bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porphyromonas gingivalis
Strain Variability and Periodontitis
Authors: Griffen Ann L. , Lyons Sharon R. , Becker Mitzi R. , Moeschberger Melvin L. , Leys Eugene J. 
Published: December 2019

ABSTRACT

To determine if there is variability in virulence among strains of
Porphyromonas gingivalis
in human periodontitis, their distribution in a group of subjects with clear indicators of periodontitis and in a healthy, age-matched control group was examined. The presence of heteroduplex types of
P. gingivalis
in the two groups was determined with a PCR-based assay. This assay relied on detection of polymorphisms in the ribosomal internal spacer region (ISR). ISR fragments generated by PCR with
P. gingivalis
-specific primers were hybridized to fragments from reference strains, and the formation of heteroduplexes from the hybridization of nonidentical sequences was observed by polyacrylamide gel electrophoresis. Characteristic fingerprints from comparison with a panel of reference strains allowed the identification of heteroduplex types in clinical samples. One hundred thirty adults with periodontitis and 181 controls were sampled. With this approach, 11 heteroduplex types of
P. gingivalis
were detected in the population. Sufficient numbers were available for statistical analysis of six of these types. Heteroduplex type hW83 was found to be very strongly associated with periodontitis (
P
= 0.0000), and two additional types, h49417 and hHG1691, were also significantly associated with disease. The remaining types, h23A4, h381, and hA7A1, were detected more frequently in subjects with periodontitis than in healthy subjects, but the difference was not significant. These data indicate that virulence in human periodontitis varies among strains of
P. gingivalis
, and they identify an apparently highly virulent subgroup.
Detection and Reporting of Organisms Producing Extended-Spectrum β-Lactamases: Survey of Laboratories in Connecticut
Authors: Tenover Fred C. , Mohammed M. Jasmine , Gorton Timothy S. , Dembek Zygmunt F. 
Published: December 2019

ABSTRACT

Extended-spectrum β-lactamases (ESBLs) are enzymes produced in some gram-negative bacilli that mediate resistance to extended-spectrum cephalosporins and aztreonam. They are most common in
Klebsiella
spp. and
Escherichia coli
but are present in a variety of
Enterobacteriaceae
. Resistance mediated by these enzymes can be difficult to detect depending on the antimicrobial agents tested. AmpC β-lactamases are related to the chromosomal enzymes of
Enterobacter
and
Citrobacter
spp. and also mediate resistance to extended-spectrum cephalosporins and aztreonam in addition to cephamycins, such as cefoxitin. Unlike ESBLs, however, AmpC β-lactamases are not inhibited by clavulanic acid or other similar compounds. To assess the abilities of various antimicrobial susceptibility testing methods to detect ESBLs, we sent three ESBL-producing organisms, one AmpC-producing organism, and a control strain that was susceptible to extended-spectrum cephalosporins to 38 laboratories in Connecticut for testing. Eight (21.0%) of 38 labs failed to detect extended-spectrum cephalosporin or aztreonam resistance in any of the ESBL- or AmpC-producing isolates. Errors were encountered with both automated and disk diffusion methods. Conversely, seven (18.4%) labs categorized at least some of the four resistant isolates as potential ESBL producers and reported the results with the extended-spectrum cephalosporins and aztreonam as resistant as suggested by current National Committee for Clinical Laboratory Standards (NCCLS) guidelines. The percentage of laboratories that failed to detect resistance in the ESBL or AmpC isolates ranged from 23.7 to 31.6% depending on the type of enzyme present in the test organism. This survey suggests that many laboratories have difficulty detecting resistance in ESBL and AmpC-producing organisms and may be unaware of the NCCLS guidelines on modifying susceptibility testing reports for ESBL-producing strains.
Direct
mecA
Detection from Blood Culture Bottles by Branched-DNA Signal Amplification
Authors: Zheng X. , Kolbert C. P. , Varga-Delmore P. , Arruda J. , Lewis M. , Kolberg J. , Cockerill F. R. , Persing D. H. 
Published: December 2019

ABSTRACT

A branched-DNA (bDNA) signal amplification method was used to detect the
mecA
gene directly from blood culture broth growing staphylococci. BACTEC blood culture bottles with positive growth indices and containing staphylococcus-like organisms as shown by Gram stain were tested for the presence of the
mecA
gene. Comparison of test results was done among 225 patients (one blood culture from each patient). Compared with PCR, the sensitivity and specificity of the bDNA method are 100 and 99%, respectively. The bDNA test is carried out in a 96-well format and requires approximately 6 h to perform. Our preliminary results suggest that direct detection of the
mecA
gene by bDNA signal amplification is (i) sensitive enough to detect
mecA
directly from blood culture bottles without the requirement for subculture and (ii) as sensitive and specific as the PCR-based method.
Evaluation of AMPLILINK Software for the COBAS AMPLICOR System
Authors: Kessler Harald H. , Jungkind Donald , Stelzl Evelyn , Direnzo Sue , Vellimedu Srinivas K. , Pierer Karen , Santner Brigitte , Marth Egon 
Published: December 2019

ABSTRACT
The use of AMPLILINK version 1.0 software was evaluated for the operation and control of one COBAS AMPLICOR instrument and for two COBAS AMPLICOR instruments run simultaneously to perform and detect nucleic acid amplification reactions. A total of 3,384 results were analyzed. The initial accuracy of the results was 99.91%. Three errors of omission of transfer of data from the COBAS AMPLICOR to the AMPLILINK system were observed. Two of these errors were from a single specimen, where both the analyte and internal control results were not transmitted. These errors did not interfere with the correctness of any other data. There were no interruptions of runs, and no data were mixed. AMPLILINK increased convenience, saved labor, and was found to be a very useful addition for clinical laboratories performing molecular-diagnostic procedures with the COBAS AMPLICOR system.
Associations between Virulence Factors of Shiga Toxin-ProducingEscherichia coliand Disease in Humans
Authors: Boerlin Patrick , McEwen Scott A. , Boerlin-Petzold Franziska , Wilson Jeffrey B. , Johnson Roger P. , Gyles Carlton L. 
Published: December 2019

ABSTRACTAssociations between known or putative virulence factors of Shiga toxin-producingEscherichia coliand disease in humans were investigated. Univariate analysis and multivariate logistic regression analysis of a set of 237 isolates from 118 serotypes showed significant associations between the presence of genes for intimin (eae) and Shiga toxin 2 (stx2) and isolates from serotypes reported in humans. Similar associations were found with isolates from serotypes reported in hemorrhagic colitis and hemolytic-uremic syndrome. The enterohemorrhagicE. coli(EHEC) hemolysin gene was significantly associated with isolates from serotypes found in severe diseases in univariate analysis but not in multivariate logistic regression models. A strong association between the intimin and EHEC-hemolysin genes may explain the lack of statistical significance of EHEC hemolysin in these multivariate models, but a true lack of biological significance of the hemolysin in humans or in disease cannot be excluded. This result warrants further investigations of this topic. Multivariate analysis revealed an interaction between theeaeandstx2genes, thus supporting the hypothesis of the synergism between the adhesin intimin and Shiga toxin 2. A strong statistical association was observed between thestx2gene and severity of disease for a set of 112 human isolates from eight major serotypes. A comparison of 77 isolates of bovine origin and 91 human isolates belonging to six major serotypes showed significant associations of the genes for Shiga toxin 1 and EspP protease with bovine isolates and an increased adherence on HEp-2 cell cultures for human isolates, particularly from diarrheic patients and healthy persons.
Identification of the Enteropathogens
Campylobacter jejuni
and
Campylobacter coli
Based on the
cadF
Virulence Gene and Its Product
Authors: Konkel Michael E. , Gray Sean A. , Kim Bong J. , Garvis Steven G. , Yoon Julie 
Published: December 2019

ABSTRACT

Campylobacter jejuni
and
Campylobacter coli
are common causes of gastroenteritis in humans. Infection with
C. jejuni
or
C. coli
is commonly acquired by eating undercooked chicken. The goal of this study was to develop specific detection assays for
C. jejuni
and
C. coli
isolates based on the
cadF
virulence gene and its product. The
cadF
gene from
C. jejuni
and
C. coli
encodes a 37-kDa outer membrane protein that promotes the binding of these pathogens to intestinal epithelial cells. A fragment of approximately 400 bp was amplified from 38 of 40 (95%)
C. jejuni
isolates and 5 of 6 (83.3%)
C. coli
isolates with primers designed to amplify an internal fragment of the
cadF
gene. PCR was then used to amplify
Campylobacter
DNA from store-bought chickens. A 400-bp band was amplified from 26 of the 27 chicken carcasses tested by the PCR-based assay. The CadF protein was detected in every
C. jejuni
and
C. coli
isolate tested, as judged by immunoblot analysis with a rabbit anti-
C. jejuni
37-kDa serum. In addition, methanol-fixed samples of whole-cell
C. jejuni
and
C. coli
were detected with the rabbit anti-37-kDa serum by using an indirect-immunofluorescence microscopy assay. These findings indicate that the
cadF
gene and its product are conserved among
C. jejuni
and
C. coli
isolates and that a PCR assay based on the
cadF
gene may be useful for the detection of
Campylobacter
organisms in food products.
Rapid Identification and Typing ofStaphylococcus aureusby PCR-Restriction Fragment Length Polymorphism Analysis of thearoAGene
Authors: Marcos Javier Yugueros , Soriano Alberto Cascón , Salazar María Sánchez , Moral Carmen Hernanz , Ramos Susana Suárez , Smeltzer Mark S. , Carrasco German Naharro 
Published: December 2019

ABSTRACTTheStaphylococcus aureus aroAgene, which encodes 5-enolpyruvylshikimate-3-phosphate synthase, was used as a target for the amplification of a 1,153-bp DNA fragment by PCR with a pair of primers of 24 and 19 nucleotides. The PCR products, which were detected by agarose gel electrophoresis, were amplified from allS. aureusstrains so far analyzed (reference strains and isolates from cows and sheep with mastitis, as well as 59 isolates from humans involved in four confirmed outbreaks). Hybridization with an internal 536-bp DNA fragment probe was positive for all PCR-positive samples. No PCR products were amplified when otherStaphylococcusspp. or genera were analyzed by using the same pair of primers. The detection limit forS. aureuscells was 20 CFU when the cells were suspended in saline; however, the sensitivity of the PCR was lower (5 × 102CFU) whenS. aureuscells were suspended in sterilized whole milk.TaqI digestion of the PCR-generated products rendered two different restriction fragment length polymorphism patterns with the cow and sheep strains tested, and these patterns corresponded to the two different patterns obtained by antibiotic susceptibility tests. Analysis of the 59 human isolates by our easy and rapid protocol rendered results similar to those of other assays.
Rapid Detection of theChlamydiaceaeand Other Families in the OrderChlamydiales: Three PCR Tests
Authors: Everett Karin D. E. , Hornung Linda J. , Andersen Arthur A. 
Published: December 2019

ABSTRACTFew identification methods will rapidly or specifically detect all bacteria in the orderChlamydiales, familyChlamydiaceae. In this study, three PCR tests based on sequence data from over 48 chlamydial strains were developed for identification of these bacteria. Two tests exclusively recognized theChlamydiaceae: a multiplex test targeting theompAgene and the rRNA intergenic spacer and a TaqMan test targeting the 23S ribosomal DNA. The multiplex test was able to detect as few as 200 inclusion-forming units (IFU), while the TaqMan test could detect 2 IFU. The amplicons produced in these tests ranged from 132 to 320 bp in length. The third test, targeting the 23S rRNA gene, produced a 600-bp amplicon from strains belonging to several families in the orderChlamydiales. Direct sequence analysis of this amplicon has facilitated the identification of new chlamydial strains. These three tests permit ready identification of chlamydiae for diagnostic and epidemiologic study. The specificity of these tests indicates that they might also be used to identify chlamydiae without culture or isolation.
Phylogenetic Relationships of Varieties and Geographical Groups of the Human Pathogenic Fungus
Histoplasma capsulatum
Darling
Authors: Kasuga Takao , Taylor John W. , White Thomas J. 
Published: December 2019

ABSTRACT

The phylogeny of 46 geographically diverse
Histoplasma capsulatum
isolates representing the three varieties
capsulatum
,
duboisii
, and
farciminosum
was evaluated using partial DNA sequences of four protein coding genes. Parsimony and distance analysis of the separate genes were generally congruent and analysis of the combined data identified six clades: (i) class 1 North American
H. capsulatum
var.
capsulatum
, (ii) class 2 North American
H. capsulatum
var.
capsulatum
, (iii) Central American
H. capsulatum
var.
capsulatum
, (iv) South American
H. capsulatum
var.
capsulatum
group A, (v) South American
H. capsulatum
var.
capsulatum
group B, and (vi)
H. capsulatum
var.
duboisii
. Although the clades were generally well supported, the relationships among them were not resolved and the nearest outgroups (
Blastomyces
and
Paracoccidioides
) were too distant to unequivocally root the
H. capsulatum
tree.
H. capsulatum
var.
farciminosum
was found within the South American
H. capsulatum
var.
capsulatum
group A clade. With the exception of the South American
H. capsulatum
var.
capsulatum
group A clade, genetic distances within clades were an order of magnitude lower than those between clades, and each clade was supported by a number of shared derived nucleotide substitutions, leading to the conclusion that each clade was genetically isolated from the others. Under a phylogenetic species concept based on possession of multiple shared derived characters, as well as concordance of four gene genealogies,
H. capsulatum
could be considered to harbor six species instead of three varieties.
Head-to-Head Evaluation of Five Chlamydia Tests Relative to a Quality-Assured Culture Standard
Authors: Newhall Wilbert J. , Johnson Robert E. , DeLisle Susan , Fine David , Hadgu Alula , Matsuda Bessie , Osmond Donna , Campbell Joyce , Stamm Walter E. 
Published: December 2019

ABSTRACT

Nucleic acid amplification tests offer superior sensitivity for the detection of
Chlamydia trachomatis
infection, but many laboratories still use nonamplification methods because of the lower cost and ease of use. In spite of their availability for more than a decade, few studies have directly compared the nonamplification tests. Such comparisons are still needed in addition to studies that directly compare individual nonamplification and amplification tests. The purpose of this study was to evaluate and compare the performance characteristics relative to culture of five different tests for the detection of
C. trachomatis
with and without confirmation of positive results. The tests were applied to endocervical specimens from 4,980 women attending family planning clinics in the northwestern United States. The five nonculture tests included Chlamydiazyme (Abbott), MicroTrak direct fluorescent antibody (DFA) (Syva), MicroTrak enzyme immunoassay (EIA) (Syva), Pace 2 (Gen-Probe), and Pathfinder EIA (Sanofi/Kallestad). All positive results obtained with a nonculture test (except MicroTrak DFA) were confirmed by testing the original specimens with a blocking antibody test (Chlamydiazyme), a cytospin DFA (MicroTrak EIA and Pathfinder EIA), and a probe competition assay (Pace 2). The prevalence of culture-proven chlamydia was 3.9%. The sensitivities of the nonculture tests were in a range from 62 to 75%, and significant differences between tests in terms of sensitivity were observed. The positive predictive value for each test was 0.85 or higher. The specificities of the nonculture tests without performance of confirmations were greater than 99%. Performing confirmatory tests eliminated nearly all of the false positives.
Antimicrobial Susceptibility Patterns of
Aeromonas jandaei
,
A. schubertii
,
A. trota
, and
A. veronii
Biotype veronii
Authors: Overman Timothy L. , Janda J. Michael 
Published: December 2019

ABSTRACT

Fifty-six isolates of four
Aeromonas
species, which have been documented as causative agents of human infections or isolated from human clinical specimens, were subjected to antimicrobial susceptibility testing using a MicroScan WalkAway conventional (overnight incubation) gram-negative panel. The four species tested and the number of isolates of each were as follows:
Aeromonas jandaei
, 17;
A. schubertii
, 12;
A. trota
, 15; and
A. veronii
biotype veronii, 12. All isolates of
A. trota
were susceptible to all antimicrobial agents tested, except cefazolin (20% of isolates were resistant) and cefoxitin (13% of isolates were resistant). All isolates of
A. schubertii
and
A. veronii
biotype veronii, as well as 88% of
A. jandaei
isolates, were resistant to ampicillin. Resistance to ampicillin-sulbactam ranged from 25% of
A. schubertii
strains to 100% of
A. veronii
biotype veronii strains. Cefazolin resistance ranged from 17% of
A. veronii
biotype veronii isolates to 59% of
A. jandaei
isolates. Imipenem resistance was detected in 65% of
A. jandaei
strains and 67% of
A. veronii
biotype veronii strains.
A. jandaei
displayed resistance to piperacillin and ticarcillin in 53 and 71% of the isolates, respectively.
A. veronii
biotype veronii strains were 100% susceptible to piperacillin and 100% resistant to ticarcillin. These antibiogram data may be useful in establishing the identification of these four species when members of the genus
Aeromonas
are isolated from human clinical sources.
Sensitivity and Specificity of Dipstick Tests for Rapid Diagnosis of Malaria in Nonimmune Travelers
Authors: Jelinek T. , Grobusch M. P. , Schwenke S. , Steidl S. , von Sonnenburg F. , Nothdurft H. D. , Klein E. , Löscher T. 
Published: December 2019

ABSTRACT

Swift diagnosis of
Plasmodium falciparum
malaria in areas where the disease is not endemic is frequently complicated by the lack of experience on the side of involved laboratory personal. Diagnostic tools based on the dipstick principle for the detection of plasmodial histidine-rich protein 2 (HRP-2) and parasite-specific lactate dehydrogenase (pLDH), respectively, have become available for the qualitative detection of
P. falciparum
malaria. In order to evaluate two of the currently available assays, specimens from 231 patients were screened during a prospective multicenter study. Among the screened specimens, samples from 53 patients (22.9%) were positive for
P. falciparum
malaria by microscopy and/or PCR. While the test kit based on the detection of HRP-2 performed with a sensitivity of 92.5% and a specificity of 98.3%, the kit for the detection of pLDH showed a sensitivity of 88.5% and a specificity of 99.4%. Dipstick tests have the potential of enhancing speed and accuracy of the diagnosis of
P. falciparum
malaria, especially if nonspecialized laboratories are involved.
Multicenter Evaluation of the BACTEC MGIT 960 System for Recovery of Mycobacteria
Authors: Hanna Bruce A. , Ebrahimzadeh Adeleh , Elliott L. Bruce , Morgan Margie A. , Novak Susan M. , Rusch-Gerdes Sabine , Acio Millie , Dunbar Denise F. , Holmes T. Michele , Rexer Charles H. , Savthyakumar Chiminyan , Vannier Ann M. 
Published: December 2019

ABSTRACT

We evaluated the BACTEC MGIT 960 system, which is a fully automated, noninvasive system for the growth and detection of mycobacteria with a capacity to incubate and continuously monitor 960 7-ml culture tubes. We studied 3,330 specimens, 2,210 respiratory and 1,120 nonrespiratory specimens, collected from 2,346 patients treated at six sites. Processed specimens were inoculated into the BACTEC MGIT 960 and BACTEC 460 TB systems, as well as onto Lowenstein-Jensen slants and Middlebrook 7H11/7H11 selective plates. From all culture systems, a total of 362 isolates of mycobacteria were recovered; these were recovered from 353 specimens collected from 247 patients. The greatest number of isolates of mycobacteria (289, or 80% of the 362 isolates) was recovered with the BACTEC MGIT 960, followed by the BACTEC 460 TB (271, or 75%) and solid media (250, or 69%). From all culture systems a total of 132 isolates of
Mycobacterium tuberculosis
complex were recovered. The greatest number of isolates of
M. tuberculosis
complex was recovered when liquid medium was combined with conventional solid media; the number recovered with BACTEC 460 TB plus solid media was 128 (97%), that recovered with BACTEC MGIT 960 plus solid media was 121 (92%), that recovered with BACTEC 460 TB was 119 (90%) and that recovered with all solid media combined was 105 (79%). The recovery with BACTEC MGIT 960 alone was 102 (77%). The mean times to detection (TTD) for
M. tuberculosis
complex were 14.4 days for BACTEC MGIT, 15.2 days for BACTEC 460 TB, and 24.1 days for solid media. The numbers of isolates of
Mycobacterium avium
complex (MAC) recovered were 172 (100%) for all systems, 147 (85%) for BACTEC MGIT 960, 123 (72%) for BACTEC 460 TB, and 106 (62%) for all solid media combined. The TTD for MAC in each system were 10.0 days for BACTEC MGIT 960, 10.4 days for BACTEC 460 TB, and 25.9 days for solid media. Breakthrough contamination rates (percentages of isolates) for each of the systems were 8.1% for BACTEC MGIT 960, 4.9% for BACTEC 460 TB, and 21.1% for all solid media combined.
Application of Dried Blood Spot Specimens for Serologic Subtyping of Human Immunodeficiency Virus Type 1 in Thailand
Authors: Chanbancherd P. , Brown A. E. , Trichavaroj R. , Tienamporn P. , Puthakird P. , Limpairojn N. , VanCott T. C. , de Souza M. S. 
Published: December 2019

ABSTRACT
Dried blood spot (DBS) specimens were assessed as an alternative to plasma for human immunodeficiency virus type 1 (HIV-1) serotyping by V3 loop peptide enzyme immunoassay. Nested PCR capable of distinguishing HIV-1 subtypes B and E was used as the reference standard. Ninety-two percent of DBS samples were typeable as either HIV-1 subtype B or E. Serotype results with DBS and plasma were identical for 254 of 257 specimens. A simple DBS collection method provides a convenient alternative for conducting HIV-1 serotype surveillance while retaining sensitivity and specificity.
Analysis with a Combination of Macrorestriction Endonucleases Reveals a High Degree of Polymorphism among
Bordetella pertussis
Isolates in Eastern France
Authors: Prevost G. , Freitas F. I. S. , Stoessel P. , Meunier O. , Haubensack M. , Monteil H. , Scheftel J. M. 
Published: December 2019

ABSTRACT

From 1990 to 1996, routine screening for whooping cough identified 399 patients with a calmodulin-dependent adenylate cyclase-positive test result and yielded 69
Bordetella pertussis
isolates. None of the patients were fully vaccinated, and most were less than 6 months old. Analysis of total DNA by pulsed-field gel electrophoresis (PFGE) after
Xba
I,
Spe
I, or
Dra
I macrorestriction yielded 19, 15, and 5 different patterns, respectively, whereas ribotyping failed to demonstrate any strain polymorphism. Discrimination among the isolates was improved by combining the PFGE profiles. Some patterns were more frequent, but the corresponding patients were not clearly epidemiologically related. The patterns for two strains obtained during a 3-month period from patients who were neighbors differed by the length of a single DNA fragment. These data strongly suggest that one type of isolate is widely spread throughout the world and is carried by individuals other than patients who develop a true illness.