzed blindly in 12 different laboratories by in-house protocols. In several laboratories a standardized PFGE protocol with a commercial kit was applied successfully as well. Eight of the centers correctly identified the genetic homogeneity of the identical isolates by both the in-house and standard protocols. Four of 12 laboratories failed to produce interpretable data by the standardized protocol, due to technical problems (primarily plug preparation). With the five related isolates, five of eight participants identified the same subtype interrelationships with both in-house and standard protocols. However, two participants identified multiple strain types in this group or classified some of the isolates as unrelated isolates rather than as subtypes. The remaining laboratory failed to distinguish differences between some of the related isolates by utilizing both the in-house and standardized protocols. There were large differences in the relative genome lengths of the isolates as calculated on the basis of the gel pictures. By visual inspection, the numbers of restriction fragments and overall banding pattern similarity in the three groups of isolates showed interlaboratory concordance, but centralized computer analysis of data from four laboratories yielded percent similarity values of only 85% for the group of identical isolates. The differences between the data sets obtained with in-house and standardized protocols could be the experimental parameters which differed with respect to the brand of equipment used, imaging software, running time (20 to 48 h), and pulsing conditions. In conclusion, it appears that the standardization of PFGE depends on controlling a variety of experimental intricacies, as is the case with other bacterial typing procedures.
Evaluation of a Commercially Available Reverse Transcription-PCR Assay for Diagnosis of Enteroviral Infection in Archival and Prospectively Collected Cerebrospinal Fluid Specimens
Authors: Pozo Francisco , Casas Inmaculada , Tenorio Antonio , Trallero Gloria , Echevarria Jose M. 
Published: December 2019

ABSTRACT
A commercially available reverse transcription (RT)-PCR method (AMPLICOR EV; Roche Diagnostic Systems, Inc., Branchburg, N.J.) was evaluated for detection of enteroviruses in cerebrospinal fluid from patients with neurological disease. This assay was compared with virus isolation in cell culture and an in-house RT-PCR method designed with a nonoverlapping region of the enteroviral genome. A panel of 200 cerebrospinal fluid specimens prospectively collected from patients with a wide variety of neurological symptoms, including 50 patients involved in three different outbreaks of acute aseptic meningitis, was assayed. A second panel of 97 archived cerebrospinal fluid specimens, stored for 2 to 5 years, from patients with aseptic meningitis associated with several enterovirus outbreaks was also studied. From the first panel, enteroviruses were detected in 13 of 50 specimens by cell culture (26%), in 43 of 50 specimens by AMPLICOR EV (86%), and in 46 of 50 specimens by the in-house assay (92%) from patients with aseptic meningitis associated with outbreak and 1 of 29, 3 of 29, and 4 of 29 specimens, respectively, from sporadic cases of aseptic meningitis. The remaining 121 cerebrospinal fluid specimens from patients with other neurological syndromes were negative by all tests. From the second panel, enteroviral RNA was detected by the AMPLICOR test (31 of 97 specimens, 32%) and the in-house assay (39 of 97 specimens, 40%). According to our results, patients with aseptic meningitis should be analyzed for enteroviral infection in cerebrospinal fluid by RT-PCR methods, and the AMPLICOR EV test is a suitable tool for performing such studies. Archival cerebrospinal fluid specimens are less suitable for evaluation of the performance of RT-PCR methods designed for enterovirus detection.
16S rRNA Sequence Diversity in
Mycobacterium celatum
Strains Caused by Presence of Two Different Copies of 16S rRNA Gene
Authors: Reischl U. , Feldmann K. , Naumann L. , Gaugler B. J. M. , Ninet B. , Hirschel B. , Emler S. 
Published: December 2019

ABSTRACT

Direct sequencing of the 16S rRNA gene (16S rDNA) of
Mycobacterium celatum
isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.
Diagnosis of Group A Streptococcal Necrotizing Fasciitis by Using PCR To Amplify the Streptococcal Pyrogenic Exotoxin B Gene
Authors: Louie Lisa , Simor Andrew E. , Louie Marie , McGeer Allison , Low Donald E. 
Published: December 2019

ABSTRACT

This study evaluated a PCR assay for detection of the streptococcal pyrogenic exotoxin B (
speB
) gene from tissue biopsy specimens of patients with necrotizing fasciitis.
speB
was detected in specimens from all 10 patients with necrotizing fasciitis due to group A streptococcus. The assay was negative for all 11 patients without culture or serologic evidence of streptococcal infection. These results suggest that the detection of
speB
by PCR may be useful for confirming group A streptococcal infection when cultures are negative or not available.
The L1 Major Capsid Protein of Human Papillomavirus Type 16 Variants Affects Yield of Virus-Like Particles Produced in an Insect Cell Expression System
Authors: Touze Antoine , El Mehdaoui Slimane , Sizaret Pierre-Yves , Mougin Christine , Muñoz Nubia , Coursaget Pierre 
Published: December 2019

ABSTRACT
The L1 major capsid proteins of six human papillomavirus type 16 (HPV-16) strains were expressed in insect cells by using recombinant baculoviruses. Virus-like particles (VLPs) which appeared similar to empty virions were identified by electron microscopy for all HPV strains investigated. However, the yield of VLPs produced varied in a range from 1 to 79 depending on the HPV-16 strain. The L1 proteins of these strains differed by up to 15 amino acids from the L1 protein of the prototype HPV-16 strain. Mutations in the amino acid region from residues 83 to 97 seemed to affect the level of expression of the L1 protein. These results are important when considering the development of HPV vaccines and serological tests. They indicate that strains inducing high levels of VLP production must be selected for the development of vaccines. Moreover, the L1 proteins of all strains investigated were able to bind with DNA. We also investigated the seroreactivities of VLPs derived from three different HPV-16 strains from Algeria, Senegal, and the Philippines by testing sera from women from 11 countries in immunoglobulin G-specific enzyme-linked immunosorbent assays. We observed a strong correlation between the reactivities of the three different VLP variants, independent of the geographical origin of the sera investigated. These results indicate that the three strains investigated are serologically cross-reactive despite the fact that their L1 proteins differ in 14 amino acids and suggest that VLPs derived from only one HPV-16 strain could be sufficient for the development of an HPV-16 vaccine and anti-HPV-16 tests.
Sudden Increase in Isolation of Group B Streptococci, Serotype V, Is Not Due to Emergence of a New Pulsed-Field Gel Electrophoresis Type
Authors: Elliott J. A. , Farmer K. D. , Facklam R. R. 
Published: December 2019

ABSTRACT

Until recently, group B streptococcus, serotype V (GBS-V), was an infrequent cause of disease. It is now recognized as a significant cause of infections in both children and adults. To determine if this increase was due to the recent introduction and spread of a single clone of GBS-V, we analyzed, by pulsed-field gel electrophoresis (PFGE), the
Sma
I chromosomal DNA digests of 45 bacteria: 41 isolated from human infections between 1986 and 1996 in the United States, 2 from human infections in Argentina, and 2 from naturally infected mice. Seventeen patterns were found and arbitrarily designated patterns A to Q. Pattern N constituted 24 (53%) of the isolates and was found in all of the years tested and from all surveillance areas, as well as in both isolates from Argentina, and was very similar to the GBS-V isolated from a mouse. Pattern P was found in three isolates, pattern F was found in two, and the remaining patterns were found in one isolate each. We concluded that the majority of isolates of GBS-V are of one PFGE subtype and that this subtype was predominate before the increase in disease caused by GBS-V and that GBS-V disease is caused by several different subtypes.
Differentiation of
Rhizomucor
Species by Carbon Source Utilization and Isoenzyme Analysis
Authors: Vastag Mária , Papp Tamás , Kasza Zsolt , Vágvölgyi Csaba 
Published: December 2019

ABSTRACT

Nineteen
Rhizomucor miehei
and
Rhizomucor pusillus
isolates were assayed for their ability to utilize 87 various substrates as a single carbon source. Besides a difference in sucrose utilization, distinctive differences were found in the utilization of glycine, phenylalanine, and β-alanine. Five isoenzyme systems also proved useful for the determination of markers of distinctive value at a species level. Data were used to obtain information about the genetic polymorphism of these species: a high degree of variability was found among the
R. pusillus
isolates, whereas the group of
R. miehei
isolates was more homogeneous genetically.
Associations between Heat-Stable (O) and Heat-Labile (HL) Serogroup Antigens of
Campylobacter jejuni
: Evidence for Interstrain Relationships within Three O/HL Serovars
Authors: Jackson C. J. , Fox A. J. , Jones D. M. , Wareing D. R. A. , Hutchinson D. N. 
Published: December 2019

ABSTRACT

A comparative examination of the heat-stable (O) and heat-labile (HL) serogrouping results for 9,024 sporadic human isolates of
Campylobacter jejuni
revealed conserved associations between specific O and HL antigens (O/HL serovars). Forty-nine percent of the isolates which grouped for both O and HL antigens belonged to one of three serovars: O 4 complex/HL 1 (17.9%), O 1/HL 2 (16.8%), or O 50/HL 7 (14.5%). Other common serovars were O 2/HL 4 (8.3%), O 6/HL 6 (8.1%), O 53/HL 11 (4.5%), O 19/HL 17 (3.3%), O 5/HL 9 (3.3%), O 9/HL 9 (3.2%), and O 23/HL 5 (3.1%). These 10 serovars accounted for 83.1% of the serogroupable isolates. A large number of strains (41.3%) could be typed by only one of the two methods or could not be serogrouped (11%). Strains belonging to three serovars, O 2/HL 4, O 50/HL 7, and O 23/HL 5, were further characterized by combining data from expressed features (O/HL serogroups, phage groups, and biotypes) with restriction fragment length polymorphism genotypes. These polyphasic data demonstrated that within each serovar, individual isolates showed substantial conservation of both genomic and phenotypic characteristics. The essentially clonal nature of the three serovars confirmed the potential of combined O and HL serogrouping as a practical and phylogenetically valid method for investigating the epidemiology of sporadic
C. jejuni
infection.
Reduction of Diagnostic Window by New Fourth-Generation Human Immunodeficiency Virus Screening Assays
Authors: Weber Bernard , Mbargane Fall El Hadji , Berger Annemarie , Doerr Hans Wilhelm 
Published: December 2019

ABSTRACT

In order to reduce the diagnostic window between the time of human immunodeficiency virus (HIV) infection and laboratory diagnosis, new screening enzyme-linked immunosorbent assays (ELISAs) which permit the simultaneous detection of HIV antigen and antibody have been developed. Two fourth-generation assays, HIV DUO (Biomérieux) and HIV Combi (Boehringer Mannheim), for the combined detection of HIV antigen and antibody, were compared with a third-generation assay (HIV-1/HIV-2 3rd Generation Plus enzyme immunoassay [EIA]; Abbott) and a p24 antigen test (HIV-1 Ag monoclonal; Abbott). A total of 17 seroconversion panels, 15 cell culture supernatants infected with different HIV type 1 (HIV-1) subtypes, and 255 potentially cross-reactive serum samples were tested. Ten seroconversions were detected an average of 8.1 days earlier with HIV DUO and 7.5 days earlier with HIV Combi than with the third-generation ELISA. Overall, in the 17 seroconversion panels tested, HIV DUO detected HIV-1 infection an average of 4.8 days and HIV Combi detected infection an average of 4.4 days earlier than HIV-1/HIV-2 3rd Generation Plus EIA. HIV antigen was detected with HIV DUO and HIV Combi in all of the 15 cell culture supernatants infected with different HIV-1 subtypes, including subtype O. With fourth-generation assays, considerably fewer false-positive results (
n
= 4 to 6) were obtained, in comparison with the third-generation EIA (
n
= 18). Fourth-generation assays permit an earlier diagnosis of HIV infection than third-generation antibody screening assays through the detection of p24 antigen, which may be present in serum samples from individuals with recent HIV infection prior to seroconversion.
Molecular Characterization of Pneumococcal Nasopharynx Isolates Collected from Children during Their First 2 Years of Life
Authors: Sluijter Marcel , Faden Howard , de Groot Ronald , Lemmens Nicole , Goessens Wil H. F. , van Belkum Alex , Hermans Peter W. M. 
Published: December 2019

ABSTRACT
Pneumococcal colonization was studied in 19 children monitored from birth through the age of 2 years. For this purpose, pneumococcal isolates were characterized by capsular typing, restriction fragment end labeling (RFEL), and penicillin-binding protein (PBP) genotyping. Fifty-eight isolates were collected and were found to belong to 10 capsular types, 31 RFEL types, and 7 PBP genotypes. Thirty-nine percent of the isolates had reduced susceptibility to penicillin. All seven highly resistant strains (MICs, >1 μg/ml) were identical to the pandemic clone 23F. Children were culture positive between one and eight times at 13 scheduled visits. Although the infants were frequently recolonized with different strains, colonization with one particular strain often persisted for several months. Isolation of a previously detected capsular type was common, and the chromosomal homogeneity tended to be high when it occurred. Horizontal transfer of capsular genes between strains of different RFEL types was demonstrated in one child. The ecological advantage of transfer of capsular genes is unclear unless survival of the organism on a mucosal surface may be linked to immunoprotective pressure against particular capsular types.
Relevant Criteria for Detecting Microsporidia in Stool Specimens
Authors: Chioralia Gabriela , Trammer Thomas , Kampen Helge , Seitz Hanns M. 
Published: December 2019

ABSTRACT

By using different staining techniques, 479 stool specimens from 212 diarrheic patients with AIDS were examined for microsporidian spores. Calcofluor fluorescence staining of 119 specimens revealed fluorescent ovoid structures of microsporidian size. Staining of these samples according to the method of Weber et al. (R. Weber, R. T. Bryan, R. L. Owen, C. M. Wilcox, L. Gorelkin, and G. S. Visvesvara, N. Engl. J. Med. 326:161–166, 1992) with trichrome produced six specimens with pinkish spores containing the characteristic microsporidian belt-like structure. The 6 specimens were processed for transmission electron microscopy, as were another 21 specimens which did not present the belt-like structure after trichrome staining but which looked highly suspicious after fluorescence staining. In these 21 samples, only fungal spores and, particularly, bacterial
Clostridium
spores were demonstrated, whereas in the 6 samples diagnosed positive after trichrome staining, the existence of microsporidia could be verified by electron microscopy. Based on our observations, we propose that the belt-like structure seen with the Weber stains in microsporidian spores corresponds to structures existing in priming-stage spores. The results suggest that routine microscopical fecal diagnosis for microsporidian infection should include a screening by fluorescence staining and, subsequently, a confirmatory viewing of fluorescence-positive samples after trichrome staining.
Genotypic Characterization of
Salmonella enteritidis
Phage Types by Plasmid Analysis, Ribotyping, and Pulsed-Field Gel Electrophoresis
Authors: Ridley A. M. , Threlfall E. J. , Rowe B. 
Published: December 2019

ABSTRACT

Pulsed-field gel electrophoresis (PFGE) was used to resolve
Xba
I and
Spe
I macrorestriction fragments from 60 defined phage type (PT) reference strains of
Salmonella enteritidis
. The level of discrimination was compared to that afforded by plasmid profile analysis and ribotyping. Twenty-eight distinct
Xba
I pulsed-field profiles (PFPs) were observed, although a single type, PFP X1, predominated. Absence of the 57-kb
spv
-associated fragment was observed for three PT reference strains, and the profile was designated PFP X1A. The
Xba
I macrorestriction profiles of a further four PT reference strains were altered by the presence of plasmid-associated bands. Twenty-six
Spe
I-generated PFPs (plus one subtype) were observed for the same strains. No
Spe
I fragment corresponding to the 38-MDa serovar-specific plasmid was detected. The distribution of
Xba
I and
Spe
I profiles did not always correspond, producing a total of 32 combined PFPs for the 60 PT reference strains. This compared with a total of 18 different plasmid profiles and three
Pvu
II ribotypes generated by the same strains. The results of this study indicate that PFGE may offer an improved level of discrimination over other genotypic typing methods for the epidemiological typing of
S. enteritidis
.
Screening of Stool Samples for Identification of Vancomycin-Resistant
Enterococcus
Isolates Should Include the Methyl-α-
d
Glucopyranoside Test To Differentiate Nonmotile
Enterococcus gallinarum
from
E. faecium
Authors: Turenne Christine Y. , Hoban Daryl J. , Karlowsky James A. , Zhanel George G. , Kabani Amin M. 
Published: December 2019

ABSTRACT

The methyl-α-
d
-glucopyranoside (MDG) test has been shown to be superior to motility testing in differentiating
Enterococcus faecium
from
E. gallinarum
. In the present study, 33 vancomycin-resistant enterococcus (VRE) isolates collected as part of a stool surveillance study were compared by using motility and MDG. Motility testing identified all 33 isolates as
E. faecium
, whereas MDG identified 11 of the 33 isolates as nonmotile
E. gallinarum
. The MDG results were confirmed by sequencing the 16S rDNA V6-to-V8 region. We conclude that the MDG test is a necessary component of routine VRE screening.
Rapid Screening for Penicillin Susceptibility of Systemic Pneumococcal Isolates by Restriction Enzyme Profiling of the
pbp2B
Gene
Authors: Beall Bernard , Facklam Richard R. , Jackson Delois M. , Starling Holly H. 
Published: December 2019

ABSTRACT

Restriction digest profiling of pneumococcal
pbp2b
-specific amplicons was effective for screening penicillin resistance. The
pbp2b
amplicon of all pneumococcal isolates for which the MICs of penicillin were ≤0.03 μg/ml had one of two different susceptible restriction profiles, and all 33 isolates for which MICs were 0.5 μg/ml or greater had one of seven distinct resistant profiles. Low-concentration penicillin resistance (MICs = 0.06 μg/ml to 0.25 μg/ml) was associated with sensitive
Hae
III profiles in some isolates; however,
Rsa
I profiling and
pbp2b
sequence analysis of such isolates revealed that some isolates contained low-level resistant
pbp2b
alleles, while others had susceptible
pbp2b
alleles. This data indicates that low-level penicillin resistance is sometimes conferred by determinants other than
pbp2b
.
Frequency of
vacA
Genotypes and Cytotoxin Activity in
Helicobacter pylori
Associated with Low-Grade Gastric Mucosa-Associated Lymphoid Tissue Lymphoma
Authors: Miehlke Stephan , Meining Alexander , Morgner Andrea , Bayerdörffer Ekkehard , Lehn Norbert , Stolte Manfred , Graham David Y. , Go Mae F. 
Published: December 2019

ABSTRACT

The
vacA
genotypes s1,m1 and s1,m2 were detected in 44 and 30% of
Helicobacter pylori
isolates, respectively, from patients with gastric mucosa-associated lymphoid tissue lymphoma, compared to 26 and 56% of isolates, respectively, from individuals with gastritis. The
vacA
s1 genotype was significantly associated with, but not predictive of, the presence of vacuolating cytotoxin activity.
Breast Abscess Associated with
Helcococcus kunzii
Authors: Chagla Abdul H. , Borczyk Alexander A. , Facklam Richard R. , Lovgren Marguerite 
Published: December 2019

ABSTRACT

Helcococcus kunzii
, a nonvirulent member of the human skin flora, has recently been implicated in causing infections in immunosuppressed patients. We report a case of breast abscess associated with
H. kunzii
in an immunocompetant patient and discuss the criteria used in its identification and our observations of susceptibility testing for this species.
Study of the Relatedness of Isolates of
Shigella flexneri
and
Shigella sonnei
Obtained in 1986 and 1987 and in 1994 and 1995 from Hong Kong
Authors: Houang E. T. S. , Chu Y.-W. , Ng T.-K. , Cheng A. F. B. 
Published: December 2019

ABSTRACT

We used pulsed-field gel electrophoresis (PFGE) to study the genetic relatedness of 235 isolates of
Shigella flexneri
and
Shigella sonnei
collected in Hong Kong (97 isolates from 1986 and 1987 and 138 isolates from 1994 and 1995). Altogether, 13 gels were run with bacteriophage lambda ladder DNA (Pharmacia) as an external reference in every sixth lane, standardized reagents and methods, and isolates randomized for species and years. For quantitative illustration of the relationships within a large body of isolates, computer-generated dendrograms were used to determine the number of isolates in pulsotypes at Dice coefficients of similarity of 75% (PT
75
) and 50% (PT
50
). For
S. flexneri
, there was a significant difference in the distribution of isolates collected during the two periods in both PT
75
and PT
50
, with 68% of isolates collected in 1994 and 1995 sharing a coefficient of similarity of ≥68%. For
S. sonnei
, a significant difference was observed in PT
50
only. We also used Upholt’s formula for an approximation of the fraction of nucleotide difference between isolates and Molecular Evolutionary Genetics Analysis to determine relative genetic distances. For both species, the relative genetic distances between isolates of the earlier collection period were significantly greater (
P
< 0.0001), i.e., they were further apart and therefore more diverse than those of the later period. We conclude that it is possible for a typical clinical laboratory to analyze a large amount of PFGE information on
Shigella
isolates obtained under controlled conditions. Such data analysis should enhance surveillance capabilities and give indications of further work to be done on various aspects of bacterial pathogenicity of the species.