bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Immunoreactivity to aStreptococcus equisubsp.zooepidemicusM-Like Protein To Confirm an Outbreak of Poststreptococcal Glomerulonephritis, and Sequences of M-Like Proteins from Isolates Obtained from Different Host Species
Authors: Nicholson Mary Lou , Ferdinand LaReesa , Sampson Jacquelyn S. , Benin Andrea , Balter Sharon , Pinto Sergio Wyton Lima , Dowell Scott F. , Facklam Richard R. , Carlone George M. , Beall Bernard 
Published: December 2019

ABSTRACTThe etiologic agent of a large 1998 outbreak of poststreptococcal acute glomerulonephritis (PSGN) in Nova Serrana, Brazil, was found likely to be a specific strain ofStreptococcus equisubsp.zooepidemicusfrom contaminated cheese (S. Balter et al., Lancet 355:1776–1780, 2000). In the present study, we used a serologic screen for a known surface-exposed virulence factor to confirm the epidemiologic findings. Using primers flanking a previously characterized M-like protein gene (J. F. Timoney et al., Infect. Immun. 63:1440–1445, 1995), we amplified and sequenced the M-like protein (designated Szp5058) gene and found it to be identical among four independent acute-phase PSGN patient isolates. Convalescent-phase sera from 33 of 44 patients in the PSGN outbreak were found to contain antibodies highly reactive to a purified Szp5058 fusion protein, compared with 1 of 17 control sera (P< 0.0001), suggesting that Szp5058 was expressed during infection and further implicating this strain as the cause of the PSGN outbreak. The predicted signal sequence and cell wall association motif of Szp5058 were highly conserved with the corresponding sequence fromS. equisubsp.zooepidemicusSzpW60, while the predicted surface-exposed portions differed markedly between these two proteins. The 5′ end of theszp5058gene, including its variable region, was identical to theszpgene from another strain associated with a previous PSGN outbreak in England (M. Barham et al., Lancet i:945–948, 1983), and the correspondingszpsequence found from the Lancefield group C type strain isolated from a guinea pig. In addition, the hypervariable (HV) portion ofszp5058was identical to a previously published HV sequence from a horse isolate (J. A. Walker and J. F. Timoney, Am. J. Vet. Res. 59:1129–1133, 1998). Three other strains ofS. equisubsp.zooepidemicus, including another strain previously associated with a PSGN outbreak, were each found to contain a distinctszpgene. Two of theseszpgenes had HV regions identical toszpregions from isolates recovered from different host species.
Detection of
Legionella pneumophila
Using a Real-Time PCR Hybridization Assay
Authors: Ballard A. L. , Fry N. K. , Chan L. , Surman S. B. , Lee J. V. , Harrison T. G. , Towner K. J. 
Published: December 2019

ABSTRACT

A real-time PCR hybridization assay for
Legionella pneumophila
is described; the assay uses LightCycler (Idaho Technology) methodology to specifically detect 2.5 CFU/reaction, equivalent to 1,000 CFU/liter of starting water sample. The assay, including DNA extraction and confirmation of product identity, is completed within 90 min of receipt of a sample.
Detection ofEhrlichia platysDNA in Brown Dog Ticks (Rhipicephalus sanguineus) in Okinawa Island, Japan
Authors: Inokuma Hisashi , Raoult Didier , Brouqui Philippe 
Published: December 2019

ABSTRACTThirty-twoRhipicephalus sanguineusfemales collected from eight free-roaming dogs in Okinawa Island, Japan, were examined for ehrlichial DNA by 16S rRNA-based PCR and subsequent sequencing. Partial sequences ofEhrlichia platys16S rRNA (678 to 679 bp) were detected in three ticks (9.4%) from two dogs. This is the first report of detection ofE. platysin Japan, and also the first report of detection in ticks.
Detection of Extended-Spectrum β-Lactamases in Klebsiellae with the Oxoid Combination Disk Method
Authors: Carter Michael W. , Oakton Karen J. , Warner Marina , Livermore David M. 
Published: December 2019

ABSTRACT
The Oxoid combination disk method for detecting extended-spectrum β-lactamases (ESBLs) depends on comparing the inhibition zones of cefpodoxime (10-μg) and cefpodoxime-plus-clavulanate (10- plus 1-μg) disks. The presence of clavulanate enlarged the zones for all of 180 ESBL-producing klebsiellae by ≥5 mm, whereas zones for cefpodoxime-susceptible isolates and cefpodoxime-resistant isolates with AmpC and K1 β-lactamases were enlarged by ≤1 mm. Good discrimination was achieved with either the NCCLS or the British disk method.
Meningoencephalitis Associated with
Globicatella sanguinis
Infection in Lambs
Authors: Vela Ana I. , Fernández Elena , las Heras Alfonso , Lawson Paul A. , Domínguez Lucas , Collins Matthew D. , Fernandez-Garayzabal Jose F. 
Published: December 2019

ABSTRACT

Thirty lambs displayed symptoms of meningoencephalitis. An unusual gram-positive coccus was isolated in pure culture from the blood and brain samples from one of the affected animals, and phenotypic and phylogenetic characterization showed this to be
Globicatella sanguinis
. This is the first report of the isolation of
G. sanguinis
in pure culture from an animal infection.
Fungal Contamination of Food in Hematology Units
Authors: Bouakline Adel , Lacroix Claire , Roux Nicole , Gangneux Jean Pierre , Derouin Francis 
Published: December 2019

ABSTRACT

The prevalence of thermotolerant fungi on non-heat-sterilizable food was determined.
Aspergillus
spp. were noted in 100% of pepper and regular tea samples, 12 to 66% of fruits, 27% of herbal teas, and 20% of freeze-dried soup samples. All soft cheese samples were contaminated by
Geotrichum
and yeast (
Candida norvegensis
) but
Candida albicans
was never identified.
Randomly Amplified Polymorphic DNA Analysis of
Erysipelothrix
spp
Authors: Okatani Alexandre Tomomitsu , Hayashidani Hideki , Takahashi Toshio , Taniguchi Takahide , Ogawa Masuo , Kaneko Ken-ichi 
Published: December 2019

ABSTRACT

The usefulness of randomly amplified polymorphic DNA method (RAPD) to identify each species of genus
Erysipelothrix
and for epidemiological analysis of this genus was studied. Eighty-one strains and 18 random primers were tested. Among the tested primers, the primers NK51 (GGTGGTGGTATC) and NK6 (CCCGCGCCCC) produced noticeable results. The primer NK51 revealed four species-specific RAPD patterns. Of the 66 strains of
E. rhusiopathiae
, 64 had the same unique band of 884 bp. Of the 12 strains of
E. tonsillarum
, 11 produced a 1,265-bp band. In addition, two strains, previously thought to be
E. rhusiopathiae
, produced the 1,265-bp band, suggesting that they had been misclassified. One strain of
E. tonsillarum
produced the 884-bp band, suggesting that it too was
E. rhusiopathiae
. The
E. rhusiopathiae
strain of serovar 13 produced a 650-bp band, and the strain of serovar 18 produced a clear 420-bp band as well as three weak bands of 1,265, 918, and 444 bp. The primer NK6 revealed 14 RAPD patterns that were not serovar specific. However, different patterns were produced among strains of the same serovar showing that the RAPD method is able to identify the genetic variations of strains of this genus and can rapidly and easily differentiate strains of the same serovar. Based on these results, we concluded that the RAPD method with primers NK51 and NK6 is a rapid and reliable method to identify the species of this genus; we also concluded that this method might be a useful tool for the epidemiological analysis of the
Erysipelothrix
species.
Bacterial Colonization of Disposable Soft Contact Lenses Is Greater during Corneal Infiltrative Events than during Asymptomatic Extended Lens Wear
Authors: Sankaridurg Padmaja R. , Sharma Savitri , Willcox Mark , Naduvilath Thomas J. , Sweeney Deborah F. , Holden Brien A. , Rao Gullapalli N. 
Published: December 2019

ABSTRACT

Microorganisms, especially gram-negative bacteria, are considered to play a role in the etiology of certain corneal infiltrative events (CIEs) observed during soft contact lens wear. This study explored the possibility of microbial colonization of soft contact lenses as a risk factor leading to CIEs. In a clinical trial conducted from March 1993 to January 1996, 330 subjects wore disposable soft contact lenses on a 6-night extended-wear and disposal schedule. During this period, 4,321 lenses (118 during CIEs; 4,203 during asymptomatic lens wear) were recovered aseptically and analyzed for microbial colonization. A greater percentage of lenses were free from microbial colonization during asymptomatic wear than during CIEs (42 versus 23%;
P
< 0.0001). The incidence of gram-positive bacteria, gram-negative bacteria and fungi was greater during CIEs than during asymptomatic lens wear (
P
< 0.05). During asymptomatic lens wear, gram-positive bacteria were isolated most frequently and were usually normal external ocular microbiota. Of the gram-positive bacteria, the incidence of
Streptococcus pneumoniae
was greater during CIE than during asymptomatic wear (7.6 versus 0.6%;
P
< 0.0001). While gram-negative bacteria were seen in few cases during asymptomatic wear, their incidence during CIE in comparison to asymptomatic wear was substantial and significant (23.7 versus 3.8%;
P
< 0.0001). Also, the level of colonization was high. Of CIEs, events of microbial keratitis, contact lens acute red eye, and asymptomatic infiltrative keratitis were associated with lens colonization with gram-negative bacteria or
S. pneumoniae
. Colonization of soft contact lenses with pathogenic bacteria, especially gram-negative bacteria and
S. pneumoniae
, appears to be a significant risk factor leading to CIE.
Diagnostic Implications of Human Cytomegalovirus Immediate Early-1 and pp67 mRNA Detection in Whole-Blood Samples from Liver Transplant Patients Using Nucleic Acid Sequence-Based Amplification
Authors: Blok M. J. , Lautenschlager I. , Goossens V. J. , Middeldorp J. M. , Vink C. , Höckerstedt K. , Bruggeman C. A. 
Published: December 2019

ABSTRACT
Nucleic acid sequence-based amplification (NASBA) was used for detection of the human cytomegalovirus (CMV) immediate early-1 (IE) and the late pp67 mRNA in 353 blood samples collected from 34 liver transplant patients. The diagnostic value of these assays was compared to that of the pp65 antigenemia assay. Overall, 95 and 42% of the antigenemia-positive samples were IE NASBA and pp67 NASBA positive, respectively. Although the results from pp67 NASBA and the antigenemia assay appeared to correspond poorly, a clear correlation was seen between pp67 NASBA-negative results and low numbers of pp65 antigen-positive cells. Twenty patients (59%) were treated with ganciclovir after the diagnosis of symptomatic CMV infection. Before initiation of the antiviral therapy, the antigenemia assay detected the onset of symptomatic infection in all patients, whereas 95 and 60% of these patients were IE NASBA and pp67 NASBA positive, respectively. Although the sensitivity of IE NASBA was very high, the positive predictive value (PPV) of this assay for the onset of a symptomatic infection was only 63%. The PPV of the antigenemia assay as well as pp67 NASBA was considerably higher (80 and 86%, respectively). Thus, the detection of IE mRNA using NASBA appears to be particularly useful as a marker for early initiation of antiviral therapy in patients at high risk for the development of a symptomatic infection. Also, IE NASBA was found to be more sensitive than the antigenemia assay for monitoring CMV infection during antiviral therapy. On the contrary, pp67 NASBA did not appear to have additional diagnostic value compared to the antigenemia assay.
Acrophialophora fusisporaBrain Abscess in a Child with Acute Lymphoblastic Leukemia: Review of Cases and Taxonomy
Authors: Al-Mohsen I. Z. , Sutton D. A. , Sigler L. , Almodovar E. , Mahgoub N. , Frayha H. , Al-Hajjar S. , Rinaldi M. G. , Walsh T. J. 
Published: December 2019

ABSTRACTA 12-year-old girl with acute lymphoblastic leukemia was referred to King Faisal Specialist Hospital and Research Center. The diagnosis without central nervous system (CNS) involvement was confirmed on admission, and chemotherapy was initiated according to the Children Cancer Group (CCG) 1882 protocol for high-risk-group leukemia. During neutropenia amphotericin B (AMB) (1 mg/kg of body weight/day) was initiated for presumed fungal infection when a computed tomography (CT) scan of the chest revealed multiple nodular densities. After 3 weeks of AMB therapy, a follow-up chest CT revealed progression of the pulmonary nodules. The patient subsequently suffered a seizure, and a CT scan of the brain was consistent with infarction or hemorrhage. Because of progression of pulmonary lesions while receiving AMB, antifungal therapy was changed to liposomal AMB (LAMB) (6 mg/kg/day). Despite 26 days of LAMB, the patient continued to have intermittent fever, and CT and magnetic resonance imaging of the brain demonstrated findings consistent with a brain abscess. Aspiration of brain abscess was performed and the Gomori methenamine silver stain was positive for hyphal elements. Culture of this material grewAcrophialophora fusispora. Lung biopsy showed necrotizing fungal pneumonia with negative culture. The dosage of LAMB was increased, and itraconazole (ITRA) was added; subsequently LAMB was discontinued and therapy was continued with ITRA alone. The patient demonstrated clinical and radiological improvement. In vitro, the isolate was susceptible to low concentrations of AMB and ITRA.A. fusisporais a thermotolerant, fast-growing fungus with neurotropic potential. We report the first case of human infection involving the CNS.AcrophialophoraresemblesPaecilomycesbut differs in having colonies that become dark and in the development of phialides along the sides or at the tips of echinulate brown conidiophores. Conidia are borne in long chains and are smooth or ornamented with fine-to-coarse echinulations, sometimes in spiral bands. The taxonomy of the genusAcrophialophorais reviewed, andAcrophialophora nainianaandAcrophialophora levisare considered as synonyms ofA. fusispora.
Development of Reverse Transcription-PCR (Oligonucleotide Probing) Enzyme-Linked Immunosorbent Assays for Diagnosis and Preliminary Typing of Foot-and-Mouth Disease: a New System Using Simple and Aqueous-Phase Hybridization
Authors: Alexandersen Soren , Forsyth Morag A. , Reid Scott M. , Belsham Graham J. 
Published: December 2019

ABSTRACT
A reverse transcription-PCR (RT-PCR)–enzyme-linked immunosorbent assay system that detects a relatively conserved region within the RNA genome of all seven serotypes of foot-and-mouth disease virus (FMDV) has been developed. The high specificity of the assay is achieved by including a rapid hybridization step with a biotin-labeled internal oligonucleotide. The assay is highly sensitive, fast, and easy to perform. A similar assay, based on a highly variable region of the FMDV genome and employing a single asymmetric RT-PCR and multiple hybridization oligonucleotides, was developed to demonstrate the method's ability to type FMDV. Based on our theoretical and practical knowledge of the methodology, we predict that similar assays are applicable to diagnosis and strain differentiation in any system amenable to PCR amplification.
Genotyping of Verocytotoxin-Producing
Escherichia coli
O157: Comparison of Isolates of a Prevalent Phage Type by Fluorescent Amplified-Fragment Length Polymorphism and Pulsed-Field Gel Electrophoresis Analyses
Authors: Smith David , Willshaw Geraldine , Stanley John , Arnold Catherine 
Published: December 2019

ABSTRACT

We applied the high-resolution genotyping technique fluorescent amplified-fragment length polymorphism (FAFLP) analysis to 71 isolates of a single phage type (PT8) of pulsed-field gel electrophoresis (PFGE)-characterized verocytotoxin-producing
Escherichia coli
O157. Twenty-seven similar, but not identical, groupings were defined by both FAFLP analysis and the PFGE profiles. Given the FAFLP analysis conditions described here, these two methods exhibited equivalent discriminatory powers.
Comparison of the Rodac Imprint Method to Selective Enrichment Broth for Recovery of Vancomycin-Resistant Enterococci and Drug-Resistant
Enterobacteriaceae
from Environmental Surfaces
Authors: Hacek Donna M. , Trick William E. , Collins Susan M. , Noskin Gary A. , Peterson Lance R. 
Published: December 2019

ABSTRACT

We compared the Rodac imprint technique to selective enrichment broth for detecting vancomycin-resistant enterococci (VRE) and multidrug-resistant
Enterobacteriaceae
(MDRE) on surfaces. Rodac plates contained tryptic soy agar with 5% sheep blood, vancomycin (6 μg/ml), ceftazidime (2 μg/ml), amphotericin B (2 μg/ml), and clindamycin (1 μg/ml). Two types of broth were used: brain heart infusion (BHI) and BHI plus vancomycin (6 μg/ml) and ceftazidime (2 μg/ml) (BHIVC). Of the 46 surfaces cultured for VRE, 12 (26%) were positive. Of the 12 VRE-positive surfaces, 11 (92%) grew from Rodac, 8 (67%) grew from BHIVC, and 7 (58%) grew from BHI. A larger study is needed for MDRE, as only 4 of 43 surfaces were MDRE positive. The Rodac imprint technique successfully recovered VRE from environmental surfaces.
Detection of
Ehrlichia chaffeensis
DNA in
Amblyomma americanum
Ticks in Connecticut and Rhode Island
Authors: Ijdo Jacob W. , Wu Caiyun , Magnarelli Louis A. , Stafford Kirby C. , Anderson John F. , Fikrig Erol 
Published: December 2019

ABSTRACT

Ehrlichia chaffeensis
, the causative agent of human monocytic ehrlichiosis, is transmitted by
Amblyomma americanum
ticks, which are most abundant in the southern United States. Because serologic evidence suggests that residents of Connecticut are exposed to
E. chaffeensis
,
A. americanum
ticks were collected in Connecticut and Rhode Island for PCR analysis to detect
E. chaffeensis
DNA. Eight of 106 (7.6%)
A. americanum
ticks from Connecticut and 6 of 52 (11.5%) from Rhode Island contained
E. chaffeensis
DNA. Thus,
E. chaffeensis
is present in ticks in southern New England and transmission of
E. chaffeensis
may occur there.
Species Identification of
Mycobacterium avium
Complex Isolates by a Variety of Molecular Techniques
Authors: Beggs Marjorie L. , Stevanova Rossina , Eisenach Kathleen D. 
Published: December 2019

ABSTRACT

Organisms in the
Mycobacterium avium
complex (MAC;
M. avium
,
M. intracellulare
, and “nonspecific or X” MAC) are emerging pathogens among individual organisms of which significant genetic variability is displayed. The objective of the present study was to evaluate various molecular methods for the rapid and definitive identification of MAC species. Isolates were obtained from both human immunodeficiency virus (HIV)-positive patients and HIV-negative patients with and without known predisposing conditions. The isolates were initially hybridized with nucleic acid probes complementary to the rRNA of the respective mycobacterial species (AccuProbe Culture Confirmation kits for
M. avium
,
M. intracellulare
, and MAC species; Gen-Probe). Isolates were also examined by PCR and in some cases by Southern blot hybridization for the insertion element IS
1245
. Two other techniques included a PCR assay that amplifies the
mig
gene, a putative virulence factor for MAC, and
hsp65
gene amplification and sequencing. This study led to the following observations. Eighty-five percent of the isolates from HIV-positive patients were
M. avium
and 86% of the isolates from HIV-negative patients were
M. intracellulare
. Fifteen of the
M. avium
isolates did not contain IS
1245
and 7% of the
M. intracellulare
isolates were found to carry IS
1245
. All of the
M. avium
strains were
mig
positive, and all of the
M. intracellulare
strains were
mig
negative.
Rapid Identification of Bacteria from Positive Blood Cultures by Fluorescence-Based PCR–Single-Strand Conformation Polymorphism Analysis of the 16S rRNA Gene
Authors: Turenne Christine Y. , Witwicki Evelyn , Hoban Daryl J. , Karlowsky James A. , Kabani Amin M. 
Published: December 2019

ABSTRACT
Bacteremia continues to result in significant morbidity and mortality, particularly in patients who are immunocompromised. Currently, patients with suspected bacteremia are empirically administered broad-spectrum antibiotics, as definitive diagnosis relies upon the use of blood cultures, which impose significant delays in and limitations to pathogen identification. To address the limitations of growth-based identification, the sequence variability of the 16S rRNA gene of bacteria was targeted for rapid identification of bacterial pathogens isolated directly from blood cultures using a fluorescence-based PCR–single-strand conformation polymorphism (SSCP) protocol. Species-specific SSCP patterns were determined for 25 of the most common bacterial species isolated from blood cultures; these isolates subsequently served as a reference collection for bacterial identification for new cases of bacteremia. A total of 272 blood-culture-positive patient specimens containing bacteria were tested. A previously determined SSCP pattern was observed for 251 (92%) specimens, with 21 (8%) specimens demonstrating SSCP patterns distinct from those in the reference collection. Time to identification from blood culture positivity ranged from 1 to 8 days with biochemical testing, whereas identification by fluorescence-based capillary electrophoresis was obtained as early as 7 h at a calculated cost of $10 (U.S. currency) per specimen when tested in batches of 10. Limitations encountered included the inability to consistently detect mixed cultures as well as some species demonstrating identical SSCP patterns. This method can be applied directly to blood cultures or whole-blood specimens, where early pathogen identification would result in a timely diagnosis with possible implications for patient management costs and the mortality and morbidity of infections.
Genomic Variations in Echovirus 30 Persistent Isolates Recovered from a Chronically Infected Immunodeficient Child and Comparison with the Reference Strain
Authors: Bailly Jean-Luc , Chambon Martine , Henquell Cécile , Icart Josette , Peigue-Lafeuille Hélène 
Published: December 2019

ABSTRACTSeven sequential isolates of echovirus type 30 (EV30) were recovered over 22 months from a child with severe combined immune deficiency syndrome. The nucleotide sequences of the 5′ halves of the genomes (4,400 nucleotides) of the first (S1) and last (S7) isolates were determined and compared with that of the EV30 Bastianni reference strain, also determined in this study. In genome regions P1 and P2, 101 variations were identified between the two isolates. Synonymous differences far outnumbered nonsynonymous differences. Amino acid changes affected both capsid and nonstructural polypeptides (particularly 2B). The VP1 nucleotide sequences of the seven isolates were determined to analyze genome evolution during the chronic infection. In the phylogenetic tree, the seven isolates were directly related to the prototype strain in an individual monophyletic group, strongly suggesting that the chronic infection in the child arose from a single persistent EV30 isolate. Four lineages were observed in the persistent isolates. Isolates S2, S4, S5, and S6 were close relatives of one another, whereas isolates S1 and S3 formed individual lineages. Isolate S7, distantly related to all other isolates, formed the fourth lineage. These findings suggest the quasispecies nature of the genomes of the seven sequential EV30 isolates. Grouping of persistent isolates on the basis of replicative capacities was consistent with phylogenetic relationships. Overall, the results indicate that genetically related EV30 variants with different replicative capacities coexisted in a carrier state, probably in the gastrointestinal tract, during the infection of the child.