bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical Identification of
Citrobacter
Species Defined by DNA Hybridization and Description of
Citrobacter gillenii
sp. nov. (Formerly
Citrobacter
Genomospecies 10) and
Citrobacter murliniae
sp. nov. (Formerly
Citrobacter
Genomospecies 11)
Authors: Brenner Don J. , O’Hara Caroline M. , Grimont Patrick A. D. , Janda J. Michael , Falsen Enevold , Aldova Eva , Ageron Elisabeth , Schindler Jiri , Abbott Sharon L. , Steigerwalt Arnold G. 
Published: December 2019

ABSTRACT

Recent work describing six named species and two unnamed genomospecies within
Citrobacter
has enlarged the genus to 11 species. DNA relatedness and phenotypic tests were used to determine how well these species can be identified. One hundred thirty-six strains were identified to species level by DNA relatedness and then identified phenotypically in a blinded fashion. By using conventional tests, 119 of the 136 strains (88%) were correctly identified to species level. Three additional strains (2%) were identified as citrobacteria but were not identified to species level, and 14 strains (10%) were misidentified as other
Citrobacter
species. Carbon source utilization tests were used to identify 86 of the strains. Eighty-four strains (98%) were correctly identified, and two strains (2%) were misidentified as other
Citrobacter
species. Additional strains of
Citrobacter
genomospecies 10 and
Citrobacter
genomospecies 11 were identified, allowing these species to be formally named as
Citrobacter gillenii
sp. nov. and
Citrobacter murliniae
sp. nov., respectively.
Diagnostic Value of Anti-Hepatitis C Virus (HCV) Core Immunoglobulin M in Recurrence of HCV Infection after Orthotopic Liver Transplantation
Authors: Casino Carmela , Lilli Daniela , Rivanera Daniela , Comanducci Antonella , Rossi Massimo , Casciaro Giovanni , Pecorella Irene , Alfani Dario , Mancini Carlo 
Published: December 2019

ABSTRACT
The significance of anti-hepatitis C virus (HCV) core immunoglobulin M (IgM) and its relationship with genotypes, alanine aminotransferase abnormality, and histological data were studied for 18 patients who had undergone orthotopic liver transplantation due to HCV-related end-stage disease. During follow-up, IgM response seemed to be associated with the recurrence of HCV infection but did not correlate with abnormal alanine aminotransferase levels and histological data. In addition, the results of this study indicated that the detection of HCV RNA is critical for diagnosis of reinfection in liver transplantation.
Phylogenetic Analysis of
Rhinosporidium seeberi
’s 18S Small-Subunit Ribosomal DNA Groups This Pathogen among Members of the Protoctistan Mesomycetozoa Clade
Authors: Herr Roger A. , Ajello Libero , Taylor John W. , Arseculeratne Sarath N. , Mendoza Leonel 
Published: December 2019

ABSTRACT

For the past 100 years the phylogenetic affinities of
Rhinosporidium seeberi
have been controversial. Based on its morphological features, it has been classified as a protozoan or as a member of the kingdom Fungi. We have amplified and sequenced nearly a full-length 18S small-subunit (SSU) ribosomal DNA (rDNA) sequence from
R. seeberi
. Using phylogenetic analysis, by parsimony and distance methods, of
R. seeberi
’s 18S SSU rDNA and that of other eukaryotes, we found that this enigmatic pathogen of humans and animals clusters with a novel group of fish parasites referred to as the DRIP clade (
Dermocystidium
, rossete agent,
Ichthyophonus
, and
Psorospermium
), near the animal-fungal divergence. Our phylogenetic analyses also indicate that
R. seeberi
is the sister taxon of the two
Dermocystidium
species used in this study. This molecular affinity is remarkable since members of the genus
Dermocystidium
form spherical structures in infected hosts, produce endospores, have not been cultured, and possess mitochondria with flat cristae. With the addition of
R. seeberi
to this clade, the acronym DRIP is no longer appropriate. We propose to name this monophyletic clade Mesomycetozoa to reflect the group’s phylogenetic association within the
Eucarya
.
Infection with Agents of Human Granulocytic Ehrlichiosis, Lyme Disease, and Babesiosis in Wild White-Footed Mice (
Peromyscus leucopus
) in Connecticut
Authors: Stafford Kirby C. , Massung Robert F. , Magnarelli Louis A. , Ijdo Jacob W. , Anderson John F. 
Published: December 2019

ABSTRACT

White-footed mice,
Peromyscus leucopus
, were captured in southern Connecticut during 1997 and 1998 to determine the prevalence of infections caused by granulocytic
Ehrlichia
sp.,
Borrelia burgdorferi
, and
Babesia microti
. Of the 50 mice captured and recaptured, 25 of 47 (53.2%) and 23 of 48 (47.9%) contained antibodies to the BDS or NCH-1
Ehrlichia
strains, respectively, as determined by indirect fluorescent antibody (IFA) staining methods. The majority (83.3%) of 48 mice also contained antibodies to
B. burgdorferi
, as determined by enzyme-linked immunosorbent assay. Moreover, 20 of 26 (76.9%) contained antibodies to
B. microti
by IFA staining methods. In nested PCR tests using the 16S rRNA gene, the DNA of the human granulocytic ehrlichiosis (HGE) agent was detected in 17 of 47 mice (36.2%), but only 4 (23.5%) of these 17 mice were PCR positive at each capture. Antibody-positive reactions to granulocytic
Ehrlichia
sp. organisms were detected in 17 of 23 (73.9%) of the PCR-positive mice. The sequences from PCR products from nine positive blood samples were identical to the HGE agent.
Ehrlichia
spp. were cultured from three of five mice captured in April 1998, including one that was PCR positive in April 1997. In addition, 2 of 14 larval
Ixodes scapularis
pools, which were attached to two PCR-positive mice, contained DNA of the HGE agent. A high percentage of white-footed mice are infected or have been infected naturally by the HGE agent with low-level persistent infection or frequent reinfection in some individual mice. However, the changes noted in the presence of DNA and antibodies in repeated blood and serum samples from individual mice over several months of field collection suggests that infection with granulocytic
Ehrlichia
is transient in most wild
P. leucopus.
Presence of α and
a
Mating Types in Environmental and Clinical Collections of
Cryptococcus neoformans
var.
gattii
Strains from Australia
Authors: Halliday C. L. , Bui T. , Krockenberger M. , Malik R. , Ellis D. H. , Carter D. A. 
Published: December 2019

ABSTRACT

Cryptococcus neoformans
var.
gattii
lives in association with certain species of eucalyptus trees and is a causative agent of cryptococcosis. It exists as two mating types, MATα and MATa, which is determined by a single-locus, two-allele system. In the closely related
C. neoformans
var.
neoformans
, the α mating type has been found to outnumber its a counterpart by at least 30:1, but there have been very limited data on the proportions of each mating type in
C. neoformans
var.
gattii
. In the present study, specific PCR primers were designed to amplify two separate α-mating-type genes from
C. neoformans
var.
gattii
strains. These were used to survey for the presence of the two mating types in clinical and environmental collections of
C. neoformans
var.
gattii
strains from Australia. Sixty-eight of 69 clinical isolates produced both α mating type-specific bands and were assumed to be of the α mating type. The majority of environmental isolates were also of the α mating type, but the a mating type was located in two separate areas. In one area, the a mating type outnumbered the α mating type by 27:2, but in the second area, the ratio of the two mating types was close to the 50:50 ratio expected for sexual recombination.
Onychomycosis Caused by
Blastoschizomyces capitatus
Authors: D’Antonio Domenico , Romano Ferdinando , Iacone Antonio , Violante Beatrice , Fazii Paolo , Pontieri Eugenio , Staniscia Tommaso , Caracciolo Claudia , Bianchini Stefano , Sferra Roberta , Vetuschi Antonella , Gaudio Eugenio , Carruba Giuseppe 
Published: December 2019

ABSTRACT

Blastoschizomyces capitatus
was cultured from the nail of a healthy patient with onychomycosis. The identity of the isolate was initially established by standard methods and ultrastructural analysis and was verified by molecular probing. Strains ATCC 200929, ATCC 62963, and ATCC 62964 served as reference strains for these analyses. To our knowledge, this is the first case of nail infection secondary to paronychia caused by this organism reported in the English literature.
Skin Carriage of Acinetobacters in Hong Kong
Authors: Chu Y. W. , Leung C. M. , Houang E. T. S. , Ng K. C. , Leung C. B. , Leung H. Y. , Cheng A. F. B. 
Published: December 2019

ABSTRACT

We studied the carriage of
Acinetobacter
spp. at five superficial sites in 79 patients from two hospitals, in 133 healthy controls from the community (medical students and new nurses), and in 198 student nurses in different classes. A total of 431 isolates from 364 positive sites of 201 subjects and 124 blood culture isolates (1997 to 1998) were genospeciated by amplified ribosomal DNA restriction analysis. Genospecies 3 was the most common species. The carriage rate of student nurses (42 of 131) was significantly lower than that of new nurses from the community (25 of 38) (chi-square test,
P
= 0.0004; odds ratio [OR], 4.08; 95% confidence limits, 1.78 to 9.41) but not significantly different (
P
= 0.1) from that of patients in the same hospital (20 of 42). Genospecies from blood cultures and subjects (acute patients and student nurses) from Prince of Wales Hospital were similar to one another but different from subjects from the community or from another hospital (chi-square test,
P
< 0.0001). Half of the subjects who were positive at at least two sites had different genospecies. Of the 28 sites examined, 68% showed strain variation among isolates of the same genospecies by random amplified polymorphic DNA analysis. Half of the 106 subjects who had samples taken again within 6 weeks or 6 months later were positive only once. In the 17 subjects who were positive on at least two occasions, each occasion yielded different genospecies in 13 subjects. Our results indicate that skin carriage in the majority of healthy subjects is characterized by low density, variation in genospecies and strains, short-term duration, and the typicality of a given locality.
Inter- and Intralaboratory Comparison of
Ehrlichia equi
and Human Granulocytic Ehrlichiosis (HGE) Agent Strains for Serodiagnosis of HGE by the Immunofluorescent-Antibody Test
Authors: Walls Jennifer J. , Aguero-Rosenfeld Maria , Bakken Johan S. , Goodman Jesse L. , Hossain Deloar , Johnson Russell C. , Dumler J. Stephen 
Published: December 2019

ABSTRACT

Human granulocytic ehrlichiosis (HGE) is usually diagnosed by immunofluorescent antibody (IFA) serology with
Ehrlichia equi
-infected neutrophils or HGE agent-infected cultured HL60 cells. The HGE agent and
E. equi
are antigenically diverse, and interpretation of serologic results is also often variable. Thus, we investigated the sensitivity and specificity of various HGE agent and
E. equi
antigens used for IFA diagnosis by three different laboratories. Serum samples from 28 patients with well-characterized HGE and 9 patients with suspected HGE who were investigated by PCR, blood smear examinations, and serology were used, along with 9 serum samples from patients with other rickettsial and ehrlichial infections. Each serum sample was tested with up to 10 different antigen preparations. Overall, qualitative IFA results agreed in 70% of the samples. Titers among antigens were similar (
r
= 0.89 to 0.96), but titers of individual samples varied by fourfold or more in 5 of 81 (6%) of the serum samples. Sensitivity ranged from 100% to 82%, and specificity varied from 100% to 67%, but these differences were not significant, even among those tested in the same laboratory or between two different laboratories. Antibodies were detected in 14 to 44% of acute-phase sera from confirmed HGE patients. Most false-positive reactions resulted with
Ehrlichia chaffeensis
; when these sera were excluded, the specificity of most antigens was 91 to 100%. These data indicate that IFA results often agree and that IFA is useful for diagnosis of HGE in convalescence. However, without further standardization, variability among serologic tests using
E. equi
and HGE agent isolates for diagnosis of HGE will occasionally provide discrepant results and confound diagnosis.
Cocirculation of Two Distinct Lineages of Equine Influenza Virus Subtype H3N8
Authors: Oxburgh L. , Klingeborn B. 
Published: December 2019

ABSTRACT
Direct amplification and sequencing of the hemagglutinin (HA) genes of equine influenza virus subtype H3N8 was undertaken in order to characterize strains of this virus circulating in Sweden. The majority of viruses from outbreaks during 1997 analyzed belonged to the American lineage of H3 equine influenza, and one strain was shown to belong to the European lineage. Furthermore, it was shown that recent American-lineage strains are mutated at amino acid position 190 of the HA during serial passage in embryonated hens’ eggs. Host cell adaptation of these viruses thus takes place at antigenic region B of the HA.
Comparison of Commercial Amies Transport Systems with In-House Amies Medium for Recovery of
Neisseria gonorrhoeae
Authors: Thompson Donna S. , French Susanne A. 
Published: December 2019

ABSTRACT

Microbiologists are still encumbered by the variable performance of Amies charcoal transport medium in recovery of
Neisseria gonorrhoeae
. The objective of this study was to evaluate and select a good quality commercial system to replace our in-house preparation. We adsorbed 0.1 ml of a suspension from 30 gonococcal isolates onto each swab type and replaced the swab into the transport medium. We plated the swabs to New York City medium at 0, 24, 48, 72, and 96 h. We compared the survival of each isolate in the commercial Amies transport systems with that in our in-house Amies transport medium. The best recovery was observed with Copan transport systems. Some systems are inadequate and unacceptable for culture of gonococci.
Isolation of
Providencia heimbachae
from Human Feces
Authors: Mohr O’Hara Caroline , Steigerwalt Arnie G. , Green Donna , McDowell Michael , Hill Bertha C. , Brenner Don J. , Miller J. Michael 
Published: December 2019

ABSTRACT

Providencia heimbachae
was first described in 1986. It has been isolated from penguin feces and an aborted bovine fetus. To date, there has been no reported isolation of this organism from human specimens. We now report the isolation of
P. heimbachae
from the stool of a 23-year-old woman with idiopathic diarrhea. The identity of the human strain was determined biochemically and by DNA relatedness to the type strain of
P. heimbachae.
Identification of and Hydrogen Peroxide Production by Fecal and Vaginal Lactobacilli Isolated from Japanese Women and Newborn Infants
Authors: Song Yu-Li , Kato Naoki , Matsumiya Yoshiko , Liu Cheng-Xu , Kato Haru , Watanabe Kunitomo 
Published: December 2019

ABSTRACT

We identified
Lactobacillus
isolates from Japanese women and newborn infants by a DNA-DNA hybridization method. The predominating lactobacilli were
Lactobacillus crispatus
and
Lactobacillus gasseri
in the women’s vaginas and the newborns’ intestines and
L. gasseri
and
Lactobacillus fermentum
in the women’s intestines. All
L. crispatus
strains were exclusively strong H
2
O
2
producers.
Third Human Isolate of a
Desulfovibrio
sp. Identical to the Provisionally Named
Desulfovibrio fairfieldensis
Authors: La Scola Bernard , Raoult Didier 
Published: December 2019

ABSTRACT

Desulfovibrio fairfieldensis
was isolated from the urine sample of a patient with a urinary tract infection and meningoencephalitis. It was identified by 16S rRNA gene amplification and sequencing.
Diarrheagenic
Escherichia coli
and Acute and Persistent Diarrhea in Returned Travelers
Authors: Schultsz C. , van den Ende J. , Cobelens F. , Vervoort T. , van Gompel A. , Wetsteyn J. C. F. M. , Dankert J. 
Published: December 2019

ABSTRACT

To determine the role of diarrheagenic
Escherichia coli
in acute and persistent diarrhea in returned travelers, a case control study was performed. Enterotoxigenic
E. coli
(ETEC) was detected in stool samples from 18 (10.7%) of 169 patients and 4 (3.7%) of 108 controls. Enteroaggregative
E. coli
(EAggEC) was detected in 16 (9.5%) patients and 7 (6.5%) controls. Diffuse adherent
E. coli
strains were commonly present in both patients (13%) and controls (13.9).
Campylobacter
and
Shigella
species were the other bacterial enteropathogens most commonly isolated (10% of patients, 2% of controls). Multivariate analysis showed that the presence of ETEC was associated with acute diarrhea (odds ratio [OR], 6.7; 95% confidence interval [CI], 1.5 to 29.1;
P
= 0.005), but not with persistent diarrhea (OR, 1.6; 95% CI, 0.4 to 7.4). EAggEC was significantly more often present in patients with acute diarrhea than in controls (
P
= 0.009), but no significant association remained after multivariate analysis. ETEC and EAggEC are frequently detected in returned travelers with diarrhea. The presence of ETEC strains is associated with acute but not with persistent diarrhea.
Brachyspira aalborgi
Infection Diagnosed by Culture and 16S Ribosomal DNA Sequencing Using Human Colonic Biopsy Specimens
Authors: Kraaz Wolfgang , Pettersson Bertil , Thunberg Ulf , Engstrand Lars , Fellström Claes 
Published: December 2019

ABSTRACT

In this study we report on the isolation and characterization of the intestinal spirochete
Brachyspira aalborgi
using human mucosal biopsy specimens taken from the colon of a young adult male with intestinal spirochetosis. A selective medium, containing 400 μg of spectinomycin/ml and 5 μg of polymyxin/ml was used for the isolation procedure. A high degree of similarity, in terms of phenotypic properties and 16S ribosomal DNA sequence, was observed between the isolated strain, named W1, and the type strain, 513A, of
B. aalborgi
. A similarity of 99.7% in the nucleotide sequence was found between W1 and 513A
T
, based on the almost-complete gene. A short segment of the 16S rRNA gene was amplified by PCR using genetic material enriched from paraffin-embedded biopsy specimens, which were taken from the patient on two occasions. The products showed 16S rRNA gene sequences virtually identical to that of strain 513A
T
in the actual region. Immunohistochemistry was performed on the colonic biopsy specimens with a polyclonal antibody raised against an intestinal spirochete isolated in a previous case of human intestinal spirochetosis. The antibody reacted strongly with the spirochete on the luminal epithelium. No immune reaction was seen within or below the surface epithelium. Routine histology did not reveal signs of colitis. Electron microscopy showed spirochetes attached end-on to the colonic mucosal surface. The isolate grew poorly on a commonly used selective medium for intestinal spirochetes, which may explain previous failures to isolate
B. aalborgi
.
Detection of Trichomonosis in Vaginal and Urine Specimens from Women by Culture and PCR
Authors: Lawing Lisa F. , Hedges Spencer R. , Schwebke Jane R. 
Published: December 2019

ABSTRACT

Vaginal trichomonosis is a highly prevalent infection which has been associated with human immunodeficiency virus acquisition and preterm birth. Culture is the current “gold standard” for diagnosis. As urine-based testing using DNA amplification techniques becomes more widely used for other sexually transmitted diseases (STDs) such as gonorrhea and chlamydia, a similar technique for trichomonosis would be highly desirable. Women attending an STD clinic for a new complaint were screened for
Trichomonas vaginalis
by wet-preparation (wet-prep) microscopy and culture and for the presence of
T. vaginalis
DNA by specific PCR of vaginal and urine specimens. The presence of trichomonosis was defined as the detection of
T. vaginalis
by direct microscopy and/or culture from either vaginal samples or urine. The overall prevalence of trichomonosis in the population was 28% (53 of 190). The sensitivity and specificity of PCR using vaginal samples were 89 and 97%, respectively. Seventy-four percent (38 of 51) of women who had a vaginal wet prep or vaginal culture positive for trichomonads had microscopic and/or culture evidence of the organisms in the urine. Two women were positive for trichomonads by wet prep or culture only in the urine. The sensitivity and specificity of PCR using urine specimens were 64 and 100%, respectively. These results indicate that the exclusive use of urine-based detection of
T. vaginalis
is not appropriate in women. PCR-based detection of
T. vaginalis
using vaginal specimens may provide an alternative to culture.
Evaluation of Amplified Fragment Length Polymorphism Analysis for Inter- and Intraspecific Differentiation of
Mycobacterium bovis
,
M. tuberculosis
, and
M. ulcerans
Authors: Huys G. , Rigouts L. , Chemlal K. , Portaels F. , Swings J. 
Published: December 2019

ABSTRACT

The usefulness of amplified fragment length polymorphism (AFLP) analysis was evaluated for the discrimination of
Mycobacterium bovis
(17 strains),
M. tuberculosis
(15 strains), and
M. ulcerans
(12 strains) at the inter- and intraspecific level. The AFLP technique is a whole-genome coverage genotypic fingerprinting method based on the selective PCR amplification of modified restriction fragments obtained through a double enzymatic digest and subsequent ligation of double-stranded restriction site-specific adapter oligonucleotides. Selective amplification of
Apa
I/
Taq
I templates with primer combination A02-T02 (both having an additional C at their 3′ end) generated autoradiographic AFLP fingerprints that were grouped by numerical analysis in two main AFLP clusters allowing clear separation of
M. ulcerans
(cluster I) from the
M. tuberculosis
complex members
M. bovis
and
M. tuberculosis
(cluster II). Calculation of similarities using the band-based Dice correlation coefficient instead of the Pearson product-moment correlation coefficient revealed a further subgrouping in cluster II. The two resulting subclusters corresponded with the phenotypic identity of
M. bovis
and
M. tuberculosis
, respectively, and could also be visually identified by two AFLP marker bands. Because of the relatively low degree of genotypic variation among the AFLP band patterns of the latter two taxa, no correlation could be found with previously reported molecular typing data or with geographical origin. The use of primer combination A02-T01 (the latter having an A as selective base) did not increase the resolving power within the
M. tuberculosis
complex but resulted in a visual subgrouping of the
M. ulcerans
strains that was not observed with primer combination A02-T02. Based on the presence or absence of a single AFLP marker band, the
M. ulcerans
isolates could be unambiguously classified in two continental types corresponding with the African and Australian origin of the strains, respectively. In conclusion, the radioactive AFLP method proved to be a reproducible and reliable taxonomic tool for the differentiation of the three mycobacterial species under study and also demonstrated its potential use for typing of
M. ulcerans
strains when employing multiple primer combinations.