bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification and PCR-Restriction Fragment Length Polymorphism Analysis of a Variant of the Ibaraki Virus from Naturally Infected Cattle and Aborted Fetuses in Japan
Authors: Ohashi Seiichi , Yoshida Kazuo , Watanabe Youichirou , Tsuda Tomoyuki 
Published: December 2019

ABSTRACT

One hundred fourteen field isolates of the Ibaraki virus (IBAV), a member of the epizootic hemorrhagic disease virus serotype 2 (EHDV-2), were isolated from blood samples of affected and apparently healthy cattle and
Culicoides
biting midges and from blood samples of dams and internal organs of aborted fetuses during an outbreak of Ibaraki disease in the southern part of Japan in 1997. In this outbreak, 242 cattle showed typical symptoms of the disease, and several hundred dams had miscarriages or stillbirths. The viruses that induced typical Ibaraki disease and reproductive problems among cattle were identical and were antigenically closely related to but distinct from previous isolates of IBAV and EHDV-2. The virus was considered to be a putative agent of this outbreak. Reverse transcription-PCR based on segment 3 of the RNA genome of EHDV-2 and restriction fragment length polymorphism analysis of the PCR products were conducted to compare the genomes of the viruses. The results suggested that the virus isolated in 1997 was a variant of IBAV and might be exotic.
Evolution and Clonal Traits of
Mycobacterium tuberculosis
Complex in Guinea-Bissau
Authors: Källenius Gunilla , Koivula Tuija , Ghebremichael Solomon , Hoffner Sven E. , Norberg Renée , Svensson Erika , Dias Francisco , Marklund Britt-Inger , Svenson Stefan B. 
Published: December 2019

ABSTRACT

Two hundred twenty-nine consecutive isolates of
Mycobacterium tuberculosis
complex from patients with pulmonary tuberculosis in Guinea-Bissau, which is located in West Africa, were analyzed for clonal origin by biochemical typing and DNA fingerprinting. By using four biochemical tests (resistance to thiophene-2-carboxylic acid hydrazide, niacin production, nitrate reductase test, and pyrazinamidase test), the isolates could be assigned to five different biovars. The characteristics of four strains conformed fully with the biochemical criteria for
M. bovis
, while those of 85 isolates agreed with the biochemical criteria for
M. tuberculosis
. The remaining 140 isolates could be allocated into one of three biovars (biovars 2 to 4) representing a spectrum between the classical bovine (biovar 1) and human (biovar 5) tubercle bacilli. By using two genotyping methods, restriction fragment length polymorphism analysis with IS
6110
(IS
6110
RFLP analysis) and spoligotyping, the isolates could be separated into three groups (groups A to C) of the
M. tuberculosis
complex. Group A (
n
= 95), which contained the majority of classical human
M. tuberculosis
isolates, had large numbers of copies of IS
6110
elements (mean number of copies, 9) and a distinctive spoligotyping pattern that lacked spacers 33 to 36. Isolates of the major group, group B (
n
= 119), had fewer IS
6110
copies (mean copy number, 5) and a spoligotyping pattern that lacked spacers 7 to 9 and 39 and mainly comprised isolates of biovars 1 to 4. Group C isolates (
n
= 15) had one to three IS
6110
copies, had a spoligotyping pattern that lacked spacers 29 to 34, and represented biovar 3 to 5 isolates. Four isolates whose biochemical characteristics conformed with those of
M. bovis
clustered with the group B isolates and had spoligotype patterns that differed from those previously reported for
M. bovis
, in that they possessed spacers 40 to 43. Interestingly, isolates of group B and, to a certain extent, also isolates of group C showed a high degree of variability in biochemical traits, despite genotypic identity in terms of IS
6110
RFLP and spoligotype patterns. We hypothesize that isolates of groups B and C have their evolutionary origin in West Africa, while group A isolates are of European descent.
Disseminated Infection with
Mycobacterium genavense
: a Challenge to Physicians and Mycobacteriologists
Authors: Thomsen Vibeke Østergaard , Dragsted Ulrik Bak , Bauer Jeanett , Fuursted Kurt , Lundgren Jens 
Published: December 2019

ABSTRACT

In the present study we compared the clinical presentations of patients with a clinical diagnosis of AIDS and disseminated
Mycobacterium genavense
infection (
n
= 12) with those of patients with AIDS and disseminated
M. avium
complex (MAC) infection (
n
= 24). Abdominal pain was seen more frequently in the group of patients infected with
M. genavense
than in patients infected with MAC (
P
= 0.003). Analysis of microbiological data revealed that stool specimens from patients infected with
M. genavense
were more often smear positive than stool specimens from patients infected with MAC (
P
= 0.00002). However,
M. genavense
could be cultured on solid media from only 15.4% of the stool specimens, whereas MAC could be cultured from 71.4% of the specimens. Bone marrow and liver biopsy specimens yielded growth of
M. genavense
within a reasonably short time, allowing species identification by DNA technology. Microbiological data clearly demonstrated the importance of acidic liquid medium for primary culture, the avoidance of pretreatment and the use of additives in culture, and the necessity for prolonged incubation if
M. genavense
is suspected. Susceptibility testing showed that
M. genavense
is sensitive to rifamycins, fluoroquinolones, and macrolides, whereas it is resistant to isoniazid. Susceptibility to ethambutol and clofazimine could not be evaluated. The mean survival times of patients in the two groups were similar.
Identification of
Porphyromonas gingivalis
Strains by Heteroduplex Analysis and Detection of Multiple Strains
Authors: Leys Eugene J. , Smith James H. , Lyons Sharon R. , Griffen Ann L. 
Published: December 2019

ABSTRACT

Heteroduplex analysis has been used extensively to identify allelic variation among mammalian genes. It provides a rapid and reliable method for determining and cataloging minor differences between two closely related DNA sequences. We have adapted this technique to distinguish among strains or clonal types of
Porphyromonas gingivalis
. The ribosomal intergenic spacer region (ISR) was amplified directly from a subgingival plaque sample by PCR with species-specific primers, avoiding the need for culturing the bacteria. The PCR products were then directly compared by heteroduplex analysis with known strains of
P. gingivalis
for identification. We identified 22 distinct but closely related heteroduplex types of
P. gingivalis
in 1,183 clinical samples. Multiple strains were found in 34% of the samples in which
P. gingivalis
was detected. Heteroduplex types were identified from these multistrain samples without separating them by culturing or molecular cloning. PCR with species-specific primers and heteroduplex analysis makes it possible to reliably and sensitively detect and identify strains of
P. gingivalis
in large numbers of samples.
Acute-Phase-Specific Heptapeptide Epitope for Diagnosis of Parvovirus B19 Infection
Authors: Kaikkonen Leena , Lankinen Hilkka , Harjunpää Irene , Hokynar Kati , Söderlund-Venermo Maria , Oker-Blom Christian , Hedman Lea , Hedman Klaus 
Published: December 2019

ABSTRACT
The major capsid protein VP2 of human parvovirus B19, when studied in a denatured form exhibiting linear epitopes, is recognized exclusively by immunoglobulin G (IgG) antibodies of patients with acute or recent B19 infection. By contrast, conformational epitopes of VP2 are recognized both by IgG of the acute phase and by IgG of past immunity. In order to localize the VP2 linear epitope(s) specific for acute-phase IgG, the entire B19 capsid protein sequence was mapped by peptide scanning using well-characterized acute-phase and control sera. A unique heptapeptide epitope showing strong and selective reactivity with the acute-phase IgG was detected and characterized. By using this linear epitope (VP2 amino acids 344 to 350) and virus-like particles exhibiting conformational VP2 epitopes, an innovative approach, second-generation epitope-typing enzyme immunoassay, was set up for improved diagnosis of primary infections by human parvovirus B19.
Phylogeny and PCR Identification of Clinically Important Zygomycetes Based on Nuclear Ribosomal-DNA Sequence Data
Authors: Voigt Kerstin , Cigelnik Elizabeth , O'donnell Kerry 
Published: December 2019

ABSTRACT

A molecular database for all clinically important Zygomycetes was constructed from nucleotide sequences from the nuclear small-subunit (18S) ribosomal DNA and domains D1 and D2 of the nuclear large-subunit (28S) ribosomal DNA. Parsimony analysis of the aligned 18S and 28S DNA sequences was used to investigate phylogenetic relationships among 42 isolates representing species of Zygomycetes reported to cause infections in humans and other animals, together with commonly cultured contaminants, with emphasis on members of the Mucorales. The molecular phylogeny provided strong support for the monophyly of the Mucorales, exclusive of
Echinosporangium transversale
and
Mortierella
spp., which are currently misclassified within the Mucorales.
Micromucor ramannianus
, traditionally classified within
Mortierella
, and
Syncephalastrum racemosum
represent the basal divergences within the Mucorales. Based on the 18S gene tree topology,
Absidia corymbifera
and
Rhizomucor variabilis
appear to be misplaced taxonomically.
A. corymbifera
is strongly supported as a sister group of the
Rhizomucor miehei-Rhizomucor pusillus
clade, while
R. variabilis
is nested within
Mucor
. The aligned 28S sequences were used to design 13 taxon-specific PCR primer pairs for those taxa most commonly implicated in infections. All of the primers specifically amplified DNA of the size predicted based on the DNA sequence data from the target taxa; however, they did not cross-react with phylogenetically related species. These primers have the potential to be used in a PCR assay for the rapid and accurate identification of the etiological agents of mucormycoses and entomophthoromycoses.
Human Antibody Responses to VlsE Antigenic Variation Protein ofBorrelia burgdorferi
Authors: Lawrenz M. B. , Hardham J. M. , Owens R. T. , Nowakowski J. , Steere A. C. , Wormser G. P. , Norris S. J. 
Published: December 2019

ABSTRACTVlsE is a 35-kDa surface-exposed lipoprotein ofBorrelia burgdorferithat was shown previously to undergo antigenic variation through segmental recombination of silentvlscassettes withvlsEduring experimental mouse infections. Previous data had indicated that sera from North American Lyme disease patients and experimentally infected animals contained antibodies reactive with VlsE. In this study, sera from patients with Lyme disease, syphilis, and autoimmune conditions as well as from healthy controls were examined for reactivity with VlsE by Western blotting and enzyme-linked immunosorbent assay (ELISA). Strong Western blot reactivity to a recombinant VlsE cassette region protein was obtained consistently with Lyme disease sera. Although sera from Lyme disease patients also reacted with a band corresponding to VlsE inB. burgdorferiB31-5A3, interpretation was complicated by low levels of VlsE expression in in vitro-culturedB. burgdorferiand by the presence of comigrating bands. An ELISA using recombinant VlsE was compared with an ELISA using sonically disruptedB. burgdorferias the antigen. For a total of 93 Lyme disease patient sera examined, the VlsE ELISA yielded sensitivities of 63% for culture-confirmed erythema migrans cases and 92% for later stages, as compared to 61 and 98%, respectively, for the “whole-cell” ELISA. The specificities of the two assays with healthy blood donor sera were comparable, but the VlsE ELISA was 90% specific with sera from syphilis patients, compared to 20% specificity for the whole-cell ELISA with this group. Neither assay showed reactivity with a panel of sera from 20 non-Lyme disease arthritis patients or 20 systemic lupus erythematosus patients. Our results indicate that VlsE may be useful in the immunodiagnosis of Lyme disease and may offer greater specificity than ELISAs using wholeB. burgdorferias the antigen.
Genetic Relatedness among Nontypeable Pneumococci Implicated in Sporadic Cases of Conjunctivitis
Authors: Barker Jason H. , Musher Daniel M. , Silberman Ronald , Phan Hoang M. , Watson David A. 
Published: December 2019

ABSTRACT

Nontypeable
Streptococcus pneumoniae
is a common cause of epidemic conjunctivitis. A previous molecular fingerprinting study identified a clone of nontypeable pneumococcus that was responsible for a recent outbreak of conjunctivitis. In the present study, we examined the extent to which pneumococci that cause sporadic cases of conjunctivitis are related to this epidemic strain. Using arbitrarily primed BOX-PCR, we have determined that, of 10 nontypeable pneumococci causing sporadic conjunctivitis, 5 were clonal and closely related to a previous outbreak strain, whereas 5 others were genetically diverse.
Scored Antibody Reactivity Determined by Immunoblotting Shows an Association between Clinical Manifestations and Presence ofBorrelia burgdorferisensu stricto,B. garinii,B. afzelii, andB. Valaisianain Humans
Authors: Ryffel Karine , Péter Olivier , Rutti Bernard , Suard André , Dayer Eric 
Published: December 2019

ABSTRACTAn immunoglobulin G immunoblot was developed with antigenic extracts ofBorrelia burgdorferisensu stricto,B. garinii,B. afzelii, andB. valaisianagenospecies and was reacted with sera from patients with neuroborreliosis, acrodermatitis, and Lyme arthritis. A detailed analysis of the reactivities of the protein bands was performed, and a two-step scoring procedure was selected to determine the preferential reactivity of sera to one particular genospecies. The discriminative potential of 5 proteins (12-kDa, 16-kDa, 18-kDa, OspA, and 66-kDa proteins) was used as a rapid first-step scoring method, followed by scoring of 14 additional protein bands if necessary. The advantage of this procedure is the low percentage of serum samples with inconclusive results for one of the four species (10% for patients with neuroborreliosis, 6% for patients with acrodermatitis chronica atrophicans, and 6% for patients with Lyme arthritis). Among 31 serum samples from patients with neuroborreliosis, 16 were more reactive toB. garinii, 7 were more reactive toB. afzelii, 3 were more reactive toB. valaisiana, and 2 were more reactive toB. burgdorferisensu stricto. Of 31 serum samples from patients with acrodermatitis, 26 showed a higher level of reactivity toB. afzelii. Of 34 serum samples from patients with Lyme arthritis, 21 were more reactive toB. burgdorferisensu stricto, 10 were more reactive toB. afzelii, and 1 was more reactive toB. valaisiana. Our results suggest an organotropism ofBorreliaspecies and provide some evidence of a pathogenic potential ofB. valaisianain humans.
Evaluation of Streck Tissue Fixative, a Nonformalin Fixative for Preservation of Stool Samples and Subsequent Parasitologic Examination
Authors: Nace Eva K. , Steurer Frank J. , Eberhard Mark L. 
Published: December 2019

ABSTRACT

We undertook a study to evaluate Streck tissue fixative (STF) as a substitute for formalin and polyvinyl alcohol (PVA) in fecal preservation. A comparison of formalin, PVA, (mercuric chloride based), and STF was done by aliquoting fecal samples into each fixative. Stool specimens were collected in Haiti, and parasites included
Cyclospora cayetanensis
,
Giardia intestinalis
,
Entamoeba coli
,
Iodamoeba butschlii
,
Endolimax nana
,
Ascaris lumbricoides
,
Trichuris trichiura
,
Strongyloides stercoralis
, and
Necator americanus
. Preserved stools were examined at various predetermined times (1 week, 1 month, and 3 months) to establish the quality of the initial preservation as well as the suitability of the fixative for long-term storage. At each time point, stool samples in fixatives were examined microscopically as follows: (i) in wet mounts (with bright-field and epifluorescence microscopy), (ii) in modified acid-fast-, trichrome-, and safranin-stained smears, and (iii) with two commercial test kits. At the time points examined, morphologic features remained comparable for samples fixed with 10% formalin and STF. For comparisons of STF- and 10% formalin-fixed samples, specific findings showed that
Cyclospora
oocysts retained full fluorescence, modified acid-fast- and safranin-stained smears of
Cryptosporidium
and
Cyclospora
oocysts were equal in staining quality, and results were comparable in the immunofluorescence assay and enzyme immunoassay commercial kits. Stool fixed in STF and stained with trichrome showed less-than-acceptable staining quality compared with stool fixed in PVA. STF provides an excellent substitute for formalin as a fixative in routine examination of stool samples for parasites. However, modifications to the trichrome staining procedures will be necessary to improve the staining quality for protozoal cysts fixed in STF to a level comparable to that with PVA.
Simultaneous Infection with Two Drug-Susceptible
Mycobacterium tuberculosis
Strains in an Immunocompetent Host
Authors: Pavlic Marion , Allerberger Franz , Dierich Manfred P. , Prodinger Wolfgang M. 
Published: December 2019

ABSTRACT

An important assumption for DNA fingerprinting of
Mycobacterium tuberculosis
is that patients are infected with only one strain at a time. Nonetheless, we demonstrate a case of simultaneous infection with two drug-susceptible strains of
M. tuberculosis
in an immunocompetent patient by IS
6110
restriction fragment length polymorphism and spoligotyping. Epidemiological data prove the patient's involvement in two independent clusters. Thus, double infections should be suspected with fingerprints showing divergent band intensities.
Rahnella aquatilis
Sepsis in an Immunocompetent Adult
Authors: Chang Chulhun Ludgerus , Jeong Joseph , Shin Jeong Hwan , Lee Eun Yup , Son Han Chul 
Published: December 2019

ABSTRACT

Rahnella aquatilis
, a rare enteric gram-negative rod which is infrequently isolated in immunocompromised patients, was isolated as a causative organism of sepsis in a 26-year-old immunocompetent male patient. The contaminated intravenous fluid was confirmed to be the source of the organism.
Development and Evaluation of a Rapid Dipstick Assay for Serodiagnosis of Acute Human Brucellosis
Authors: Smits Henk L. , Basahi M. A. , Díaz Ramon , Marrodan T. , Douglas James T. , Rocha Alice , Veerman Jaques , Zheludkov M. M. , Witte Olav W. M. , de Jong Joop , Gussenhoven George C. , Goris Marga G. A. , van der Hoorn Menno A. W. G. 
Published: December 2019

ABSTRACTA dipstick assay for the detection of brucella-specific immunoglobulin M antibodies was evaluated with 707 sera from 247 laboratory-confirmed brucellosis patients and 342 control sera from brucellosis-free individuals. These sera were collected from six different countries. The assay was found to be highly sensitive and specific. In addition, the test is easy to use and does not require specialized training or equipment, and the components are stable without a requirement for refrigeration. All of these factors make the test ideal for developing countries and rural settings.
Associations of
Streptococcus suis
Serotype 2 Ribotype Profiles with Clinical Disease and Antimicrobial Resistance
Authors: Rasmussen S. R. , Aarestrup F. M. , Jensen N. E. , Jorsal S. E. 
Published: December 2019

ABSTRACT

A total of 122
Streptococcus suis
serotype 2 strains were characterized thoroughly by comparing clinical and pathological observations, ribotype profiles, and antimicrobial resistance. Twenty-one different ribotype profiles were found and compared by cluster analysis, resulting in the identification of three ribotype clusters. A total of 58% of all strains investigated were of two ribotypes belonging to different ribotype clusters. A remarkable relationship existed between the observed ribotype profiles and the clinical-pathological observations because strains of one of the two dominant ribotypes were almost exclusively isolated from pigs with meningitis, while strains of the other dominant ribotype were never associated with meningitis. This second ribotype was isolated only from pigs with pneumonia, endocarditis, pericarditis, or septicemia. Cluster analysis revealed that strains belonging to the same ribotype cluster as one of the dominant ribotypes came from pigs that showed clinical signs similar to those of pigs infected with strains with the respective dominant ribotype profiles. Furthermore, strains belonging to different ribotype clusters had totally different patterns of resistance to antibiotics because strains isolated from pigs with meningitis were resistant to sulfamethazoxazole and strains isolated from pigs with pneumonia, endocarditis, pericarditis, or septicemia were resistant to tetracycline.
Vancomycin-Resistant
Enterococcus faecium
Colonization in Children
Authors: Singh-Naz Nalini , Sleemi Ambreen , Pikis Andreas , Patel Kantilal M. , Campos Joseph M. 
Published: December 2019

ABSTRACT

Nosocomial vancomycin-resistant
Enterococcus
(VRE) infections have been described in only small numbers of pediatric patients. In none of these studies were multivariate analyses performed to assess which factors were independent risk factors in these patients. In the present cohort study of patients admitted to our hematology/oncology unit, surveillance cultures revealed a colonization rate of 24% and all isolates were identified as
Enterococcus faecium
. Risk factors associated with colonization with VRE identified by multiple logistic regression analysis included young age and chemotherapy with antineoplastic agents, cefotaxime, vancomycin, and ceftazidime. A molecular epidemiological tool, pulsed-field gel electrophoresis, was used to determine the relatedness of the VRE isolates detected. DNA analysis by this method identified two major clusters of VRE isolates. Young children with gastrointestinal colonization with VRE, without evidence of clinical infection, can serve as a reservoir for the spread of VRE.
Simple, Reliable, and Cost-Effective Yeast Identification Scheme for the Clinical Laboratory
Authors: Koehler Ann P. , Chu Kai-Cheong , Houang Elizabeth T. S. , Cheng Augustine F. B. 
Published: December 2019

ABSTRACT
The appearance of colonies on the chromogenic medium CHROMagar Candida combined with observation of morphology on corn meal–Tween 80 agar was used for the identification of 353 clinical yeast isolates. The results were compared with those obtained with API yeast identification kits. The accuracy of identification and the turnaround time were equivalent for each method, and our cultural method was less expensive.