bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of PCR for Diagnosis of Melioidosis
Authors: Haase Antje , Brennan Maree , Barrett Siobhan , Wood Yvonne , Huffam Sarah , O’Brien Daniel , Currie Bart 
Published: December 2019

ABSTRACT

Previously published PCR-based diagnostic tests for melioidosis were evaluated for clinical usefulness. A
Burkholderia pseudomallei
16S rRNA-derived primer set had a sensitivity approaching 100% for clinical samples from 22 culture-confirmed cases of melioidosis and enabled diagnosis of 3 culture-negative cases. However, samples from 10 of 30 inpatients from Royal Darwin Hospital with other diagnoses were positive by PCR, giving a specificity of 67% and a positive predictive value of only 70%. Although there are a number of intriguing possible explanations for our results, concerns of inappropriate therapy resulting from a positive result by PCR have led us to forgo the advantage of rapid PCR diagnosis for melioidosis until a better system is validated.
Detection of
Mycobacterium tuberculosis
Complex in Cattle by PCR Using Milk, Lymph Node Aspirates, and Nasal Swabs
Authors: Vitale Fabrizio , Capra Giuseppina , Maxia Letizia , Reale Stefano , Vesco Gesualdo , Caracappa Santo 
Published: December 2019

ABSTRACT

The PCR technique was applied to the diagnosis of tuberculosis in live cattle, and both skin-test-negative and skin-test-positive animals were studied. DNA was taken from various sources including specimens of lymph node aspirates, milk, and nasal swabs. After slaughter and visual inspection, tissues such as lymph nodes, lungs, and udders from tuberculin reactors were tested by the same technique. Specific oligonucleotide primers internal to the IS
6110
insertion element were used to amplify a 580-bp fragment. A 182-bp fragment was obtained by designating a nested PCR from the first amplification product. This fragment was cloned and sequenced, and after being labeled it was employed in dot blot hybridization. A total of 100 cattle were tested, and PCR analysis was performed using nasal swab, milk, and lymph node aspirate. Sixty skin-test-positive cows were also tested to detect mycobacterial DNA in tissue samples from lymph nodes, lungs, and udders, and the infection was confirmed in all of the animals. Using PCR analysis of tissue samples from slaughtered animals as a “gold standard” we calculated 100% values for sensitivity, specificity, and positive and negative predictive values for milk and lymph node aspirate samples. The respective values for nasal swab samples were 58, 100, 100, and 28%. The respective values for all of the samples were 74, 100, 100, and 35%, while for visual inspection the values were 81, 100, 100, and 58%, respectively. PCR analysis of specimens of lymph node aspirates, milk, and nasal swabs from skin-test-negative animals showed that 52% of these skin test results were false negatives. These animals, not being removed from the farms, represent a potential source of further infection.
Sensitivity and Specificity of an Improved Rapid Latex Agglutination Test for Identification of Methicillin-Sensitive and -Resistant
Staphylococcus aureus
Isolates
Authors: Smole Sandra C. , Aronson Elyssa , Durbin Annette , Brecher Stephen M. , Arbeit Robert D. 
Published: December 2019

ABSTRACT

The performance of a second-generation rapid agglutination kit, Slidex Staph Plus (SSP; bioMérieux), was compared to those of the Slidex Staph (SS; bioMérieux), Staphaurex (SRX; Murex Diagnostics), and BBL Staphyloslide (BBL; Becton Dickinson) kits by using 508 clinical isolates composed of 150 methicillin-sensitive
Staphylococcus aureus
(MSSA) organisms, 154 methicillin-resistant
S. aureus
(MRSA) organisms, and 204 non-
S. aureus Staphylococcus
spp. Of the 508 isolates tested, 75% were fresh clinical isolates, with the remainder taken from five different freezer collections. All four agglutination tests had comparable sensitivities for MSSA and MRSA. However, the SS kit was significantly less specific (93.1%) than the three other tests (
P
> 0.05, McNemar test). These results demonstrate that the new rapid latex agglutination kit, SSP, was more specific for the identification of
S. aureus
than the previous version and performed comparably to the SRX and BBL kits.
Group A Streptococcal Vir Types Are M-Protein Gene (emm) Sequence Type Specific
Authors: Gardiner Don L. , Goodfellow Alison M. , Martin Diana R. , Sriprakash Kadaba S. 
Published: December 2019

ABSTRACTThe M-protein genes (emmgenes) of 103 separate impetiginousStreptococcus pyogenesisolates were sequenced and the sequence types were compared to the types obtained by Vir typing. Vir typing is based on restriction fragment length polymorphism (RFLP) analysis of a 4- to 7-kb pathogenicity island encodingemmand other virulence genes. By using bothHaeIII andHinfI to generate RFLP profiles, complete concordance between Vir type andemmsequence type was found. Comparison of theemmsequences with those in GenBank revealed new sequence types sharing less than 90% identity with known types. Diversity in theemmsequence was generated by corrected frameshift mutations, point mutations, and small in-frame mutations.
Epidemiology of a Dominant Clonal Strain of Vancomycin-Resistant
Enterococcus faecium
at Separate Hospitals in Boston, Massachusetts
Authors: Fridkin Scott K. , Yokoe Deborah S. , Whitney Cynthia G. , Onderdonk Andrew , Hooper David C. 
Published: December 2019

ABSTRACT

In 1996, the dominant (43%) strain of vancomycin-resistant enterococci (VRE; type A) at Massachusetts General Hospital was identified at Brigham and Women’s Hospital (BWH). To characterize the epidemiology of infection with type A isolates of VRE at BWH, we collected demographic and clinical data for all patients from whom VRE were isolated from a clinical specimen through September 1996. The first clinical isolates from all BWH patients from whom VRE were isolated were typed by pulsed-field gel electrophoresis of
Sma
I digests of chromosomal DNA. Among patients hospitalized after the first patient at BWH infected with a type A isolate of VRE was identified, exposures were compared between patients who acquired type A isolates of VRE and those who acquired other types of VRE. Isolates from 99 patients identified to have acquired VRE were most commonly from blood (
n
= 27), urine (
n
= 19), or wounds (
n
= 19). Three months after the index patient arrived at BWH and at a time when ≥12 types of strains of VRE were present, type A isolates of VRE became dominant; 39 of 75 (52%) of the study cohort had acquired type A isolates of VRE. We found no association between the acquisition of type A isolates of VRE and transfer from another institution or temporal overlap by service, ward, or floor with patients known to have acquired type A isolates of VRE. By multivariate analysis, only residence in the medical intensive care unit (adjusted odds ratio [OR], 3.2; 95% confidence interval [CI], 1.4 to 107) and the receipt of two or more antibiotics per patient-day (adjusted OR, 12.2; 95% CI, 1.2 to 9.0) were associated with the acquisition of strain A. This strain of VRE, dominant at two Boston hospitals, was associated with intensity of antibiotic exposures (i.e., two or more antibiotics per patient-day). We hypothesize that this strain may have unidentified properties providing a mechanism favoring its spread and dominance over other extant isolates, and further studies are needed to define these properties.
Panfungal PCR Assay for Detection of Fungal Infection in Human Blood Specimens
Authors: Van Burik Jo-Anne , Myerson David , Schreckhise Randall W. , Bowden Raleigh A. 
Published: December 2019

ABSTRACT
A novel panfungal PCR assay which detects the small-subunit rRNA gene sequence of the two major fungal organism groups was used to test whole-blood specimens obtained from a series of blood or bone marrow transplant recipients. The 580-bp PCR product was identified after amplification by panfungal primers and hybridization to a 245-bp digoxigenin-labeled probe. The lower limit of detection of the assay was approximately four organisms per milliliter of blood. Multiple whole-blood specimens from five patients without fungal infection or colonization had negative PCR results. Specimens from 11 infected patients had positive PCR results. Blood from three patients with pulmonary aspergillosis had positive PCR results: one patient’s blood specimen obtained in the week prior to the diagnosis of infection by a positive bronchoalveolar lavage fluid culture result was positive by PCR, and blood specimens obtained from two patients 1 to 2 days after lung biopsy and which were sterile by culture were positive by PCR. The blood of four patients with candidemia, three patients with mixed fungal infections, and one patient with fusariosis also had positive PCR signals. The panfungal PCR assay can detect multiple fungal genera and may be used as an adjunct to conventional methods for the detection of fungal infection or for describing the natural history of fungal infection. Further studies are needed to define the sensitivity and specificity of this assay for the diagnosis of fungal infection prior to the existence of other clinical or laboratory indications of invasive fungal infection.
Immunoglobulin A-Specific Capture Enzyme-Linked Immunosorbent Assay for Diagnosis of Dengue Fever
Authors: Talarmin Antoine , Labeau Bhety , Lelarge Josiane , Sarthou Jean-Louis 
Published: December 2019

ABSTRACT
Dengue fever (DF) is usually diagnosed by testing for dengue virus immunoglobulin M (IgM) by a capture enzyme-linked immunosorbent assay (ELISA) (MAC-ELISA). However, IgM can last for months, and its presence might reflect a previous infection. We have tested the use of anti-dengue virus IgA capture ELISA (AAC-ELISA) for the diagnosis of DF by comparing the results of MAC-ELISAs and AAC-ELISAs for 178 serum samples taken from patients with confirmed cases of DF. IgM appears more rapidly (mean delay of positivity, 3.8 days after the onset of DF) than IgA (4.6 days) but lasts longer; the peak IgA titer is obtained on day 8. The specificity and the positive predictive value of AAC-ELISA are 100%; its sensitivity and negative predictive value (NPV) are also 100% between days 6 and 25 after the onset of DF, but they decrease drastically when data for tests conducted with specimens from the first days of infection are included, because the IgA titers, like the IgM titers, have not yet risen. AAC-ELISA is a simple method that can be performed together with MAC-ELISA and that can help in interprating DF serology.
Limitations of the Current Microbial Identification System for Identification of Clinical Yeast Isolates
Authors: Kellogg James A. , Bankert David A. , Chaturvedi Vishnu 
Published: December 2019

ABSTRACT

The ability of the rapid, computerized Microbial Identification System (MIS; Microbial ID, Inc.) to identify a variety of clinical isolates of yeast species was compared to the abilities of a combination of tests including the Yeast Biochemical Card (bioMerieux Vitek), determination of microscopic morphology on cornmeal agar with Tween 80, and when necessary, conventional biochemical tests and/or the API 20C Aux system (bioMerieux Vitek) to identify the same yeast isolates. The MIS chromatographically analyzes cellular fatty acids and compares the results with the fatty acid profiles in its database. Yeast isolates were subcultured onto Sabouraud dextrose agar and were incubated at 28°C for 24 h. The resulting colonies were saponified, methylated, extracted, and chromatographically analyzed (by version 3.8 of the MIS YSTCLN database) according to the manufacturer’s instructions. Of 477 isolates of 23 species tested, 448 (94%) were given species names by the MIS and 29 (6%) were unidentified (specified as “no match” by the MIS). Of the 448 isolates given names by the MIS, only 335 (75%) of the identifications were correct to the species level. While the MIS correctly identified only 102 (82%) of 124 isolates of
Candida glabrata
, the predictive value of an MIS identification of unknown isolates as
C. glabrata
was 100% (102 of 102) because no isolates of other species were misidentified as
C. glabrata
. In contrast, while the MIS correctly identified 100% (15 of 15) of the isolates of
Saccharomyces cerevisiae
, the predictive value of an MIS identification of unknown isolates as
S. cerevisiae
was only 47% (15 of 32), because 17 isolates of
C. glabrata
were misidentified as
S. cerevisiae
. The low predictive values for accuracy associated with MIS identifications for most of the remaining yeast species indicate that the procedure and/or database for the system need to be improved.
Ultrastructure, Immunofluorescence, Western Blot, and PCR Analysis of Eight Isolates ofEncephalitozoon(Septata)intestinalisEstablished in Culture from Sputum and Urine Samples and Duodenal Aspirates of Five Patients with AIDS
Authors: del Aguila C. , Croppo G. P. , Moura H. , Da Silva A. J. , Leitch G. J. , Moss D. M. , Wallace S. , Slemenda S. B. , Pieniazek N. J. , Visvesvara G. S. 
Published: December 2019

ABSTRACTMicrosporidia are ancient, intracellular, eukaryotic protozoan parasites that form spores and that lack mitochondria. Currently, as many as eight species included under six genera are known to infect humans, mostly patients with AIDS. Among these,Enterocytozoon bieneusi, the agent of gastrointestinal (GI) disease, is the most frequently identified microsporidian in clinical laboratories in the United States.Encephalitozoon(Septata)intestinalis, the agent that causes a disseminated infection including infection of the GI tract, is the second most frequently identified microsporidian parasite. In spite of this, not many isolates ofE. intestinalishave been established in culture. We describe here the continuous cultivation of eight isolates ofE. intestinalisobtained from different samples including the urine, sputum, and duodenal aspirate or biopsy specimens from five AIDS patients originating from California, Colorado, and Georgia. The specific identification was made on the bases of ultrastructural, antigenic, and PCR analyses.
Three Cases of
Anaerobiospirillum succiniciproducens
Bacteremia Confirmed by 16S rRNA Gene Sequencing
Authors: Tee Wee , Korman Tony M. , Waters Mary Jo , Macphee Andrew , Jenney Adam , Joyce Linda , Dyall-Smith Michael L. 
Published: December 2019

ABSTRACT

We describe three cases of
Anaerobiospirillum succiniciproducens
bacteremia from Australia. We believe one of these cases represents the first report of
A. succiniciproducens
bacteremia in a human immunodeficiency virus (HIV)-infected individual. The other two patients had an underlying disorder (one patient had bleeding esophageal varices complicating alcohol liver disease and one patient had non-Hodgkin’s lymphoma). A motile, gram-negative, spiral anaerobe was isolated by culturing blood from all patients. Electron microscopy showed a curved bacterium with bipolar tufts of flagella resembling
Anaerobiospirillum
spp. Sequencing of the 16S rRNA genes of the isolates revealed no close relatives (organisms likely to be in the same genus) in the sequence databases, nor were any sequence data available for
A. succiniciproducens
. This report presents for the first time the 16S rRNA gene sequence of the type strain of
A. succiniciproducens
, strain ATCC 29305. Two of the three clinical isolates have sequences identical to that of the type strain, while the sequence of the other strain differs from that of the type strain at 4 nucleotides.
Detection of
Ureaplasma urealyticum
in Endotracheal Tube Aspirates from Neonates by PCR
Authors: Nelson S. , Matlow A. , Johnson G. , Th’ng C. , Dunn M. , Quinn P. 
Published: December 2019

ABSTRACT

A PCR-based test was optimized for the detection of
Ureaplasma urealyticum
from neonatal respiratory specimens, with primers directed against the multiple-banded antigen gene (L. J. Teng, X. Zheng, J. I. Glass, H. Watson, J. Tsai, and G. H. Cassell, J. Clin. Microbiol. 32:1464–1469, 1994). Endotracheal tube aspirates (225) from 103 low-birth-weight neonates (<1,250 g) were taken, when possible, at days 0, 4, and 14 after birth and examined by culture and by PCR. Of 77 specimens positive by either method, 73 were detected by PCR and 60 were detected by culture. Overall, 36% of the neonates were positive for
U. urealyticum
by either method. Of 16 patients with PCR-positive–culture-negative results, 13 had positive cultures at another sampling point, and one additional patient had a twin with positive cultures. Of 11 patients with day 0 specimens positive by PCR alone, 9 subsequently became culture positive, demonstrating the utility of this test in early detection. Multiple serovars were present in over 50% of positive specimens, with serovars 3 and 14 in combination being most prevalent. The amplicon size generated from the specimen by PCR correctly predicted the biovars isolated in over 85% of positive specimens. Thus, this PCR test was valuable in allowing early detection of
U. urealyticum
in neonatal respiratory specimens, as well as in providing biovar information.
Effects of Ammonia Inhalation and Acetic Acid Pretreatment on Colonization Kinetics of Toxigenic
Pasteurella multocida
within Upper Respiratory Tracts of Swine
Authors: Hamilton T. D. C. , Roe J. M. , Hayes C. M. , Webster A. J. F. 
Published: December 2019

ABSTRACT

Pigs reared in intensive production systems are continuously exposed to ammonia released by the microbial degradation of their excrement. Exposure to this gas has been shown to increase the severity of the disease progressive atrophic rhinitis by facilitating colonization of the pig’s upper respiratory tract by
Pasteurella multocida
. The etiological mechanism responsible for this synergy was investigated by studying the colonization kinetics of
P. multocida
enhanced by ammonia and comparing them with those evoked by an established disease model. Three-week-old Large White piglets were weaned and allocated to five experimental groups (groups A to E). Pigs in groups A and B were exposed continuously to ammonia at 20 ppm for the first 2 weeks of the study. Pigs in group C were pretreated with 0.5 ml of 1% acetic acid per nostril on days −2 and −1 of the study. On day 0 all the pigs in groups A, C, and D were inoculated with 1.4 × 10
8
toxigenic
P. multocida
organisms given by the intranasal route. The kinetics of
P. multocida
colonization were established by testing samples obtained at weekly intervals throughout the study. The study was terminated on day 37, and the extent of turbinate atrophy was determined by using a morphometric index. The results of the study showed that exposure to aerial ammonia for a limited period had a marked effect on the colonization of toxigenic
P. multocida
in the nasal cavities of pigs, which resulted in the almost total exclusion of commensal flora. In contrast, ammonia had only a limited effect on
P. multocida
colonization at the tonsil. The exacerbation of
P. multocida
colonization by ammonia was restricted to the period of ammonia exposure, and the number of
P. multocida
organisms colonizing the upper respiratory tract declined rapidly upon the cessation of exposure to ammonia. During the exposure period, the ammonia levels in mucus recovered from the nasal cavity and tonsil were found to be 7- and 3.5-fold higher, respectively, than the levels in samples taken from unexposed controls. Acetic acid pretreatment also induced marked colonization of the nasal cavity which, in contrast to that induced by ammonia, persisted throughout the time course of the study. Furthermore, acetic acid pretreatment induced marked but transient colonization of the tonsil. These findings suggest that the synergistic effect of ammonia acts through an etiological mechanism different from that evoked by acetic acid pretreatment. A strong correlation was found between the numbers of
P. multocida
organisms isolated from the nasal cavity and the severity of clinical lesions, as determined by using a morphometric index. The data presented in the paper highlight the potential importance of ammonia as an exacerbating factor in respiratory disease of intensively reared livestock.
Identification and Analysis of a New
vacA
Genotype Variant of
Helicobacter pylori
in Different Patient Groups in Germany
Authors: Strobel Sonja , Bereswill Stefan , Balig Peter , Allgaier Peter , Sonntag Hans-Günther , Kist Manfred 
Published: December 2019

ABSTRACT

The vacuolating cytotoxin of
Helicobacter pylori
(VacA) is known to cause cell damage to mammalian cells and is suspected to give rise to gastric epithelial lesions that might lead to peptic ulcer disease. As shown recently, the gene encoding VacA exhibits genetic variation, with three different families of signal sequences (s1a, s1b, and s2) and two families of midregion sequences (m1 and m2). In order to investigate the relationship between the presence of specific
vacA
genotypes and peptic ulceration, the
vacA
genotypes of 158 clinical isolates of
H. pylori
were determined. The study group consisted of 106 patients with duodenal ulceration; 52 patients with nonulcer dyspepsia (NUD) were used as controls.
H. pylori
of genotype s1 was isolated from 96% of the patients with ulcerations, whereas genotype s2 was only present in 4%, indicating a strong correlation between the
vacA
genotype and peptic ulceration (
P
< 0.001). In contrast, 31% of the patients from the NUD control group were infected with strains of
vacA
genotype s2. Particular midregion genotypes (m1 and m2) were not associated with clinical manifestations. The midregions from 18% of the isolates could not be classified by the proposed scheme. DNA sequencing revealed high homology between the untypeable midregions and that of genotype m1, with multiple base pair exchanges, some affecting the primer annealing site. Compared to those of m1 and m2 alleles, the divergent midregions from untypeable strains showed clustering, indicating the presence of a further subfamily of sequences in the midregion of
vacA
in German isolates, for which we propose the term “m1a.” A new specific primer that we designed for typing m1a isolates might be useful in other studies.
Comparison of Nine Commercially Available Enzyme-Linked Immunosorbent Assays for Detection of
Giardia lamblia
in Fecal Specimens
Authors: Aldeen William E. , Carroll K. , Robison A. , Morrison M. , Hale D. 
Published: December 2019

ABSTRACT

Overall performance, including ease of use, total hands-on time, incubation and processing times, sensitivity, and specificity, of each of nine enzyme-linked immunosorbent assays (ELISAs) were compared by using 222 individual fecal samples submitted for the detection of
Giardia lamblia
. The assays evaluated were manufactured by Alexon, Inc., Cambridge Biotech Corp., Meridian, Inc., and Trend Scientific, Inc. All assays used polyclonal antibodies except the “new and improved” Microplate (direct and diluted methods) by Alexon, which is a monoclonal antibody assay. Seventy specimens were positive for
G. lamblia
by ELISA, ova and parasite test, and/or direct fluorescent-antibody assay. One hundred fifty two were negative by all three methods. Sensitivities and specificities ranged from 88.6 to 100% and 99.3 to 100%, respectively. The total hands-on time needed to run one specimen ranged from 1 min to 2 min 17 s per specimen. All except one commercially available ELISA were found to be rapid, sensitive, and specific for the detection of
G. lamblia
in fecal specimens.