bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid Method for Species-Specific Identification of
Vibrio cholerae
Using Primers Targeted to the Gene of Outer Membrane Protein OmpW
Authors: Nandi Bisweswar , Nandy Ranjan K. , Mukhopadhyay Sarmishtha , Nair G. Balakrish , Shimada Toshio , Ghose Asoke C. 
Published: December 2019

ABSTRACT

The distribution of genes for an outer membrane protein (OmpW) and a regulatory protein (ToxR) in
Vibrio cholerae
and other organisms was studied using respective primers and probes. PCR amplification results showed that all (100%) of the 254
V. cholerae
strains tested were positive for
ompW
and 229 (∼98%) of 233 were positive for
toxR
. None of the 40 strains belonging to other
Vibrio
species produced amplicons with either
ompW
- or
toxR
-specific primers, while 80 bacterial strains from other genera tested were also found to be negative by the assay. These studies were extended with representative number of strains using
ompW
- and
toxR
-specific probes in DNA dot blot assay. While the
V. cholerae
strains reacted with
ompW
probe, only one (
V. mimicus
) out of 60 other bacterial strains tested showed weak recognition. In contrast, several strains belonging to other
Vibrio
species (e.g.,
V. mimicus
,
V. splendidus
,
V. alginolyticus
,
V. fluvialis
,
V. proteolyticus
,
V. aestuarianus
,
V. salmonicida
,
V. furnissii
, and
V. parahaemolyticus
) showed weak to strong reactivity to the
toxR
probe. Restriction fragment length polymorphism analysis and nucleotide sequence data revealed that the
ompW
sequence is highly conserved among
V. cholerae
strains belonging to different biotypes and/or serogroups. All of these results suggest that the
ompW
gene can be targeted for the species-specific identification of
V. cholerae
strains. The scope of this study was further extended through the development of a one-step multiplex PCR assay for the simultaneous amplification of
ompW
and
ctxA
genes which should be of considerable value in the screening of both toxigenic and nontoxigenic
V. cholerae
strains of clinical as well as environmental origin.
Comparison of the BACTEC MGIT 960 and ESP Culture System II for Growth and Detection of Mycobacteria
Authors: Williams-Bouyer Natalie , Yorke Rebecca , Lee Hung I. , Woods Gail L. 
Published: December 2019

ABSTRACT

The performances of two continuously monitoring mycobacterial culture systems—ESP Culture System II (ESP II; Trek Diagnostics, Inc., Westlake, Ohio) and BACTEC MGIT 960 (BD Biosciences, Sparks, Md.)—were compared. In addition to both liquid media, all specimens were plated onto Middlebrook 7H11/7H11 selective agar. A total of 3,151 specimens of all types (56.3% were respiratory specimens) were cultured; 231 (7.3%) yielded mycobacteria. The most common species recovered were
Mycobacterium avium
complex (69 isolates) and
Mycobacterium tuberculosis
complex (MTBC; 65 isolates). The recovery rates for ESP II, BACTEC MGIT 960, and Middlebrook agar, respectively, were 71.2, 63.9, and 61.8% for all mycobacteria; 70.2, 72.6, and 66.3% for all mycobacteria except
Mycobacterium gordonae
; and 73.8, 84.6, and 87.7% for MTBC. For liquid plus solid medium combinations, recovery rates for all mycobacteria and for MTBC, respectively, were 84.1 and 92.3% for ESP II plus Middlebrook agar and 81.5 and 98.5% for BACTEC MGIT 960 plus Middlebrook agar. The differences in recovery of all mycobacteria by ESP II and by BACTEC MGIT 960 were not significant; for the individual species, the only significant difference was recovery of more isolates of
M. gordonae
by ESP II. For those isolates recovered in both automated systems, mean times to detection of all mycobacteria and MTBC, respectively, were 15.8 and 17.4 days for ESP II and 12.5 and 11.9 days for BACTEC MGIT 960 (
P
< 0.05). False-positive signals occurred with 23 (0.7%) BACTEC MGIT 960 cultures and 84 (2.7%) ESP II cultures (
P
< 0.01). Overall contamination rates were 17.1% for BACTEC MGIT 960, 18.9% for ESP II, and 11.0% for Middlebrook agar. In summary, the ESP II and BACTEC MGIT 960 systems performed comparably with regard to growth and detection of mycobacteria, and the contamination rates were similar. However, with ESP II, times to detection of all mycobacteria and of MTBC were significantly longer, the recovery rate of
M. gordonae
was significantly higher, and the number of false-positive signals was greater than with BACTEC MGIT 960.
Comparison of Intertypic Antigenicity of Aino Virus Isolates by Dot Immunobinding Assay Using Neutralizing Monoclonal Antibodies
Authors: Yoshida Kazuo , Ohashi Seiichi , Kubo Tomomi , Tsuda Tomoyuki 
Published: December 2019

ABSTRACT
Neutralizing monoclonal antibodies (MAbs) against the Aino virus were prepared, and the neutralizing epitopes of the virus were defined by competitive binding assay. Seven continuous and overlapping neutralizing epitopes existed on the G1 glycoprotein of the Aino virus. Two antigenic domains were identified and were designated I and II, with domain II consisting of six epitopes. Dot immunobinding assays (DIAs) were performed with MAbs that recognized these seven neutralizing epitopes. DIAs were performed with 1 Australian strain and 21 isolates found in Japan between the years 1964 and 1995. The MAb response patterns of all isolates were divided into four groups. The Japanese isolates did not show large differences in antigenicity, but the antigenicity of the Australian strain collected in 1968 was significantly different from that of the Japanese strains; the Australian strain lacked reactivity to three epitopes and showed only low reactivity to one epitope.
Extensive Sequence Divergence among Bovine Respiratory Syncytial Viruses Isolated during Recurrent Outbreaks in Closed Herds
Authors: Larsen L. E. , Tjørnehøj K. , Viuff B. 
Published: December 2019

ABSTRACTThe nucleotides coding for the extracellular part of the G glycoprotein and the full SH protein of bovine respiratory syncytial virus (BRSV) were sequenced from viruses isolated from numerous outbreaks of BRSV infection. The isolates included viruses isolated from the same herd (closed dairy farms and veal calf production units) in different years and from all confirmed outbreaks in Denmark within a short period. The results showed that identical viruses were isolated within a herd during outbreaks and that viruses from recurrent infections varied by up to 11% in sequence even in closed herds. It is possible that a quasispecies variant swarm of BRSV persisted in some of the calves in each herd and that a new and different highly fit virus type (master and consensus sequence) became dominant and spread from a single animal in connection with each new outbreak. Based on the high level of diversity, however, the most likely explanation was that BRSV was (re)introduced into the herd prior to each new outbreak. These findings are highly relevant for the understanding of the transmission patterns of BRSV among calves and human respiratory syncytial virus among humans.
Rapid-Cycle PCR for Detection and Typing of
Mycoplasma pneumoniae
in Clinical Specimens
Authors: Kong Fanrong , Gordon Susanna , Gilbert Gwendolyn L. 
Published: December 2019

ABSTRACT

We designed several new primers and modified previously described species- and type-specific primers targeting the
Mycoplasma pneumoniae
P1 adhesin gene. Optimized thermal profiles allowed one-step or nested PCR to be completed in less than 1 h. In 10 patients with pneumonia,
M. pneumoniae
type 1 was identified in 3 and type 2 in 7.
Persistent
Legionella
Infection in a Patient after Bone Marrow Transplantation
Authors: Schindel C. , Siepmann U. , Han S.-R. , Ullmann A. J. , Mayer E. , Fischer T. , Maeurer M. 
Published: December 2019

ABSTRACT

We report on a patient who developed
Legionella
pneumonia after bone marrow transplantation. Despite appropriate antibiotic treatment, disease progressed. The patient developed a lung abscess from which
Legionella
and
Prevotella
were isolated. Cure was achieved by surgical resection. The resected material was sterile, but 16S ribosomal DNA analysis revealed
Legionella
DNA.
Diarrhea in Children under 5 Years of Age from Ifakara, Tanzania: a Case-Control Study
Authors: Gascón J. , Vargas M. , Schellenberg D. , Urassa H. , Casals C. , Kahigwa E. , Aponte J. J. , Mshinda H. , Vila J. 
Published: December 2019

ABSTRACT

A matched case-control study was conducted in the Maternal and Child Health Clinic (MCH) in Ifakara, Tanzania, during the rainy season in order to elucidate the risk factors for and etiology of diarrheal diseases in children under 5 years of age. Cases (103) and controls (206) were matched for sex and age group. Precoded questionnaires with demographic details, clinical history, and physical signs were completed. Stools samples were collected for bacterial, parasitological, and viral studies. A high number of siblings (odds ratio [OR], 0.86;
P
= 0.027), the number of siblings surviving (OR, 0.82;
P
= 0.007), the birth order (OR, 0.85;
P
= 0.018) and the distance from the house to the water source (OR, 0.33;
P
= 0.011) were associated with the risk of diarrhea. There were high rates of enteropathogen isolates in stool samples from children without diarrhea (52.23%).
Shigella
species were the only enteropathogen statistically related with diarrhea (OR, 2.90;
P
< 0.029). Enterotoxigenic, enteropathogenic, and enteroaggregative strains of
Escherichia coli
were not related with diarrhea, and neither were
Giardia lamblia
or
Salmonella
species.
Carried Meningococci in the Czech Republic: a Diverse Recombining Population
Authors: Jolley K. A. , Kalmusova J. , Feil E. J. , Gupta S. , Musilek M. , Kriz P. , Maiden M. C. J. 
Published: December 2019

ABSTRACT

Population and evolutionary analyses of pathogenic bacteria are frequently hindered by sampling strategies that concentrate on isolates from patients with invasive disease. This is especially so for the gram-negative diplococcus
Neisseria meningitidis
, a cause of septicemia and meningitis worldwide. Meningococcal isolate collections almost exclusively comprise organisms originating from patients with invasive meningococcal disease, although this bacterium is a commensal inhabitant of the human nasopharynx and very rarely causes pathological effects. In the present study, molecular biology-based techniques were used to establish the genetic relationships of 156 meningococci isolated from healthy young adults in the Czech Republic during 1993. None of the individuals sampled had known links to patients with invasive disease. Multilocus sequence typing (MLST) showed that the bacterial population was highly diverse, comprising 71 different sequence types (STs) which were assigned to 34 distinct complexes or lineages. Three previously identified hyperinvasive lineages were present: 26 isolates (17%) belonged to the ST-41 complex (lineage 3); 4 (2.6%) belonged to the ST-11 (electrophoretic type [ET-37]) complex, and 1 (0.6%) belonged to the ST-32 (ET-5) complex. The data were consistent with the view that most nucleotide sequence diversity resulted from the reassortment of alleles by horizontal genetic exchange.
Transfusion-Acquired, Autochthonous Human Babesiosis in Japan: Isolation of
Babesia microti
-Like Parasites with hu-RBC-SCID Mice
Authors: Saito-Ito Atsuko , Tsuji Masayoshi , Wei Qiang , He Shenyi , Matsui Toshimitsu , Kohsaki Masatoshi , Arai Satoru , Kamiyama Tsuneo , Hioki Kyoji , Ishihara Chiaki 
Published: December 2019

ABSTRACT

We have isolated piroplasms from a patient who developed the first case of human babesiosis in Japan by using NOD/shi-
scid
mice whose circulating erythrocytes (RBCs) had been replaced with human RBCs (hu-RBC-SCID mice). Following inoculation of the patient's blood specimen into hu-RBC-SCID mice, parasites proliferated within the human RBCs in the mice, resulting in a high level of parasitemia. Parasite DNA was prepared from blood samples of the patient and the mice, and the nuclear small-subunit rRNA gene (rDNA) was amplified and sequenced. Both DNA samples gave rise to identical sequences which showed the highest degree of homology (99.2%) with the
Babesia microti
rDNA. Because the patient had received a blood transfusion before the onset of babesiosis, we investigated the eight donors who were involved. Their archived blood samples were analyzed for specific antibody and parasite DNA; only a single donor was found to be positive by both tests, and the parasite rDNA sequence from the donor coincided with that derived from the patient. The donor's serum exhibited a high antibody titer against the isolate from the patient, whereas it exhibited only a weak cross-reaction against
B. microti
strains isolated in the United States. We conclude that the first Japanese babesiosis case occurred due to a blood transfusion and that the etiological agent is an indigenous Japanese parasite which may be a geographical variant of
B. microti
. Our results also demonstrated the usefulness of hu-RBC-SCID mice for isolation of parasites from humans and for maintenance of the parasite infectivity for human RBCs.
Genomic and Phylogenetic Analysis of Hepatitis C Virus Isolates from Argentine Patients: a Six-Year Retrospective Study
Authors: Quarleri J. F. , Robertson B. H. , Mathet V. L. , Feld M. , Espı́nola L. , Requeijo M. P. , Mandó O. , Carballal G. , Oubiña J. R. 
Published: December 2019

ABSTRACT

Typing of hepatitis C virus (HCV) isolates from Argentine patients was performed by using different methodologies in a population of 243 patients. HCV subtype was assigned based upon restriction fragment length polymorphism (RFLP). HCV RNA genomes obtained from serum samples were classified as belonging to clade 1 (53.5%), 2 (23.0%), or 3 (8.6%); 14.8% of samples showed HCV mixed infections, more frequently implying different subtypes within the same clade. In addition to RFLP typing, phylogenetic relatedness among sequences from both 5′ untranslated region (
n
= 50) and nonstructural 5B coding region (
n
= 15) was established.
Vibrio parahaemolyticus
Serovar O3:K6 as Cause of Unusually High Incidence of Food-Borne Disease Outbreaks in Taiwan from 1996 to 1999
Authors: Chiou Chien-Shun , Hsu Shih-Yuan , Chiu Shiou-Ing , Wang Tien-Kuei , Chao Cheng-Shun 
Published: December 2019

ABSTRACT

The occurrence of food-borne disease outbreaks in Taiwan increased dramatically in 1996, and the incidence has since remained elevated. This increase in outbreaks is correlated with a high rate of isolation of
Vibrio parahaemolyticus
, which caused between 61 and 71% of the total outbreaks for the period 1996 to 1999. By serotyping, 40 serovars were identified from 3743
V. parahaemolyticus
isolates, of which O3:K6 was the most frequently detected. The O3:K6 serovar could have emerged in Taiwan as early as October 1995 and at that time accounted for only 0.6% of the
V. parahaemolyticus
infections. This level increased suddenly to 50.1% in 1996 and reached a peak (83.8%) in 1997. Comparison of the outbreak profiles for the etiology groups indicates that the high incidence of food-borne disease outbreaks during 1996 to 1999 can be attributed to the extraordinarily high O3:K6 infections. In 1999, the O3:K6 serovar was still prevalent, and accounted for 61.3% of all
V. parahaemolyticus
infections. Due to its extraordinarily high infection frequency and its capability to spread globally, this organism needs to be intensively monitored internationally.
Comparison of Human Papillomavirus Detection and Typing by Cycle Sequencing, Line Blotting, and Hybrid Capture
Authors: Vernon Suzanne D. , Unger Elizabeth R. , Williams Deon 
Published: December 2019

ABSTRACT

We compared the results of human papillomavirus (HPV) detection and typing from 781 cervical samples assayed by three methods: L1 consensus PCR followed by cycle sequencing, L1 consensus PCR with biotinylated primers followed by hybridization to a line blot, and Hybrid Capture assay. Both PCR assays used L1 consensus PCR with primers MY09 and MY11. We evaluated the amplification efficiencies of both PCR assays and also compared the specific HPV types detected by each method. The samples positive by the Hybrid Capture assay were compared to the specific types detected by the PCR-based assays. The concordance between the two PCR assays in producing an HPV amplicon visible by gel electrophoresis or in detecting any HPV type was moderate: kappa values were 0.61 (95% confidence interval [CI] = 0.56 to 0.67) and 0.51 (95% CI = 0.46 to 0.58), respectively. The McNemar test for correlated proportions indicated that biotinylated PCR was less likely to produce a band (
P
= 0.001) and to detect an HPV type (
P
= 0.001) than the other PCR assay. In comparing the Hybrid Capture assay results with the HPV types detected by the PCR-based assays, we found that positivity by the Hybrid Capture assay for a number of samples may be due to cross-hybridization with HPV types not included in the Hybrid Capture assay probe cocktails.
SimulFluor Respiratory Screen for Rapid Detection of Multiple Respiratory Viruses in Clinical Specimens by Immunofluorescence Staining
Authors: Landry Marie L. , Ferguson David 
Published: December 2019

ABSTRACT
A new rapid direct immunofluorescence assay (DFA) respiratory screen reagent for detection of seven common respiratory viruses (respiratory syncytial virus [RSV], influenza A and B viruses, parainfluenza virus types 1 to 3, and adenovirus) was compared with standard single or dual DFA reagents and culture. In total, 1,531 respiratory samples were adequate for testing with both SimulFluor Respiratory Screen (RS) reagent (Chemicon International, Temecula, Calif.) and single or dual DFA reagents. The RS DFA reagent detected 367 (98.4%) and single or dual DFA reagents detected 368 (98.7%) of 373 DFA-positive samples. In addition, the RS DFA reagent was equivalent to or better than culture for detection of all viruses except adenovirus. Only 15 of 799 (1.9%) RS-negative samples inoculated into cell cultures yielded respiratory virus isolates (one RSV, five influenza A virus, two influenza B virus, one parainfluenza virus, and six adenovirus). Sixty-six other virus isolates (13 rhinovirus, 24 cytomegalovirus, 28 herpes simplex virus type 1, and 1 enterovirus) were also recovered in culture. With cytospin preparation of slides, only 7.5% of samples submitted were deemed inadequate for DFA. The availability of a rapid DFA screening reagent for detection of multiple common respiratory viruses within 1 to 2 h of sample collection should be of great benefit in terms of patient management and infection control.
Pathogenic Clones versus Environmentally Driven Population Increase: Analysis of an Epidemic of the Human Fungal Pathogen
Coccidioides immitis
Authors: Fisher Matthew C. , Koenig Gina L. , White Thomas J. , Taylor John W. 
Published: December 2019

ABSTRACT

For many pathogenic microbes that utilize mainly asexual modes of reproduction, it is unknown whether epidemics are due to either the emergence of pathogenic clones or environmentally determined increases in the population size of the organism. Descriptions of the genetic structures of epidemic populations, in conjunction with analyses of key environmental variables, are able to distinguish between these competing hypotheses. A major epidemic of coccidioidomycosis (etiologic agent,
Coccidioides immitis
) occurred between 1991 and 1994 in central California, representing an 11-fold increase above the mean number of cases reported from 1955 to 1990. Molecular analyses showed extensive genetic diversity, a lack of linkage disequilibria, and little phylogenetic structure, demonstrating that a newly pathogenic strain was not responsible for the observed epidemic. Epidemiological analyses showed that morbidity caused by
C. immitis
was best explained by the interaction between two variables, the lengths of droughts preceding epidemics and the amounts of rainfall. This shows that the principal factors governing this epidemic of
C. immitis
are environmental and not genetic. An important implication of this result is that the periodicity of cyclical environmental factors regulates the population size of
C. immitis
and is instrumental in determining the size of epidemics. This knowledge provides an important tool for predicting outbreaks of this pathogen, as well as a general framework that may be applied to determine the causes of epidemics of other fungal diseases.
Bacteremia Caused by a Strain of
Desulfovibrio
Related to the Provisionally Named
Desulfovibrio fairfieldensis
Authors: Loubinoux Julien , Mory Francine , Pereira Ines A. C. , Le Faou Alain E. 
Published: December 2019

ABSTRACT

Eight isolates of
Desulfovibrio
spp. have been obtained over 5 years from abdominal or brain abscesses or blood. In seven patients these strains were part of a mixed flora. One strain was isolated in pure culture from the blood of a patient with peritonitis of appendicular origin. According to the 16S rRNA gene sequences, this strain was close to
Desulfovibrio fairfieldensis
. The present report describes the fourth isolate of this recently described species to be isolated in pure culture or as a predominant part of the flora and to be associated with infectious processes. Thus,
D. fairfieldensis
may possess a higher pathogenic potential than other
Desulfovibrio
species.
PCR Detection of Granulocytic Ehrlichiae in
Ixodes ricinus
Ticks and Wild Small Mammals in Western Switzerland
Authors: Liz Jorge S. , Anderes Laurence , Sumner John W. , Massung Robert F. , Gern Lise , Rutti Bernard , Brossard Michel 
Published: December 2019

ABSTRACT

The presence of granulocytic ehrlichiae was demonstrated by PCR in
Ixodes ricinus
ticks and wild small mammals in Switzerland in two areas of endemicity for bovine ehrlichiosis. Six ticks (three females and three nymphs) (1.4%) of 417
I. ricinus
ticks collected by flagging vegetation contained ehrlichial DNA. A total of 201 small mammals from five species, wood mouse (
Apodemus sylvaticus
), yellow-necked mouse (
Apodemus flavicollis
), earth vole (
Pitymys subterraneus
), bank vole (
Clethrionomys glareolus
), and common shrew (
Sorex araneus
), were trapped. The analysis of
I. ricinus
mammals collected on 116 small mammals showed that nine
C. glareolus
voles and two
A. sylvaticus
mice hosted infected tick larvae. In these rodents, granulocytic ehrlichia infection was also detected in blood, spleen, liver, and ear samples. Further examinations of 190 small mammals without ticks or with noninfected ticks showed the presence of ehrlichial DNA in spleen and other tissues from six additional
C. glareolus
, three
A. flavicollis
, and one
S. araneus
mammals. This study suggests that
A. sylvaticus
,
A. flavicollis
,
S. araneus
, and particularly
C. glareolus
are likely to be natural reservoirs for granulocytic ehrlichiae. Partial 16S rRNA gene sequences of granulocytic ehrlichiae from ticks and rodents showed a high degree of homology (99 to 100%) with granulocytic ehrlichiae isolated from humans. In contrast,
groESL
heat shock operon sequence analysis showed a strong divergence (approximately 5%) between the sequences in samples derived from rodents and those derived from samples from questing ticks or from other published ehrlichia sequences. Dual infections with granulocytic ehrlichia and
Borrelia burgdorferi
were found in ticks and small mammals.