bluuebunny/crossref_metadata_2025_split huggingface dataset:
Malignant Catarrhal Fever-Like Disease in Barbary Red Deer (Cervus elaphus barbarus) Naturally Infected with a Virus Resembling Alcelaphine Herpesvirus 2
Authors: Klieforth Robert , Maalouf Gabriel , Stalis Ilse , Terio Karen , Janssen Donald , Schrenzel Mark 
Published: August 2002

ABSTRACTEight Barbary red deer (Cervus elaphus barbarus) developed clinical signs suggestive of malignant catarrhal fever (MCF) over a 28-day period. These animals were housed outdoors with four other species of ruminants. Affected red deer had lethargy, ocular signs, and nasal discharge and were euthanatized within 48 h. Lesions included ulcers of the muzzle, lips, and oral cavity associated with infiltrates of neutrophils and lymphocytes. Serologically, six of seven red deer tested during the outbreak were positive by competitive enzyme-linked immunosorbent assay for antibodies to a shared MCF virus antigen. PCR using oligonucleotide primers designed for a conserved protein of alcelaphine herpesviruses 1 (AlHV-1) and 2 (AlHV-2) and for conserved regions of a herpesvirus DNA polymerase gene was positive for tissues from all eight clinically affected animals and negative for eight out of eight red deer without clinical signs of MCF. DNA sequencing of PCR amplicons from the diseased red deer indicated that they were infected with a novel herpesvirus closely related to AlHV-2; immunohistochemistry using polyclonal anti-AlHV-2 serum and in situ hybridization demonstrated the presence of virus within salivary glands adjacent to oral lesions of affected animals. A survey of other ruminants near the outbreak subsequently showed that normal Jackson's hartebeest (Alcelaphus buselaphus jacksoni) that were cohoused with the diseased red deer were infected with the same virus and were shedding the virus in nasal excretions. These findings suggest that a herpesvirus closely related to AlHV-2 caused the MCF-like disease epizootic in Barbary red deer and that the virus may have originated from Jackson's hartebeest.
Practical Approach for Typing Strains of
Leishmania infantum
by Microsatellite Analysis
Authors: Bulle Béatrice , Millon Laurence , Bart Jean-Mathieu , Gállego Montserrat , Gambarelli Françoise , Portús Montserrat , Schnur Lee , Jaffe Charles L. , Fernandez-Barredo Salceda , Alunda José María , Piarroux Renaud 
Published: August 2002

ABSTRACT

Currently the universally accepted standard procedure for characterizing and identifying strains of
Leishmania
is isoenzyme analysis. However, in the Mediterranean area, despite their very wide geographical distribution, most
Leishmania infantum
strains belong to zymodeme MON-1. In order to increase our understanding of polymorphism in strains of
L. infantum
, we developed PCR assays amplifying 10 microsatellites and sequenced PCR products. The discriminative power of microsatellite analysis was tested by using a panel of 50
L. infantum
strains collected from patients and dogs from Spain, France, and Israel, including 32 strains belonging to zymodeme MON-1, 8 strains belonging to zymodemes MON-24, MON-29, MON-33, MON-34, or MON-80, and 10 untyped strains. Five of the microsatellites were polymorphic, revealing 22 genotypes, whereas the five remaining microsatellites were not variable. In particular, MON-1 strains could be separated into 13 different closely related genotypes. MON-33 and MON-34 strains also gave two additional genotypes closely related to MON-1, while MON-29, MON-24, and MON 80 strains exhibited more divergent genotypes. Among the foci examined, the Catalonian focus displayed a high polymorphism, probably reflecting isoenzyme polymorphism, while the Israeli focus exhibited a low polymorphism that could be consistent with the recent reemergence and rapid spread of canine leishmaniasis in northern and central Israel. The strains originating from the south of France and the Madrid, Spain, area displayed significant microsatellite polymorphism even though they were monomorphic by isoenzyme analysis. In conclusion, microsatellite polymorphism exhibits a high discriminative power and appears to be suitable for characterization of closely related strains of
L. infantum
in epidemiological studies.
Mycobacterium africanum
Subtype II Is Associated with Two Distinct Genotypes and Is a Major Cause of Human Tuberculosis in Kampala, Uganda
Authors: Niemann S. , Rüsch-Gerdes S. , Joloba M. L. , Whalen C. C. , Guwatudde D. , Ellner J. J. , Eisenach K. , Fumokong N. , Johnson J. L. , Aisu T. , Mugerwa R. D. , Okwera A. , Schwander S. K. 
Published: August 2002

ABSTRACT

The population structure of 234
Mycobacterium tuberculosis
complex strains obtained during 1995 and 1997 from tuberculosis patients living in Kampala, Uganda (East Africa), was analyzed by routine laboratory procedures, spoligotyping, and IS
6110
restriction fragment length polymorphism (RFLP) typing. According to biochemical test results, 157 isolates (67%) were classified as
M. africanum
subtype II (resistant to thiophen-2-carboxylic acid hydrazide), 76 isolates (32%) were classified as
M. tuberculosis
, and 1 isolate was classified as classical
M. bovis
. Spoligotyping did not lead to clear differentiation of
M. tuberculosis
and
M. africanum
, but all
M. africanum
subtype II isolates lacked spacers 33 to 36, differentiating them from
M. africanum
subtype I. Moreover, spoligotyping was not sufficient for differentiation of isolates on the strain level, since 193 (82%) were grouped into clusters. In contrast, in the IS
6110
-based dendrogram,
M. africanum
strains were clustered into two closely related strain families (Uganda I and II) and clearly separated from the
M. tuberculosis
isolates. A further characteristic of both
M. africanum
subtype II families was the absence of spoligotype spacer 40. All strains of family I also lacked spacer 43. The clustering rate obtained by the combination of spoligotyping and RFLP IS
6110
analysis was similar for
M. africanum
and
M. tuberculosis
, as 46% and 49% of the respective isolates were grouped into clusters. The results presented demonstrate that
M. africanum
subtype II isolates from Kampala, Uganda, belong to two closely related genotypes, which may represent unique phylogenetic branches within the
M. tuberculosis
complex. We conclude that
M. africanum
subtype II is the main cause of human tuberculosis in Kampala, Uganda.
Fluorescent Amplified Fragment Length Polymorphism Analysis ofSalmonella entericaSerovar Typhimurium Reveals Phage-Type- Specific Markers and Potential for Microarray Typing
Authors: Hu Honghua , Lan Ruiting , Reeves Peter R. 
Published: August 2002

ABSTRACTFluorescent amplified fragment length polymorphism (AFLP) was applied to 46Salmonella entericaserovar Typhimurium isolates of Australian origin comprising nine phage types, by using the restriction enzymesMseI andEcoRI and all 16 possibleMseI +1-EcoRI +1 primer pair combinations. AFLP in the present study showed a very good discrimination power with a Simpson index of diversity of 0.98, and 35 different AFLP patterns were observed in the 46 isolates. AFLP grouped most serovar Typhimurium isolates by phage type and enabled differentiation of phage types. Furthermore, 84 phage-type-specific polymorphic AFLP fragments, for which presence or absence correlated with phage type (including 25 with one exception to phage type specificity) were observed in the 46 strains studied. Eighteen phage-type-specific AFLP fragments were cloned and sequenced. Fifteen are of known genes or have a homologue in the databases. Three sequences are plasmid related, eight are phage related, and four relate to chromosomal genes. Twelve of the 18 fragments are polymorphic because the DNA is present or absent as indicated by Southern hybridization, and we see good potential to use sequences of these fragments as the basis for multiplex PCR and development of a microarray-based molecular phage-typing method for serovar Typhimurium.
Biological and Biochemical Characterization of Sheep Scrapie in Japan
Authors: Horiuchi Motohiro , Nemoto Takuya , Ishiguro Naotaka , Furuoka Hidefumi , Mohri Shirou , Shinagawa Morikazu 
Published: August 2002

ABSTRACT

Due to the apparent absence of an agent-specific nucleic acid genome, scrapie strains cannot be classified by genome characterization, which is commonly used for the classification of many viruses. However, scrapie strains can be distinguished to some extent by biological properties such as transmissibility to experimental animals and distribution of neuropathological lesions and by biochemical properties such as the molecular mass and relative protease-resistance of the disease-specific isoform of prion protein (PrP
Sc
). In order to preliminarily characterize the scrapie strains that are prevalent in Japan, we analyzed the transmissibility of sheep scrapie isolates to mice and the relative proteinase K (PK) resistance of the corresponding PrP
Sc
. The results indicate that Japanese scrapie strains can be divided into at least three groups based on biological and biochemical properties. The first group includes isolates which cause disease in mice with an incubation period of ∼400 days and possess PrP
Sc
with relatively high PK resistance. Isolates of the second group contain PrP
Sc
that is highly resistant to PK digestion but transmit poorly to mice. The final group consists of isolates that cause disease in mice with an incubation period of less than 300 days and are associated with PrP
Sc
with reduced PK resistance. Sheep scrapie has occurred sporadically in Japan since1982, with only ∼60 officially reported cases so far. However, the diversity of scrapie strains in the field suggested by our data raises the concern that a scrapie strain similar to the parental agent of bovine spongiform encephalopathy could exist or emerge in Japan. Thus, continuous surveillance for scrapie will be required to prevent the further spread of scrapie, not only among the sheep population but also to other species, and to eliminate any potential risk of sheep scrapie to public health.
Actinomyces cardiffensis
sp. nov. from Human Clinical Sources
Authors: Hall Val , Collins Mattew D. , Hutson Roger , Falsen Enevold , Duerden Brian I. 
Published: August 2002

ABSTRACT

Eight strains of a previously undescribed catalase-negative
Actinomyces
-like bacterium were recovered from human clinical specimens. The morphological and biochemical characteristics of the isolates were consistent with their assignment to the genus
Actinomyces
, but they did not appear to correspond to any recognized species. 16S rRNA gene sequence analysis showed the organisms represent a hitherto unknown species within the genus
Actinomyces
related to, albeit distinct from, a group of species which includes
Actinomyces turicensis
and close relatives. Based on biochemical and molecular genetic evidence, it is proposed that the unknown isolates from human clinical sources be classified as a new species,
Actinomyces cardiffensis
sp. nov. The type strain of
Actinomyces cardiffensis
is CCUG 44997
T
.
Serodiagnosis of Imported Schistosomiasis by a Combination of a Commercial Indirect Hemagglutination Test withSchistosoma mansoniAdult Worm Antigens and an Enzyme-Linked Immunosorbent Assay withS. mansoniEgg Antigens
Authors: van Gool Tom , Vetter Hans , Vervoort Tony , Doenhoff Michael J. , Wetsteyn Jose , Overbosch David 
Published: August 2002

ABSTRACTA commercial indirect hemagglutination (IHA) test using erythrocytes coated withSchistosoma mansoniadult worm antigens (WA) and an enzyme-linked immunosorbent assay (ELISA) withS. mansoniegg antigens (SEA) were assessed for their use in serodiagnosis of imported schistosomiasis (hereafter these tests are designated WA/IHA and SEA/ELISA, respectively). The sensitivity of the tests was evaluated with sera from 75 patients with provenS. mansoniinfection, 25 with provenS. haematobiuminfection, and 10 with clinical Katayama fever. The specificity was assessed with sera from 283 patients with various parasitic, bacterial, viral, and fungal infections and sera containing autoimmune antibodies. Sensitivities of the WA/IHA with a cutoff titer of 1:160 (WA/IHA160) in detectingS. mansoni,S. haematobium,S. mansoniandS. haematobiumcombined, and clinical Katayama fever were 88.0, 80.0, 86.0, and 70.0%, respectively, with a specificity of 98.9%. The WA/IHA with a cutoff of 1:80 (WA/IHA80) showed sensitivities of 94.7, 92.0, 94.0, and 90.0%, respectively, with a specificity of 94.7%. The comparable values of SEA/ELISA were 93.3, 92.0, 93.0, and 50.0%, respectively, with a specificity of 98.2%. Combined use of ELISA and WA/IHA80gave sensitivities of 100% forS. mansoni,S. haematobium, andS. mansoniandS. haematobiumcombined and 90% for Katayama fever. The specificity of this combination in detecting schistosomiasis was 92.9%. Combination of SEA/ELISA with WA/IHA160gave sensitivities of 98.7, 96.0, 98.0, and 80% with a specificity of 97.2%. Our findings suggest that WA/IHA and SEA/ELISA are each sensitive and specific serological tests that are easy to use for the diagnosis of imported schistosomiasis. The combined use of these two tests enabled the serological diagnosis of schistosomiasis to be achieved with very high degrees of both sensitivity and specificity.
Taxonomic Subgroups of
Pasteurella multocida
Correlate with Clinical Presentation
Authors: Chen Henry I. , Hulten Kristina , Clarridge Jill E. 
Published: August 2002

ABSTRACT

Pasteurella multocida
is a small nonmotile gram-negative coccobacillus that is found in the nasopharynx and gastrointestinal tract of many wild and domesticated animals. In humans it most commonly causes cellulitis and localized superficial skin abscesses following an animal bite or scratch. The respiratory tract is the second most common site of infection for
Pasteurella
. Of the more than 17 species of
Pasteurella
known,
Pasteurella multocida
subsp.
multocida
and
Pasteurella multocida
subsp.
septica
are among the most common pathogens in humans. With the use of molecular techniques, distinction between different subspecies of
P
.
multocida
can be made more easily and accurately. We used the sequence of the 16S ribosomal DNA (rDNA) and repetitive extragenic palindromic sequence-PCR (REP-PCR) to characterize 20 strains (14 of
P
.
multocida
subsp.
multocida
and 6 of
P
.
multocida
subsp.
septica
; the 16S rDNA is identical for
P
.
multocida
subsp.
multocida
and
Pasteurella multocida
subsp.
gallicida
but differs from that of
P
.
multocida
subsp.
septica
) isolated from various anatomic sites. We found excellent correlation between the 16S rDNA sequence (a marker for a small conserved region of the genome), REP-PCR (a marker for a large portion of the genome), and biochemical tests (trehalose and sorbitol). We also found a correlation between the clinical presentation and the taxonomic group, with
P
.
multocida
subsp.
septica
more often associated with wounds than with respiratory infections (67 versus 17%, respectively) (
P
< 0.05, Z test) and
P
.
multocida
subsp.
multocida
more often associated with respiratory infections than with wounds (71 versus 14%, respectively) (
P
< 0.05, Z test).
Genotypic Diversity of Clinical
Actinomyces
Species: Phenotype, Source, and Disease Correlation among Genospecies
Authors: Clarridge Jill E. , Zhang Qing 
Published: August 2002

ABSTRACT

We determined the frequency distribution of
Actinomyces
spp. recovered in a routine clinical laboratory and investigated the clinical significance of accurate identification to the species level. We identified 92 clinical strains of
Actinomyces
, including 13 strains in the related
Arcanobacterium-Actinobaculum
taxon, by 16S rRNA gene sequence analysis and recorded their biotypes, sources, and disease associations. The clinical isolates clustered into 21 genogroups. Twelve genogroups (74 strains) correlated with a known species, and nine genogroups (17 strains) did not. The individual species had source and disease correlates.
Actinomyces turicensis
was the most frequently isolated species and was associated with genitourinary tract specimens, often with other organisms and rarely with inflammatory cells.
Actinomyces radingae
was most often associated with serious, chronic soft tissue abscesses of the breast, chest, and back.
Actinomyces europaeus
was associated with skin abscesses of the neck and genital areas.
Actinomyces lingnae
,
Actinomyces gravenitzii
,
Actinomyces odontolyticus
, and
Actinomyces meyeri
were isolated from respiratory specimens, while
A. odontolyticus
-like strains were isolated from diverse sources. Several of the species were commonly coisolated with a particular bacterium:
Actinomyces israelii
was the only
Actinomyces
spp. coisolated with
Actinobacillus
(
Haemophilus
)
actinomycetemcomitans
;
Actinomyces meyeri
was coisolated with
Peptostreptococcus micros
and was the only species other than
A. israelii
associated with sulfur granules in histological specimens. Most genogroups had consistent biotypes (as determined with the RapID ANA II system); however, strains were misidentified, and many codes were not in the database. One biotype was common to several genogroups, with all of these isolates being identified as
A. meyeri
. Despite the recent description of new
Actinomyces
spp., 19% of the isolates recovered in our routine laboratory belonged to novel genospecies. One novel group with three strains,
Actinomyces houstonensis
sp. nov., was phenotypically similar to
A. meyeri
and
A. turicensis
but was genotypically closest to
Actinomyces neuii. A. houstonensis
sp. nov. was associated with abscesses. Our data documented consistent site and disease associations for 21 genogroups of
Actinomyces
spp. that provide greater insights into appropriate treatments. However, we also demonstrated a complexity within the
Actinomyces
genus that compromises the biochemical identification of
Actinomyces
that can be performed in most clinical laboratories. It is our hope that this large group of well-defined strains will be used to find a simple and accurate biochemical test for differentiation of the species in routine laboratories.
Quantitative Multiprobe PCR Assay for Simultaneous Detection and Identification to Species Level of Bacterial Pathogens
Authors: Yang Samuel , Lin Shin , Kelen Gabor D. , Quinn Thomas C. , Dick James D. , Gaydos Charlotte A. , Rothman Richard E. 
Published: August 2002

ABSTRACT

We describe a novel adaptation of the TaqMan PCR assay which potentially allows for highly sensitive detection of any eubacterial species with simultaneous species identification. Our system relies on a unique multiprobe design in which a single set of highly conserved sequences encoded by the 16S rRNA gene serves as the primer pair and is used in combination with both an internal highly conserved sequence, the universal probe, and an internal variable region, the species-specific probe. A pre-PCR ultrafiltration step effectively decontaminates or removes background DNA. The TaqMan system described reliabAly detected 14 common bacterial species with a detection limit of 50 fg. Further, highly sensitive and specific pathogen detection was demonstrated with a prototype species-specific probe designed to detect
Staphylococcus aureus
. This assay has broad potential in the clinical arena for rapid and specific diagnosis of infectious diseases.
Characterization of Hepatitis C Virus Quasispecies by Matrix-Assisted Laser Desorption Ionization-Time of Flight (Mass Spectrometry) Mutation Detection
Authors: Ayers Melissa , Siu Karen , Roberts Eve , Garvin Alex M. , Tellier Raymond 
Published: August 2002

ABSTRACT
Hepatitis C virus (HCV), the causative agent of hepatitis C, frequently causes chronic infection. The mechanisms of viral persistence continue to be the object of investigation. An important aspect of HCV chronic infection is the quasispecies nature of the viral population, which has been particularly well documented in the hypervariable region 1 of the E2 glycoprotein. Recent studies show that characterization of the quasispecies diversity at the amino acid level can help to predict the outcome of HCV infection. Currently the accurate characterization of HCV quasispecies requires the cloning of PCR products, followed by the sequencing of many clones. In this study we present a new method to characterize HCV quasispecies, based on in vitro translation of the amplicons, followed by mass spectrometry analysis of the resulting peptide mix. The assay was used on reference HCV samples and on clinical samples. In principle, this method could be applied to other chronic viral infections in which quasispecies play a role.
Molecular Typing of Papillomatous Digital Dermatitis-Associated
Treponema
Isolates Based on Analysis of 16S-23S Ribosomal DNA Intergenic Spacer Regions
Authors: Stamm L. V. , Bergen H. L. , Walker R. L. 
Published: August 2002

ABSTRACT

Papillomatous digital dermatitis (PDD), an emerging infectious disease of cattle, is characterized by painful, ulcerative foot lesions. The detection of high numbers of invasive spirochetes in PDD lesions suggests an important role for these organisms in the pathogenesis of PDD. PDD-associated spirochetes have phenotypic characteristics consistent with members of the genus
Treponema
. Partial 16S ribosomal DNA (rDNA) sequence analysis of clonal isolates from California cattle showed that they comprise three phylotypes which cluster closely with human-associated
Treponema
spp. of the oral cavity (
T. denticola
and
T. medium/T. vincentii
) or genital area (
T. phagedenis
). The goal of our study was to apply 16S-23S rDNA intergenic spacer region (ISR) sequence analysis to the molecular typing of U.S. PDD-associated
Treponema
isolates. This methodology has potentially greater discriminatory power for differentiation of closely related bacteria than 16S rDNA analysis. We PCR amplified, cloned, and sequenced the ISRs from six California PDD-associated
Treponema
isolates and, for comparative purposes, one strain each of
T. denticola
,
T. medium
,
T. vincentii
, and
T. phagedenis.
Two ISRs that varied in length and composition were present in all the PDD-associated
Treponema
isolates and in
T. denticola
,
T. medium
, and
T. phagedenis
. ISR1 contained a tRNA
Ala
gene, while ISR2 contained a tRNA
Ile
gene. Only a single ISR (ISR1) was identified in
T. vincentii.
Comparative analyses of the ISR1 and ISR2 sequences indicated that the California PDD-associated
Treponema
isolates comprised three phylotypes, in agreement with the results of 16S rDNA analysis. PCR amplification of the 16S-tRNA
Ile
region of ISR2 permitted rapid phylotyping of California and Iowa PDD-associated
Treponema
isolates based on product length polymorphisms.
Molecular Analysis of the Pathogenicity Locus and Polymorphism in the Putative Negative Regulator of Toxin Production (TcdC) among
Clostridium difficile
Clinical Isolates
Authors: Spigaglia Patrizia , Mastrantonio Paola 
Published: August 2002

ABSTRACT

The pathogenicity locus (PaLoc) of
Clostridium difficile
contains toxin A and B genes and three accessory genes, including
tcdD
and
tcdC
, which are supposed to code for the positive and negative regulators of toxin expression, respectively. Different studies have described variations in
C. difficile
toxin A and B genes, but little is known about
C. difficile
variants for the accessory genes. The PaLoc of several
C. difficile
clinical isolates was investigated by three different PCR methods with the aim to identify variant strains. Of the toxinogenic
C. difficile
strains examined, 25% showed variations. No correlation between
C. difficile
variant strains and key patient groups was found. Interestingly, all of these strains showed a variant
tcdC
gene. Three different
tcdC
alleles were identified, and one of these had a nonsense mutation which reduced the TcdC protein from 232 to 61 amino acids. It is possible that different TcdC variants affect toxin production differently, a hypothesis with important implications for the pathogenic potential of variant
C. difficile
strains.