bluuebunny/crossref_metadata_2025_split huggingface dataset:
Use of Molecular Subtyping To Document Long-Term Persistence of
Corynebacterium diphtheriae
in South Dakota
Authors: Popovic Tanja , Kim Chung , Reiss Jonathan , Reeves Mike , Nakao Hiroshi , Golaz Anne 
Published: December 2019

ABSTRACT

Enhanced surveillance of patients with upper respiratory symptoms in a Northern Plains community revealed that approximately 4% of them were infected by toxigenic
Corynebacterium diphtheriae
of both mitis and gravis biotypes, showing that the organism is still circulating in the United States. Toxigenic
C. diphtheriae
was isolated from five members of four households. Four molecular subtyping methods—ribotyping, multilocus enzyme electrophoresis (MEE), random amplified polymorphic DNA (RAPD), and single-strand conformation polymorphism—were used to molecularly characterize these strains and compare them to 17 archival South Dakota strains dating back to 1973 through 1983 and to 5 isolates collected from residents of diverse regions of the United States. Ribotyping and RAPD clearly demonstrated the household transmission of isolates and provided precise information on the circulation of several distinct strains within three households. By MEE, most recent and archival South Dakota strains were identified as closely related and clustered within the newly identified ET (electrophoretic type) 215 complex. Furthermore, three recent South Dakota isolates and eight archival South Dakota isolates were indistinguishable by both ribotyping and RAPD. All of these molecular methods showed that recent South Dakota isolates and archival South Dakota isolates were more closely related to each other than to the
C. diphtheriae
strains isolated in other parts of the United States or worldwide. The data also supported the improbability of importation of
C. diphtheriae
into this area and rather strongly suggest the long-term persistence of the organism in this region.
Strain Variation in Adenovirus Serotypes 4 and 7a Causing Acute Respiratory Disease
Authors: Crawford-Miksza Leta K. , Nang Roberto N. , Schnurr David P. 
Published: December 2019

ABSTRACTIn order to determine the suitability of vaccine strains established in the 1960s for a new vaccine, a comprehensive study of strain variation of adenovirus serotype 4 (AV 4) and AV 7 was undertaken. A 1,500-bp region of the hexon gene containing the AV neutralization epitopes from prototype, vaccine, and community-acquired strains and from wild-type strains from military personnel that cause acute respiratory disease (ARD) was sequenced and analyzed. The whole hexon gene from prototype strains, vaccine strains, and selected isolates was sequenced. AV 7 and AV 7a were found to have distinct genotypes, and all vaccine and wild-type strains recovered from 1963 to 1997 had the AV 7a genotype. There was no significant strain variation in the neutralization epitopes of the AV 7a genotype over a 42-year period. The evolution of AV 4 was more complex, with continuous genetic drift punctuated by replacement with a new strain. The current strain of AV 4, which has been in circulation since 1995, is significantly different from the AV 4 prototype and the vaccine strains. Genetic differences were confirmed to be antigenic differences by neutralization tests, which define the new strain as an AV 4 variant. A type-specific PCR for AV 4, AV 7/7a, and AV 21 was developed, and this PCR facilitated the rapid identification of isolates from outbreaks of ARD.
Genetic Diversity of the 28-Kilodalton Outer Membrane Protein Gene in Human Isolates ofEhrlichia chaffeensis
Authors: Yu Xue-Jie , McBride Jere W. , Walker David H. 
Published: December 2019

ABSTRACTTheEhrlichia chaffeensis28-kDa outer membrane protein (p28) gene was sequenced completely by genomic walking with adapter PCR. The DNA sequence of the p28 gene was nearly identical to the previously reported sequence (N. Ohashi, N. Zhi, Y. Zhang, and Y. Rikihisa, Infect. Immun. 66:132–139, 1998), but analysis of a further 75 bp on the 5′ end of the gene revealed DNA that encoded a 25-amino-acid signal sequence. The leader sequence was removed from the N terminus of a 30-kDa precursor to generate the mature p28 protein. A monoclonal antibody (MAb), 1A9, recognizing four outer membrane proteins ofE. chaffeensis(Arkansas strain) including the 25-, 26-, 27-, and 29-kDa proteins (X.-J. Yu, P. Brouqui, J. S. Dumler, and D. Raoult, J. Clin. Microbiol. 31:3284–3288, 1993) reacted with the recombinant p28 protein. This result indicated that the four proteins recognized by MAb 1A9 were encoded by the multiple genes of the 28-kDa protein family. DNA sequence alignment analysis revealed divergence of p28 among all five human isolates ofE. chaffeensis. TheE. chaffeensisstrains could be divided into three genetic groups on the basis of the p28 gene. The first group consisted of the Sapulpa and St. Vincent strains. They had predicted amino acid sequences identical to each other. The second group contained strain 91HE17 and strain Jax, which only showed 0.4% divergence from each other. The third group contained the Arkansas strain only. The amino acid sequences of p28 differed by 11% between the first two groups, by 13.3% between the first and third groups, and by 13.1% between the second and third groups. The presence of antigenic variants of p28 among the strains ofE. chaffeensisand the presence of multiple copies of heterogeneous genes suggest a possible mechanism by whichE. chaffeensismight evade the host immune defenses. Whether or not immunization with the p28 of one strain ofE. chaffeensiswould confer cross-protection against other strains needs to be investigated.
Rapid Film-Based Determination of Antibiotic Susceptibilities of
Mycobacterium tuberculosis
Strains by Using a Luciferase Reporter Phage and the Bronx Box
Authors: Riska Paul F. , Su Ya , Bardarov Svetoslav , Freundlich Lawrence , Sarkis Gary , Hatfull Graham , Carrière Christian , Kumar Vanaja , Chan John , Jacobs William R. 
Published: December 2019

ABSTRACT

Detecting antibiotic resistance in
Mycobacterium tuberculosis
is becoming increasingly important with the global recognition of drug-resistant strains and their adverse impact on clinical outcomes. Current methods of susceptibility testing are either time-consuming or costly; rapid, reliable, simple, and inexpensive methods would be highly desirable, especially in the developing world where most tuberculosis is found. The luciferase reporter phage is a unique reagent well-suited for this purpose: upon infection with viable mycobacteria, it produces quantifiable light which is not observed in mycobacterial cells treated with active antimicrobials. In this report, we describe a modification of our original assay, which allows detection of the emitted light with a Polaroid film box designated the Bronx Box. The technique has been applied to 25
M. tuberculosis
reference and clinical strains, and criteria are presented which allow rapid and simple discrimination among strains susceptible or resistant to isoniazid and rifampin, the major antituberculosis agents.
Fatal Disseminated
Trichoderma longibrachiatum
Infection in an Adult Bone Marrow Transplant Patient: Species Identification and Review of the Literature
Authors: Richter S. , Cormican M. G. , Pfaller M. A. , Lee C. K. , Gingrich R. , Rinaldi M. G. , Sutton D. A. 
Published: December 2019

ABSTRACT

Trichoderma longibrachiatum
was recovered from stool surveillance cultures and a perirectal ulcer biopsy specimen from a 29-year-old male who had received an allogeneic bone marrow transplant for acute lymphoblastic leukemia. The amphotericin B (2.0 μg/ml) and itraconazole (1.0 μg/ml) MICs for the organism were elevated. Therapy with these agents was unsuccessful, and the patient died on day 58 posttransplantation. At autopsy, histologic sections from the lungs, liver, brain, and intestinal wall showed infiltration by branching septate hyphae. Cultures were positive for
Trichoderma longibrachiatum
. While
Trichoderma
species have been recognized to be pathogenic in profoundly immunosuppressed hosts with increasing frequency, this is the first report of probable acquisition through the gastrointestinal tract. Salient features regarding the identification of molds in the
Trichoderma longibrachiatum
species aggregate are presented.
Identification of
Vibrio parahaemolyticus
Strains at the Species Level by PCR Targeted to the
toxR
Gene
Authors: Kim Yung Bu , Okuda Jun , Matsumoto Chiho , Takahashi Naoki , Hashimoto Satoru , Nishibuchi Mitsuaki 
Published: December 2019

ABSTRACT

The DNA colony hybridization test with the polynucleotide probe for
Vibrio parahaemolyticus toxR
gene was performed. All 373 strains of
V. parahaemolyticus
gave positive results, and the strains belonging to four other
Vibrio
species including
Vibrio alginolyticus
gave weakly positive results, suggesting that
toxR
sequence variation may reflect the phylogenetic relationships of
Vibrio
species. We then established a
toxR
-targeted PCR protocol for the specific detection of
V. parahaemolyticus
.
Aspergillus
Meningitis: Diagnosis by Non-Culture-Based Microbiological Methods and Management
Authors: Verweij Paul E. , Brinkman Kees , Kremer Herbert P. H. , Kullberg Bart-Jan , Meis Jacques F. G. M. 
Published: December 2019

ABSTRACT

The performance of antibody detection, antigen detection, and
Aspergillus
genus-specific PCR for diagnosing
Aspergillus
meningitis was investigated with 26 cerebrospinal fluid (CSF) samples obtained from a single patient with proven infection caused by
Aspergillus fumigatus
. Immunoglobulin G antibodies directed against
Aspergillus
were not detected by enzyme-linked immunosorbent assay in CSF or serum. The antigen galactomannan was detected in the CSF 45 days before a culture became positive, and
Aspergillus
DNA was detected 4 days prior to culture. Decline of the galactomannan antigen titer in the CSF during treatment with intravenous and intraventricular amphotericin B and intravenous voriconazole corresponded with the clinical response to treatment.
Identification of a Novel Genotype of Hepatitis G Virus in Southeast Asia
Authors: Naito Hideo , Win Khin Maung , Abe Kenji 
Published: December 2019

ABSTRACT
Hepatitis G virus (HGV) isolates obtained from 20 Myanmarese and 10 Vietnamese subjects were analyzed. A cluster of isolates not belonging to any known genotype of HGV was found in five Myanmarese subjects and three Vietnamese subjects by phylogenetic analysis, and we classified this new genotype as type 4. These results revealed that the HGV genome can be classified into at least four major genotypes.
PCR-Based Restriction Pattern Typing of the
vacA
Gene Provides Evidence for a Homogeneous Group among
Helicobacter pylori
Strains Associated with Peptic Ulcer Disease
Authors: Donati Manuela , Storni Elisa , D’Apote Lucia , Moreno Sandra , Tucci Antonio , Poli Loris , Cevenini Roberto 
Published: December 2019

ABSTRACT

The results of PCR-based molecular typing of
Helicobacter pylori
strains by restriction fragment length polymorphism analysis of a 1,161-bp nucleotide sequence of the midregion of the
vacA
gene are reported. A total of 48
H. pylori
strains isolated from gastric biopsy specimens obtained from 18 patients with peptic ulcer dyspepsia, 15 patients with nonulcer dyspepsia, and 15 asymptomatic
H. pylori
-infected subjects were studied. Highly heterogeneous restriction patterns were obtained by digestion of PCR products with
Sau
II,
Bgl
II, and
Hha
I, whereas
Hae
III digestion resulted in a strictly homogeneous profile for
H. pylori
strains isolated from 14 of 18 (77.7%) patients with peptic ulcer dyspepsia, but a strictly homogeneous profile was found for strains from only 8 of 15 (53.3%) patients with nonulcer dyspepsia (
P
= 0.163) and 5 of 15 (33.3%) asymptomatic
H. pylori
-infected subjects (
P
= 0.014). A potentially important aspect of the results obtained is the clinical relevance, since a single restriction pattern seems to be able to identify the majority of
H. pylori
strains associated with peptic ulcer disease.
Identification of Nonlipophilic Corynebacteria Isolated from Dairy Cows with Mastitis
Authors: Hommez Jozef , Devriese Luc A. , Vaneechoutte Mario , Riegel Philippe , Butaye Patrick , Haesebrouck Freddy 
Published: December 2019

ABSTRACT

Nonlipophilic corynebacteria associated with clinical and subclinical mastitis in dairy cows were found to belong to four species:
Corynebacterium amycolatum
,
Corynebacterium ulcerans
,
Corynebacterium pseudotuberculosis
, and
Corynebacterium minutissimum
. These species may easily be confused. However, clear-cut differences between
C. ulcerans
and
C. pseudotuberculosis
were found in their acid production from maltotriose and ethylene glycol, susceptibility to vibriostatic agent O129, and alkaline phosphatase. Absence of growth at 20°C and lack of α-glucosidase and 4MU-α-
d
-glycoside hydrolysis activity differentiated
C. amycolatum
from
C. pseudotuberculosis
and
C. ulcerans
. The mastitis
C. pseudotuberculosis
strains differed from the biovar equi and ovis reference strains and from caprine field strains in their colony morphologies and in their reduced inhibitory activity on staphylococcal β-hemolysin.
C. amycolatum
was the most frequently isolated nonlipophilic corynebacterium.
Molecular Markers Demonstrate that the First Described Multidrug-Resistant
Mycobacterium bovis
Outbreak Was Due to
Mycobacterium tuberculosis
Authors: Gutiérrez M. C. , Galán J. C. , Blázquez J. , Bouvet E. , Vincent V. 
Published: December 2019

ABSTRACT

We genetically characterized multidrug-resistant
Mycobacterium tuberculosis
complex strains which caused a nosocomial outbreak of tuberculosis affecting six human immunodeficiency virus (HIV)-positive patients and one HIV-negative staff member (E. Bouvet, E. Casalino, G. Mendoza-Sassi, S. Lariven, E. Vallée, M. Pernet, S. Gottot, and F. Vachon, AIDS 7:1453–1460, 1993). The strains showed all the phenotypic characteristics of
Mycobacterium bovis
. They presented a high copy number of IS
6110
, the spacers 40 to 43 in the direct repeat locus, and the
mtp40
fragment. They lacked the G-A mutation at position 285 in the
oxyR
gene and the C-G mutation at position 169 in the
pncA
gene. These genetic characteristics revealed that these were dysgonic, slow-growing
M. tuberculosis
strains mimicking the
M. bovis
phenotype, probably as a consequence of cellular alterations associated with the multidrug resistance. Spoligotyping and IS
6110
restriction fragment length polymorphism (RFLP) analysis confirmed that the outbreak was due to a single strain. However, the IS
6110
RFLP pattern of the strain isolated from the last patient, diagnosed three years after the index case, differed slightly from the patterns of the other six strains. A model of a possible genetic event is presented to explain this divergence. This study stresses the value of using several independent molecular markers to identify multidrug-resistant tubercle bacilli.
Molecular Evidence for Heterogeneity of the Multiple-Drug-Resistant
Mycobacterium tuberculosis
Population in Scotland (1990 to 1997)
Authors: Fang Z. , Doig C. , Rayner A. , Kenna D. T. , Watt B. , Forbes K. J. 
Published: December 2019

ABSTRACT

Multiple-drug-resistant
Mycobacterium tuberculosis
(MDR-MTB) has been well studied in hospitals or health care institutions and in human immunodeficiency virus-infected populations. However, the characteristics of MDR-MTB in the community have not been well investigated. An understanding of its prevalence and circulation within the community will help to estimate the problem and optimize the strategies for control and prevention of its development and transmission. In this study, MDR-MTB isolates from Scotland collected between 1990 and 1997 were characterized, along with non-drug-resistant isolates. The results showed that they were genetically diverse, suggesting they were unrelated to each other and had probably evolved independently. Several new alleles of
rpoB
,
katG
, and
ahpC
were identified:
rpoB
codon 525 (ACC→AAC; Thr525Asn);
katG
codon 128 (CGG→CAG; Arg128Gln) and codon 291 (GCT→CCT; Ala291Pro); and the
ahpC
synonymous substitution at codon 6 (ATT→ATC). One of the MDR-MTB isolates from an Asian patient had an IS
6110
restriction fragment length polymorphism pattern very similar to that of the MDR-MTB W strain and had the same drug resistance-related alleles but did not have any epidemiological connection with the W strains. Additionally, a cluster of
M. tuberculosis
isolates was identified in our collection of 715 clinical isolates; the isolates in this cluster had genetic backgrounds very similar to those of the W strains, one of which had already developed multiple drug resistances. The diverse population of MDR-MTB in Scotland, along with a low incidence of drug-resistant
M. tuberculosis
, has implications for the control of the organism and prevention of its spread.
Age-Dependent Acquisition of Hepatitis G Virus/GB Virus C in a Nonrisk Population: Detection of the Virus by Antibodies
Authors: Feucht Heinz-Hubert , Schröter Matthias , Zöllner Bernhard , Polywka Susanne , Laufs Rainer 
Published: December 2019

ABSTRACT
Until now there have been few seroepidemiological data for hepatitis G virus/GB virus type C (HGV/GBV-C). A four-antigen HGV/GBV-C immunoblot was established to examine 446 serum specimens from healthy individuals without risk factors for parenteral viral transmission. These individuals were divided into seven groups according to age. Seroprevalence rates were low for children and adolescents (5.6%) and increased for the age groups assumed to be the most sexually active (15.3 to 26.8%). Remarkably, none of the 80 individuals who tested positive for HGV/GBV-C antibodies were simultaneously positive for HGV/GBV-C viremia. From our data we conclude that HGV/GBV-C infection is widespread in the general population (16 to 25%). The development of an antibody response is associated with clearance of HGV/GBV-C viremia. Due to the lack of risk factors for HGV/GBV-C infection of blood, other efficient transmission routes must exist. It must be assumed that HGV/GBV-C transmission may be linked to sexual activity.
Multicenter Comparison of PCR Assays for Detection of Human Herpesvirus 8 DNA in Semen
Authors: Pellett Philip E. , Spira Thomas J. , Bagasra Omar , Boshoff Chris , Corey Lawrence , de Lellis Laura , Huang Meei-Li , Lin Jung-Chung , Matthews Steve , Monini Paolo , Rimessi Paola , Sosa Carlos , Wood Charles , Stewart John A. 
Published: December 2019

ABSTRACT

Reported prevalences of human herpesvirus 8 (HHV-8) (Kaposi’s sarcoma-associated herpesvirus) in semen have ranged widely. This is possibly due to differences in assay sensitivity, geographic or population-based differences in the true presence of the virus in semen, and PCR contamination. This study assessed interlaboratory sensitivity and reproducibility in the analysis of blinded experimental panels, each consisting of 48 specimens and being composed of semen specimens from different healthy artificial-insemination donors (
n
= 30) and human immunodeficiency virus (HIV)-infected patients (
n
= 7) plus positive (
n
= 4) and negative (
n
= 7) controls. The experimental panels analyzed in each laboratory were identical except for being independently coded. Of 10 experiments done in five laboratories, 5 experiments from three laboratories had evidence of PCR contamination; all instances of contamination were in the context of nested PCR procedures. In the experiments with no false-positive results, HHV-8 DNA was detected in three (8%) of the 37 semen specimens (two from artificial-insemination donors and one from an HIV-positive patient) but in only 3 (1.6%) of the 184 PCRs in which these specimens were analyzed. This suggests that HHV-8 DNA is present in semen at concentrations that can be too low to allow its consistent detection. This study emphasizes the importance of performing blinded, multi-institution experiments to provide a coherent basis for comparing results and to motivate standardization of methods.
Discrimination of
Burkholderia multivorans
and
Burkholderia vietnamiensis
from
Burkholderia cepacia
Genomovars I, III, and IV by PCR
Authors: Bauernfeind Adolf , Schneider Ines , Jungwirth Renate , Roller Carsten 
Published: December 2019

ABSTRACT

We present a PCR procedure for identification of
Burkholderia cepacia
,
Burkholderia multivorans
, and
Burkholderia vietnamiensis
. 16S and 23S ribosomal DNAs (rDNAs) of
B. multivorans
and
B. vietnamiensis
were sequenced and aligned with published sequences for definition of species-specific 18-mer oligonucleotide primers. Specific antisense 16S rDNA primers (for
B. cepacia
, 5′-AGC ACT CCC RCC TCT CAG-3′; for
B. multivorans
, 5′-AGC ACT CCC GAA TCT CTT-3′) and 23S rDNA primers (for
B. vietnamiensis
, 5′-TCC TAC CAT GCG TGC AA-3′) were paired with a general sense primer of 16S rDNAs (5′-AGR GTT YGA TYM TGG CTC AG-3′) or with a sense primer of 23S rDNA (5′-CCT TTG GGT CAT CCT GGA-3′). PCR with these primers under optimized conditions is appropriate to specifically and rapidly identify
B. multivorans
,
B. vietnamiensis
, and
B. cepacia
(genomovars I, III, and IV are not discriminated). In comparison with the polyphasic taxonomic analyses presently necessary for species and genomovar identification within the
B. cepacia
complex, our procedure is more rapid and easier to perform and may contribute to clarifying the clinical significance of individual members of the complex in cystic fibrosis.
High Aspartyl Proteinase Production and Vaginitis in Human Immunodeficiency Virus-Infected Women
Authors: de Bernardis F. , Mondello F. , Scaravelli G. , Pachì A. , Girolamo A. , Agatensi L. , Cassone A. 
Published: December 2019

ABSTRACT

Vaginal isolates of
Candida albicans
from human immunodeficiency virus-positive (HIV
+
) and HIV
−
women with or without candidal vaginitis were examined for secretory aspartyl proteinase (Sap) production in vitro and in vivo and for the possible correlation of Sap production with pathology and antimycotic susceptibility in vitro. HIV
+
women with candidal vaginitis were infected by strains of
C. albicans
showing significantly higher levels of Sap, a virulence enzyme, than strains isolated from HIV
+
,
C. albicans
carrier subjects and HIV
−
subjects with vaginitis. The greater production of Sap in vitro was paralleled by greater amounts of Sap in the vaginal fluids of infected subjects. In an estrogen-dependent, rat vaginitis model, a strain of
C. albicans
producing a high level of Sap that was isolated from an HIV
+
woman with vaginitis was more pathogenic than a strain of
C. albicans
that was isolated primarily from an HIV
−
,
Candida
carrier. In the same model, pepstatin A, a strong Sap inhibitor, exerted a strong curative effect on experimental vaginitis. No correlation was found between Sap production and antimycotic susceptibility, as most of the isolates were fully susceptible to fluconazole, itraconazole, and other antimycotics, regardless of their source (subjects infected with strains producing high or low levels of Sap, subjects with vaginitis or carrier subjects, or subjects with or without HIV). Thus, high Sap production is associated with virulence of
C. albicans
but not with fungal resistance to fluconazole in HIV-infected subjects, and Sap is a potentially new therapeutic target in candidal vaginitis.