bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of
Shigella flexneri
Subserotype 1c in Rural Egypt
Authors: El-Gendy Atef , El-Ghorab Nemat , Lane Edward M. , Elyazeed Remon Abu , Carlin Nils I. A. , Mitry Mary M. , Kay Bradford A. , Savarino Stephen J. , Peruski Leonard F. 
Published: December 2019

ABSTRACT

In a population-based study of diarrhea in rural, northern Egypt, 60
Shigella flexneri
strains were identified, of which 10 could not be definitively serotyped. Serological analysis with commercial reagents suggested that they were serotype 1, but the strains failed to react with subserotype 1a- or 1b-specific antibodies. All 10 strains reacted with MASF 1c, a monoclonal antibody specific for a provisional
S. flexneri
subserotype, 1c, first identified in Bangladesh and not previously detected outside of that region. Our results show that
S. flexneri
subserotype 1c is not unique to Bangladesh and that the inability to detect it may reflect both the limited use of suitable screening methods and the rarity of this subserotype.
Comparison of Isolation Media for Recovery of
Burkholderia cepacia
Complex from Respiratory Secretions of Patients with Cystic Fibrosis
Authors: Henry Deborah , Campbell Maureen , McGimpsey Colleen , Clarke Alison , Louden Laurie , Burns Jane L. , Roe Martha H. , Vandamme Peter , Speert David 
Published: December 2019

ABSTRACT

Burkholderia cepacia
selective agar (BCSA) has previously been devised for isolation of
B. cepacia
from respiratory secretions of patients with cystic fibrosis and tested under research laboratory conditions. Here we describe a study in which BCSA, oxidation-fermentation polymyxin bacitracin lactose agar (OFPBL), and
Pseudomonas cepacia
agar (PCA) were compared in routine culture procedures for the ability to grow
B. cepacia
and inhibit other organisms. Three hundred twenty-eight specimens from 209 patients at two pediatric centers and 328 specimens from 109 adults were tested. Plates were inoculated, incubated, and read for quality and quantity of growth at 24, 48, and 72 h. Five (1.5%) specimens from 4 (1.9%) children and 75 (22.9%) specimens from 16 (14.7%) adults grew
B. cepacia
complex. At 24, 48, and 72 h, BCSA achieved 43, 93, and 100% detection, respectively; OFPBL achieved 26, 84, and 96%, respectively; and PCA achieved 33, 74, and 84% detection, respectively. Quality was assessed as pinpoint or good growth. At 24 h, most cultures growing
B. cepacia
complex had pinpoint colonies. By 48 and 72 h, 48 and 69% of
B. cepacia
complex cultures, respectively, had good growth on BCSA, while on OFPBL 19 and 30%, respectively, had good growth and on PCA 11 and 18%, respectively, had good growth. BCSA was superior to OFPBL and PCA in suppressing organisms other than
B. cepacia
complex; 40 non-
B. cepacia
complex organisms were isolated from BCSA, 263 were isolated from OFPBL, and 116 were isolated from PCA. We conclude that BCSA is superior to OFPBL and PCA in its ability to support the growth of
B. cepacia
complex and to suppress other respiratory organisms.
Evaluation of Modified BACTEC 12B Radiometric Medium and Solid Media for Culture ofMycobacterium aviumsubsp.paratuberculosisfrom Sheep
Authors: Whittington R. J. , Marsh I. , McAllister S. , Turner M. J. , Marshall D. J. , Fraser C. A. 
Published: December 2019

ABSTRACTDefinitive diagnosis of Johne’s disease in ruminants depends on confirming the presence of the causative bacterium,Mycobacterium aviumsubsp.paratuberculosis, in tissues of the host. This is readily achieved in most ruminant species by culture. However, culture of clinical specimens from sheep in many countries has been unrewarding. Such a culture from sheep was achieved recently in Australia by using a radiometric culture medium. The aims of the present study were to evaluate the culture ofM. aviumsubsp.paratuberculosisfrom sheep by using modified BACTEC 12B radiometric medium, to determine the sensitivity of culture in relation to histopathology, and to evaluate a range of solid media. Culture ofM. aviumsubsp.paratuberculosisfrom sheep with Johne’s disease is a sensitive method of diagnosis: intestinal tissues from all 43 animals with multibacillary disease and all 22 animals with paucibacillary disease were culture positive, while 98% of feces from 53 animals with multibacillary disease and 48% of feces from 31 animals with paucibacillary disease were culture positive. Of sheep without histological evidence of Johne’s disease from infected flocks, intestinal tissue from 32% of 41 were culture positive, while feces from 17% of 41 were culture positive. Consequently, culture is recommended as the “gold standard” test for detection of ovine Johne’s disease. Of the wide range of solid media that were evaluated, only modified Middlebrook 7H10 and 7H11 agars, which were very similar in composition to modified BACTEC 12B medium, yielded growth of ovine strains ofM. aviumsubsp.paratuberculosis. The sensitivity of detection ofM. aviumsubsp.paratuberculosison solid media was slightly lower than that in modified BACTEC 12B radiometric medium. Both egg yolk and mycobactin J were essential additives for growth of ovine strains ofM. aviumsubsp.paratuberculosisin both liquid and solid media.
Human Immunodeficiency Virus Antibody Testing by Enzyme-Linked Fluorescent and Western Blot Assays Using Serum, Gingival-Crevicular Transudate, and Urine Samples
Authors: Martínez Prudencio Martínez , Torres Antonio Rodríguez , Ortiz de Lejarazu Raul , Montoya Ana , Martín José Francisco , Eiros José María 
Published: December 2019

ABSTRACT
The aim of the present study was to evaluate the possible utilization of saliva and urine as alternative samples to serum for the diagnosis of human immunodeficiency virus (HIV) infection. A total of 302 individuals participated in the study: 187 HIV-infected individuals (106 had Centers for Disease Control and Prevention [CDC] stage II infection, 19 had CDC stage III infection, and 62 had CDC stage IV infection) and 115 noninfected persons (46 of the noninfected persons were blood donors and 69 belonged to a group at high risk of HIV infection). Paired saliva and urine samples were taken from each of the participants in the study. The presence of HIV-specific antibodies was detected by an enzyme-linked fluorescent assay (ELFA), and the result was confirmed by Western blot analysis (WB). The ELFA with saliva gave maximum sensitivity and specificity values, while ELFA had lower sensitivity (95.2%) and specificity (97.4%) values for detection of HIV antibody in urine samples. WB with all saliva samples fulfilled the World Health Organization criterion for positivity, while only 96.8% of the urine samples were confirmed to be positive by WB. Among the four reactivity patterns found by WB of these alternative samples, the most frequent included bands against three groups of HIV structural proteins (was ENV, POL, and GAG). The reactivity bands most frequently observed were those for the proteins gp160 and gp120. The least common reactivity band was the band for protein p17. The detection of HIV antibodies in saliva samples by means of ELFA with the possibility of later confirmation by WB makes saliva an alternative to serum for possible use in the diagnosis of infection. In contrast, HIV antibody detection in urine samples by the same methodology (ELFA) could be taken into consideration for use in epidemiological studies.
Detection of Epstein-Barr Virus DNA in Sera from Transplant Recipients with Lymphoproliferative Disorders
Authors: Limaye Ajit P. , Huang Meei-Li , Atienza Ederlyn E. , Ferrenberg James M. , Corey Lawrence 
Published: December 2019

ABSTRACT

Early diagnosis of Epstein-Barr Virus (EBV)-associated posttransplant lymphoproliferative disease (PTLD) is important because many patients respond to reduction in immunosuppression, especially if PTLD is detected at an early stage. Previous studies have found elevated EBV DNA levels in blood from patients with PTLD, but these assays required isolation of cellular blood fractions and quantitation. We evaluated the presence of cell-free EBV DNA in serum from solid-organ transplant recipients as a marker for PTLD. Five of 6 transplant recipients with histopathologically documented PTLD had EBV DNA detected in serum at the time of diagnosis (sensitivity = 83%), compared with 0 of 16 matched transplant recipients without PTLD (specificity = 100%) (
P
< 0.001 [Fisher’s exact test]). Furthermore, EBV DNA was detected in serum 8 and 52 months prior to the diagnosis of PTLD in two of three patients for whom stored sera were analyzed. Detection of EBV DNA in serum appears to be a useful marker for the early detection of PTLD in solid-organ transplant recipients. Further studies to define the role of such assays in evaluating solid-organ transplant patients at risk for PTLD are warranted.
Bartonella koehlerae
sp. nov., Isolated from Cats
Authors: Droz Sara , Chi Banghee , Horn Elke , Steigerwalt Arnold G. , Whitney Anne M. , Brenner Don J. 
Published: December 2019

ABSTRACT

Two of the 25
Bartonella
isolates recovered during a prevalence study of
Bartonella henselae
bacteremia in domestic cats from the greater San Francisco Bay region were found to differ phenotypically and genotypically from all prior
B. henselae
isolates. These isolates, C-29 and C-30, which were recovered from the blood of two pet cats belonging to the same household, grew on chocolate agar as pinpoint colonies following 14 days of incubation at 35°C in a candle jar but failed to grow on heart infusion agar supplemented with 5% rabbit blood. Additional phenotypic characteristics distinguished the isolates C-29 and C-30 from other feline
B. henselae
isolates. The restriction patterns obtained for C-29 and C-30 by citrate synthase PCR-restriction fragment length polymorphism (RFLP) analysis as well as by genomic RFLP could not be distinguished from each other but were distinctly different from that of the
B. henselae
type strain. In reciprocal reactions, DNAs from strains C-29 and C-30 were 97 to 100% related under optimal and stringent DNA reassociation conditions, with 0 to 0.5% divergence within related sequences. Labeled DNA from the type strain of
B. henselae
was 61 to 65% related to unlabeled DNAs from strains C-29 and C-30 in 55°C reactions, with 5.0 to 5.5% divergence within the related sequences, and 31 to 41% related in stringent, 70°C reactions. In reciprocal reactions, labeled DNAs from strains C-29 and C-30 were 68 to 92% related to those of the
B. henselae
type strain and other
B. henselae
strains, with 5 to 7% divergence. The 16S rRNA gene sequence of strain C-29 was 99.54% homologous to that of the type strain of
B. henselae
. On the basis of these findings, the two isolates C-29 and C-30 are designated a new species of
Bartonella
, for which we propose the name
Bartonella koehlerae
. The type strain of
Bartonella koehlerae
is strain C-29 (ATCC 700693).
Facklamia languida
sp. nov., Isolated from Human Clinical Specimens
Authors: Lawson Paul A. , Collins Matthew D. , Falsen Enevold , Sjöden Berit , Facklam Richard R. 
Published: December 2019

ABSTRACT

Three strains of a gram-positive catalase-negative, facultatively anaerobic coccus-shaped organism originating from human clinical samples were characterized by phenotypic and molecular taxonomic methods. Sequencing of genes encoding 16S rRNA showed that the strains are phylogenetically closely related (99.9 to 100% sequence similarity) and represent a new subline within the genus
Facklamia
. The unknown bacterium was readily distinguished from all currently described species of the genus
Facklamia
(viz.,
Facklamia hominis
,
Facklamia ignava
, and
Facklamia sourekii
) by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified as
Facklamia languida
sp. nov. The type strain of
F. languida
is CCUG 37842.
Rapid Identification of
Staphylococcus aureus
by Using Fluorescent Staphylocoagulase Assays
Authors: Holliday M. G. , Ford M. , Perry J. D. , Gould F. K. 
Published: December 2019

ABSTRACT

Two rapid (1-h) assays for the detection of
Staphylococcus aureus
staphylocoagulase were developed by using the fluorogenic thrombin substrates
N-t
-boc-Val-Pro-Arg-7-amido-4-methylcoumarin (VPA) and
N-t
-boc-β-benzyl-Asp-Pro-Arg-7-amido-4-methylocoumarin (BB). The assays were compared to the tube coagulase test and latex agglutination (LA) (Sanofi Diagnostics Pasteur, Guildford, Surrey, United Kingdom) by using 406 clinical isolates of staphylococci, and they produced positive and negative predictive values of 99.2 and 99.1% for LA, 98.9 and 92.7% for VPA, and 98.9 and 99.1% for BB. Fluorescent assays used colonies from solid media, thereby eliminating the need for broth cultures, and were performed in microtiter trays, thus making them suitable for large-scale screening.
Comparison of Levels of Human Immunodeficiency Virus Type 1 RNA in Plasma as Measured by the NucliSens Nucleic Acid Sequence-Based Amplification and Quantiplex Branched-DNA Assays
Authors: Ginocchio C. C. , Tetali S. , Washburn D. , Zhang F. , Kaplan M. H. 
Published: December 2019

ABSTRACT

This study compared levels of human immunodeficiency virus type 1 RNA in plasma as measured by the Quantiplex branched-DNA and NucliSens nucleic acid sequence-based amplification assays. RNA was detectable in 118 of 184 samples (64.13%) by the Quantiplex assay and in 171 of 184 samples (92.94%) by the NucliSens assay. Regression analysis indicated that a linear relationship existed between the two sets of values (
P
< 0.0001), although the Quantiplex and NucliSens values were significantly different (
P
< 0.001), with the NucliSens values being approximately 0.323 log higher. Spearman correlation analysis indicated that the overall changes in patient viral load patterns were highly correlative between the two assays:
r
= 0.912,
P
< 0.0001. The lower limits of sensitivity were determined to be approximately 100 copies/ml and 1,200 to 1,400 copies/ml for the NucliSens and Quantiplex assays, respectively.
Serum Is More Suitable than Whole Blood for Diagnosis of Systemic Candidiasis by Nested PCR
Authors: Bougnoux M.-E. , Dupont C. , Mateo J. , Saulnier P. , Faivre V. , Payen D. , Nicolas-Chanoine M.-H. 
Published: December 2019

ABSTRACT

PCR assays for the diagnosis of systemic candidiasis can be performed either on serum or on whole blood, but results obtained with the two kinds of samples have never been formally compared. Thus we designed a nested PCR assay in which five specific inner pairs of primers were used to amplify specific targets on the rRNA genes of
Candida albicans
,
C. tropicalis
,
C. parapsilosis
,
C. krusei
, and
C. glabrata
. In vitro, the lower limit of detection of each nested PCR assay was 1 fg of purified DNA from the corresponding
Candida
species. In rabbits with candidemia of 120 minutes’ duration following intravenous (i.v.) injection of 10
8
CFU of
C. albicans
, the sensitivities of the PCR in serum and whole blood were not significantly different (93 versus 86%). In other rabbits, injected with only 10
5
CFU of
C. albicans
, detection of candidemia by culture was possible for only 1 min, whereas DNA could be detected by PCR in whole blood and in serum for 15 and 150 min, respectively. PCR was more often positive in serum than in whole blood in 40 culture-negative samples (27 versus 7%;
P
< 0.05%). Lastly, experiments with rabbits injected i.v. with 20 or 200 μg of purified
C. albicans
DNA showed that PCRs were positive in serum from 30 to at least 120 min after injection, suggesting that the clearance of free DNA is slow. These results suggest that serum is the sample of choice, which should be used preferentially over whole blood for the diagnosis of systemic candidiasis by PCR.
Amplification of the Six Major Human Herpesviruses from Cerebrospinal Fluid by a Single PCR
Authors: Minjolle Sophie , Michelet C. , Jusselin I. , Joannes M. , Cartier F. , Colimon R. 
Published: December 2019

ABSTRACT
We used a novel type of primer system, a system that uses stair primers, in which the primer sequences are based on consensus sequences in the DNA polymerase gene of herpesvirus to detect herpesviruses by PCR. A single PCR in a single tube detected the six major herpesviruses that infect the central nervous system: herpes simplex virus type 1 (HSV-1), and type 2 (HSV-2), cytomegalovirus (CMV), Epstein-Barr virus (EBV), varicella-zoster virus (VZV), and human herpesvirus 6 (HHV-6). We used the technique to analyze 142 cerebrospinal fluid (CSF) samples that had been stored at −80°C and compared the results with those obtained previously for the same samples by standard, targeted PCR. Four hundred one targeted PCR tests had been run with the 142 samples to detect HSV-1, HSV-2, CMV, and VZV; screening for EBV and HHV-6 was not prescribed when the samples were initially taken. Eighteen CSF samples tested positive by classic targeted PCR. The herpesvirus consensus PCR detected herpesviruses in 37 samples, including 3 samples with coinfections and 17 viral isolates which were not targeted. Two samples identified as infected by the targeted PCR tested negative by the consensus PCR, and eight samples that tested positive by the consensus PCR were negative by the targeted PCR. One hundred three samples scored negative by both the targeted and the consensus PCRs. This preliminary study demonstrates the value of testing for six different herpesviruses simultaneously by a sensitive and straightforward technique rather than screening only for those viruses that are causing infections as suggested by clinical signs.
Multicenter Comparison of the Digene Hybrid Capture CMV DNA Assay (Version 2.0), the pp65 Antigenemia Assay, and Cell Culture for Detection of Cytomegalovirus Viremia
Authors: Mazzulli Tony , Drew Lawrence W. , Yen-Lieberman Belinda , Jekic-McMullen Dragana , Kohn Debra J. , Isada Carlos , Moussa George , Chua Robert , Walmsley Sharon 
Published: December 2019

ABSTRACT
We compared the Digene Hybrid Capture CMV DNA Assay version 2.0, the pp65 antigenemia assay, traditional tube culture, and shell vial culture for the detection of cytomegalovirus (CMV) viremia in several patient populations at three centers. Of 561 blood specimens collected from 402 patients, complete clinical and laboratory data were available for 489. Using consensus definitions for true positives and true negatives, the sensitivities of the Hybrid Capture assay, antigenemia, shell vial, and tube culture were 95, 94, 43, and 46%, respectively. The specificities of the Hybrid Capture assay and antigenemia were 95 and 94%, respectively. At all three study sites, the detected level of CMV viremia was significantly higher with the Hybrid Capture assay or antigenemia than with shell vial and tube culture. In a group of 131 healthy nonimmunosuppressed volunteers, the Hybrid Capture assay demonstrated a specificity of over 99%. The Hybrid Capture assay is a standardized assay that is simple to perform and can utilize whole blood specimens that have been stored for up to 48 h. The high sensitivity and specificity of the Hybrid Capture assay along with its simplicity and flexibility make it a clinically useful assay for the detection of CMV viremia in immunocompromised or immunosuppressed patients. Further evaluation to determine its role in predicting CMV disease and for monitoring the therapeutic response to anti-CMV therapy is needed.
Detection of
Bartonella henselae
DNA by Two Different PCR Assays and Determination of the Genotypes of Strains Involved in Histologically Defined Cat Scratch Disease
Authors: Sander Anna , Posselt Miriam , Böhm Norbert , Ruess Michael , Altwegg Martin 
Published: December 2019

ABSTRACT

Cat scratch disease (CSD) is a common cause of subacute regional lymphadenopathy, not only in children but also in adults. Serological and molecular studies demonstrated that
Bartonella henselae
is the etiologic agent in most cases of CSD. Amplification of
B. henselae
DNA in affected tissue and detection of antibodies to
B. henselae
are the two mainstays in the laboratory diagnosis of CSD. We designed a retrospective study and investigated formalin-fixed, paraffin-embedded lymph nodes from 60 patients (25 female, 35 male) with histologically suspected CSD by PCR amplification. The sensitivities of two different PCR assays were compared. The first primer pair amplified a 296-bp fragment of the 16S rRNA gene in 36 of the 60 samples, corresponding to a sensitivity of 60%. The second primer pair amplified a 414-bp fragment of the
htrA
gene in 26 of the 60 lymph nodes, corresponding to a sensitivity of 43.3%.
Bartonella
DNA could be detected in a total of 39 (65%) of the 60 lymph nodes investigated. However, histopathologic findings are typical but not specific for CSD and cannot be considered as a “gold standard” for diagnosis of CSD. The sensitivity of the PCR assays increased from 65 to 87% if two criteria (histology and serology) were used in combination for diagnosis of CSD. Two genotypes (I and II) of
B. henselae
are described as being involved in CSD. Genotype I was found in 23 (59%) and genotype II was found in 9 (23%) of the 39 PCR-positive lymph nodes. Seven (18%) lymph nodes were negative in both type-specific PCR assays. Thirty (50%) of our 60 patients were younger than 20 years old (15 were younger than 10 years), 20 (33%) were between 21 and 40 years old, and 10 (17%) patients were between 41 and 84 years old. Our data suggest that detection of
Bartonella
DNA in patients’ samples might confirm the histologically suspected diagnosis of CSD.
Studies of Genetic Relationships between Bovine, Caprine, Cervine, and Rangiferine Alphaherpesviruses and Improved Molecular Methods for Virus Detection and Identification
Authors: Ros Carlos , Belák Sándor 
Published: December 2019

ABSTRACT
The glycoprotein B (gB) and D (gD) genes from five ruminant alphaherpesviruses, bovine herpesvirus 1 (BHV-1), bovine herpesvirus 5 (BHV-5), caprine herpesvirus 1 (CapHV-1), cervine herpesvirus 1, and rangiferine herpesvirus 1, were partially sequenced. The nucleotide sequence alignments revealed a highly conserved gB gene, with homologies ranging between 87.2 and 99.6%, and a more variable gD gene, with homologies ranging between 71.3 and 98.9%. The phylogenetic analysis of the gB and gD nucleotide and deduced amino acid sequences revealed that BHV-5 is the most closely related virus to the BHV-1 subtype 1 and BHV-1 subtype 2 cluster and that CapHV-1 is the most distantly related virus. The phylogenetic data showed a close relationship of all the studied viruses with suid herpesvirus 1. On the basis of sequence data for the gB gene, a nested PCR combined with restriction enzyme analysis (REA) of the PCR products was developed for the simultaneous detection and identification of the viruses that were studied. Nested primers from highly conserved sequence stretches were selected in order to amplify a region of 294 bp in all five viruses, and a subsequent REA of the PCR products allowed specific identification. A mimic molecule that served as an internal standard of the amplification efficiency was constructed. The practical diagnostic applicability of the assay was evaluated with clinical samples consisting of semen and organ specimens from experimentally infected animals.