bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clonal and Spontaneous Origins of Fluconazole Resistance in
Candida albicans
Authors: Xu Jianping , Ramos Adela R. , Vilgalys Rytas , Mitchell Thomas G. 
Published: December 2019

ABSTRACT

The genotypes and susceptibilities to fluconazole of 78 strains of the human pathogenic yeast
Candida albicans
were compared. The strains comprised two sets of samples from Durham, N.C.: one from patients infected with the human immunodeficiency virus (HIV) and the other from healthy volunteers. For each strain, the MIC of fluconazole was determined by the standard National Committee for Clinical Laboratory Standards protocol. Genotypes were determined by PCR fingerprinting with five separate primers. The analysis revealed little evidence for genotypic clustering according to HIV status or body site. However, a small group of fluconazole-resistant strains isolated from patients infected with HIV formed a distinct cluster. In addition, two fluconazole-resistant strains were isolated from individuals who never took fluconazole, one from a patient infected with HIV and the other from a healthy person. The results suggest both clonal and spontaneous origins of fluconazole resistance in
C. albicans
.
Two Liquid Medium Systems, Mycobacteria Growth Indicator Tube and MB Redox Tube, for
Mycobacterium tuberculosis
Isolation from Sputum Specimens
Authors: Heifets L. , Linder T. , Sanchez T. , Spencer D. , Brennan J. 
Published: December 2019

ABSTRACT

Two manual liquid medium systems, the Mycobacteria Growth Indicator Tube (MGIT) and MB Redox tube systems, were evaluated in comparison to the radiometric BACTEC-460 semiautomated system for recovery of
Mycobacterium tuberculosis
from sputum specimens. The highest level of recovery, from a total of 77 culture-positive specimens, occurred with the BACTEC-460 system (92.2%), followed by the MB Redox tube (80.5%) and the MGIT (63.6%) systems. The shortest time to detection was observed also among the cultures in BACTEC-460: a mean of 12 days to a growth index (GI) of 10 and 15 days to a GI of 500. The mean times for the other systems were 16 days for the MB Redox tube system and 17.4 days for the MGIT system. The proportion of cultures grown after more than 3 weeks of incubation was only 2.8 or 8.4% in BACTEC-460 (for a GI of 10 or 500) but 17.7% in MB Redox and 22.5% in MGIT. Despite these differences in comparison to the BACTEC-460 system and some differences between the MGIT and MB Redox tube systems, either of the two manual liquid medium systems presents a reasonable alternative to the BACTEC-460 system, especially for laboratories with a limited workload, and a valuable element in the laboratory protocol, in conjunction with solid media, for obtaining rapid detection of growth from about 80% of culture-positive specimens and for better overall recovery of
M. tuberculosis
.
Growth of
Cowdria ruminantium
, the Causative Agent of Heartwater, in a Tick Cell Line
Authors: Bell-Sakyi Lesley , Paxton Edith A. , Munderloh Ulrike G. , Sumption Keith J. 
Published: December 2019

ABSTRACT

The tick-borne rickettsia
Cowdria ruminantium
has been propagated continuously for over 500 days in the
Ixodes scapularis
tick cell line IDE8 by using the Gardel isolate from bovine endothelial cells as an inoculum. Infection of the tick cells was confirmed by PCR, karyotyping, electron microscopy, and reinfection of bovine cells.
Epidemiological Analysis of Non-M-Typeable Group A Streptococcus Isolates from a Thai Population in Northern Thailand
Authors: Pruksakorn Sumalee , Sittisombut Nopporn , Phornphutkul Charlie , Pruksachatkunakorn Chulabhorn , Good Michael F. , Brandt Evelyn 
Published: December 2019

ABSTRACTInfection with group A streptococci (GAS) can lead to the development of severe postinfectious sequelae such as rheumatic fever (RF). In Thailand, RF and rheumatic heart disease (RHD) remain important health problems. More than 80% of GAS circulating in this population are non-M antigen typeable by conventional M serotyping methods. In this study, we determine the M protein sequence types of GAS isolates found in northern Thailand. Theemmgenes from 53 GAS isolates, collected between 1985 and 1995 from individuals with pharyngitis, impetigo, acute RF (ARF), RHD, or meningitis as well as from individuals without infections, were amplified by PCR and sequenced. Thirteen new sequence types that did not show homology to previously published sequences were characterized. Six of these sequence types could be isolated from both skin and throat sites of impetigo and pharyngitis/ARF patients, respectively. In many cases we could not specifically differentiate skin strains or throat strains that could be associated with ARF or acute glomerulonephritis. Antigenic variations in theemmgene of the isolates investigated, compared to published M protein sequences, were predominantly due to point mutations, small deletions, and insertions in the hypervariable region. One group of isolates with homology to M44 exhibited corrected frameshift mutations. A new M type isolated from an RHD patient exhibited nucleotide sequence corresponding to the N terminus of M58 and the C terminus of M25, suggesting that recombination between the two types may have occurred. This study provided epidemiological data relating to GAS endemic to northern Thailand which could be useful for identification of vaccine candidates in a specific region of endemicity.
Helminthic Transmission and Isolation ofEhrlichia risticii, the Causative Agent of Potomac Horse Fever, by Using Trematode Stages from Freshwater Stream Snails
Authors: Pusterla Nicola , Madigan John E. , Chae Joon-Seok , DeRock Elfriede , Johnson Eileen , Pusterla Jeannine Berger 
Published: December 2019

ABSTRACTWe report successful helminthic transmission ofEhrlichia risticii, the causative agent of Potomac horse fever, using trematode stages collected fromJuga yrekaensissnails. The ehrlichial agent was isolated from the blood of experimentally infected horses by culture in murine monocytic cells and identified asE. risticiiultrastructurally and by characterization of three different genes.
Resolution of the Pathways of Poliovirus Type 1 Transmission during an Outbreak
Authors: Shulman Lester M. , Handsher Rachel , Yang Chen-Fu , Yang Su-Ju , Manor Joseph , Vonsover Ami , Grossman Zehava , Pallansch Mark , Mendelson Ella , Kew Olen M. 
Published: December 2019

ABSTRACT
An outbreak of poliomyelitis with 20 cases occurred in Israel, Gaza, and the West Bank from October 1987 to October 1988. The wild type 1 poliovirus associated with the outbreak was most closely related to viruses found in the Nile Delta. The epidemiologic links among patients involved in the outbreak and patients with community-acquired infections during the outbreak were inferred from the evolutionary relationships among isolates of the outbreak virus. Complete VP1 sequences (906 nucleotides) were determined for 12 clinical and 4 sewage isolates. A total of 58 nucleotide differences were found among the 16 isolates; 74% of all substitutions were synonymous third-position transitions. An evolutionary tree, representing both the pathways of VP1 sequence evolution and the inferred chains of virus transmission during the outbreak, was constructed under the assumption that each substitution had occurred only once. The combined epidemiologic and molecular data suggest that a single founder strain was introduced into Israel from the vicinity of Gaza in the fall of 1987. Poliovirus circulation was apparently localized to southern communities during the winter and spread north by the following summer into the Hadera subdistrict of Israel, where it radiated via multiple chains of transmission into other communities in northern Israel and the West Bank. The close sequence matches (>99%) between clinical and sewage isolates from the same communities confirm the utility of environmental sampling as a tool for monitoring wild poliovirus circulation.
Molecular Analysis of
CAP59
Gene Sequences from Five Serotypes of
Cryptococcus neoformans
Authors: Nakamura Yuka , Kano Rui , Watanabe Shinichi , Hasegawa Atsuhiko 
Published: December 2019

ABSTRACT

The nucleotide sequences of
CAP59
genes from five serotypes of
Cryptococcus neoformans
were analyzed for their phylogenetic relationships. Approximately 600-bp genomic DNA fragments of the
CAP59
gene were amplified from each isolate by PCR and sequenced. The
CAP59
nucleotide sequences of
C. neoformans
showed more than 90% similarity among the five serotypes. By phylogenetic analysis, their sequences were divided into three clusters: serotypes A and AD, serotypes B and C, and serotype D. In addition, the results of reduced amino acid sequences were similar to the nucleotide sequence data. These data revealed that serotype AD was genetically close to serotype A rather than serotype D, although it had been considered to be a mixed type of serotype A and D by serological analysis. Furthermore, the nucleotide sequences of the serotype B and C isolates of
C. neoformans
were very similar to each other. These results indicated that serotype B and C isolates belonging to
C. neoformans
var.
gattii
were genetically homogeneous and closely related. The molecular analysis of the
CAP59
gene will provide useful information for the differentiation of serotypes of
C. neoformans
and for an understanding of their phylogenetic relationships.
Newly Recognized Herpesvirus Causing Malignant Catarrhal Fever in White-Tailed Deer (
Odocoileus virginianus
)
Authors: Li Hong , Dyer Neil , Keller Janice , Crawford Timothy B. 
Published: December 2019

ABSTRACT

Malignant catarrhal fever (MCF) was diagnosed by clinical signs and lesions in five out of six white-tailed deer (
Odocoileus virginianus
) in a North American zoo. The clinical signs and histopathological lesions in these deer were typical of MCF. Antibody to an epitope conserved among the MCF viruses was detected in the sera collected from the deer. PCR failed to amplify viral sequences from DNA extracted from peripheral blood leukocytes (PBL) and/or spleens of the deer with primers specific for ovine herpesvirus 2 (OHV-2) or specific for alcelaphine herpesvirus 1 (AHV-1). By using degenerate primers targeting a conserved region of a herpesviral DNA polymerase gene, a DNA fragment was amplified from the PBL or spleens of all six deer and sequenced. Alignment of the sequences demonstrated that the virus in the deer belongs to the
Gammaherpesvirinae
subfamily, exhibiting 82% identity to OHV-2, 71% to AHV-1, and 60% to a newly identified bovine lymphotropic herpesvirus. This virus, which causes classical MCF in white-tailed deer, is a newly recognized agent belonging to the MCF group of gammaherpesviruses. It is the third reported pathogenic MCF virus, genetically distinct but closely related to OHV-2 and AHV-1. The reservoir for the virus has not been identified.
Genomic Analysis of
Blastocystis hominis
Strains Isolated from Two Long-Term Health Care Facilities
Authors: Yoshikawa Hisao , Abe Niichiro , Iwasawa Mizue , Kitano Syoko , Nagano Isao , Wu Zhiliang , Takahashi Yuzo 
Published: December 2019

ABSTRACT

The genotype
Blastocystis hominis
is highly polymorphic. Therefore, a genetic marker would be a powerful tool for the identification or classification of
B. hominis
subtypes and could be used as a means to resolve the transmission route or origin of the parasite. To this end, 32
B. hominis
isolates were collected from patients and/or staff members of two long-term health care facilities (facilities A and B), and these organisms were subjected to genotype analysis based on diagnostic PCR primers and restriction fragment length polymorphism (RFLP) of small subunit rRNA gene (rDNA). Based on PCR amplification using diagnostic primers which were developed from randomly amplified polymorphic DNA analysis of known strains of
B. hominis
, the 32 isolates of
B. hominis
were classified into three different subtypes. Thirty isolates, including twenty-four that were isolated from patients and a staff member, from facility A and all isolates isolated from six patients from facility B showed the same genotype. Two of six patients of facility B had been transferred from facility A, and these two patients also had the same-genotype
B. hominis
that corresponded to 24 isolates from facility A. This genotype strain may have been transmitted by these two patients from facility A to facility B, suggesting human-to-human transmission. In contrast, 2 of 26 isolates from facility A showed distinct genotypes, suggesting that the colonization by these two isolates is attributable to another infectious route. These different subtypes were subjected to RFLP analysis, and the RFLP profiles were correlated with the results obtained by diagnostic PCR primers. This study presents the first molecular evidence of possible human-to-human
B. hominis
infection between and/or among two small communities.
New
Ehrlichia
Species Closely Related to
Ehrlichia chaffeensis
Isolated from
Ixodes ovatus
Ticks in Japan
Authors: Shibata Shin-ichiro , Kawahara Makoto , Rikihisa Yasuko , Fujita Hiromi , Watanabe Yuriko , Suto Chiharu , Ito Tadahiko 
Published: December 2019

ABSTRACT

Seven
Ehrlichia
strains (six HF strains and one Anan strain) that were obtained from laboratory mice by intraperitoneally inoculating homogenates of adult
Ixodes ovatus
collected in Japan were characterized. 16S rRNA sequences of all six HF strains were identical, and the sequences were 99.7, 98.2, and 97.7% identical to those of Anan strain,
Ehrlichia chaffeensis
(human monocytic ehrlichiosis agent), and
E. muris
, respectively. Partial GroEL amino acid sequencing also revealed that the six HF strains had identical sequences, which were 99.0, 98.5, and 97.3% identical to those of
E. chaffeensis
, the Anan strain, and
E. canis
, respectively. All HF strains were lethal to mice at higher dosages and intraperitoneal inoculation, whereas the Anan or
E. muris
strain induced only mild clinical signs. Light and electron microscopy of moribund mice inoculated with one of the HF strains revealed severe liver necrosis and the presence of numerous ehrlichial inclusions (morulae) in various organs. The study revealed that members of
E. canis
genogroup are naturally present in
Ixodes
ticks. HF strains that can cause severe illness in immunocompetent laboratory mice would be valuable in studying the pathogenesis and the roles of both cellular and humoral immune responses in ehrlichiosis caused by
E. canis
genogroup.
Heterogeneous Antimicrobial Resistance Patterns in Polyclonal Populations of Coagulase-Negative Staphylococci Isolated from Catheters
Authors: García de Viedma Darío , Martín Rabadán Pablo , Díaz Marisol , Cercenado Emilia , Bouza Emilio 
Published: December 2019

ABSTRACT
Most cases of nosocomial bacteremia are catheter related, and coagulase-negative staphylococci (CoNS) are the microorganisms most frequently associated with these infections. Subtle morphological differences are frequently found among CoNS colonies cultured from infected catheters. The aim of this study was to analyze the significance of the morphological heterogeneity observed in these CoNS populations. With this purpose in mind, the clonal composition of the CoNS populations obtained from a selection of nine catheters was analyzed by two different molecular techniques, arbitrarily primed-PCR and DNA macrorestriction analysis by pulsed-field gel electrophoresis. Twenty CoNS morphotypes were included for analysis, and four single colonies representative of each morphotype were selected. Morphological differences between colonies were found to correlate in all cases with differences at the molecular level. Unique fingerprints were also obtained for some isolates which were indistinguishable from other representatives of the same morphotypes. Differences in the molecular patterns among the isolates were associated in most of the cases with differences in the antimicrobial susceptibility patterns. The frequent isolation of polyclonal CoNS populations from catheters, with heterogeneous antimicrobial susceptibility patterns, has relevant epidemiologic and therapeutic implications in the context of catheter-related infections.
Rapid Enzyme Immunoassay for Determination of Toxigenicity among Clinical Isolates of Corynebacteria
Authors: Engler Kathryn H. , Efstratiou Androulla 
Published: December 2019

ABSTRACT

A rapid enzyme immunoassay (EIA) was developed for the phenotypic detection of diphtheria toxin among clinical isolates of corynebacteria. The assay uses equine polyclonal antitoxin as the capture antibody and an alkaline phosphatase-labeled monoclonal antibody, specific for fragment A of the toxin molecule, as the detecting antibody. The assay is rapid, sensitive, and specific: a final result is available within 3 h of colony selection, and the limits of detection are 0.1 ng of pure diphtheria toxin/ml. Toxigenicity could be detected with isolates grown on a diverse range of culture media, including selective agars. Toxin detection using the EIA was compared to that with the Elek test and PCR detection of fragment A of the diphtheria toxin (
tox
) gene, using 245 isolates of corynebacteria. The results for the EIA were in complete concordance with those of the Elek test: 87 toxigenic and 158 nontoxigenic isolates. Ten of the phenotypically nontoxigenic strains were found to contain fragment A of the
tox
gene but did not express the toxin protein. These isolates were found to be nontoxigenic in the Vero cell tissue culture cytotoxicity assay and were therefore nontoxigenic for diagnostic purposes. The EIA is a simple rapid phenotypic test which provides a definitive result on toxigenicity within one working day.
Identification of
Aspergillus
Species Using Internal Transcribed Spacer Regions 1 and 2
Authors: Henry Travis , Iwen Peter C. , Hinrichs Steven H. 
Published: December 2019

ABSTRACT

Aspergillus
species are the most frequent cause of invasive mold infections in immunocompromised patients. Although over 180 species are found within the genus, 3 species,
Aspergillus flavus
,
A. fumigatus
, and
A. terreus
, account for most cases of invasive aspergillosis (IA), with
A. nidulans
,
A. niger
, and
A. ustus
being rare causes of IA. The ability to distinguish between the various clinically relevant
Aspergillus
species may have diagnostic value, as certain species are associated with higher mortality and increased virulence and vary in their resistance to antifungal therapy. A method to identify
Aspergillus
at the species level and differentiate it from other true pathogenic and opportunistic molds was developed using the 18S and 28S rRNA genes for primer binding sites. The contiguous internal transcribed spacer (ITS) region, ITS 1–5.8S–ITS 2, from referenced strains and clinical isolates of aspergilli and other fungi were amplified, sequenced, and compared with non-reference strain sequences in GenBank. ITS amplicons from
Aspergillus
species ranged in size from 565 to 613 bp. Comparison of reference strains and GenBank sequences demonstrated that both ITS 1 and ITS 2 regions were needed for accurate identification of
Aspergillus
at the species level. Intraspecies variation among clinical isolates and reference strains was minimal. Sixteen other pathogenic molds demonstrated less than 89% similarity with
Aspergillus
ITS 1 and 2 sequences. A blind study of 11 clinical isolates was performed, and each was correctly identified. Clinical application of this approach may allow for earlier diagnosis and selection of effective antifungal agents for patients with IA.
Comparison of Enhanced
Mycobacterium tuberculosis
Amplified Direct Test with COBAS AMPLICOR
Mycobacterium tuberculosis
Assay for Direct Detection of
Mycobacterium tuberculosis
Complex in Respiratory and Extrapulmonary Specimens
Authors: Scarparo Claudio , Piccoli Paola , Rigon Alessandra , Ruggiero Giuliana , Scagnelli Mariuccia , Piersimoni Claudio 
Published: December 2019

ABSTRACT

The new Roche COBAS AMPLICOR
Mycobacterium tuberculosis
Assay was compared to the Gen-Probe enhanced
Mycobacterium tuberculosis
Amplified Direct Test (AMTDII). A total of 486 specimens (296 respiratory and 190 extrapulmonary) collected from 323 patients were tested in parallel with both assays. Results were compared with those of acid-fast staining and culture, setting the combination of culture and clinical diagnosis as the “gold standard.” After resolution of discrepant results, the sensitivity, specificity, and positive and negative predictive values for AMTDII were 85.7, 100, 100, and 90.4% for respiratory specimens and 82.9, 100, 100, and 95.5% for extrapulmonary specimens, respectively. The corresponding values for AMPLICOR were 94.2, 100, 100, and 96.6% for respiratory specimens and 85, 100, 100, and 96.1% for extrapulmonary specimens, respectively. No significant differences were observed between the results of both assays or, within each one, between respiratory and extrapulmonary specimens. The difference between AMTDII and AMPLICOR sensitivities was related to the presence of inhibitory samples, which the former assay, lacking an internal amplification control (IAC), could not detect. The overall inhibition rate for the AMPLICOR assay was 3.9% (19 specimens). It is concluded that, although both amplification assays proved to be rapid and specific for the detection of
M. tuberculosis
complex in clinical samples, AMPLICOR, by a completely automated amplification and detection procedure, was shown to be particularly feasible for a routine laboratory setting. Finally, AMTDII is potentially an excellent diagnostic technique for both respiratory and extrapulmonary specimens, provided that an IAC is included with the assay.
Genetic Structure of Population of
Bacillus cereus
and
B. thuringiensis
Isolates Associated with Periodontitis and Other Human Infections
Authors: Helgason Erlendur , Caugant Dominique A. , Olsen Ingar , Kolstø Anne-Brit 
Published: December 2019

ABSTRACT

The genetic diversity and relationships among 35
Bacillus cereus
and
Bacillus thuringiensis
isolates recovered from marginal and apical periodontitis in humans and from various other human infections were investigated using multilocus enzyme electrophoresis. The strains were isolated in Norway, except for three strains isolated from periodontitis patients in Brazil. The genetic diversity of these strains was compared to that of 30 isolates from dairies in Norway and Finland. Allelic variation in 13 structural gene loci encoding metabolic enzymes was analyzed. Twelve of the 13 loci were polymorphic, and 48 unique electrophoretic types (ETs) were identified, representing multilocus genotypes. The mean genetic diversity among the 48 genotypes was 0.508. The genetic diversity of each source group of isolates varied from 0.241 (periodontal infection) to 0.534 (dairy). Cluster analysis revealed two major groups separated at a genetic distance of greater than 0.6. One cluster, ETs 1 to 13, included solely isolates from dairies, while the other cluster, ETs 14 to 49, included all of the human isolates as well as isolates from dairies in Norway and Finland. The isolates were serotyped using antiflagellar antiserum. A total of 14 distinct serotypes were observed. However, little association between serotyping and genotyping was seen. Most of the strains were also analyzed with pulsed-field gel electrophoresis, showing the presence of extrachromosomal DNA in the size range of 15 to 600 kb. Our results indicate a high degree of heterogeneity among dairy strains. In contrast, strains isolated from humans had their genotypes in one cluster. Most strains from patients with periodontitis belonged to a single lineage, suggesting that specific clones of
B. cereus
and
B. thuringiensis
are associated with oral infections.