bluuebunny/crossref_metadata_2025_split huggingface dataset:
Community Strain of Methicillin-Resistant
Staphylococcus aureus
Involved in a Hospital Outbreak
Authors: O’Brien F. G. , Pearman J. W. , Gracey M. , Riley T. V. , Grubb W. B. 
Published: December 2019

ABSTRACT

Western Australia (WA) has been able to prevent methicillin-resistant
Staphylococcus aureus
(MRSA) strains from outside of the state from becoming established in its hospitals. Recently, a single-strain outbreak of MRSA occurred in a WA metropolitan teaching hospital following admission of an infected patient from a remote community. The strain responsible for the outbreak was unrelated to any imported strains and spread rapidly in the hospital. Screening of two remote communities in the region from which the index case came revealed that 42% of the people in one community and 24% in the other carried MRSA. Isolates were typed by resistance pattern, plasmid analysis, contour-clamped homogeneous electric field electrophoresis, bacteriophage pattern, and coagulase gene restriction fragment length polymorphism. It was found that of the people carrying MRSA, 39% in the former community and 17% in the latter community were carrying an MRSA strain which was indistinguishable from the strain that caused the hospital outbreak.
Antigenic Domains of the Open Reading Frame 2-Encoded Protein of Hepatitis E Virus
Authors: Khudyakov Yury E. , Lopareva Elena N. , Jue Danny L. , Crews Tamara K. , Thyagarajan S. P. , Fields Howard A. 
Published: December 2019

ABSTRACT
The antigenic composition of the hepatitis E virus (HEV) protein encoded by open reading frame 2 (ORF2) was determined by using synthetic peptides. Three sets of overlapping 18-, 25-, and 30-mer peptides, with each set spanning the entire ORF2 protein of the HEV Burma strain, were synthesized. All synthetic peptides were tested by enzyme immunoassay against a panel of 32 anti-HEV-positive serum specimens obtained from acutely HEV-infected persons. Six antigenic domains within the ORF2 protein were identified. Domains 1 and 6 located at the N and C termini of the ORF2 protein, respectively, contain strong immunoglobulin G (IgG) and IgM antigenic epitopes that can be efficiently modeled with peptides of different sizes. In contrast, antigenic epitopes identified within the two central domains (3 and 4) were modeled more efficiently with 30-mer peptides than with either 18- or 25-mers. Domain 2 located at amino acids (aa) 143 to 222 was modeled best with 25-mer peptides. A few 30-mer synthetic peptides derived from domain 5 identified at aa 490 to 579 demonstrated strong IgM antigenic reactivity. Several 30-mer synthetic peptides derived from domains 1, 4, and 6 immunoreacted with IgG or IgM with more than 70% of anti-HEV-positive serum specimens. Thus, the results of this study demonstrate the existence of six diagnostically relevant antigenic domains within the HEV ORF2 protein.
Genotypes of Canine Distemper Virus Determined by Analysis of the Hemagglutinin Genes of Recent Isolates from Dogs in Japan
Authors: Mochizuki Masami , Hashimoto Michiru , Hagiwara Shigeyuki , Yoshida Yoshio , Ishiguro Shinryo 
Published: December 2019

ABSTRACTCanine distemper of domestic dogs is caused by canine distemper virus (CDV), a member of the morbilliviruses. It has been a highly contagious disease of great veterinary importance for centuries, but for the last several decades it has been controlled satisfactorily by modified live vaccines. In the 1990s, however, it was described that CDV strains genetically different from vaccine strains may have caused the disease in vaccinated dogs. The highest antigenic variation is found in the H protein. Therefore, in the present study, hemagglutinin (H) genes obtained from current vaccines and field isolates and amplified directly from clinical specimens were genetically analyzed by restriction fragment length polymorphism assay and sequencing. Phylogenetic analysis of the H-gene amino acid sequences revealed that at least two CDV genotypes are circulating among dogs in Japan; one is a genotype to which almost all Japanese CDV isolates belong and the other has not been previously described. Both are separate and independent from the other lineages or genotypes of vaccine strains, as well as European and U.S. CDV isolates. The results suggest that CDV has also evolved in Japan, and further studies will be needed for an evaluation and possible improvement of the efficacies of current CDV vaccines.
Hepatitis B Virus (HBV) Mutations Associated with Resistance to Lamivudine in Patients Coinfected with HBV and Human Immunodeficiency Virus
Authors: Thibault Vincent , Benhamou Yves , Seguret Christophe , Bochet Marie , Katlama Christine , Bricaire François , Opolon Pierre , Poynard Thierry , Agut Henri 
Published: December 2019

ABSTRACT

Mutations associated with hepatitis B virus (HBV) resistance to lamivudine have not been extensively addressed in human immunodeficiency virus (HIV)-HBV coinfection. We have studied the HBV polymerase sequences from nine coinfected patients who experienced HBV recurrence while under lamivudine treatment. In seven of these nine patients, Met
550
, belonging to the highly conserved YMDD motif, was mutated to Val and was associated with a substitution of Met for Leu
526
in each case. In the two remaining patients, we found a Met
550
-to-Ile change that was associated in only one case with a Leu
526
-to-Met mutation. No mutation was observed in three control patients not receiving lamivudine. This study demonstrates the emergence of particular genetic profiles in HBV-HIV-coinfected patients experiencing a loss of control of HBV infection despite high doses of lamivudine.
Phenotypic and Genetic Characterization of a Novel
Borrelia burgdorferi
Sensu Lato Isolate from a Patient with Lyme Borreliosis
Authors: Wang Guiqing , van Dam Alje P. , Dankert Jacob 
Published: December 2019

ABSTRACT

Borrelia burgdorferi
sensu lato A14S was cultured from a skin biopsy specimen of a patient with erythema migrans in The Netherlands. This isolate had a unique DNA fingerprint pattern compared to 135 other
B. burgdorferi
sensu lato isolates. In this study, the isolate A14S was further characterized by protein analysis with sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and reactivity with various monoclonal antibodies. In addition, the 16S rRNA,
ospA
, and
ospC
genes, as well as the 5S-23S rRNA intergenic spacer DNA, were amplified by PCR, cloned, and sequenced. SDS-PAGE protein profiles and phylogenetic analysis based on all of the analyzed genes confirmed that
B. burgdorferi
sensu lato A14S was phenotypically and genetically different from the three human pathogenic species
B. burgdorferi
sensu stricto,
Borrelia garinii
, and
Borrelia afzelii
, as well as from other
B. burgdorferi
sensu lato species. Our findings indicate that
Borrelia
genomic groups or isolates other than the three well-known human pathogenic species may also cause human Lyme borreliosis.
Rapid Detection of Methicillin Resistance in
Staphylococcus aureus
Isolates by the MRSA-Screen Latex Agglutination Test
Authors: van Leeuwen Willem B. , van Pelt Cindy , Luijendijk Ad , Verbrugh Henri A. , Goessens Wil H. F. 
Published: December 2019

ABSTRACT

The slide agglutination test MRSA-Screen (Denka Seiken Co., Niigata, Japan) was compared with the
mecA
PCR (“gold standard”) for the detection of methicillin resistance in
Staphylococcus aureus
. The MRSA-Screen test detected the penicillin-binding protein 2a (PBP2a) antigen in 87 of 90 genetically diverse methicillin-resistant
S. aureus
(MRSA) stock culture strains, leading to a sensitivity of 97%. The three discrepant MRSA strains displayed positive results only after induction of the
mecA
gene by exposure to methicillin. Both
mecA
PCR and MRSA-Screen displayed negative results among the methicillin-susceptible
S. aureus
strains (
n
= 106), as well as for
Micrococcus
spp. (
n
= 10), members of the family
Enterobacteriaceae
(
n
= 10),
Streptococcus pneumoniae
(
n
= 10), and
Enterococcus
spp. (
n
= 10) (specificity = 100%). Producing the same PBP2a antigen, all 10 methicillin-resistant
Staphylococcus epidermidis
strains score positived in both the latex test and the
mecA
PCR. Consequently, the MRSA-Screen test should be applied only after identification of the MRSA strain to the species level to rule out coagulase-negative staphylococci. In conclusion, due to excellent specificity and sensitivity the MRSA-Screen latex test has the potential to be successfully used for routine applications in the microbiology laboratory.
Analysis by Enzyme-Linked Immunosorbent Assay and PCR of Human Liver Abscess Aspirates from Patients in China for
Entamoeba histolytica
Authors: Zengzhu G. , Bracha R. , Nuchamowitz Y. , Cheng-I W. , Mirelman D. 
Published: December 2019

ABSTRACT

Aspirates of liver abscesses were analyzed for
Entamoeba histolytica
. PCR detected a gene encoding a 30-kDa protein in all samples but detected the ribosomal DNA gene in only 14 (33.3%) samples. Enzyme-linked immunosorbent assay detected antigen in 41 (97.6%) samples. PCR analysis of a strain-specific antigen (SSG) revealed that abscesses were caused by various strains.
Evaluation of the Effects of Storage in Two Different Swab Fabrics and under Three Different Transport Conditions on Recovery of Aerobic and Anaerobic Bacteria
Authors: Roelofsen E. , van Leeuwen M. , Meijer-Severs G. J. , Wilkinson M. H. F. , Degener J. E. 
Published: December 2019

ABSTRACT
Recovery of six anaerobic and five aerobic pathogens from viscose swabs and polyurethane swabs (Culturette EZ) was evaluated quantitatively, and transport in aerobic dry tubes, aerobic Amies transport medium (Transwab), and anaerobic universal transport medium (Port-a-Cul) was compared. The Culturette EZ in aerobic dry tubes gave the highest recovery levels. Data obtained with clinical specimens confirmed these results.
Evaluation of the Leukocyte Esterase and Nitrite Urine Dipstick Screening Tests for Detection of Bacteriuria in Women with Suspected Uncomplicated Urinary Tract Infections
Authors: Semeniuk Heather , Church Deirdre 
Published: December 2019

ABSTRACT
A positive dipstick urinalysis (i.e., leukocyte esterase test and/or nitrite test) did not reliably detect significant bacteriuria in 479 ambulatory women with suspected uncomplicated urinary tract infection; 18.9% of the urine samples that demonstrated significant bacteriuria would have been rejected by the laboratory based on a negative urinalysis screen.
Characterization of Enterovirus Isolates from Patients with Heart Muscle Disease in a Selenium-Deficient Area of China
Authors: Peng Tianqing , Li Yanwen , Yang Yingzhen , Niu Cunlong , Morgan-Capner Peter , Archard Leonard C. , Zhang Hongyi 
Published: December 2019

ABSTRACTAn association of enterovirus infection with endemic cardiomyopathy (Keshan disease [KD]) and outbreaks of myocarditis in selenium-deficient rural areas of southwestern China has been established. Enteroviruses have been isolated from patients with KD or during outbreaks of myocarditis in last two decades. Six of these isolates grew readily in cell lines (Vero or HEp-2) and were investigated by a novel molecular typing method apart from serotyping and pathogenicity. A neutralization assay identified two isolates from KD as coxsackievirus serotype B2 (CVB2) and two isolates from myocarditis as coxsackievirus serotype B6 (CVB6) but failed to type the remaining two isolates, also from myocarditis. Direct nucleotide sequencing of reverse transcription-PCR products amplified from the 5′ nontranslated region (5′NTR) of these viruses confirmed that they belong to a phylogenetic cluster consisting of coxsackie B-like viruses, including some echovirus serotypes. Sequence analysis of the coding region for viral capsid protein VP1 showed that two isolates serotyped as CVB2 have the highest amino acid sequence homology with CVB2 and that the remaining four isolates, two CVB6 and the two unknown serotypes, are most closely related to the sequence of CVB6. Sequences among these isolates varied from 82.3 to 99% in the 5′NTR and from 69 to 99% in VP1, indicating no cross contamination. The pathogenicity of these viruses in adult and suckling mice was assessed. None caused pathologic changes in the hearts of adult MF-1 or SWR mice, although pancreatitis was evident. However, the four CVB6-like viruses caused death in suckling mice, similar to a virulent coxsackievirus group B3 laboratory strain. In conclusion, the sequence data confirm that coxsackievirus group B serotypes are predominant in the region in which KD is endemic and may be the etiological agents in outbreaks of myocarditis. VP1 genotyping of enteroviruses is accurate and reliable. Animal experiments indicate that isolates may differ in pathogenicity.
Rapid Differentiation of Fermentative from Nonfermentative Gram-Negative Bacilli in Positive Blood Cultures by an Impedance Method
Authors: Chang Tsung Chain , Huang Ay Huey 
Published: December 2019

ABSTRACT
Rapid differentiation of fermentative gram-negative bacilli (fermenters) from nonfermentative gram-negative bacilli (nonfermenters) in positive blood cultures may help physicians to narrow the choice of appropriate antibiotics for empiric treatment. An impedance method for direct differentiation of fermenters from nonfermenters was investigated. The bacterial suspensions (or positive culture broths containing gram-negative bacteria) were inoculated into the module wells of a Bactometer (bioMérieux, Inc., Hazelwood, Mo.) containing 1 ml of Muller-Hinton broth. The inoculated modules were incubated at 35°C, and the change in impedance in each well was continuously monitored. The amount of time required to cause a series of significant deviations from baseline impedance values was defined as the detection time (DT). The percent change of impedance was defined as the change of impedance at the time interval from DT to DT plus 1 h. After testing 857 strains of pure cultures (586 strains of fermenters and 271 strains of nonfermenters), a breakpoint (2.98%) of impedance change was obtained by discriminant analysis. Strains displaying impedance changes of greater than 2.98% were classified as fermenters; the others were classified as nonfermenters. By using this breakpoint, 98.6% (340 of 345) of positive blood cultures containing fermenters and 98% (98 of 100) of positive blood cultures containing nonfermenters were correctly classified. The impedance method was simple, and the results were normally available within 2 to 4 h after direct inoculation of positive blood culture broths.
Evaluation of
d
-Xylose and 1% Methyl-α-
d
-Glucopyranoside Fermentation Tests for Distinguishing
Enterococcus gallinarum
from
Enterococcus faecium
Authors: Chen D. K. , Pearce L. , McGeer A. , Low D. E. , Willey B. M. 
Published: December 2019

ABSTRACT

To determine the validity of the rapid xylose and methyl-α-
d
-glucopyranoside (MDG) fermentation tests in distinguishing
Enterococcus gallinarum
from
Enterococcus faecium
, 156 well-characterized clinical isolates of enterococci (55
E. gallinarum
, 91
E. faecium
, and 10
Enterococcus faecalis
isolates) known to be of different clones were examined in a blinded fashion. Species identification was confirmed by PCR of the
ddl
ligase genes of
E. faecium
and
E. faecalis
and the
vanC1
gene of
E. gallinarum
. Xylose tests were performed with
d
-xylose tablets by using a heavy bacterial suspension and were interpreted after 2 h of incubation. Standard MDG fermentation tests were read after 24 h of incubation. The xylose fermentation test had a sensitivity of 98% (54 of 55) and a specificity of 99% (100 of 101) in distinguishing
E. gallinarum
from
E. faecium
and
E. faecalis
. The standard MDG test had a sensitivity of 100% (55 of 55) and a specificity of 95% (96 of 101) after 24 h. The xylose fermentation test is a simple method, easily incorporated into laboratory protocols, that distinguishes
E. gallinarum
from
E. faecium
with high sensitivity and specificity in 2 h. The standard MDG test has high sensitivity and can be useful in ruling out the presence of
E. gallinarum
but requires overnight incubation.
Genotyping of Rotaviruses in Environmental Water and Stool Samples in Southern Switzerland by Nucleotide Sequence Analysis of 189 Base Pairs at the 5′ End of the VP7 Gene
Authors: Baggi Franca , Peduzzi Raffaele 
Published: December 2019

ABSTRACT
Stool specimens from children (<4 years old) with diarrhea were collected over a 1-year period in Ticino (southern region of Switzerland). During the same period, environmental samples were collected from surface waters in the proximity of major water treatment plants. From treatment plants, samples were collected from the raw sewage and before the release of the treated water. From rivers, samples were collected before and after receiving the treated waters. A single-step reverse transcription (RT)-PCR amplification of the entire VP7 gene from extracted double-stranded RNA was developed. For the water samples, a further nested PCR was necessary to increase sensitivity. All amplified viral products were sequenced, and the sequence profile was compared to that of the VP7 genes of human and animal rotaviruses from GenBank. Rotavirus strains are characterized by outer capsid proteins G (glycoprotein) and P (protease-cleaved protein). Correct G genotyping of viral sequences from stool and water samples was possible by analyzing only 189 bp at the 5′ end of the VP7 gene. In the Ticino region, the most predominant G genotype among clinical and water samples was G1. Genotypes G2 and G4 were found only among clinical samples. We also detected rotavirus G1-type sequences in feces from a healthy adult. This finding corroborates the hypothesis that healthy adults act as potential reservoirs for the spread of rotavirus in the environment. In our experiments, this RT-PCR-based method for rotavirus genotyping has proven to be a useful tool for epidemiological investigations.
Immunodiagnosis of
Echinococcus
Infections: Confirmatory Testing and Species Differentiation by a New Commercial Western Blot
Authors: Liance Martine , Janin Veronique , Bresson-Hadni Solange , Vuitton Dominique-Angele , Houin Rene , Piarroux Renaud 
Published: December 2019

ABSTRACT

The
Echinococcus
Western Blot IgG (LDBIO Diagnostics, Lyon, France), using a whole larval antigen from
Echinococcus multilocularis
, was evaluated for serodiagnosis and differentiation between two human parasitic infections of worldwide importance: cystic echinococcosis, due to
Echinococcus granulosus
, and alveolar echinococcosis, due to
E. multilocularis
. Fifty and 61 serum samples from patients with cystic and alveolar echinococcosis, respectively, were used for assessing diagnostic sensitivity. The sensitivity of the assay was compared with those of screening tests used for these applications. Sera used for assessing cross-reactivities were from 154 patients with other diseases, either parasitic or not. The assay allowed the detection of serum immunoglobulin G antibodies in 97% of
Echinococcus
-infected patients. It had a higher sensitivity than screening assays for the detection for each echinococcosis. The assay allowed us to correctly distinguish between
E. granulosus
- and
E. multilocularis
-infected patients in 76% of cases. It did not allow us to distinguish active from inactive forms of both echinococcoses. The occurrence of cross-reactivities with neurocysticercosis indicates the necessity for retesting sera with species-specific antigens, for rare patients with neurologic disorders. This study shows the usefulness of the commercially available
Echinococcus
Western Blot IgG for the serological confirmation of human echinococcosis.
Development of a PCR-Based Line Probe Assay for Identification of Fungal Pathogens
Authors: Martin Cara , Roberts David , van der Weide Marjo , Rossau Rudi , Jannes Geert , Smith Terry , Maher Majella 
Published: December 2019

ABSTRACT

We report on a reverse-hybridization line probe assay (LiPA) which when combined with PCR amplification detects and identifies clinically significant fungal pathogens including
Candida
,
Aspergillus
, and
Cryptococcus
species. DNA probes have been designed from the internal transcribed-spacer (ITS) regions of
Candida albicans
,
Candida parapsilosis
,
Candida glabrata
,
Candida tropicalis
,
Candida krusei
,
Candida dubliniensis
,
Cryptococcus neoformans
,
Aspergillus fumigatus
,
Aspergillus versicolor
,
Aspergillus nidulans
and
Aspergillus flavus
. The probes were incorporated into a LiPA for detection of biotinylated ITS PCR products, and the specificity of the probes was evaluated. We established LiPA detection limits for ITS 1 and for full ITS amplicons for genomic DNA from
C. albicans
,
A. fumigatus
, and
C. neoformans
. Further evaluation of the LiPA was carried out on clinical fungal isolates. One hundred twenty-seven isolates consisting of dimorphic yeasts and dermatophytic and filamentous fungi were tested by the LiPA, which correctly identified 77 dimorphic yeasts and 23 of the filamentous isolates; the remaining 27 isolates represented species of fungi for which probes were not included in the LiPA. The fungal-PCR-LiPA technology was applied to blood samples inoculated with
Candida
cells which were pretreated by minibead beating to mechanically disrupt the cells, with the DNA extracted by either a previously described guanidium thiocyanate-silica method or the commercially available QIAmp tissue kit. PCR amplification of the extracted DNA and subsequent DNA probe hybridization in the LiPA assay yielded detection limits of 2 to 10 cells/ml. An internal standard control was included in the PCR amplification to monitor for PCR inhibition. This fungal PCR-LiPA assay is robust and sensitive and can easily be integrated into a clinical-testing laboratory with the potential for same-day diagnosis of fungal infection.
Comparison of the CMV Brite Turbo Assay and the Digene Hybrid Capture CMV DNA (Version 2.0) Assay for Quantitation of Cytomegalovirus in Renal Transplant Recipients
Authors: Ho Stephen K. N. , Li Fu-Keung , Lai Kar-Neng , Chan Tak-Mao 
Published: December 2019

ABSTRACT

We compared the CMV Brite Turbo Kit (BT) and the Digene Hybrid Capture CMV DNA (version 2.0) assay (HC2) in the quantitation of pp65 antigenemia and cytomegalovirus (CMV) DNA levels in immunosuppressed renal transplant recipients. Of 123 blood specimens collected from 24 renal transplant recipients, BT and HC2 assays detected 35 and 39 positive samples, respectively. The overall concordance rate between the two assays was 90%. Discordant results were observed at low levels of viremia, so that 8 samples were HC2 positive but BT negative and another 4 were BT positive but HC2 negative. There was good correlation (
R
2
= 0.766;
P
< 0.01) between the levels of CMV DNA and pp65 antigenemia in the 31 concordant positive samples. Correlation between results obtained with the two assays was confirmed by longitudinal studies for a patient who developed clinical CMV disease. HC2 may be more sensitive at low viremia levels and allow earlier detection of impending CMV disease. The BT assay offered the advantage of a rapid (2-h) turnaround time. We conclude that BT and HC2 assays have similar sensitivity and efficacy in the diagnosis and monitoring of CMV infection and disease in renal transplant recipients. While the HC2 assay would be appropriate for centers that handle a large number of samples, the BT test may be more suitable for small sample numbers or when results are needed urgently.