bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diagnosis of Human Ehrlichiosis by PCR Assay of Acute-Phase Serum
Authors: Comer James A. , Nicholson William L. , Sumner John W. , Olson James G. , Childs James E. 
Published: December 2019

ABSTRACTA PCR assay of 43 acute-phase serum samples was evaluated as a method for early detection of human granulocytic ehrlichiosis (HGE) and determination of etiology when serologic testing is inconclusive. Sequence-confirmed products of the HGE agent were amplified from three individuals residing or having exposure history in Minnesota or Wisconsin, and similarly confirmed products fromEhrlichia chaffeensiswere amplified from three individuals from Florida or Maryland. Etiology, as determined by PCR and serology, was the same whenever there was a fourfold difference between the maximum titers of antibodies to both antigens, indicating that presumptive determination of etiology may be based on fourfold differences in titers. PCR testing determined thatE. chaffeensiswas the etiologic agent for one individual who had similar titers of antibodies to both agents. PCR assay of acute-phase serum in the absence of whole blood specimens may be a useful method for early detection of human ehrlichiosis and determination of etiology when serologic testing is inconclusive.
Heterogeneously Vancomycin-Resistant
Staphylococcus epidermidis
Strain Causing Recurrent Peritonitis in a Dialysis Patient during Vancomycin Therapy
Authors: Sieradzki Krzysztof , Roberts Richard B. , Serur David , Hargrave Judie , Tomasz Alexander 
Published: December 2019

ABSTRACT

Methicillin-resistant
Staphylococcus epidermidis
(MRSE) was recovered over a 2-month period from the dialysis fluid of a peritoneal dialysis (PD) patient who experienced recurrent episodes of peritonitis during therapeutic and prophylactic use of vancomycin. Characterization of five consecutive MRSE isolates by molecular and microbiological methods showed that they were representatives of a single strain, had reduced susceptibility to vancomycin, did not react with DNA probes specific for the enterococcal
vanA
or
vanB
gene, and showed characteristics reminiscent of the properties of a recently described vancomycin-resistant laboratory mutant of
Staphylococcus aureus
. Cultures of these MRSE isolates were heterogeneous: they contained—with a frequency of 10
−4
to 10
−5
—bacteria for which vancomycin MICs were high (25 to 50 μg/ml) which could easily be selected to “take over” the cultures by using vancomycin selection in the laboratory. In contrast, the five consecutive MRSE isolates recovered from the PD patient during virtually continuous vancomycin therapy showed no indication for a similar enrichment of more resistant subpopulations, suggesting the existence of an “occult” infection site in the patient (presumably at the catheter exit site) which was not accessible to the antibiotic.
Mycobacterium
Species Identification and Rifampin Resistance Testing with High-Density DNA Probe Arrays
Authors: Troesch A. , Nguyen H. , Miyada C. G. , Desvarenne S. , Gingeras T. R. , Kaplan P. M. , Cros P. , Mabilat C. 
Published: December 2019

ABSTRACT

Species identification within the genus
Mycobacterium
and subsequent antibiotic susceptibility testing still rely on time-consuming, culture-based methods. Despite the recent development of DNA probes, which greatly reduce assay time, there is a need for a single platform assay capable of answering the multitude of diagnostic questions associated with this genus. We describe the use of a DNA probe array based on two sequence databases: one for the species identification of mycobacteria (82 unique 16S rRNA sequences corresponding to 54 phenotypical species) and the other for detecting
Mycobacterium tuberculosis
rifampin resistance (
rpoB
alleles). Species identification or rifampin resistance was determined by hybridizing fluorescently labeled, amplified genetic material generated from bacterial colonies to the array. Seventy mycobacterial isolates from 27 different species and 15 rifampin-resistant
M. tuberculosis
strains were tested. A total of 26 of 27 species were correctly identified as well as all of the
rpoB
mutants. This parallel testing format opens new perspectives in terms of patient management for bacterial diseases by allowing a number of genetic tests to be simultaneously run.
Clinical Spectrum of Infections Due to the Newly Described
Actinomyces
Species
A. turicensis
,
A. radingae
, and
A. europaeus
Authors: Sabbe Luc J. M. , Van De Merwe Dick , Schouls Leo , Bergmans Anneke , Vaneechoutte Mario , Vandamme Peter 
Published: December 2019

ABSTRACT

Over a 7-year period, we isolated 294
Actinomyces
-like organisms (ALOs) which were not clearly identifiable. Using well-defined probes coding for sequences specific for recently described
Actinomyces
species (
A. turicensis
,
A. radingae
, and
A. europaeus
), we were able to identify 128 strains. The majority belonged to the
A. turicensis
species.
A. radingae
was found only in patients with skin-related pathologies.
A. europaeus
was also detected in patients with urinary tract infections. The main sources of
A. turicensis
were genital infections, followed by skin-related and urinary tract infections. Additional clinical pictures were appendicitis, cholecystitis, ear, nose, and throat infections, and bacteremia. In a small number of patients these ALOs were found as the only pathogen. Strains of the three species were tested by two widely used biochemical identification methods.
A. turicensis
was easily identifiable by both these methods. We conclude that these ALOs are not infrequent pathogens and are found in a wide range of human infections. At least
A. turicensis
is easily identifiable by clinical diagnostic laboratories.
Typing and Characterization of Mechanisms of Resistance of
Shigella
spp. Isolated from Feces of Children under 5 Years of Age from Ifakara, Tanzania
Authors: Navia Margarita M. , Capitano Liliana , Ruiz Joaquin , Vargas Martha , Urassa Honorati , Schellemberg David , Gascon Joaquim , Vila Jordi 
Published: December 2019

ABSTRACT

Eighty-six strains of
Shigella
spp. were isolated during the dry season from stool samples of children under 5 years of age in Ifakara, Tanzania. The epidemiological relationship as well as the antimicrobial susceptibility and mechanisms of resistance to ampicillin, chloramphenicol, and co-trimoxazole were investigated. Four different epidemiological tools, pulsed-field gel electrophoresis (PFGE), repetitive extragenic palindromic (REP)-PCR, plasmid analysis, and antibiogram, were compared for typing
Shigella
strains. Seventy-eight (90%) strains were
Shigella flexneri
and were distributed into four groups, by either PFGE or REP-PCR, with 51, 17, 7, and 3 strains. The four strains of
Shigella dysenteriae
belonged to the same group, and the four strains of
Shigella sonnei
were distributed in two groups with three and one strain each. Plasmid analysis showed a high level of heterogeneity among strains belonging to the same PFGE group, while the antibiogram was less discriminative. REP-PCR provided an alternative, rapid, powerful genotyping method for
Shigella
spp. Overall, antimicrobial susceptibility testing showed a high level of resistance to ampicillin (81.8%), chloramphenicol (72.7%), tetracycline (96.9%), and co-trimoxazole (87.9%). Ampicillin resistance was related to an integron-borne OXA-1-type β-lactamase in 85.1% of the cases and to a TEM-1-type β-lactamase in the remaining 14.8%. Resistance to co-trimoxazole was due to the presence of a
dhfr Ia
gene in all groups except one of
S. flexneri
, where a
dhfr VII
gene was found within an integron. Chloramphenicol resistance was associated in every case with positive chloramphenicol acetyltransferase activity. All strains were susceptible to nalidixic acid, ciprofloxacin, ceftazidime, cefotaxime, and cefoxitin. Therefore, these antimicrobial agents may be good alternatives for the treatment of diarrhea caused by
Shigella
in Tanzania.
Autopsy-Controlled Prospective Evaluation of Serial Screening for Circulating Galactomannan by a Sandwich Enzyme-Linked Immunosorbent Assay for Hematological Patients at Risk for Invasive Aspergillosis
Authors: Maertens Johan , Verhaegen Jan , Demuynck Hilde , Brock Penelope , Verhoef Gregor , Vandenberghe Peter , Van Eldere Johan , Verbist Ludo , Boogaerts Marc 
Published: December 2019

ABSTRACT

Efforts to improve the diagnosis of invasive aspergillosis (IA) have been directed towards the detection of fungal antigens, including galactomannan (GM). However, previous evaluations of GM detection have been hampered by a lack of proven cases of IA and by a nonserial study design. This prospective study assessed the diagnostic value of serial screening for circulating GM by using a recently developed sandwich enzyme-linked immunosorbent assay (ELISA) for prolonged-neutropenic and/or steroid-treated patients with hematological disorders. Serum GM levels were monitored twice weekly for 186 consecutive patients at increased risk for IA. The patients were stratified according to the likelihood of IA (proven, probable, possible, and no evidence of IA) by using stringent criteria. Proven IA was defined by characteristic histopathological findings together with a positive culture for
Aspergillus
species. Autopsy and culture from autopsy specimens was used to verify both positive and negative test results. A total of 2,172 serum samples were tested from 243 episodes (mean, 9 samples/episode). Based on the analysis of 71 patients with confirmed disease status (culture and histology), the sensitivity and specificity of serial GM monitoring were 92.6 and 95.4%, respectively. The positive predictive value was almost 93%, the negative predictive value was 95%, and the efficacy was 94%. False-positive reactions occurred at a rate of nearly 8%, although this figure might have been overestimated. Less than 1% of all tested sera were considered inconclusive. In more than half of the cases, antigenemia was detected before clinical suspicion of IA (median, 6 days before). Serial determination of serum GM by the sandwich ELISA technique is a sensitive tool for the diagnosis of IA in hematological patients at risk. This approach may substantially influence clinical management with regard to preemptive and empirical antifungal therapy.
Isolation ofHelicobacter canisfrom a Colony of Bengal Cats with Endemic Diarrhea
Authors: Foley Janet E. , Marks Stanley L. , Munson Linda , Melli Ann , Dewhirst Floyd E. , Yu Shilu , Shen Zeli , Fox James G. 
Published: December 2019

ABSTRACTOn the basis of biochemical, phenotypic, and 16S rRNA analyses,Helicobacter caniswas isolated from Bengal cats with and without chronic diarrhea. Because the cats were coinfected with other potential pathogens, includingCampylobacter helveticus, and becauseH. caniswas isolated from nondiarrheic cats, the causal role ofH. canisin producing the diarrhea could not be proven. Histologically, the colons of the four affected cats were characterized by mild to moderate neutrophilic, plasmacytic, and histocytic infiltrates in the lamina propria. Rare crypt abscesses were also noted for three cats but were a more prominent feature of the colonic lesions noted for the fourth cat. This is the first observation ofH. canisin cats and raises the possibility thatH. canis, likeH. hepaticusandH. bilisin mice, can cause inflammation of the colon, particularly in hosts with immune dysregulation. Further studies are needed to determine the importance ofH. canisas a primary enteric pathogen in cats and the role of cats in the possible zoonotic spread ofH. canisto humans.
Dusky-Footed Wood Rats (Neotoma fuscipes) as Reservoirs of Granulocytic Ehrlichiae (Rickettsiales:Ehrlichieae) in Northern California
Authors: Nicholson William L. , Castro Martin B. , Kramer Vicki L. , Sumner John W. , Childs James E. 
Published: December 2019

ABSTRACTDusky-footed wood rats (Neotoma fuscipes) andPeromyscussp. mice (P. maniculatusandP. truei) were collected from one site in Placer County, one site in Santa Cruz County, and two sites in Sonoma County in northern California. Serum or plasma samples from 260 rodents were tested for antibodies to the agent of human granulocytic ehrlichiosis. Of these, samples from 25 wood rats (34% of those tested) and 10 (8%)Peromyscussp. mice were found to be seropositive, but only those from one site. PCR assays targeting thegroESLheat shock operon were conducted on all seropositive specimens and a subset of seronegative blood specimens. Ehrlichial DNA was identified in 17 (68%) of the 25 seropositive wood rat blood samples and in 1 of the 10 (10%)Peromyscussp. specimens. None of 40 seronegative blood samples was PCR positive. Both seropositive and PCR-positive animals were collected during each trapping period. One male tick out of 84Ixodes pacificusadults collected was PCR positive; samples ofDermacentor occidentalisnymphs and adults were negative. Nucleotide sequences of amplicons from three wood rat blood specimens and from the single PCR-positive tick differed by one and two bases, respectively, from a sequence previously obtained fromEhrlichia equi. At one site in Sonoma County, wood rats had a concurrent high prevalence of seropositivity and PCR positivity, while other sigmodontine rodents collected at the site were only occasionally infected. We suggest that dusky-footed wood rats serve as reservoirs of granulocytic ehrlichial agents in certain areas of northern California. The tick species involved in the transmission of granulocytic ehrlichiae among wood rats remains unknown.
Detection of
Helicobacter pylori
Antibodies in a Pediatric Population: Comparison of Three Commercially Available Serological Tests and One In-House Enzyme Immunoassay
Authors: Sunnerstam Bengt , Kjerstadius Torbjörn , Jansson Lillemor , Giesecke Johan , Bergström Mats , Ejderhamn Jan 
Published: December 2019

ABSTRACT

A serum immunoglobulin G enzyme immunoassay (EIA) for
Helicobacter pylori
antibodies already in use in adults was evaluated with 99 pediatric serum samples to determine its usefulness for the study of
H. pylori
disease in children. The reference method used was either the
13
C-urea breath test or a biopsy culture of gastric mucosa. In children, an EIA cutoff of 0.35 absorbancy unit yielded sensitivity, specificity, and positive and negative predictive values of 93, 97, 93, and 97%, respectively. The cutoff recommended when this EIA was published for use in adults was 0.70 absorbancy unit (H. Gnarpe, P. Unge, C. Blomqvist, and S. Mäkitalo, APMIS 96:128–132, 1988). Another subset of 169 serum samples taken from children was analyzed by four serological tests in order to compare the performance of the in-house EIA with the Pyloriset, HM-CAP, and Helico-G kits. For the 169 samples, 10 (5.9%) false-positives and no false-negatives occurred with the Helico-G, 3 (1.8%) false-positives and no false-negatives occurred with the Pyloriset, and 3 (1.8%) false-positives and 1 (0.6%) false-negative occurred with the HM-CAP. For the 169 samples, 1 (0.6%) false-positive and no false-negatives occurred with the in-house EIA. Serological detection of
H. pylori
antibodies with our EIA seems to be valuable in diagnosing
H. pylori
infection in children, but only if a lowered, specific pediatric cutoff is established. The commercial kits, particularly the Helico-G, seem to overdiagnose pediatric
H. pylori
infection. A positive serological test for
H. pylori
infection, particularly for children, needs to be confirmed by a reference method because of the possibility of spontaneous eradication of infection, with a lingering serological response.
Quantitation of Ergosterol Content: Novel Method for Determination of Fluconazole Susceptibility of
Candida albicans
Authors: Arthington-Skaggs Beth A. , Jradi Hoda , Desai Tejal , Morrison Christine J. 
Published: December 2019

ABSTRACT
MIC end points for the most commonly prescribed azole antifungal drug, fluconazole, can be difficult to determine because its fungistatic nature can lead to excessive “trailing” of growth during susceptibility testing by National Committee for Clinical Laboratory Standards broth macrodilution and microdilution methods. To overcome this ambiguity, and because fluconazole acts by inhibiting ergosterol biosynthesis, we developed a novel method to differentiate fluconazole-susceptible from fluconazole-resistant isolates by quantitating ergosterol production in cells grown in 0, 1, 4, 16, or 64 μg of fluconazole per ml. Ergosterol was isolated from whole yeast cells by saponification, followed by extraction of nonsaponifiable lipids with heptane. Ergosterol was identified by its unique spectrophotometric absorbance profile between 240 and 300 nm. We used this sterol quantitation method (SQM) to test 38 isolates with broth microdilution end points of ≤8 μg/ml (susceptible), 16 to 32 μg/ml (susceptible dose-dependent [SDD]), or ≥64 μg/ml (resistant) and 10 isolates with trailing end points by the broth microdilution method. No significant differences in mean ergosterol content were observed between any of the isolates grown in the absence of fluconazole. However, 18 susceptible isolates showed a mean reduction in ergosterol content of 72% after exposure to 1 μg of fluconazole/ml, an 84% reduction after exposure to 4 μg/ml, and 95 and 100% reductions after exposure to 16 and 64 μg of fluconazole/ml, respectively. Ten SDD isolates showed mean ergosterol reductions of 38, 57, 73, and 99% after exposure to 1, 4, 16, and 64 μg of fluconazole/ml, respectively. In contrast, 10 resistant isolates showed mean reductions in ergosterol content of only 25, 38, 53, and 84% after exposure to the same concentrations of fluconazole. The MIC of fluconazole, by using the SQM, was defined as the lowest concentration of the drug which resulted in 80% or greater inhibition of overall mean ergosterol biosynthesis compared to that in the drug-free control. Of 38 isolates which gave clear end points by the broth microdilution method, the SQM MIC was within 2 dilutions of the broth microdilution MIC for 33 (87%). The SQM also discriminated between resistant and highly resistant isolates and was particularly useful for discerning the fluconazole susceptibilities of 10 additional isolates which gave equivocal end points by the broth microdilution method due to trailing growth. In contrast to the broth microdilution method, the SQM determined trailing isolates to be susceptible rather than resistant, indicating that the SQM may predict clinical outcome more accurately. The SQM may provide a means to enhance current methods of fluconazole susceptibility testing and may provide a better correlation of in vitro with in vivo results, particularly for isolates with trailing end points.
Two Sensitive PCR-Based Methods for Detection of Hepatitis B Virus Variants Associated with Reduced Susceptibility to Lamivudine
Authors: Allen Marchelle I. , Gauthier Josee , DesLauriers Manon , Bourne Eric J. , Carrick Kevin M. , Baldanti Fausto , Ross Lisa L. , Lutz Michael W. , Condreay Lynn D. 
Published: December 2019

ABSTRACT

Two novel assays, a restriction fragment length polymorphism (RFLP) assay and an assay based on the 5′-nuclease activity of
Taq
DNA polymerase, were developed for screening viral variants in lamivudine-treated patients’ sera containing <1,000 copies of the hepatitis B virus (HBV) genome per ml. Both assays were designed to detect single-nucleotide changes within the HBV DNA polymerase gene that are associated with lamivudine resistance in vitro and have been used to screen a number of patients’ sera for variant virus. Results obtained with these assays and standard sequencing technology were compared with regard to throughput, ability to detect individual virus species present at low concentrations, and ability to detect, distinguish, and quantitate wild-type (wt) and HBV tyrosine methionine
552
aspartate aspartate motif variants in mixed viral populations. Unlike DNA sequencing, both assays are amenable to high-throughput screening and were shown to be able to quantitatively detect variant virus in the presence of a background of wt virus. As with DNA sequencing, both new assays incorporate a PCR amplification step and are able to detect the relatively low amounts of virus found in lamivudine-treated patients’ sera. However, these assays are far less labor intensive than the DNA-sequencing techniques presently in use. Overall, the RFLP assay was more sensitive than DNA sequencing in detecting and determining the ratios of wt to variant virus. Furthermore, the RFLP assay and 5′-nuclease assay were equally sensitive in the detection of mixed viral species, but the RFLP assay was superior to the 5′-nuclease assay in the quantitation of mixed viral species. These assays should prove useful for further understanding of virological response to therapy and disease progression.
Molecular Characterization of a Shiga Toxigenic
Escherichia coli
O113:H21 Strain Lacking
eae
Responsible for a Cluster of Cases of Hemolytic-Uremic Syndrome
Authors: Paton Adrienne W. , Woodrow Matthew C. , Doyle Robyn M. , Lanser Janice A. , Paton James C. 
Published: December 2019

ABSTRACT

Shiga toxigenic
Escherichia coli
(STEC) strains are a diverse group of organisms capable of causing severe gastrointestinal disease in humans. Within the STEC family, certain strains appear to have greater virulence for humans. STEC strains carrying
eae
and belonging to serogroup O157 or O111 have been responsible for the vast majority of outbreaks of STEC disease reported to date. Here we describe a STEC O113:H21 strain lacking
eae
that was responsible for a cluster of three cases of hemolytic-uremic syndrome. This strain produces a single Stx2-related toxin and adheres efficiently to Henle 407 cells.
Comparison of Four Methodologies for Rapid and Cost-Effective Identification of
Candida glabrata
Authors: Fenn JoAnn P. , Billetdeaux Erick , Segal Helene , Skodack-Jones Lisa , Padilla Pamela E. , Bale Martha , Carroll Karen 
Published: December 2019

ABSTRACT

To improve turnaround time and decrease the cost of the identification of
Candida glabrata
, we evaluated four methods for the detection of trehalose assimilation or fermentation. These methods were compared with the API 20C method (bioMERIEUX, Hazelwood, Mo.) to determine accuracy. We recommend the use of Remel Rapid Trehalose Assimilation Broth because of its rapid, 3-h results, reasonable sensitivity, and low number of false positives.
Transmission of an Azole-Resistant Isogenic Strain of
Candida albicans
among Human Immunodeficiency Virus-Infected Family Members with Oropharyngeal Candidiasis
Authors: Müller Frank-Michael C. , Kasai Miki , Francesconi Andrea , Brillante Beth , Roden Maureen , Peter Joanne , Chanock Stephen J. , Walsh Thomas J. 
Published: December 2019

ABSTRACT

We report transmission of an azole-resistant, isogenic strain of
Candida albicans
in a human immunodeficiency virus (HIV)-infected family of two children with symptomatic oropharyngeal candidiasis and a mother with asymptomatic colonization over a 5-year period. These findings were confirmed by three different molecular epidemiology methods: interrepeat PCR, Southern hybridization with a
C. albicans
repetitive element 2 probe, and electrophoretic karyotyping. This study contributes to an evolving understanding of the mode of transmission of
C. albicans
, particularly in children, and underscores the importance of monitoring specimens from family members of HIV-infected patients.