bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular Epidemiology of
Entamoeba
spp.: Evidence of a Bottleneck (Demographic Sweep) and Transcontinental Spread of Diploid Parasites
Authors: Ghosh Sudip , Frisardi Marta , Ramirez-Avila Lynn , Descoteaux Steven , Sturm-Ramirez Katherine , Newton-Sanchez Oscar Alberto , Santos-Preciado Jose Ignacio , Ganguly Chaiti , Lohia Anuradha , Reed Sharon , Samuelson John 
Published: December 2019

ABSTRACT

Entamoeba histolytica
causes amebic colitis and liver abscess in developing countries such as Mexico and India.
Entamoeba dispar
is morphologically identical but is not associated with disease. Here we determined the ploidy of
E. histolytica
and developed PCR-based methods for distinguishing field isolates of
E. histolytica
or
E. dispar
. Fluorescence in situ hybridization showed that
E. histolytica
trophozoites are diploid for five “single-copy” probes tested. Intergenic sequences between
superoxide dismutase
and
actin 3
genes of clinical isolates of
E. histolytica
from the New and Old Worlds were identical, as were those of
E. dispar
. These results suggest a bottleneck or demographic sweep in entamoebae which infect humans. In contrast,
E. histolytica
and
E. dispar
genes encoding repeat antigens on the surface of trophozoites (Ser-rich protein) or encysting parasites (chitinase) were highly polymorphic.
chitinase
alleles suggested that the early axenized strains of
E. histolytica
, HM-1 from Mexico City, Mexico, and NIH-200 from Calcutta, India, are still present and that similar
E. dispar
parasites can be identified in both the New and Old Worlds.
Ser-rich protein
alleles, which suggested the presence of the HM-1 strain in Mexico City, included some
E. histolytica
genes that predicted Ser-rich proteins with very few repeats. These results, which suggest diversifying selection at
chitinase
and
Ser-rich protein
loci, demonstrate the usefulness of these alleles for distinguishing clinical isolates of
E. histolytica
and
E. dispar
.
Evaluation of the Abbott LCx HIV-1 RNA Quantitative, a New Assay for Quantitative Determination of Human Immunodeficiency Virus Type 1 RNA
Authors: Zanchetta Nadia , Nardi Giampiero , Tocalli Loredana , Drago Lorenzo , Bossi Carla , Pulvirenti Francesco Renato , Galli Claudio , Gismondo Maria Rita 
Published: December 2019

ABSTRACT

A new quantitative reverse transcription (RT)-PCR assay for human immunodeficiency virus type 1 (HIV-1) RNA (Abbott LCx HIV RNA Quantitative assay) has been compared with the Organon NucliSens assay on 521 retrospective samples obtained from HIV-1-positive patients monitored during highly active antiretroviral therapy, 79 of whom were assayed also by the Chiron Quantiplex 3.0 system and on characterized panels. The LCx system showed a moderate correlation (
r
= 0.795) and gave higher results than the NucliSens system on 245 of 327 concordant positive samples, with similar sensitivity. Correlation with Quantiplex system results was higher (
r
= 0.943). LCx reproducibility was very good; the procedure was simple, well controlled, and rapid (up to 48 results in 7 h). The HIV RNA quantitative assay on the LCx system is suitable for routine use.
Results of a Quality Assurance Program for Detection of Cytomegalovirus Infection in the Pediatric Pulmonary and Cardiovascular Complications of Vertically Transmitted Human Immunodeficiency Virus Infection Study
Authors: Demmler Gail J. , Istas Allison , Easley Kirk A. , Kovacs Andrea ,   the Pediatric Pulmonary and Cardiovascular Complications of Vertically Transmitted HIV-1 Infection Study Group
Published: December 2019

ABSTRACT
A quality assurance program was established by the Pediatric Pulmonary and Cardiovascular Complications of Vertically Transmitted Human Immunodeficiency Virus Type 1 Infection Study Group for monitoring cytomegalovirus (CMV) antibody and culture results obtained from nine different participating laboratories. Over a 3-year period, every 6 months, each laboratory was sent by the designated reference laboratory six coded samples: three urine samples for CMV detection and three serum samples for CMV immunoglobulin G (IgG) and IgM antibody determination. Overall, the participating laboratories exhibited the following composite performance statistics, relative to the reference laboratory (sensitivity and specificity, respectively): 100 and 97.4% for CMV cultures, 95.5 and 94.4% for CMV IgG antibody assays, and 92.6 and 90.2% for CMV IgM assays. The practice of having individual laboratories use different commercial methods and reagents for CMV detection and antibody determination was successfully monitored and provided useful information on the comparable performance of different assays.
Diversity of Domain V of 23S rRNA Gene Sequence in Different
Enterococcus
Species
Authors: Tsiodras Sotirios , Gold Howard S. , Coakley Eoin P. G. , Wennersten Christine , Moellering Robert C. , Eliopoulos George M. 
Published: December 2019

ABSTRACT

The highly conserved central loop of domain V of 23S RNA (nucleotides 2042 to 2628;
Escherichia coli
numbering) is implicated in peptidyltransferase activity and represents one of the target sites for macrolide, lincosamide, and streptogramin B antibiotics. DNA encoding domain V (590 bp) of several species of
Enterococcus
was amplified by PCR. Twenty enterococcal isolates were tested, including
Enterococcus faecium
(six isolates),
Enterococcus faecalis
,
Enterococcus avium
,
Enterococcus durans
,
Enterococcus gallinarum
,
Enterococcus casseliflavus
(two isolates of each), and
Enterococcus raffinosus
,
Enterococcus mundtii
,
Enterococcus malodoratus
, and
Enterococcus hirae
(one isolate of each). For all isolates, species identification by biochemical testing was corroborated by 16S rRNA gene sequencing. The sequence of domain V of the 23S rRNA gene from
E. faecium
and
E. faecalis
differed from those of all other enterococci. The domain V sequences of
E. durans
and
E. hirae
were identical. This was also true for
E. gallinarum
and
E. casseliflavus. E. avium
differed from
E. casseliflavus
by 23 bases, from
E. durans
by 16 bases, and from
E. malodoratus
by 2 bases.
E. avium
differed from
E. raffinosus
by one base. Despite the fact that domain V is considered to be highly conserved, substantial differences were identified between several enterococcal species.
Molecular and Pathogenic Characterization ofBorrelia burgdorferiSensu Lato Isolates from Spain
Authors: Escudero Raquel , Barral Marta , Pérez Azucena , Vitutia M. Mar , García-Pérez Ana L. , Jiménez Santos , Sellek Ricela E. , Anda Pedro 
Published: December 2019

ABSTRACTFifteenBorrelia burgdorferisensu lato isolates from questing ticks and skin biopsy specimens from erythema migrans patients in three different areas of Spain were characterized. Four different genospecies were found (nineBorrelia garinii, including the two human isolates, threeB. burgdorferisensu stricto, twoB. valaisiana, and oneB. lusitaniae), showing a diverse spectrum ofB. burgdorferisensu lato species.B. gariniiisolates were highly variable in terms of pulsed-field gel electrophoresis pattern and OspA serotype, with four of the seven serotypes described. One of the human isolates was OspA serotype 5, the same found in four of seven tick isolates. The second human isolate was OspA serotype 3, which was not present in ticks from the same area. SevenB. gariniiisolates were able to disseminate through the skin of C3H/HeN mice and to cause severe inflammation of joints. One of the twoB. valaisianaisolates also caused disease in mice. Only oneB. burgdorferisensu stricto isolate was recovered from the urinary bladder. One isolate each ofB. valaisianaandB. lusitaniaewere not able to disseminate through the skin of mice or to infect internal organs. In summary, there is substantial diversity in the species and in the pathogenicity ofB. burgdorferisensu lato in areas in northern Spain where Lyme disease is endemic.
Real-Time Quantitative PCR for Human Herpesvirus 6 DNA
Authors: Locatelli Giuseppe , Santoro Fabio , Veglia Fabrizio , Gobbi Alberto , Lusso Paolo , Malnati Mauro S. 
Published: December 2019

ABSTRACT

The diagnosis of human herpesvirus 6 (HHV-6) infection represents a complex issue because the most widely used diagnostic tools, such as immunoglobulin G antibody titer determination and qualitative DNA PCR with blood cells, are unable to distinguish between latent (clinically silent) and active (often clinically relevant) infection. We have developed a new, highly sensitive, quantitative PCR assay for the accurate measurement of HHV-6 DNA in tissue-derived cell suspensions and body fluids. The test uses a 5′ nuclease, fluorogenic assay combined with real-time detection of PCR amplification products with the ABI PRISM 7700 sequence detector system. The sensitivity of this method is equal to the sensitivity of a nested PCR protocol (lower detection limit, 1 viral genome equivalent/test) for both the A and the B HHV-6 subgroups and shows a wider dynamic range of detection (from 1 to 10
6
viral genome equivalents/test) and a higher degree of accuracy, repeatability, and reproducibility compared to those of a standard quantitative-competitive PCR assay developed with the same reference DNA molecule. The novel technique is versatile, showing the same sensitivity and dynamic range with viral DNA extracted from different fluids (i.e., culture medium or plasma) or from tissue-derived cell suspensions. Furthermore, by virtue of its high-throughput format, this method is well suited for large epidemiological surveys.
Coyotes (Canis latrans) as the Reservoir for a Human PathogenicBartonellasp.: Molecular Epidemiology ofBartonella vinsoniisubsp.berkhoffiiInfection in Coyotes from Central Coastal California
Authors: Chang Chao-Chin , Kasten Rickie W. , Chomel Bruno B. , Simpson Darren C. , Hew Carrie M. , Kordick Dorsey L. , Heller Remy , Piemont Yves , Breitschwerdt Edward B. 
Published: December 2019

ABSTRACTBartonella vinsoniisubsp.berkhoffiiwas originally isolated from a dog suffering infectious endocarditis and was recently identified as a zoonotic agent causing human endocarditis. Following the coyote bite of a child who developed clinical signs compatible withBartonellainfection in Santa Clara County, Calif., this epidemiological study was conducted. Among 109 coyotes (Canis latrans) from central coastal California, 31 animals (28%) were found to be bacteremic withB. vinsoniisubsp.berkhoffiiand 83 animals (76%) hadB. vinsoniisubsp.berkhoffiiantibodies. These findings suggest these animals could be the wildlife reservoir ofB. vinsoniisubsp.berkhoffii. PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of thegltAand 16S rRNA genes for these 31 isolates yielded similar profiles that were identical to those ofB. vinsoniisubsp.berkhoffii. Partial sequencing of thegltAand 16S rRNA genes, respectively, indicated 99.5 and 100% homology between the coyote isolate andB. vinsoniisubsp.berkhoffii(ATCC 51672). PCR-RFLP analysis of the 16S-23S intergenic spacer region showed the existence of two different strain profiles, as has been reported in dogs. Six (19%) of 31Bartonellabacteremic coyotes exhibited the strain profile that was identified in the type strain of a canine endocarditis case (B. vinsoniisubsp.berkhoffiiATCC 51672). The other 25 bacteremic coyotes were infected with a strain that was similar to the strains isolated from healthy dogs. Based on whole bacterial genome analysis by pulsed-field gel electrophoresis (PFGE) withSmaI restriction endonuclease, there was more diversity in fingerprints for the coyote isolates, which had at least 10 major variants compared to the two variants described for domestic dog isolates from the eastern United States. By PFGE analysis, threeBartonellabacteremic coyotes were infected by a strain identical to the one isolated from three healthy dog carriers. Further studies are necessary to elucidate the mode of transmission ofB. vinsoniisubsp.berkhoffii, especially to identify potential vectors, and to determine how humans become infected.
Serodiagnosis of
Bartonella bacilliformis
Infection by Indirect Fluorescence Antibody Assay: Test Development and Application to a Population in an Area of Bartonellosis Endemicity
Authors: Chamberlin Judith , Laughlin Larry , Gordon Scott , Romero Sofia , Solórzano Nelson , Regnery Russell L. 
Published: December 2019

ABSTRACT

Bartonella bacilliformis
causes bartonellosis, a potentially life-threatening emerging infectious disease seen in the Andes Mountains of South America. There are no generally accepted serologic tests to confirm the disease. We developed an indirect fluorescence antibody (IFA) test for the detection of antibodies to
B. bacilliformis
and then tested its performance as an aid in the diagnosis of acute bartonellosis. The IFA is 82% sensitive in detecting
B. bacilliformis
antibodies in acute-phase blood samples of laboratory-confirmed bartonellosis patients. When used to examine convalescent-phase sera, the IFA is positive in 93% of bartonellosis cases. The positive predictive value of the test is 89% in an area of Peru where
B. bacilliformis
is endemic and where the point prevalence of infection is 45%.
Avian Pneumovirus (APV) RNA from Wild and Sentinel Birds in the United States Has Genetic Homology with RNA from APV Isolates from Domestic Turkeys
Authors: Shin Hyun-Jin , Njenga M. Kariuki , McComb Brian , Halvorson David A. , Nagaraja Kakambi V. 
Published: December 2019

ABSTRACT
Nasal turbinates or swabs were collected from wild ducks, geese, owls, sparrows, swallows, and starlings and from sentinel ducks placed next to turkey farms experiencing avian pneumovirus (APV) infections and were analyzed for APV genome and infectious particles. APV RNA was detected in samples examined from geese, sparrows, and starlings. APV RNA and antibodies were also detected in two different groups of sentinel ducks. Infectious APV was recovered from sentinel duck samples. The APV M gene isolated from the wild birds had over 96% predicted amino acid identity with APV/Minnesota 2A, which was isolated earlier from domestic turkeys showing respiratory illness, suggesting that wild birds may be involved in spreading APV infection.
Application of Representational Difference Analysis to Genomic Fragments of Marek's Disease Virus
Authors: Endoh Daiji , Cho Kyoung-Oh , Tsukamoto Kenji , Morimura Toshifumi , Kon Yasuhiro , Hayashi Masanobu 
Published: December 2019

ABSTRACT

A rapid and simple method for isolation of DNA fragments of Marek's disease virus (MDV) based on representational difference analysis (RDA) was developed. Multiple viral DNA fragments, the sizes of which were restricted to 0.3 to 3.5 kbp, were simultaneously amplified after subtraction of chicken DNA from
Bam
HI-,
Bgl
II-,
Eco
RI-,
Hin
dIII-, or
Xho
I-digested DNA fragments of MDV-infected cells. Nucleotide sequence of two RDA-derived fragments coincided with the sequence determined from direct sequencing of the MDV genome. We detected an interstrain difference in the size of restriction enzyme-digested fragments on agarose gel. This method was used on a single feather pulp to generate sufficient MDV DNA for cloning.
Rapid Genotyping of Varicella-Zoster Virus Vaccine and Wild-Type Strains with Fluorophore-Labeled Hybridization Probes
Authors: Loparev Vladimir N. , McCaustland Karen , Holloway Brian P. , Krause Philip R. , Takayama Michiko , Schmid D. Scott 
Published: December 2019

ABSTRACT
We developed a single-tube rapid method for the detection and differentiation of varicella-zoster virus (VZV) vaccine and wild-type strains that combines rapid-cycle PCR with wild-type-specific fluorescent probe melting profiles for product genotyping. A region including the polymorphic site in VZV open reading frame (ORF) 62 was amplified in the presence of two fluorescence-labeled hybridization probes. During the annealing step of the thermal cycling, both probes bound to their complementary sequences in the amplicon, resulting in resonance energy transfer, thus providing real-time fluorescence monitoring of PCR. Continuous acquisition of fluorescence data during a melting curve analysis at the completion of PCR revealed that loss of fluorescence occurred in a strain-specific manner as the detection probe, which was fully complementary to the wild-type VZV ORF 62 region, melted off the template. Use of this method allowed genotyping of samples within minutes after the completion of PCR, eliminating the need for post-PCR sample manipulation. In addition to reducing the time required to produce a result, this method substantially reduces the risk of contamination of the final product as well as the risk of sample tracking errors. The genotypes of 79 VZV-positive samples determined by this fluorescent resonance energy transfer (FRET) method were identical to the genotypes obtained by conventional PCR and restriction fragment length polymorphism analysis. The genotyping of VZV strains by the FRET method is a rapid and reliable method that is suitable for typing and that is also practical for use for the processing of large numbers of specimens.
Dissemination of CTX-M-3 and CMY-2 β-Lactamases among Clinical Isolates of
Escherichia coli
in Southern Taiwan
Authors: Yan Jing-Jou , Ko Wen-Chien , Tsai Shu-Huei , Wu Hsiu-Mei , Jin Ying-Tai , Wu Jiunn-Jong 
Published: December 2019

ABSTRACT

A total of 1,210 clinical isolates of
Escherichia coli
collected from a university hospital in southern Taiwan were screened for production of extended-spectrum β-lactamases (ESBLs). Expression of classical ESBLs (resistant to extended-spectrum β-lactam agents and susceptible to β-lactam inhibitors) was inferred in 18 isolates by the phenotypic confirmatory test. These included 10 isolates producing CTX-M-3, 2 strains carrying SHV-12, 1 strain harboring SHV-5, 1 strain expressing TEM-10, and 4 strains producing unidentifiable ESBLs with a pI of 8.05, 8.0, or 7.4. Eighteen isolates that showed decreased susceptibilities to ceftazidime and/or cefotaxime, negative results for the confirmatory test, and high-level resistance to cefoxitin (MICs of ≥128 μg/ml) were also investigated. Five isolates were found to produce CMY-2 AmpC enzymes, one isolate carried both CTX-M-3 and CMY-2, and the remaining three and nine isolates expressed putative AmpC β-lactamases with pIs of >9.0 and 8.9, respectively. Thus, together with the isolate producing CTX-M-3 and CMY-2, 19 (1.6%) isolates produced classical ESBLs. Pulsed-field gel electrophoresis revealed that all isolates carrying CTX-M-3 and/or CMY-2 were genetically unrelated, indicating that dissemination of resistance plasmids was responsible for the spread of these two enzymes among
E. coli
in this area. Among the 16 isolates expressing CTX-M-3 and/or CMY-2, 5 might have colonized outside the hospital environment. Our data indicate that CTX-M-3 and CMY-2, two β-lactamases initially identified in Europe, have been disseminated to and are prevalent in Taiwan.
Comparison of Sequencing of the
por
Gene and Typing of the
opa
Gene for Discrimination of
Neisseria gonorrhoeae
Strains from Sexual Contacts
Authors: Viscidi Raphael P. , Demma James C. , Gu Jing , Zenilman Jonathan 
Published: December 2019

ABSTRACT

Typing of gonococcal strains is a valuable tool for the biological confirmation of sexual contacts. We have developed a typing method based on DNA sequencing of two overlapping
por
gene fragments generated by a heminested PCR. We compared sequencing of the
por
gene (POR sequencing) and typing of the
opa
gene (OPA typing) for the characterization of strains from 17 sexual partnerships. Both methods were highly discriminatory. A different genotype was detected in 15 of the 17 epidemiologically unconnected couples by POR sequencing and in 16 of the 17 couples by OPA typing with restriction enzyme
Hpa
II. Within partnerships, identical genotypes were obtained from 16 of the 17 known sex contacts by POR sequencing and from 15 of the 17 by OPA typing. Compared to OPA typing, which relies on interpretation of bands in a gel, DNA sequence data offer the advantage of being objective and portable. As costs for sequencing decline, the method should become affordable for most laboratory personnel who wish to type gonococcal strains.
Simple and Inexpensive but Highly Discriminating Method for Computer-Assisted DNA Fingerprinting of
Pseudomonas aeruginosa
Authors: Al-Samarrai Taha H. , Zhang Ningxin , Lamont Iain L. , Martin Lois , Kolbe John , Wilsher Margaret , Morris Arthur J. , Schmid Jan 
Published: December 2019

ABSTRACT

We describe here a method for computer-assisted fingerprinting of
Pseudomonas aeruginosa
. In this method, DNA is digested with
Sal
I, and bands with molecular sizes of ≥9.7 kb are visually scored after electrophoresis on agarose gels. Pattern scores are entered into a Microsoft Excel database. In scoring, the number of bands within each of a set of molecular size ranges is scored, rather than the absolute molecular size of each band, substantially enhancing the speed and reproducibility of the method, while eliminating the need for using expensive gel scanning equipment and software. Pattern scores are used to generate matrices of genetic distance values, which can be visualized in neighbor-joining trees. The method reliably distinguishes two epidemiologically unrelated isolates in 99.3% of all comparisons. The genetic relationships between isolates observed with the method were consistent with those obtained by analysis of two
P. aeruginosa
genes, indicating that it provides valid estimates of genetic divergence between isolates. Using the method, respiratory tract isolates from cystic fibrosis patients in Green Lane Hospital in Auckland, New Zealand, were shown to be genetically less diverse than epidemiologically unrelated isolates from other patients. This finding was not due to the existence of clusters of related strains specialized toward colonization of the respiratory tract and thus was indicative of transmission between patients. Analysis of multiple isolates from individual cystic fibrosis patients suggested that up to five separate clusters of genetically related strains may simultaneously be present in a patient. The method described should significantly enhance our ability to investigate the epidemiology of
P. aeruginosa.
Evaluation of Etest for Susceptibility Testing of Multidrug-Resistant Isolates of
Mycobacterium tuberculosis
Authors: Hazbón Manzour Hernando , del Socorro Orozco Maria , Labrada Luz Angela , Tovar Rafael , Weigle Kristen A. , Wanger Audrey 
Published: December 2019

ABSTRACT

To prescribe effective treatment schemes for patients with tuberculosis, more-efficient susceptibility testing techniques for
Mycobacterium tuberculosis
are needed, especially in regions with multidrug resistance. Etest (AB BIODISK, Solna, Sweden) is a simple technique that provides quantitative drug susceptibility results for
M. tuberculosis
in 5 to 10 days from a culture grown at low cost. The performance of Etest was compared to that of the reference proportion method, using 95
M. tuberculosis
clinical isolates of which 42.1% (40 of 95) were resistant to at least one antibiotic by the reference method. Overall agreement between Etest and the reference method was 98.9% (94 of 95) for detection of multidrug resistance; for resistance to individual drugs, agreement was 97.9% (93 of 95) for rifampin, 96.0% (92 of 95) for ethambutol, 94.7% (90 of 95) for isoniazid, and 85.3% (81 of 95) for streptomycin. This study supports the utility of Etest for timely detection of drug resistance in
M. tuberculosis
and for use in tuberculosis control programs.