bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the Etest Method for Determining Voriconazole Susceptibilities of 312 Clinical Isolates of
Candida
Species by Using Three Different Agar Media
Authors: Pfaller M. A. , Messer S. A. , Houston A. , Mills K. , Bolmstrom A. , Jones R. N. 
Published: December 2019

ABSTRACT

Performance of the Etest for voriconazole susceptibility testing of 312 isolates of
Candida
spp. was assessed against that of the National Committee for Clinical Laboratory Standards (NCCLS) microdilution broth method. The NCCLS method employed RPMI 1640 broth medium, and MICs were read after incubation for 48 h at 35°C. Etest MICs were determined with RPMI agar containing 2% glucose (RPG), Casitone agar (CAS), and antibiotic medium 3 (AM3) agar and were read after incubation for 48 h at 35°C. The
Candida
spp. isolates included
C. albicans
(
n
= 174),
C. glabrata
(
n
= 55),
C. tropicalis
(
n
= 31),
C. parapsilosis
(
n
= 39),
C. krusei
(
n
= 5),
C. lusitaniae
(
n
= 2), and
C. guilliermondii
(
n
= 6). The Etest results obtained using RPG correlated well with the reference MICs. Overall agreement ranged from 91% for
C. glabrata
to 100% for
C. tropicalis
,
C. parapsilosis
,
C. guilliermondii
,
C. krusei
, and
C. lusitaniae
. When CAS was used, agreement ranged from 80% for
C. krusei
to 100% for
C. parapsilosis
,
C. guilliermondii
, and
C. lusitaniae
. With AM3, agreement ranged from 58% for
C. glabrata
to 100% for
C. lusitaniae
and
C. guilliermondii
. The Etest method using RPG appears to be a useful method for determining voriconazole susceptibilities of
Candida
species.
Molecular and Antigenic Characterization of a Highly Evolved Derivative of the Type 2 Oral Poliovaccine Strain Isolated from Sewage in Israel
Authors: Shulman Lester M. , Manor Yosef , Handsher Rachel , Delpeyroux Francis , McDonough Michael J. , Halmut Tova , Silberstein Ilana , Alfandari Jacklyn , Quay Jacqueline , Fisher Tamar , Robinov Jana , Kew Olen M. , Crainic Radu , Mendelson Ella 
Published: December 2019

ABSTRACT

An unusual, highly diverged derivative of the Sabin type 2 oral poliovaccine (OPV) strain was recovered from environmental samples during routine screening for wild polioviruses. Virus was cultivated in L20B cells and then passaged on BGM cells at 40°C (RCT [reproductive capacity at supraoptimal temperature]-positive marker) to select against most OPV strains. All but 1 of 25 RCT-positive OPV-derived environmental isolates were antigenically and genetically (>99.5% VP1 sequence match) similar to the respective Sabin strains. However, isolate PV2/4568-1/ISR98 (referred to below as 4568-1) escaped neutralization with Sabin 2-specific monoclonal antibodies and cross-adsorbed sera, and had multiple nucleotide substitutions (220 of 2,646; 8.3%) in the P1 capsid region. Fourteen of the 44 associated amino acid substitutions in the capsid mapped to neutralizing antigenic sites. Neutralizing titers in the sera of 50 Israeli children 15 years old were significantly lower to 4568-1 (geometric mean titer [GMT], 47) than to Sabin 2 (GMT, 162) or to the prototype wild strain, PV2/MEF-1/EGY42 (GMT, 108). Two key attenuating sites had also reverted in 4568-1 (A
481
to G in the 5′ untranslated region and the VP1 amino acid I
143
to T), and the isolate was highly neurovirulent for transgenic mice expressing the poliovirus receptor (PVR-Tg21 mice). The extensive genetic divergence of 4568-1 from the parental Sabin 2 strain suggested that the virus had replicated in one or more people for ∼6 years. The presence in the environment of a highly evolved, neurovirulent OPV-derived poliovirus in the absence of polio cases has important implications for strategies for the cessation of immunization with OPV following global polio eradication.
Phenotypic and Genetic Characterization of
Lactococcus garvieae
Isolated in Spain from Lactococcosis Outbreaks and Comparison with Isolates of Other Countries and Sources
Authors: Vela A. I. , Vázquez J. , Gibello A. , Blanco M. M. , Moreno M. A. , Liébana P. , Albendea C. , Alcalá B. , Mendez A. , Domínguez L. , Fernández-Garayzábal J. F. 
Published: December 2019

ABSTRACT

The phenotypic and genetic analysis results for 84 isolates of
Lactococcus garvieae
(including 62 strains from trout with lactococcosis from four different countries, 7 strains from cows and water buffalos with subclinical mastitis, 3 from water, and 10 from human clinical samples) are presented. There was great phenotypic heterogeneity (13 different biotypes) based on the acidification of saccharose, tagatose, mannitol, and cyclodextrin and the presence of the enzymes pyroglutamic acid arylamidase and
N
-acetyl-β-glucosaminidase.
L. garvieae
also exhibited high genetic diversity by pulsed-field gel electrophoresis (PFGE), with 19 different pulsotypes among the isolates of
L. garvieae
studied. Only epidemiologically related strains, like the Spanish and Italian fish isolates and the cow and water buffalo isolates, displayed a close genetic relationship by PFGE, while the strains isolated from sporadic clinical cases, like the human isolates, were genetically unrelated. Overall, a general correlation between phenotypic and genetic data was observed. Epidemiological analysis of biotype and PFGE results indicated that the trout lactococcosis outbreaks in Spain and Portugal and those in France and Italy were produced by genetically unrelated clones. In Spain, two different clones were detected; the outbreaks diagnosed from 1995 onward were produced by a clone (biotype 2, pulsotype A1) which, although genetically related, was different from the one that was responsible for the outbreaks studied between 1991 and 1994 (biotype 1, pulsotype B). The Portuguese isolate had a biochemical profile identical to that of the Spanish strain isolated from 1995 onward and is also genetically closely related to this strain (pulsotype A2). There was a close relationship between the two pulsotypes (E and F) found in the Italian isolates. The French isolate (biotype 3, pulsotype D) was not genetically related to any other
L. garvieae
fish isolate. These results suggest the existence of diverse infection sources for the different lactococcosis outbreaks.
Utility of Tissue Culture for Detection of
Toxoplasma gondii
in Vitreous Humor of Patients Diagnosed with Toxoplasmic Retinochoroiditis
Authors: Miller Darlene , Davis Janet , Rosa Robert , Diaz Martha , Perez Edith 
Published: December 2019

ABSTRACT

Laboratory recovery and confirmation of the etiologic agent in necrotizing retinochoroiditis are problematic. Tissue culture and intraocular antibody titers were compared as adjuncts to clinical diagnosis for toxoplasmic retinochoroiditis: the correlations were 91 and 67%, respectively. Isolation of
Toxoplasma gondii
may establish a definitive diagnosis in patients with toxoplasmic retinochoroiditis.
A Probable New
Helicobacter
Species Isolated from a Patient with Bacteremia
Authors: Tee Wee , Hinds Suzanne , Montgomery Janet , Dyall-Smith Michael L. 
Published: December 2019

ABSTRACT

A probable new
Helicobacter
species was isolated from the blood of a 14-month-old aboriginal child who presented with vomiting, diarrhea, fever, and dry cough. The most similar 16S rRNA gene sequence was that of
Helicobacter fennelliae
CCUG 18820
T
but the new sequence differed from it by at least 32 base substitutions and by the presence of a large (353-nucleotide) intervening sequence.
Evaluation of the Alexon-Trend ProSpecT
Campylobacter
Microplate Assay
Authors: Tolcin Rita , LaSalvia Margaret M. , Kirkley Barbara A. , Vetter Emily A. , Cockerill Franklin R. , Procop Gary W. 
Published: December 2019

ABSTRACT

We evaluated stool specimens known to contain or be free of
Campylobacter
by traditional culture, using the ProSpecT
Campylobacter
microplate assay (Alexon-Trend, Ramsey, Minn.). This rapid enzyme immunoassay for the detection of
Campylobacter
-specific antigens demonstrated 96% sensitivity and 99% specificity and is an acceptable alternative method of
Campylobacter
detection.
Community Acquisition of Gentamicin-Sensitive Methicillin-Resistant
Staphylococcus aureus
in Southeast Queensland, Australia
Authors: Nimmo Graeme R. , Schooneveldt Jacqueline , O'Kane Gabrielle , McCall Brad , Vickery Alison 
Published: December 2019

ABSTRACT

Community-acquired methicillin-resistant
Staphylococcus aureus
(MRSA) susceptible to gentamicin has been reported in a number of countries in the 1990s. To study the acquisition of gentamicin-sensitive MRSA (GS-MRSA) in southeast Queensland and the relatedness of GS-MRSA to other strains of MRSA, 35 cases of infection due to GS-MRSA from October 1997 through September 1998 were examined retrospectively to determine the mode of acquisition and risk factors for MRSA acquisition. Thirty-one isolates from the cases were examined using a variety of methods (antibiotyping, phage typing, pulsed-field gel electrophoresis [PFGE] fingerprinting, and coagulase typing by restriction analysis of PCR products) and were compared with strains of local hospital-acquired gentamicin-resistant MRSA (GR-MRSA) and of Western Australian MRSA (WA-MRSA). Only 6 of 23 cases of community-acquired GS-MRSA had risk factors for MRSA acquisition. Twenty of 21 isolates from cases of community-acquired infection were found to be related by PFGE and coagulase typing and had similar phage typing patterns. Hospital- and nursing home-acquired GS-MRSA strains were genetically and phenotypically diverse. Community-acquired GS-MRSA strains were not related to nosocomial GR-MRSA or WA-MRSA, but phage typing results suggest that they are related to GS-MRSA previously reported in New Zealand.
Outbreak of Nosocomial Infections Due to Extended-Spectrum β-Lactamase-Producing Strains of Enteric Group 137, a New Member of the Family
Enterobacteriaceae
Closely Related to
Citrobacter farmeri
and
Citrobacter amalonaticus
Authors: Warren John R. , Farmer J. J. , Dewhirst Floyd E. , Birkhead Karen , Zembower Teresa , Peterson Lance R. , Sims Lola , Bhattacharya Mondira 
Published: December 2019

ABSTRACT

A member of the
Enterobacteriaceae
initially identified as
Kluyvera cryocrescens
by the MicroScan Gram-Negative Combo 13 panel caused an outbreak of nosocomial infections in four patients (pneumonia,
n
= 2; urinary tract infection,
n
= 1; wound infection,
n
= 1) and urinary tract colonization in one patient. When the strains were tested by the Enteric Reference Laboratory of the Centers for Disease Control and Prevention, biochemical results were most compatible with
Yersinia intermedia
,
Kluyvera cryocrescens
, and
Citrobacter farmeri
but identification scores were low and test results were discrepant. However, when the biochemical test profile was placed in the computer database as a new organism, all strains were identified as the organism with high identification scores (0.999968 to 0.999997) and no discrepant test results. By 16S rRNA sequence analysis the organism clustered most closely with, but was distinct from,
Citrobacter farmeri
and
Citrobacter amalonaticus
. Based on its unique biochemical profile and rRNA sequence, this organism is designated Enteric Group 137. Restriction endonuclease analysis and taxonomic antibiograms of strains causing the outbreak demonstrated a single clone of Enteric Group 137, and antibiotic susceptibility testing revealed the presence of extended-spectrum β-lactamase (ESBL) resistance. Enteric Group 137 appears to be a new opportunistic pathogen that can serve as a source of ESBL resistance in the hospital.
Polymorphism in the Gene Coding for the Immunodominant Antigen gp43 from the Pathogenic Fungus
Paracoccidioides brasiliensis
Authors: Morais Flavia V. , Barros Tânia F. , Fukada Márcio K. , Cisalpino Patrícia S. , Puccia Rosana 
Published: December 2019

ABSTRACT

The gp43 glycoprotein is an immune-dominant antigen in patients with paracoccidioidomycosis (PCM). It is protective against murine PCM and is a putative virulence factor. The gp43 gene of
Paracoccidioides brasiliensis
B-339 is located in a 1,329-bp DNA fragment that includes two exons, a 78-bp intron, and a leader peptide-coding region of 105 bp. Polymorphism in gp43 has been suggested by the occurrence, in the same isolate or among different fungal samples, of isoforms with distinct isoelectric points. In the present study we aligned and compared with a consensus sequence the gp43 precursor genes of 17
P. brasiliensis
isolates after sequencing two PCR products from each fungal sample. The genotypic types detected showed 1 to 4 or 14 to 15 informative substitution sites, preferentially localized between 578 and 1166 bp. Some nucleotide differences within individual isolates (noninformative sites) resulted in a second isoelectric point for the deduced protein. The most polymorphic sequences were also phylogenetically distant from the others and encoded basic gp43 isoforms. The three isolates in this group were from patients with chronic PCM, and their DNA restriction patterns were distinct in Southern blots. The nucleotides encoding the inner core of the murine T-cell-protective epitope of gp43 were conserved, offering hope for the development of a universal vaccine.
Detection of Immunoglobulin M Antibodies to P35 Antigen of
Toxoplasma gondii
for Serodiagnosis of Recently Acquired Infection in Pregnant Women
Authors: Suzuki Yasuhiro , Ramirez Raymund , Press Cindy , Li Shuli , Parmley Stephen , Thulliez Philippe , Remington Jack S. 
Published: December 2019

ABSTRACT

We examined the efficiency of detection of immunoglobulin M (IgM) antibodies to a 35-kDa antigen (P35) of
Toxoplasma gondii
for serodiagnosis of acute infection in pregnant women. A double-sandwich enzyme-linked immunosorbent assay (ELISA) with recombinant P35 antigen (P35-IgM-ELISA) was used for this purpose. On the basis of the clinical history and the combination of results from the toxoplasma serological profile (Sabin-Feldman dye test, conventional IgM and IgA ELISAs, and the differential agglutination test), the patients were classified into three groups: group I, status suggestive of recently acquired infection; group II, status suggestive of infection acquired in the distant past; group III, status suggestive of persisting IgM antibodies. Eighteen (90.0%) of 20 serum samples from group I patients were positive by the P35-IgM-ELISA, whereas none of the 33 serum samples from group II patients were positive. Only 4 (25.0%) of 16 serum samples from group III patients were positive by the P35-IgM-ELISA, whereas all these serum samples were positive by the conventional IgM ELISA. These results indicate that demonstration of IgM antibodies against P35 by the P35-IgM-ELISA is more specific for the acute stage of the infection than demonstration of IgM antibodies by the ELISA that uses a whole-lysate antigen preparation. Studies with sera obtained from four pregnant women who seroconverted (IgG and IgM antibodies) during pregnancy revealed that two of them became negative by the P35-IgM-ELISA between 4 and 6 months after seroconversion, whereas the conventional IgM ELISA titers remained highly positive. The P35-IgM-ELISA appears to be useful for differentiating recently acquired infection from those acquired in the distant past in pregnant women.
Molecular Epidemiological Analysis of
Cryptosporidium
spp. in the United Kingdom: Results of Genotyping
Cryptosporidium
spp. in 1,705 Fecal Samples from Humans and 105 Fecal Samples from Livestock Animals
Authors: McLauchlin J. , Amar C. , Pedraza-Díaz S. , Nichols G. L. 
Published: December 2019

ABSTRACT

Cryptosporidium
present in 1,705 fecal samples from humans and 105 from livestock animals were analyzed by PCR-restriction fragment length polymorphism of the
Cryptosporidium
oocyst wall protein. Overall, genotype 1 (human exclusive type) was detected in 37.8% of the samples from humans, genotype 2 (broad host range) was detected in 61.5%, a third genotype designated genotype 3 (
Cryptosporidium meleagridis
) was detected in 0.3%, and both genotypes 1 and 2 were recovered from 0.4%. All samples from livestock yielded genotype 2. Among 469 patients infected during eight drinking water-related outbreaks, five outbreaks were predominantly due to genotype 1, and three were due to genotype 2. Fifty-four samples were collected from patients involved with five swimming pool-associated outbreaks: two outbreaks were due to genotype 1, one was due to genotype 2, and the remaining two involved both genotypes 1 and 2. Among 26 family outbreaks and 1 children's nursery outbreak (2 to 3 members per group), the same genotype was recovered from the different members of each outbreak: 13 were due to genotype 1, and 14 were due to genotype 2. In eighteen patients reporting contact with animals and/or farms, genotype 1 was recovered from one patient and genotype 2 was recovered from the remaining 17. Among the sporadic cases, there were distinct geographical and temporal variations in the distribution of the genotypes. The spring peak in cases was due to genotype 2. Genotype 1 was significantly more common in patients infected during the late-summer–autumn peak and in those with a history of foreign travel.
Evaluation of an Immunocapture-Agglutination Test (Brucellacapt) for Serodiagnosis of Human Brucellosis
Authors: Orduña Antonio , Almaraz Ana , Prado Ana , Gutierrez M. Purificación , Garcia-Pascual Agustina , Dueñas Ana , Cuervo Milagros , Abad Ramon , Hernández Beatriz , Lorenzo Belen , Bratos Miguel A. , Torres Antonio Rodriguez 
Published: December 2019

ABSTRACT

We evaluated the validity and the usefulness of a new test for the diagnosis of human brucellosis based on an immunocapture-agglutination technique. A total of 315 sera from 82 patients with a diagnosis of brucellosis, 157 sera from patients in whom brucellosis was suspected but not confirmed, and 412 sera from people living in rural areas with endemic brucellosis were studied. The seroagglutination test (SAT), Coombs anti-Brucella test, and Brucellacapt test were evaluated. All the initial sera from the 82 patients proved to be positive in Brucellacapt and Coombs tests, while only 75 (91.4%) were positive in the SAT. If a ≥1/160 diagnostic threshold titer was defined for the Brucellacapt test, Coombs test, and SAT, the sensitivities were 95.1, 91.5, and 65.8%, respectively. Taking the same diagnostic threshold titer for the 157 sera from the unconfirmed but suspected patients, the specificities of the Brucellacapt, Coombs, and SAT were 81.5, 96.2, and 100%, respectively; for the 412 control sera, the specificities were 99.0, 99.8, and 100%. The diagnostic efficiency (area below the receiver operating characteristic curve) of Brucellacapt was 0.987852 (95% confidence interval [CI], 0.95109 to 0.99286), very similar to the diagnostic efficiency of the Coombs test (0.97611; 95% CI, 0.94781 to 0.99146) and higher than that of SAT (0.91013; 95% CI, 0.86649 to 0.94317). The results of the Brucellacapt test were compared with those of the Coombs test (correlation coefficient, 0.956;
P
= 0.000) and SAT (correlation coefficient, 0.866;
P
= 0.000). The study shows very good correlation between the Brucellacapt and Coombs tests, with a high concordance between titers obtained in the two tests. Nevertheless, lower correlation and concordance were found between the Brucellacapt and Coombs tests when the results for titers of ≥1/160 were compared (0.692;
P
= 0.000). In acute brucellosis, the Brucellacapt and Coombs tests render positive titers of ≥1/160. When the titers are lower, they increase significantly in the following 30 days, despite the evolution of SAT titers. In contrast, Brucellacapt and Coombs titers are always high (≥1/640) in brucellosis with long evolution, whether SAT titers are higher or lower than 1/160.
Serological Relationships of
Cryptococcus
spp.: Distribution of Antigenic Factors in
Cryptococcus
and Intraspecies Diversity
Authors: Ikeda Reiko , Sugita Takashi , Shinoda Takako 
Published: December 2019

ABSTRACT

The antigenic formulas of 34 species in the genus
Cryptococcus
were determined by using type strains and eight factor sera prepared from adsorption experiments with
Cryptococcus neoformans
serotypes. These antigenic factors were shared by 19 species. The strains used could be divided into eight serological groups. The patterns of groups 1, 2, 3, 5, and 6 were the same as the patterns of
C. neoformans
serotypes A, D, A-D, B, and C, respectively. The species belonging to group 4 reacted to factor sera 1, 2, and 3. Group 7 contained one species that reacted only to factor serum 1. The 15 species in group 8 did not react to any of the factor sera used. Compared to the reported molecular phylogenetic tree, the serological and phylogenetic data were correlated in the
Filobasidium
lineage. All the members of the albidus clade in the
Filobasidium
lineage had antigens 1, 2, and 3, and all the strains in the magnus clade belonged to serogroup 8. Moreover, intraspecies diversity was examined using strains of
C. curvatus
,
C. humicolus
, and
C. laurentii
. Serological heterogeneity was observed in the species
C. humicolus
and
C. laurentii
, as well as in phylogenetic relationships previously published. Using serological features, similarities and differences between
Cryptococcus
species were demonstrated. Our study contributes to a better description of the genus
Cryptococcus
and related species phenotypically and phylogenetically.
Detection of Influenza A Viruses from Different Species by PCR Amplification of Conserved Sequences in the Matrix Gene
Authors: Fouchier Ron A. M. , Bestebroer Theo M. , Herfst Sander , Van Der Kemp Liane , Rimmelzwaan Guus F. , Osterhaus Albert D. M. E. 
Published: December 2019

ABSTRACT
The recently raised awareness of the threat of a new influenza pandemic has stimulated interest in the detection of influenza A viruses in human as well as animal secretions. Virus isolation alone is unsatisfactory for this purpose because of its inherent limited sensitivity and the lack of host cells that are universally permissive to all influenza A viruses. Previously described PCR methods are more sensitive but are targeted predominantly at virus strains currently circulating in humans, since the sequences of the primer sets display considerable numbers of mismatches to the sequences of animal influenza A viruses. Therefore, a new set of primers, based on highly conserved regions of the matrix gene, was designed for single-tube reverse transcription-PCR for the detection of influenza A viruses from multiple species. This PCR proved to be fully reactive with a panel of 25 genetically diverse virus isolates that were obtained from birds, humans, pigs, horses, and seals and that included all known subtypes of influenza A virus. It was not reactive with the 11 other RNA viruses tested. Comparative tests with throat swab samples from humans and fecal and cloacal swab samples from birds confirmed that the new PCR is faster and up to 100-fold more sensitive than classical virus isolation procedures.
Species-Specific Identification of Human Adenoviruses by a Multiplex PCR Assay
Authors: Xu WanHong , McDonough Mike C. , Erdman Dean D. 
Published: December 2019

ABSTRACT
A multiplex PCR assay was developed by using primers to the fiber gene that could differentiate human adenovirus (Ad) species A through F in a single amplification reaction. The assay correctly identified the species of all 49 recognized Ad prototype strains as well as 180 geographically and temporally diverse Ad field isolates. Ad serotype 6 (Ad6) (species C), Ad16 (species B), Ad31 (species A), and Ad40 and Ad41 (species F) could also be distinguished by amplicon size within each respective species. In comparison, a previously described Ad species-specific multiplex PCR assay that used primers to the Ad hexon gene gave equivocal results with several serotypes of species B, whereas our multiplex assay amplified all species B serotypes equally well. Our multiplex PCR assay will permit rapid, accurate, and cost-effective classification of Ad isolates.