bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of Different Test Conditions on MICs of Food Animal Growth-Promoting Antibacterial Agents for Enterococci
Authors: Butaye Patrick , Devriese Luc A. , Haesebrouck Freddy 
Published: December 2019

ABSTRACT

The influence of the addition of sheep blood to Mueller-Hinton II agar and the effects of aerobic incubation with or without CO
2
and of anaerobic incubation were tested with bacitracin, tylosin, avoparcin, virginiamycin, avilamycin, narasin, and flavomycin on enterococci. The antibacterial activity of bambermycin (Flavomycin) was strongly inhibited by the addition of blood, except with the species
Enterococcus faecium
,
Enterococcus mundtii
,
Enterococcus hirae
,
Enterococcus casseliflavus
, and
Enterococcus gallinarum
, which were not susceptible to this antibiotic on blood-free medium. With all other antimicrobials except avoparcin and tylosin, the presence of blood resulted in MIC increases of 1 to 3 log
2
differences. Incubation in aerobic or anaerobic atmospheres enriched with CO
2
lowered the susceptibility of enterococci to tylosin and increased their susceptibility to avilamycin, narasin, and avoparcin. This effect was most pronounced in tests on blood-free media. Results of susceptibility tests incubated under anaerobiosis and in a CO
2
-enriched atmosphere did not differ. For all enterococcal species, the preferred conditions for testing the susceptibility are Mueller-Hinton II medium supplemented with blood and incubation in a CO
2
-enriched atmosphere. However, when only
E. faecium
and
Enterococcus faecalis
are being tested, Mueller-Hinton II medium without blood incubated aerobically gives satisfactory results.
Molecular Characterization of Vancomycin-Resistant Enterococci from Hospitalized Patients and Poultry Products in The Netherlands
Authors: van den Braak Nicole , van Belkum Alex , van Keulen Marrit , Vliegenthart John , Verbrugh Henri A. , Endtz Hubert P. 
Published: December 2019

ABSTRACT

Vancomycin-resistant enterococci (VRE) pose an emerging health risk, but little is known about the precise epidemiology of the genes coding for vancomycin resistance. To determine whether the bacterial flora of consumer poultry serves as a gene reservoir, the level of contamination of poultry products with VRE was determined. VRE were genotyped by pulsed-field gel electrophoresis (PFGE), and transposon structure mapping was done by PCR. The
vanX-vanY
intergenic regions of several strains were further analyzed by sequencing. A total of 242 of 305 (79%) poultry products were found to be contaminated with VRE. Of these VRE, 142 (59%) were high-level-vancomycin-resistant
Enterococcus faecium
strains (VREF). PFGE revealed extensive VREF heterogeneity. Two genotypes were found nationwide on multiple occasions: type A (22 of 142 VREF [15%]) and type B (14 of 142 VREF [10%]). No PFGE-deduced genetic overlap was found when VREF from humans were compared with VREF from poultry. Two
vanA
transposon types were identified among poultry strains. In 59 of 142 (42%) of the poultry VREF, the size of the intergenic region between
vanX
and
vanY
was ∼1,300 bp. This transposon type was not found in human VREF. In contrast, all human strains and 83 of 142 (58%) of the poultry VREF contained an intergenic region 543 bp in size. Sequencing of this 543-bp intergenic
vanX-vanY
region demonstrated full sequence conservation. Though preliminary, these data suggest that dissemination of the resistance genes carried on transposable elements may be of greater importance than clonal dissemination of resistant strains. This observation is important for developing strategies to control the spread of glycopeptide resistance.
Survey of Incidence of
Clostridium difficile
Infection in Canadian Hospitals and Diagnostic Approaches
Authors: Alfa Michelle J. , Du Tim , Beda Gabi 
Published: December 2019

ABSTRACT

A questionnaire relating to
Clostridium difficile
disease incidence and diagnostic practices was sent to 380 Canadian hospitals (all with >50 beds). The national questionnaire response rate was 63%. In-house testing was performed in 17.6, 61.5, and 74.2% of the hospitals with <300, 300 to 500, and >500 beds, respectively. The average test positivity rates were 17.2, 15.3, and 13.2% for hospitals with <300, 300 to 500, and >500 beds, respectively. The average disease incidences were 23.5, 30.8, and 40.3 cases per 100,000 patient days in the hospitals with <300, 300 to 500, and >500 beds, respectively. In the 81 hospitals where in-house testing was performed, cytotoxin testing utilizing tissue culture was most common (44.4%), followed by enzyme-linked immunosorbent assay (38.3%), culture for toxigenic
C. difficile
(32.1%), and latex agglutination (13.6%). The clinical criteria for
C. difficile
testing were variable, with 85% of hospitals indicating that a test was done automatically if ordered by a doctor. Our results show that
C. difficile
-associated diarrhea is a major problem in hospitals with ≥200 beds. Despite a lower disease incidence in smaller hospitals, there was a higher diagnostic test positivity rate. This may reflect the preference of smaller hospitals for culture and latex agglutination tests.
Coryneform Bacteria in Throat Cultures of Healthy Individuals
Authors: von Graevenitz Alexander , Pünter-Streit Verena , Riegel Philippe , Funke Guido 
Published: December 2019

ABSTRACT

Throat swabs from 113 healthy individuals from Hamburg, Germany, and Zurich, Switzerland, were investigated for coryneform bacteria with nonselective and selective media. Ninety specimens contained 123 strains. Surprisingly, 76% of them were strains of
Corynebacterium durum
(47%) and
Rothia dentocariosa
(29%). Only two were strains of
Corynebacterium pseudodiphtheriticum
, and none were strains of
C. striatum
,
C. amycolatum
, or
C. diphtheriae.
Clonal Nature of Enterotoxigenic
Escherichia coli
Serotype O6:H16 Revealed by Randomly Amplified Polymorphic DNA Analysis
Authors: Pacheco Ana B. F. , Soares Kelen C. , de Almeida Darcy F. , Viboud Gloria I. , Binsztein Norma , Ferreira Luis C. S. 
Published: December 2019

ABSTRACT

The genetic relatedness among 29 enterotoxigenic
Escherichia coli
strains of serotype O6:H16 was investigated by randomly amplified polymorphic DNA (RAPD) analysis. The strains were isolated in different parts of the world, displayed CS1-CS3 or CS2-CS3 profiles, and expressed heat-labile toxin (LT) and heat-stable toxin; a single strain expressed only LT. Ten RAPD types were distinguished and showed significant similarity, having on average 82% of the amplified bands in common. These results indicated that, irrespective of the different geographical origin or virulence factors, these strains belonged to a widespread clonal group.
Identification of Toxin A-Negative, Toxin B-Positive
Clostridium difficile
by PCR
Authors: Kato Haru , Kato Naoki , Watanabe Kunitomo , Iwai Naoichi , Nakamura Haruhi , Yamamoto Toshinobu , Suzuki Kanzo , Kim Shin-Moo , Chong Yunsop , Wasito Eddy Bagus 
Published: December 2019

ABSTRACT

Toxigenic strains of
Clostridium difficile
have been reported to produce both toxins A and B nearly always, and nontoxigenic strains have been reported to produce neither of these toxins. Recent studies indicate that it is not always true. We established a PCR assay to differentiate toxin A-negative, toxin B-positive (toxin A−, toxin B+) strains from both toxin-positive (toxin A+, toxin B+) strains and both toxin-negative (toxin A−, toxin B−) strains as an alternative to cell culture assay and enzyme-linked immunosorbent assay (ELISA). By using the PCR primer set NK11 and NK9 derived from the repeating sequences of the toxin A gene, a shorter segment (ca. 700 bp) was amplified from toxin A−, toxin B+ strains compared to the size of the segment amplified from toxin A+, toxin B+ strains (ca. 1,200 bp), and no product was amplified from toxin A−, toxin B− strains. We examined a total of 421
C. difficile
isolates by PCR. Of these, 48 strains showed a shorter segment by the PCR, were negative by ELISAs for the detection of toxin A, and were positive by cell culture assay. Although the cytotoxin produced by the toxin A−, toxin B+ strains was neutralized by anti-toxin B serum, the appearance of the cytotoxic effects on Vero cell monolayers was distinguishable from that of toxin A+, toxin B+ strains. By immunoblotting, the 44 toxin A−, toxin B+ strains were typed to serogroup F and the remaining four strains were serogroup X. Pulsed-field gel electrophoresis separated the 48 strains into 19 types. The PCR assay for the detection of the repeating sequences combined with PCR amplification of the nonrepeating sequences of either the toxin A or the toxin B gene is indicated to be useful for differentiating toxin A−, toxin B+ strains from toxin A+, toxin B+ and toxin A−, toxin B− strains and will contribute to elucidation of the precise role of toxin A−, toxin B+ strains in intestinal diseases.
A Novel Toxinotyping Scheme and Correlation of Toxinotypes with Serogroups of
Clostridium difficile
Isolates
Authors: Rupnik Maja , Avesani Véronique , Janc Miha , von Eichel-Streiber Christoph , Delmée Michel 
Published: December 2019

ABSTRACT

Two hundred nineteen
Clostridium difficile
isolates from 22 serogroups were screened for changes in the genes coding for toxin B (
tcdB
) and toxin A (
tcdA
). Parts of the toxin genes were amplified, and the PCR fragments were checked for length polymorphisms and cut with several restriction enzymes to monitor restriction fragment length polymorphisms (RFLPs). For 47 strains (21%), differences in the toxin genes were found compared to the toxin genes of reference strain VPI 10463. Polymorphisms were usually observed in both toxin genes. RFLPs were more commonly found in the
tcdB
gene, in which a single restriction enzyme could give up to five different patterns. Restriction sites seemed to be less heterogeneous in the
tcdA
gene, in which for most enzymes only two different RFLPs were recognized. However, deletions were observed in
tcdA
, and four new types of shortened
tcdA
genes are described. According to the changes in their toxin genes, variant strains could be divided into 10 groups (toxinotypes I to X). A toxinotype was characterized by similar patterns of changes in the toxin genes and in other regions of the pathogenicity locus and also similar pulsed-field gel electrophoresis patterns. Variant toxinotypes were found in 9 of the 22 serogroups studied, and some toxinotypes were clearly associated with specific serogroups. Toxinotype VIII is characteristic for all strains of serogroup F. Other serogroups in which variant toxinotypes were commonly found are A1, A15, E, and X. Testing of variability in
C. difficile
toxin genes not only might be useful as a molecular typing system but also could have implications in diagnostics and pathogenesis.
Evaluation of Mannitol Salt Agar for Detection of Oxacillin Resistance in
Staphylococcus aureus
by Disk Diffusion and Agar Screening
Authors: Kampf Günter , Lecke Christoph , Cimbal Ann-Katrin , Weist Klaus , Rüden Henning 
Published: December 2019

ABSTRACT

Mannitol salt agar was evaluated for detection of oxacillin resistance in 136
Staphylococcus aureus
isolates. All
mecA
-positive isolates (
n
= 54) were correctly categorized as oxacillin resistant by the disk diffusion test (1-μg disk; zone diameter, <16 mm); the specificity was 97.6%. Agar screening (2 μg of oxacillin per ml) revealed a sensitivity of 98.1% and a specificity of 95.1%.
Microsatellite Markers for Typing
Aspergillus fumigatus
Isolates
Authors: Bart-Delabesse Emmanuelle , Humbert Jean-François , Delabesse Éric , Bretagne Stéphane 
Published: December 2019

ABSTRACT

The use of microsatellites as highly polymorphic DNA markers for the typing of isolates of
Aspergillus fumigatus
was investigated. Four CA repeats were selected by screening an
A. fumigatus
DNA library with a (CA)
10
oligonucleotide. Primers flanking these CA repeats were designed to amplify each locus. One primer of each pair was labeled with a fluorophore, and the PCR products were analyzed with an automatic sequencer and the GeneScan software. For each primer set and for a given isolate, one band was detected and was assigned to an allele because
A. fumigatus
is haploid. With 50 clinical isolates, 50 environmental isolates, and 2 reference strains we obtained 12, 11, 10, and 23 different alleles for the four CA microsatellites, respectively (discriminatory power, 0.994). The results were identical by whatever DNA extraction technique was used. Interestingly, no clustering between environmental and clinical isolates was observed, suggesting that every isolate is potentially pathogenic. Microsatellite markers appear suitable for use in large epidemiological studies of invasive aspergillosis.
Rapid Identification of
Candida dubliniensis
by Indirect Immunofluorescence Based on Differential Localization of Antigens on
C. dubliniensis
Blastospores and
Candida albicans
Germ Tubes
Authors: Bikandi Joseba , Millán Rosario San , Moragues María D. , Cebas Gontzal , Clarke Mary , Coleman David C. , Sullivan Derek J. , Quindós Guillermo , Pontón José 
Published: December 2019

ABSTRACT

There is a clear need for the development of a rapid and reliable test for the identification of
Candida dubliniensis
and for the discrimination of this species from
Candida albicans
. In the present study we have investigated the potential use of
C. dubliniensis
-specific antigens as a basis for its identification. We produced an anti-
C. dubliniensis
serum which, after adsorption with
C. albicans
blastospores, was found to differentially label
C. dubliniensis
isolates in an indirect immunofluorescence test. In this test, the antiserum reacted with blastospores and germ tubes of
C. dubliniensis
and with blastospores of
Candida krusei
and
Rhodotorula rubra
but did not react with blastospores of several other
Candida
species including
C. albicans
. The antiserum also reacted with
C. albicans
germ tubes. The anti-
C. dubliniensis
adsorbed serum reacted with specific components of 25, 28, 37, 40, 52, and 62 kDa in the
C. dubliniensis
extract and with a variety of antigens from other yeast species. The antigens from non-
C. dubliniensis
yeasts showing reactivity with the anti-
C. dubliniensis
adsorbed serum are mostly expressed within the cell walls of these yeast species, and this reactivity does not interfere with the use of the anti-
C. dubliniensis
adsorbed serum in an indirect immunofluorescence test for the rapid identification of
C. dubliniensis
.
Comparison of Amplified Ribosomal DNA Restriction Analysis, Random Amplified Polymorphic DNA Analysis, and Amplified Fragment Length Polymorphism Fingerprinting for Identification ofAcinetobacterGenomic Species and Typing ofAcinetobacter baumannii
Authors: Koeleman Johannes G. M. , Stoof Jeroen , Biesmans Dennis J. , Savelkoul Paul H. M. , Vandenbroucke-Grauls Christina M. J. E. 
Published: December 2019

ABSTRACTThirty-one strains ofAcinetobacterspecies, including type strains of the 18 genomic species and 13 clinical isolates, were compared by amplified ribosomal DNA restriction analysis (ARDRA), random amplified polymorphic DNA analysis (RAPD), and amplified fragment length polymorphism (AFLP) fingerprinting. ARDRA, performed with five different enzymes, showed low discriminatory power for differentiatingAcinetobacterat the species and strain level. The standardized commercially available RAPD kit clearly enabled the discrimination of allAcinetobactergenomic species but showed great polymorphism between isolates ofAcinetobacter baumannii. AFLP fingerprinting with radioactively as well as fluorescently labelled primers showed high discriminatory power for the identification of 18Acinetobactergenomic species and typing of 13 clinicalAcinetobacterisolates. Compared to radioactive AFLP, fluorescent AFLP was technically fast and simple to perform, and it permitted analysis with an automated DNA sequencer. Fluorescent AFLP seems particularly well suited for studying the epidemiology of nosocomial infections and outbreaks caused byAcinetobacterspecies.
Development of rRNA-Targeted PCR and In Situ Hybridization with Fluorescently Labelled Oligonucleotides for Detection of
Yersinia
Species
Authors: Trebesius Karlheinz , Harmsen Dag , Rakin Alexander , Schmelz Jochen , Heesemann Jürgen 
Published: December 2019

ABSTRACT

In this report, we present details of two rapid molecular detection techniques based on 16S and 23S rRNA sequence data to identify and differentiate
Yersinia
species from clinical and environmental sources. Near-full-length 16S rRNA gene (rDNA) sequences for three different
Yersinia
species and partial 23S rDNA sequences for three
Y. pestis
and three
Y. pseudotuberculosis
strains were determined. While 16S rDNA sequences of
Y. pestis
and
Y. pseudotuberculosis
were found to be identical, one base difference was identified within a highly variable region of 23S rDNA. The rDNA sequences were used to develop primers and fluorescently tagged oligonucleotide probes suitable for differential detection of
Yersinia
species by PCR and in situ hybridization, respectively. As few as 10
2
Yersinia
cells per ml could be detected by PCR with a seminested approach. Amplification with a subgenus-specific primer pair followed by a second PCR allowed differentiation of
Y. enterocolitica
biogroup 1B from biogroups 2 to 5 or from other pathogenic
Yersinia
species. Moreover, a set of oligonucleotide probes suitable for rapid (3-h) in situ detection and differentiation of the three pathogenic
Yersinia
species (in particular
Y. pestis
and
Y. pseudotuberculosis
) was developed. The applicability of this technique was demonstrated by detection of
Y. pestis
and
Y. pseudotuberculosis
in spiked throat and stool samples, respectively. These probes were also capable of identifying
Y. enterocolitica
within cryosections of experimentally infected mouse tissue by the use of confocal laser scanning microscopy.
Stable Phenotypic Resistance of
Candida
Species to Amphotericin B Conferred by Preexposure to Subinhibitory Levels of Azoles
Authors: Vazquez Jose A. , Arganoza Maria T. , Boikov Dina , Yoon Stephanie , Sobel Jack D. , Akins Robert A. 
Published: December 2019

ABSTRACT

The fungicidal activity of amphotericin B (AmB) was quantitated for several
Candida
species.
Candida albicans
and
C. tropicalis
were consistently susceptible to AmB, with less than 1% survivors after 6 h of exposure to AmB.
C. parapsilosis
and variants of
C. lusitaniae
and
C. guilliermondii
were the most resistant, demonstrating 50 to 90% survivors in this time period and as high as 1% survival after a 24-h exposure time. All
Candida
species were killed (<1% survivors) after 24 h of exposure to AmB. In contrast, overnight exposure to either fluconazole or itraconazole resulted in pronounced increases in resistance to subsequent exposures to AmB. Most dramatically,
C. albicans
was able to grow in AmB cultures after azole preexposure. Several other
Candida
species did not grow in AmB but showed little or no reduction in viability after up to 24 h in AmB. Depending on the growth conditions,
Candida
cells preexposed to azoles may retain AmB resistance for days after the azoles have been removed. If this in vitro antagonism applies to the clinical setting, treatment of patients with certain antifungal combinations may not be beneficial. The ability of some
Candida
isolates to survive transient exposures to AmB was not reflected in the in vitro susceptibility changes as measured by standard MIC assays. This finding should be considered in studies attempting to correlate patient outcome with in vitro susceptibilities of clinical fungal isolates. Patients who fail to respond to AmB may be infected with isolates that are classified as susceptible by standard in vitro assays but that may be resistant to transient antifungal exposures which may be more relevant in the clinical setting.
Low False-Negative Rate of PCR Analysis for Detecting Human Papillomavirus-Related Cervical Lesions
Authors: Zazove Philip , Reed Barbara D. , Gregoire Lucie , Ferenczy Alex , Gorenflo Daniel W. , Lancaster Wayne D. 
Published: December 2019

ABSTRACT

Although PCR analysis is a sensitive test for detection of human papillomavirus (HPV) in the cervix, the proportion of cases of cervical dysplasia missed, or the false-negative rate, has been unknown. We determined the accuracy of PCR analysis for HPV DNA as a predictor of HPV-related cervical lesions in a cross-sectional study of sexually active women, aged 18 to 50 years, from the University of Michigan Family Medicine HPV study. Of 133 eligible participants, 41 underwent colposcopy because of a positive result for HPV of the cervix by the PCR method and 92 underwent screening colposcopy with biopsy prior to knowing the HPV PCR results. Twenty-four of those screened were subsequently found to also be HPV DNA positive. In those found to be HPV positive, histological studies revealed the presence of condyloma or cervical intraepithelial neoplasia in 16 women (24.6%) and changes suggestive of condyloma in 5 (7.6%). No HPV-negative woman had an abnormal biopsy or cytology report (
P
= 0.000001). The false-negative rate (1 − sensitivity) for HPV PCR analysis for detection of the presence of a cervical HPV-related lesion was 0% (95% confidence interval, 0 to 0.047), and the specificity was 60.7%. In summary, PCR analysis for HPV DNA had a very low false-negative rate for predicting HPV-related lesions of the cervix in a community-based population. This supports the validity of using the absence of HPV at the cervix, as determined by PCR testing, as an inclusion criterion for patients in control groups in studies dealing with low-grade cervical lesions.
Detection of Rotavirus Types G8 and G10 among Brazilian Children with Diarrhea
Authors: Santos Norma , Lima Rita C. C. , Pereira Cláudio F. A. , Gouvea Vera 
Published: December 2019

ABSTRACT
Characterization of 49 rotavirus-positive stool specimens from children with diarrhea in the state of Rio de Janeiro, Brazil, in 1996 and 1997 revealed a great diversity of rotavirus G types. Conventional types G1 and G3 accounted for 27 and 12% of the infections, respectively, whereas 60% of the infections were caused by unconventional types G5 (25%), G10 (16%), and G8 (4%) and mixed G types (16%).
Phenotypic and Genotypic Characterization of Virulent
Yersinia enterocolitica
Strains Unable To Ferment Sucrose
Authors: Guiyoule Annie , Guinet Françoise , Martin Liliane , Benoit Catherine , Desplaces Nicole , Carniel Elisabeth 
Published: December 2019

ABSTRACT

Several atypical sucrose-negative
Yersinia
strains, isolated from clinical samples and sometimes associated with symptoms, proved to have full virulence potential in in vitro and in vivo testings. DNA-relatedness studies revealed that they were authentic
Yersinia enterocolitica
strains. Therefore, atypical sucrose-negative
Yersinia
isolates should be analyzed for their virulence potential.