bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection and Species Determination of Malaria Parasites by PCR: Comparison with Microscopy and with ParaSight-F and ICT Malaria Pf Tests in a Clinical Environment
Authors: Tham Jill M. , Lee Szu Hee , Tan Theresa M. C. , Ting Robert C. Y. , Kara Ursula A. K. 
Published: December 2019

ABSTRACT

A rapid procedure for the diagnosis of malaria infections directly from dried blood spots by PCR amplification was evaluated with samples from 52 patients.
Plasmodium
infections were identified with a genus-specific primer set, and species differentiation between
Plasmodium falciparum
and
Plasmodium vivax
was analyzed by multiplex PCR. The PCR test with any of the three primer sets was able to detect as few as four parasites per microliter by gel electrophoresis or by nonisotopic paper hybridization chromatography. The diagnoses obtained by PCR correlated closely with those obtained by Giemsa staining except for two samples observed to have mixed
P. falciparum-P. vivax
infections. These were initially missed by microscopic analysis. In comparison with antigen-capture assays for
P. falciparum
, the PCR assays were able to detect three infections that were missed by the ParaSight-F test. The PCR test was negative for nine ParaSight-F-positive samples and one ICT Malaria Pf-positive sample, and these were confirmed to be false-positive results. The PCR thus gave no false-negative or false-positive results. Patients undergoing antimalarial therapy were also monitored by the PCR assay. Four of seven patients who were PCR positive for
P. vivax
at the time of discharge were later readmitted to the hospital with a recurrence of
P. vivax
infection. We would like to propose that PCR is a sensitive and easy method that can serve as a useful addition to microscopy for the diagnosis and the clinical monitoring of treatment of malaria.
GB Virus C/Hepatitis G Virus Groups and Subgroups: Classification by a Restriction Fragment Length Polymorphism Method Based on Phylogenetic Analysis of the 5′ Untranslated Region
Authors: Quarleri J. F. , Mathet V. L. , Feld M. , Ferrario D. , della Latta M. P. , Verdun R. , Sánchez D. O. , Oubiña J. R. 
Published: December 2019

ABSTRACT

A phylogenetic tree based on 150 5′ untranslated region sequences deposited in GenBank database allowed segregation of the sequences into three major groups, including two subgroups, i.e., 1, 2a, 2b, and 3, supported by bootstrap analysis. Restriction site analysis of these sequences predicted that
Hin
fI and either
Aat
II or
Aci
I could be used for genomic typing with 99.4% accuracy. cDNA sequencing and subsequent alignment of 21 Argentine GB virus C/hepatitis G virus strains confirmed restriction fragment length polymorphism patterns theoretically predicted. This method may be useful for a rapid screening of samples when either epidemiological or transmission studies of this agent are carried out.
Detection of Multidrug-Resistant
Salmonella enterica
Serotype
typhimurium
DT104 Based on a Gene Which Confers Cross-Resistance to Florfenicol and Chloramphenicol
Authors: Bolton Lance F. , Kelley Lynda C. , Lee Margie D. , Fedorka-Cray Paula J. , Maurer John J. 
Published: December 2019

ABSTRACT

Salmonella enterica
serotype
typhimurium
(
S. typhimurium
) DT104 (DT104) first emerged as a major pathogen in Europe and is characterized by its pentadrug-resistant pattern. It has also been associated with outbreaks in the United States. The organism typically carries resistance to ampicillin, chloramphenicol, streptomycin, sulfonamides, and tetracycline. The mechanism of chloramphenicol resistance in DT104 was determined by producing antibiotic-resistant
Escherichia coli
host strain clones from DT104 DNA. DNA from chloramphenicol-resistant clones was sequenced, and probes specific for the genes

flo
S. typhimurium

(

flo
St

),
int
,
invA
, and
spvC
were produced for colony blot hybridizations. One hundred nine
Salmonella
isolates, including 44 multidrug-resistant DT104 isolates, were tested to evaluate the specificities of the probes. The gene

flo
St

, reported in this study, confers chloramphenicol and florfenicol resistance on
S. typhimurium
DT104. Florfenicol resistance is unique to
S. typhimurium
DT104 and multidrug-resistant
S. typhimurium
isolates with the same drug resistance profile among all isolates evaluated. Of 44 DT104 isolates tested, 98% were detected based on phenotypic florfenicol resistance and 100% had the

flo
St

-positive genotype. Resistances to florfenicol and chloramphenicol are conferred by the gene

flo
St

, described in this paper. Presumptive identification of
S. typhimurium
DT104 can be made rapidly based on the presence of the

flo
St

gene or its resulting phenotype.
Comparison of Cytomegalovirus Loads in Plasma and Leukocytes of Patients with Cytomegalovirus Retinitis
Authors: Jabs Douglas A. , Forman Michael , Enger Cheryl , Jackson J. Brooks 
Published: December 2019

ABSTRACT

Cytomegalovirus (CMV) DNA loads in paired leukocyte and plasma samples from 199 patient visits by 66 patients with CMV retinitis were determined. Leukocyte CMV load determinations had a greater range of values (mean, 24,587 copies/10
6
leukocytes; maximum, 539,000) than did plasma CMV load determinations (mean, 10,302 copies/ml; maximum, 386,000), and leukocyte viral loads were detectable in a greater proportion of patients at the time of diagnosis of CMV retinitis prior to initiation of anti-CMV therapy (82%) than were plasma viral loads (64%) (
P
= 0.0078). Agreement with CMV blood cultures was slightly better for plasma (κ = 0.68) than for leukocytes (κ = 0.53), due to a greater proportion of patients with detectable viral loads in leukocytes having negative blood cultures.
Methicillin-ResistantStaphylococcus aureusOutbreak in a Veterinary Teaching Hospital: Potential Human-to-Animal Transmission
Authors: Seguin Jennifer C. , Walker Robert D. , Caron John P. , Kloos Wesley E. , George Carol G. , Hollis Richard J. , Jones Ronald N. , Pfaller Michael A. 
Published: December 2019

ABSTRACTDuring a 13-month period, 11 equine patients visiting a veterinary teaching hospital for various diagnostic and surgical procedures developed postprocedural infections from which methicillin (oxacillin)-resistantStaphylococcus aureus(MRSA) strains were isolated. TheS. aureusisolates were identified by conventional methods that included Gram staining, tests for colonial morphology, tests for clumping factor, and tests for coagulase and urease activities and were also tested with the API STAPH IDENT system. Antimicrobial susceptibility tests were performed by the disk diffusion method. The biochemical profile and antibiogram of each isolate suggested that the isolates may have come from a common source. Because MRSA strains are very uncommon animal isolates but are rather common human isolates, a nasal swab specimen for culture was collected voluntarily from five persons associated with equine surgery and recovery in an attempt to identify a possible source of the organisms. MRSA strains were isolated from three of the five people, with one person found to be colonized with two biotypes of MRSA. The MRSA isolates from the people appeared to be identical to the isolates from horses. Further study of the isolates includedSmaI andEagI macrorestriction analysis by pulsed-field gel electrophoresis conducted in two different laboratories. The results indicated that both the equine and human isolates were members of a very closely related group which appear to have originated from a common source. On the basis of the pattern associated with the infection, it is speculated that the members of the Veterinary Teaching Hospital staff were the primary source of the infection, although the specific mode of transmission is unclear.
Mycoplasma penetrans
and Other Mycoplasmas in Urine of Human Immunodeficiency Virus-Positive Children
Authors: Hussain Althaf I. , Robson William Lane M. , Kelley Robin , Reid Tanya , Gangemi J. David 
Published: December 2019

ABSTRACT

Urine samples from children with human immunodeficiency virus (HIV) infection and healthy controls were examined for mycoplasmas by culture. Standard biochemical assays, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and PCR (16S and 16S-23S spacer rRNA region) were used for identification of isolates. Mycoplasmas were identified from 13 (87%) of 15 HIV-positive patients and 3 (20%) of 15 HIV-negative control patients. The frequency and type of mycoplasma varied with the severity of HIV infection.
Mycoplasma penetrans
,
Mycoplasma pirum
,
Mycoplasma fermentans
, and
Mycoplasma genitalium
were isolated from patients with severe immunodeficiency.
Mycoplasma hominis
and
Ureaplasma urealyticum
were isolated more frequently from children in the early stages of HIV infection and from HIV-negative patients.
Mycoplasma penetrans
was isolated from one (50%) of two patients in Centers for Disease Control and Prevention (CDC) group B and from five (55.5%) of nine pediatric patients with AIDS (CDC group C). This is the first report that indicates that “AIDS-associated” mycoplasmas are more common in HIV-infected children than in HIV-negative controls.
Clinical and Pathologic Evaluation of ChronicBartonella henselaeorBartonella clarridgeiaeInfection in Cats
Authors: Kordick Dorsey L. , Brown Talmage T. , Shin KwangOk , Breitschwerdt Edward B. 
Published: December 2019

ABSTRACTHumanBartonellainfections result in diverse medical presentations, whereas many cats appear to tolerate chronic bacteremia without obvious clinical abnormalities. Eighteen specific-pathogen-free cats were inoculated withBartonella henselae- and/orBartonella clarridgeiae-infected cat blood and monitored for 454 days. Relapsing bacteremia did not correlate with changes in protein profiles or differences in antigenic protein recognition. Intradermal skin testing did not induce a delayed type hypersensitivity reaction to cat scratch disease skin test antigen. Thirteen cats were euthanatized at the end of the study. Despite persistent infection, clinical signs were minimal and gross necropsy results were unremarkable. Histopathology revealed peripheral lymph node hyperplasia (in all of the 13 cats), splenic follicular hyperplasia (in 9 cats), lymphocytic cholangitis/pericholangitis (in 9 cats), lymphocytic hepatitis (in 6 cats), lymphoplasmacytic myocarditis (in 8 cats), and interstitial lymphocytic nephritis (in 4 cats). Structures suggestive ofBartonellawere visualized in some Warthin-Starry stained sections, andBartonellaDNA was amplified from the lymph node (from 6 of the 13 cats), liver (from 11 cats) heart (from 8 cats), kidney (from 9 cats), lung (from 2 cats), and brain (from 9 cats). This study indicates thatB. henselaeorB. clarridgeiaecan induce chronic infection following blood transfusion in specific-pathogen-free cats and thatBartonellaDNA can be detected in blood, brain, lymph node, myocardium, liver, and kidney tissues of both blood culture-positive cats and blood culture-negative cats. Detection of histologic changes in these cats supports a potential etiologic role forBartonellaspecies in several idiopathic disease processes in cats.
Ability of a Rapid Serology Test To Detect Seroconversion to Herpes Simplex Virus Type 2 Glycoprotein G Soon after Infection
Authors: Ashley Rhoda L. , Eagleton Marie , Pfeiffer Natasha 
Published: December 2019

ABSTRACT

Sera (
n
= 188) from 29 patients with first-episode genital herpes simplex virus type 2 (HSV-2) infections were tested by POCkit-HSV-2 and Western blot (WB) to determine the speed of seroconversion. The median time to detection of HSV-2 antibody was 13 days (range, 3 to 102 days) by the POCkit-HSV-2 test versus 13 days (range, 2 to 58 days) for WB.
Cytolethal Distending Toxin Genes in
Campylobacter jejuni
and
Campylobacter coli
Isolates: Detection and Analysis by PCR
Authors: Eyigor Aysegul , Dawson Karl A. , Langlois Bruce E. , Pickett Carol L. 
Published: December 2019

ABSTRACT

Campylobacter jejuni
produces a toxin called cytolethal distending toxin (CDT). Knowledge of the prevalence and homogeneity of
Campylobacter
sp.
cdt
genes is incomplete. In this work, we identified four PCR primer pairs that collectively amplified
cdt
genes in all of the
C. jejuni
and
Campylobacter coli
strains tested. Restriction analyses of the
cdt
PCR products showed clear differences between the
cdt
genes of these two species, yet there were few heterogeneities noted between members of the same species. Consequently, it may be possible to speciate
C. jejuni
and
C. coli
isolates on the basis of restriction patterns within their
cdt
genes.
Assessment of Strain Relatedness among
Salmonella
Serotypes Salinatis, Duisburg, and Sandiego by Biotyping, Ribotyping, IS
200
Fingerprinting, and Pulsed-Field Gel Electrophoresis
Authors: Old David C. , Rankin Shelley C. , Crichton Pamela B. 
Published: December 2019

ABSTRACT

Salinatis (antigenic formula, 4,12:d:eh:enz
15
) is a rare
Salmonella
serotype currently designated a triphasic variant of the diphasic serotype Duisburg (
1
,4,12,
27
:d:enz
15
) (underlining indicates that the O antigen is determined by phage lysogenization). Salinatis could also be related to serotype Sandiego (4,[5],12:eh:enz
15
), from which it might have been derived by loss of H-d flagellin genes. Nineteen
Salmonella
strains of serotypes Salinatis, Duisburg, and Sandiego were examined by biotyping,
Pvu
II and
Sma
I ribotyping, IS
200
fingerprinting, and pulsed-field gel electrophoretic profiling. Results from these methods, used alone or together, indicate that serotype Salinatis is more likely to be related to serotype Sandiego than to serotype Duisburg. For future lists of serotype names, it is recommended that Salinatis be considered a variant of Sandiego.
Use of a Murine O-Antigen-Specific Monoclonal Antibody To IdentifyAcinetobacterStrains of Unnamed Genomic Species 13 Sensu Tjernberg and Ursing
Authors: Pantophlet Ralph , Brade Lore , Brade Helmut 
Published: December 2019

ABSTRACTA monoclonal antibody against the O-antigenic polysaccharide chain of the lipopolysaccharide (LPS) ofAcinetobacterstrains belonging to the unnamed genomic species 13 Sensu Tjernberg and Ursing (13TU) was obtained after immunization of BALB/c mice with heat-killed bacteria and was characterized by enzyme immunoassay and Western blot analysis, by use of LPS and proteinase K-treated bacterial lysates, analyses in which the antibody was shown to be highly specific for the homologous antigen. In addition, when tested in dot and Western blots, reactivity was observed with 9 of 18Acinetobacterstrains of genomic species 13TU which had been isolated in Germany and Denmark; no reactivity was observed with strains of other genomic species, including the closely related genomic groups 1 (A. calcoaceticus), 2 (A. baumannii), and 3 (unnamed), or with other gram-negative bacteria. The antibody described here represents a convenient reagent for the simple, economical, and accurate differentiation of clinical isolates of genomic species 13TU from otherAcinetobacterstrains. Although the antibody does not identify all isolates of this genomic group, it is evident that it will be a useful reagent in the development of a serotyping scheme for clinical laboratories.
High Prevalence of TT Virus Infection in Healthy Children and Adults and in Patients with Liver Disease in Taiwan
Authors: Hsieh Sen-Yung , Wu Yin-Hua , Ho Yu-Pin , Tsao Kuo-Chien , Yeh Chau-Ting , Liaw Yun-Fan 
Published: December 2019

ABSTRACT
A newly identified DNA virus, named TT virus (TTV), was found to be related to transfusion-associated hepatitis. We conducted the following experiments to evaluate its pathogenic role in liver disease and potential modes of transmission. We used PCR to detect TTV DNA in serum. The rates of TTV viremia in 13 patients with idiopathic acute hepatitis, 14 patients with idiopathic fulminant hepatitis, 22 patients with chronic hepatitis, and 19 patients with cirrhosis of the liver were 46, 64, 55, and 63%, respectively, and were not significantly different from those in 50 healthy control subjects (53%). PCR products derived from seven patients with liver disease and three healthy controls were cloned and then subjected to phylogenetic analyses, which failed to link a virulent strain of TTV to severe liver disease. TTV infection was further assessed in an additional 148 subjects with normal liver biochemical tests, including 30 newborns (sera collected from the umbilical cord), 23 infants, 16 preschool children, 21 individuals of an age prior to that of sexual experience (aged 6 to 15 years), 15 young adults (aged under 30 years), and 43 individuals older than 30 years. The rates of TTV viremia were 0, 17, 25, 33, 47, and 54%, respectively. These findings suggest that TTV is transmitted mainly via nonparenteral daily contact and frequently occurs very early in life and that TTV infection does not have a significant effect on liver disease.
Serotyping of Adenoviruses on Conjunctival Scrapings by PCR and Sequence Analysis
Authors: Takeuchi Satoshi , Itoh Norihiko , Uchio Eiichi , Aoki Koki , Ohno Shigeaki 
Published: December 2019

ABSTRACT
To detect and identify adenovirus (Ad), we investigated hypervariable regions (HVRs) of Ad by using a combination of PCR and direct sequencing (PCR-sequence) method. Primers for nested PCR to amplify the conserved region in the hexon protein containing HVRs were designed based on hexon gene sequences derived from GenBank. These two primer sets amplified a DNA fragment of 7 HVRs from 16 prototypes of Ad, which were divided into five subgenera, including seven serotypes that are the predominant causative agents of acute conjunctivitis in Japan, and from 31 recent conjunctival scraping specimens from patients with adenoviral conjunctivitis. HVR DNA sequences were determined by means of universal sequence primers. Analysis of the predicted amino acid homology of HVRs among Ad prototypes suggested three regions, HVR4, -5, and -7, to be candidates for the neutralization epitopes. The clinical serotype of specimens was determined by the PCR-sequence method with reference to these three HVRs. The serotype determined according to this method was identical to that obtained by culture isolation and the neutralization test (NT) in all scraping samples, whereas the results of this method did not match PCR and restriction fragment length polymorphism (PCR-RFLP) analysis in five samples. It took only three days to detect Ad and to identify the serotype, in contrast to culture isolation-NT, which took at least 2 weeks. These findings indicate that our newly developed PCR-sequence method is applicable for the detection and serotyping of human Ads.
Evaluation of Three Nucleic Acid Amplification Methods for Direct Detection of
Mycobacterium tuberculosis
Complex in Respiratory Specimens
Authors: Wang S. X. , Tay L. 
Published: December 2019

ABSTRACT

Two hundred thirty respiratory specimens from 230 patients were analyzed by using COBAS AMPLICOR PCR, Amplified
Mycobacterium tuberculosis
Direct Test, and ligase chain reaction methods. Results were compared with those of smear microscopy and radiometric culture (Bactec) methods. No significant differences were observed among the results of the three methods, which are acceptable for direct detection of
M. tuberculosis
complex in respiratory specimens.
Development of a High-Throughput Quantitative Assay for Detecting Herpes Simplex Virus DNA in Clinical Samples
Authors: Ryncarz Alexander J. , Goddard James , Wald Anna , Huang Meei-Li , Roizman Bernard , Corey Lawrence 
Published: December 2019

ABSTRACT

We have developed a high-throughput, semiautomated, quantitative fluorescence-based PCR assay to detect and type herpes simplex virus (HSV) DNA in clinical samples. The detection assay, which uses primers to the type-common region of HSV glycoprotein B (gB), was linear from <10 to 10
8
copies of HSV DNA/20 μl of sample. Among duplicate samples in reproducibility runs, the assay showed less than 5% variability. We compared the fluorescence-based PCR assay with culture and gel-based liquid hybridization system with 335 genital tract specimens from HSV type 2 (HSV-2)-seropositive persons attending a research clinic and 380 consecutive cerebrospinal fluid (CSF) samples submitted to a diagnostic virology laboratory. Among the 162 culture-positive genital tract specimens, TaqMan PCR was positive for 157 (97%) specimens, whereas the quantitative-competitive PCR was positive for 144 (89%) specimens. Comparisons of the mean titer of HSV DNA detected by the two assays revealed that the mean titer detected by the gel-based system was slightly higher (median, 1 log). These differences in titers were in part related to the fivefold difference in the amount of HSV DNA used in the amplicon standards with the two assays. Among the 380 CSF samples, 42 were positive by both assays, 13 were positive only by the assay with the agarose gel, and 3 were positive only by the assay with the fluorescent probe. To define the subtype of HSV DNA detected in the screening assay, we also designed one set of primers which amplifies the gG regions of both types of HSV and probes which are specific to either HSV-1 (gG1) or HSV-2 (gG2). These probes were labeled with different fluorescent dyes (6-carboxyfluorescein for gG2 and 6-hexachlorofluorescein for gG1) to enable detection in a single PCR. In mixing experiments the probes discriminated the correct subtype in mixtures with up to a 7-log-higher concentration of the opposite subtype. The PCR typing results showed 100% concordance with the results obtained by assays with monoclonal antibodies against HSV-1 or HSV-2. Thus, while the real-time PCR is slightly less sensitive than the gel-based liquid hybridization system, the high throughput, the lack of contamination during processing, the better reproducibility, and the better ability to type the isolates rapidly make the real-time PCR a valuable tool for clinical investigation and diagnosis of HSV infection.
Characterization of
Bacteroides forsythus
Strains from Cat and Dog Bite Wounds in Humans and Comparison with Monkey and Human Oral Strains
Authors: Hudspeth M. K. , Gerardo S. Hunt , Maiden M. F. J. , Citron D. M. , Goldstein E. J. C. 
Published: December 2019

ABSTRACT

Bacteroides forsythus
strains recovered from cat and dog bite wound infections in humans (
n
= 3), monkey oral strains (
n
= 3), and the human oral ATCC 43037 type strain were characterized by using phenotypic characteristics, enzymatic tests, whole cell fatty acid analysis, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) analysis, PCR fingerprinting, and 16S rDNA (genes coding for rRNA) sequencing. All three bite wound isolates grew on brucella agar supplemented with 5% sheep blood, vitamin K
1
, and hemin. These strains, unlike the ATCC strain and previously described monkey oral and human clinical strains, did not require
N
-acetylmuramic acid supplementation for growth as pure cultures. However, their phenotypic characteristics, except for catalase production, were similar to those of previously identified strains. PCR fingerprinting analysis showed differences in band patterns from the ATCC strain. Also, SDS-PAGE and whole cell fatty acid analysis indicated that the dog and cat bite wound strains were similar but not identical to the human
B. forsythus
ATCC 43037 type strain and the monkey oral strains. The rDNA sequence analysis indicated that the three bite wound isolates had 99.93% homology with each other and 98.9 and 99.22% homology with the human ATCC 43037 and monkey oral strains, respectively. These results suggest that there are host-specific variations within each group.