bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nosocomial
Candida glabrata
Colonization: an Epidemiologic Study
Authors: Vazquez Jose A. , Dembry Louise M. , Sanchez Veronica , Vazquez Mary A. , Sobel Jack D. , Dmuchowski Carl , Zervos Marcus J. 
Published: December 2019

ABSTRACT

Candida glabrata
has emerged as an important nosocomial pathogen, yet little is known about its epidemiology. We prospectively followed 98 patients admitted to a medical intensive care unit and the bone marrow transplant unit of a university hospital. Samples from environmental surfaces and the hands of hospital personnel were also cultured. Patients with newly acquired
C. glabrata
strains were compared to controls who were culture negative for
C. glabrata. C. glabrata
was recovered from multiple sites from 24 patients and three environmental surfaces. Sixteen patients (17%) acquired
C. glabrata
after admission to the study units. Significant risk factors for the nosocomial acquisition of
C. glabrata
were prolonged duration of hospitalization in the unit and prior antimicrobial use. Strain delineation by restriction enzyme analysis revealed 28 different strains of
C. glabrata
; three strain types were common to nine patients. The environmental isolates were of the same strain type and common to five patients (four patients with newly acquired strains). These results suggest the possibility of exogenous nosocomial acquisition of
C. glabrata
, including the possible acquisition from the hospital environment. Transmission may be by indirect contact since identical strains of
C. glabrata
were recovered from patients who were geographically and temporally associated.
Performance of a PCR Assay for Detection of
Pneumocystis carinii
from Respiratory Specimens
Authors: Caliendo Angela M. , Hewitt Peter L. , Allega Jessica M. , Keen Anne , Ruoff Kathryn L. , Ferraro Mary Jane 
Published: December 2019

ABSTRACT

This study evaluates the performance of a PCR assay for the detection of
Pneumocystis carinii
from respiratory specimens that has been designed for use in the clinical microbiology laboratory. The test includes a simple method for nucleic acid extraction and amplification, a colorimetric probe hybridization technique for detection of amplicons, and an internal control to evaluate for the presence of inhibitors of amplification. Two hundred thirty-two clinical specimens (120 induced-sputum [IS] and 112 bronchoalveolar lavage [BAL] specimens) from 168 patients were tested by both immunofluorescent (direct fluorescent-antibody [DFA]) staining and PCR. Of the 112 BAL specimens, 17 were positive for
P. carinii
by DFA staining and PCR. An additional two specimens were DFA negative and PCR positive. For BAL specimens, the sensitivity and specificity of PCR compared to DFA were 100 and 98%, respectively. Eighteen IS specimens were positive for
P. carinii
by DFA, and 27 were positive by PCR. One of the 18 DFA-positive IS specimens was negative by PCR; this patient had just completed therapy for
P. carinii
pneumonia. Of the 10 specimens that were PCR positive and DFA negative, 4 were from patients who had a subsequent BAL specimen that was positive by DFA and PCR. For IS specimens, the sensitivity of DFA and PCR was 82 and 95%, respectively. The specificity of PCR for IS specimens was 94%. Due to the high sensitivity of PCR for the detection of
P. carinii
from IS specimens, a PCR-based diagnostic test may be a useful screening test and may alleviate the need for bronchoscopy in some patients.
Rapid Screening Tests for Determining In Vitro Susceptibility of Herpes Simplex Virus Clinical Isolates
Authors: de la Iglesia Pedro , Melón Santiago , López Beatriz , Rodriguez Mercedes , Blanco Maria I. , Mellado Purificación , de Oña Maria 
Published: December 2019

ABSTRACT
The susceptibility of human herpes simplex virus (HSV) to acyclovir (ACV) was determined with the use of a single dose of the drug (1 and 2 μg of ACV per ml for HSV-1 and HSV-2, respectively) in two rapid assays: a rapid cytopathic effect inhibitory assay (Rapid CIA) and a rapid dye uptake assay (Rapid DUA). These tests allow the simultaneous determination of virus titer and susceptibility to ACV at a determined viral concentration (100 50% tissue culture infective doses and 100 50% dye uptake units). These tests were compared with a conventional susceptibility assay (dye uptake assay) and showed similar results. Indeterminate results with the Rapid CIA appeared in 3 of 30 samples. With the use of both Rapid CIA and Rapid DUA, we were able to determine the susceptibility of 100% of the isolates. The rapid tests, unlike conventional assays, are able to provide susceptibility results within 3 days after the virus has been isolated from a clinical specimen and could thus play a direct role in therapeutic decisions.
Can Results Obtained with Commercially Available MicroScan Microdilution Panels Serve as an Indicator of β-Lactamase Production among
Escherichia coli
and
Klebsiella
Isolates with Hidden Resistance to ExpandedSpectrum Cephalosporins and Aztreonam?
Authors: Moland Ellen Smith , Sanders Christine C. , Thomson Kenneth S. 
Published: December 2019

ABSTRACT

Among clinical isolates of
Escherichia coli
,
Klebsiella pneumoniae
, and
Klebsiella oxytoca
, there is an ever-increasing prevalence of β-lactamases that may confer resistance to newer β-lactam antibiotics that is not detectable by conventional procedures. Therefore, 75 isolates of these species producing well-characterized β-lactamases were studied using two MicroScan conventional microdilution panels, Gram Negative Urine MIC 7 (NU7) and Gram Negative MIC Plus 2 (N+2), to determine if results could be utilized to provide an accurate indication of β-lactamase production in the absence of frank resistance to expanded-spectrum cephalosporins and aztreonam. The enzymes studied included Bush groups 1 (AmpC), 2b (TEM-1, TEM-2, and SHV-1), 2be (extended spectrum β-lactamases [ESBLs] and K1), and 2br, alone and in various combinations. In tests with
E. coli
and
K. pneumoniae
and the NU7 panel, cefpodoxime MICs of ≥2 μg/ml were obtained only for isolates producing ESBLs or AmpC β-lactamases. Cefoxitin MICs of >16 μg/ml were obtained for all strains producing AmpC β-lactamase and only 1 of 33 strains producing ESBLs. For the N+2 panel, ceftazidime MICs of ≥4 μg/ml correctly identified 90% of ESBL producers and 100% of AmpC producers among isolates of
E. coli
and
K. pneumoniae
. Cefotetan MICs of ≥ 8 μg/ml were obtained for seven of eight producers of AmpC β-lactamase and no ESBL producers. For tests performed with either panel and isolates of
K. oxytoca
, MICs of ceftazidime, cefotaxime, and ceftizoxime were elevated for strains producing ESBLs, while ceftriaxone and aztreonam MICs separated low-level K1 from high-level K1 producers within this species. These results suggest that microdilution panels can be used by clinical laboratories as an indicator of certain β-lactamases that may produce hidden but clinically significant resistance among isolates of
E. coli
,
K. pneumoniae
, and
K. oxytoca
. Although it may not always be possible to differentiate between strains that produce ESBLs and those that produce AmpC, this differentiation is not critical since therapeutic options for patients infected with such organisms are similarly limited.
Development of Specific Nested Oligonucleotide PCR Primers for the
Streptococcus iniae
16S-23S Ribosomal DNA Intergenic Spacer
Authors: Berridge Brian R. , Fuller Jeffrey D. , de Azavedo Joyce , Low Donald E. , Bercovier Herve , Frelier Paul F. 
Published: December 2019

ABSTRACT

Streptococcus iniae
is a cause of septicemia, meningoencephalitis, and death in farmed fish and of cellulitis in human beings. A set of nested oligonucleotide PCR primers that specifically amplified a 373-bp subunit from a variety of clinical isolates from farmed fish and human patients were constructed from a 524-bp consensus sequence of the
S. iniae
16S-23S ribosomal DNA intergenic spacer.
Follow-Up of
Staphylococcus aureus
Nasal Carriage after 8 Years: Redefining the Persistent Carrier State
Authors: VandenBergh Marjolein F. Q. , Yzerman Ed P. F. , van Belkum Alex , Boelens Hélène A. M. , Sijmons Marly , Verbrugh Henri A. 
Published: December 2019

ABSTRACT

Studies of
Staphylococcus aureus
nasal carriage have distinguished three carriage patterns: persistent, intermittent, and noncarriage. The criteria used to identify these carriage patterns have been inconsistent. In 1988 the
S. aureus
nasal carrier index, i.e., the proportion of nasal swab specimen cultures yielding
S. aureus
, was determined for 91 staff members of various departments of a large university hospital by obtaining weekly nasal swab specimens for culture over a 12-week period. Thirty-three (36%) persons had carrier indices of 0.80 or higher, 15 (17%) had indices between 0.1 and 0.7, and 43 (47%) had indices of zero. In 1995, 17 individuals with carrier indices of 0.80 or higher in 1988 were available for reexamination. For 12 (71%) of these individuals,
S. aureus
was again isolated from a single nasal swab, i.e., from each individual with a 1988 carrier index of 1.0 but from only half of those with indices below 1.0. Genotyping (by randomly amplified polymorphic DNA analysis and pulsed-field gel electrophoresis) of all
S. aureus
strains showed that strains isolated from only three individuals, all with 1988 carrier indices of 1.0, in 1988 and 1995 showed genetic similarity. In conclusion, persistent
S. aureus
nasal carriage is a unique characteristic of a fraction of the population, and the attribute “persistent” should be confined to those individuals for whom serial nasal swab specimen cultures consistently yield
S. aureus
.
Amplified-Fragment Length Polymorphism Fingerprinting of
Mycoplasma
Species
Authors: Kokotovic Branko , Friis Niels F. , Jensen Jørgen S. , Ahrens Peter 
Published: December 2019

ABSTRACT

Amplified-fragment length polymorphism (AFLP) is a whole-genome fingerprinting method based on selective amplification of restriction fragments. The potential of the method for the characterization of mycoplasmas was investigated in a total of 50 strains of human and animal origin, including
Mycoplasma genitalium
(
n
= 11),
Mycoplasma pneumoniae
(
n
= 5),
Mycoplasma hominis
(
n
= 5),
Mycoplasma hyopneumoniae
(
n
= 9),
Myco plasma flocculare
(
n
= 5),
Mycoplasma hyosynoviae
(
n
= 10), and
Mycoplasma dispar
(
n
= 5). AFLP templates were prepared by the digestion of mycoplasmal DNA with
Bgl
II and
Mfe
I restriction endonucleases and subsequent ligation of corresponding site-specific adapters. The amplification of AFLP templates with a single set of nonselective primers resulted in reproducible fingerprints of approximately 60 to 80 fragments in the size range of 50 to 500 bp. The method was able to discriminate the analyzed strains at species and intraspecies levels as well. Each of the tested
Mycoplasma
species developed a banding pattern entirely different from those obtained from other species under analysis. Subtle intraspecies genomic differences were detected among strains of all of the
Mycoplasma
species analyzed. The extent of polymorphism varied markedly between the analyzed mycoplasmas, comprising pattern similarity levels from 61.7% detected among
M. dispar
strains to 95.9% detected among
M. genitalium
strains. The results of the present study provide evidence of the high discriminatory power of AFLP analysis, suggesting the possible applicability of this method to the molecular characterization of mycoplasmas.
Natural History of Intestinal Microsporidiosis among Patients Infected with Human Immunodeficiency Virus
Authors: Dascomb Kristin , Clark Rebecca , Aberg Judith , Pulvirenti Joseph , Hewitt Ross G. , Kissinger Patricia , Didier Elizabeth S. 
Published: December 2019

ABSTRACT
A chart review of 73 human immunodeficiency virus (HIV)-infected patients with enteric microsporidiosis was conducted to define the natural history of microsporidiosis. A substantial proportion of patients remained symptomatic after 6 months (54.8% with persistent diarrhea and 51.2% with weight loss). Predictors for persistent diarrhea included high HIV RNA viral load and no initiation of protease inhibitor therapy.
Serodiagnosis of Human Granulocytic Ehrlichiosis by a Recombinant HGE-44-Based Enzyme-Linked Immunosorbent Assay
Authors: Ijdo Jacob W. , Wu Caiyun , Magnarelli Louis A. , Fikrig Erol 
Published: December 2019

ABSTRACT
Current antibody testing for human granulocytic ehrlichiosis relies predominantly on indirect fluorescent-antibody assays and immunoblot analysis. Shortcomings of these techniques include high cost and variability of test results associated with the use of different strains of antigens derived from either horses or cultured HL-60 cells. We used recombinant protein HGE-44, expressed and purified as a maltose-binding protein (MBP) fusion peptide, as an antigen in a polyvalent enzyme-linked immunosorbent assay (ELISA). Fifty-five normal serum samples from healthy humans served as a reference to establish cutoff levels. Thirty-three of 38 HGE patient serum samples (87%), previously confirmed by positive whole-cell immunoblotting, reacted positively in the recombinant ELISA. In specificity analyses, serum samples from patients with Lyme disease, syphilis, rheumatoid arthritis, and human monocytic ehrlichiosis (HME) did not react with HGE-44–MBP antigen, except for one sample (specificity, 98%). We conclude that recombinant HGE-44 antigen is a suitable antigen in an ELISA for the laboratory diagnosis and epidemiological study of HGE.
Novel Bacterium Isolated from a Lung Transplant Patient with Cystic Fibrosis
Authors: Pitulle Christian , Citron Diane M. , Bochner Barry , Barbers Richard , Appleman Maria D. 
Published: December 2019

ABSTRACTThe major clinical problem for patients with cystic fibrosis (CF) is progressive loss of pulmonary function, usually due to chronic bacterial infections. A patient with CF and a lung transplant was severely infected with a previously unidentified gram-negative bacterium. We isolated this organism (strain DS15158) from the patient and characterized it by phylogenetic analysis of the small-subunit rRNA and biochemically by the BIOLOG GN MicroPlate assay, fatty acid analysis, and various standard laboratory tests. No close match to any other organism could be found. Isolate DS15158 represents a new genus-level divergence within the bacterial subdivision α-Proteobacteriaon the basis of the 16S rRNA gene analysis.
Multiplex Reverse Transcriptase PCR Assay for Simultaneous Detection of Three Fish Viruses
Authors: Williams K. , Blake S. , Sweeney A. , Singer J. T. , Nicholson B. L. 
Published: December 2019

ABSTRACT
A multiplex reverse transcriptase (RT)-PCR assay was developed for the simultaneous detection of three different fish viruses: infectious pancreatic necrosis virus (IPNV), infectious hematopoietic necrosis virus (IHNV), and viral hemorrhagic septicemia virus (VHSV). The sensitivity levels of the multiplex RT-PCR assay were 100, 1, and 32 50% tissue culture infective doses/ml for IPNV, IHNV, and VHSV, respectively.
Posttreatment Follow-Up of Brucellosis by PCR Assay
Authors: Morata Pilar , Queipo-Ortuño María Isabel , Reguera JoséMaría , García-Ordoñez Miguel Angel , Pichardo Cristina , Colmenero Juan de Dios 
Published: December 2019

ABSTRACT
In order to evaluate the usefulness of a peripheral blood PCR assay in the posttreatment follow-up of brucellosis, a cohort of 30 patients was studied by means of blood cultures, rose Bengal, seroagglutination, Coombs' antibrucella tests, and PCR assay at the time of diagnosis, at the end of treatment, and 2, 4, and 6 months later. Of the 29 patients whose PCR assays were initially positive, 28 (96.5%) were negative at the conclusion of the treatment. PCR was positive for the two patients who had relapses and negative for another four who had suspected but unconfirmed relapses. PCR was negative for 98.3% of the follow-up samples from those patients who had a favorable evolution. In conclusion, PCR appears to be a very useful technique, not only for the initial diagnosis of the disease, but also for posttreatment follow-up and the early detection of relapses.
Evaluation of AMPLICOR
Neisseria gonorrhoeae
PCR Using
cppB
Nested PCR and 16S rRNA PCR
Authors: Farrell David J. 
Published: December 2019

ABSTRACT

Certain strains of
Neisseria subflava
and
Neisseria cinerea
are known to produce false-positive results with the AMPLICOR
Neisseria gonorrhoeae
PCR (Roche Diagnostic Systems, Branchburg, N.J.). The analytical sensitivity and analytical specificity of three PCR tests were assessed with 3 geographically diverse
N. gonorrhoeae
strains and 30 non-
N. gonorrhoeae Neisseria
spp. The sensitivities of the in-house nested
cppB
gene and the 16S rRNA PCR methods were greater than that of the AMPLICOR
N. gonorrhoeae
PCR with purified DNA from all 3
N. gonorrhoeae
strains. Six of 14 clinical strains of
N. subflava
(1 from a vaginal swab, 5 from respiratory sites) produced false-positive AMPLICOR
N. gonorrhoeae
PCR results and were negative by the two other PCR methods. When applied to 207 clinical specimens selected from a population with a high prevalence (∼9%) of infection, the results for 15 of 96 (15.6%) AMPLICOR-positive specimens and 14 of 17 (82.3%) AMPLICOR-equivocal specimens were not confirmed by the more sensitive nested
cppB
PCR method. Only 2 of 94 (2.1%) of AMPLICOR
N. gonorrhoeae
PCR-negative specimens from the same population tested positive by the nested
cppB
method. These results suggest that for this population the AMPLICOR
N. gonorrhoeae
PCR test is suitable as a screening test only and all positive results should be confirmed by a PCR method that is more specific and at least as sensitive. This study also illustrates that caution should be used when introducing commercially available nucleic acid amplification-based diagnostic tests into the regimens of tests used for populations not previously tested with these products.
The IS
6110
Restriction Fragment Length Polymorphism in Particular Multidrug-Resistant
Mycobacterium tuberculosis
Strains May Evolve Too Fast for Reliable Use in Outbreak Investigation
Authors: Alito Alicia , Morcillo Nora , Scipioni Silvia , Dolmann Alberto , Romano María I. , Cataldi Angel , van Soolingen Dick 
Published: December 2019

ABSTRACT

To study possible nosocomial transmission of multidrug-resistant (MDR)
Mycobacterium tuberculosis
, strain types and other information on 24, mostly human immunodeficiency virus-positive patients, were collected. Isolates from 11 patients had identical IS
6110
restriction fragment length polymorphism (RFLP) patterns as well as spoligotype patterns and resistance profiles. Noticeably, nine other isolates from related cases also exhibited identical spoligotypes but slightly different RFLP patterns. These results indicate that for some MDR strains, the evolutionary clock of IS
6110
RFLP may run too fast for reliable interpretation of strain typing results over a period of a few years.
Unexpected Cross-Reaction with
Fusobacterium necrophorum
in a PCR for Detection of Mycoplasmas
Authors: Jensen Jørgen Skov , Bruun Brita , Gahrn-Hansen Bente 
Published: December 2019

ABSTRACT

Cross-reactions with
Fusobacterium necrophorum
were found in a PCR designed for detection of a wide range of mycoplasma species. Twenty-five strains of
Fusobacterium
were examined; all 14
F. necrophorum
strains reacted positively, whereas all 7
Fusobacterium nucleatum
strains reacted negatively. Two strains that were not
F. necrophorum
yielded variable results.
Detection of Enzootic Babesiosis in Baboons (Papio cynocephalus) and Phylogenetic Evidence Supporting Synonymy of the GeneraEntopolypoidesandBabesia
Authors: Bronsdon Melinda A. , Homer Mary J. , Magera Jennifer M. H. , Harrison Carol , Andrews Robert G. , Bielitzki Joseph T. , Emerson Carol L. , Persing David H. , Fritsche Thomas R. 
Published: December 2019

ABSTRACTBlood smear evaluation of two baboons (Papio cynocephalus) experiencing acute hemolytic crises following experimental stem cell transplantation revealed numerous intraerythrocytic organisms typical of the genusBabesia. Both animals had received whole-blood transfusions from two baboon donors, one of which was subsequently found to display rare trophozoites ofEntopolypoides macaci. An investigation was then undertaken to determine the prevalence of hematozoa in baboons held in our primate colony and to determine the relationship, if any, between the involved species. Analysis of thick and thin blood films from 65 healthy baboons (23 originating from our breeding facility, 26 originating from an out-of-state breeding facility, and 16 imported from Africa) for hematozoa revealed rareE. macaciparasites in 31%, with respective prevalences of 39, 35, and 12%. Phylogenetic analysis of nuclear small-subunit rRNA gene sequences amplified from peripheral blood of a baboon chronically infected withE. macacidemonstrated this parasite to be most closely related toBabesia microti(97.9% sequence similarity); sera from infected animals did not react in indirect fluorescent-antibody tests withBabesia microtiantigen, however, suggesting that they represent different species. These results support an emerging view that the genusEntopolypoidesMayer 1933 is synonymous with that of the genusBabesiaStarcovici 1893 and that the morphological variation noted among intracellular forms is a function of alteration in host immune status. The presence of an underrecognized, but highly enzootic,Babesiasp. in baboons may result in substantial, unanticipated impact on research programs. The similarity of this parasite to the known human pathogenB. microtimay also pose risks to humans undergoing xenotransplantation, mandating effective screening of donor animals.
Septic Shock Due to
Helicobacter fennelliae
in a Non-Human Immunodeficiency Virus-Infected Heterosexual Patient
Authors: Hsueh Po-Ren , Teng Lee-Jene , Hung Chien-Chin , Chen Yu-Chi , Yang Pan-Chyr , Ho Shen-Wu , Luh Kwen-Tay 
Published: December 2019

ABSTRACT

Helicobacter fennelliae
(formerly
Campylobacter fennelliae
) has been reported to cause bacteremia in homosexual men with or without human immunodeficiency virus (HIV) infection. We report here a 48-year-old, non-HIV-infected, heterosexual man with diabetes mellitus and cirrhosis of the liver who developed bacteremia and septic shock due to
H. fennelliae
. The patient was treated successfully initially with intravenous ampicillin-sulbactam and ceftazidime, followed by ampicillin-sulbactam only. These agents were active in vitro against the isolate by E-test results. To our knowledge, this is the first documented case of septic shock due to
H. fennelliae
in a non-HIV-infected, heterosexual, immunocompromised patient.
Amplification of a 500-Base-Pair Fragment from Cultured Isolates of
Mycobacterium bovis
Authors: Rodríguez Juan Germán , Fissanoti Juan Carlos , Del Portillo Patricia , Patarroyo Manuel Elkin , Romano María Isabel , Cataldi Angel 
Published: December 2019

ABSTRACT

The presence of a 500-bp fragment which amplifies a region from the genome of
Mycobacterium bovis
(J. G. Rodriguez, G. A. Meija, P. Del Portillo, M. E. Patarroyo, and L. A. Murillo, Microbiology 141:2131–2138, 1995) was evaluated by carrying out PCR on 121
M. bovis
isolates. The
M. bovis
strains, previously characterized by culture and biochemical tests, were isolated from cattle in different regions of Argentina, Mexico, and Colombia. Four additional strains isolated from sea lions that belong to the
M. tuberculosis
complex were also included in the study. All of the isolates tested were PCR positive, rendering the expected 500-bp band and giving a correlation of 100% with previous microbiological characterization. Southern blot analysis revealed a common band of 1,800 bp and a polymorphic high-molecular-mass hybridization pattern. The results show that this assay may be useful for diagnosis and identification of
M. bovis
in cattle.