bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretation of Trailing Endpoints in Antifungal Susceptibility Testing by the National Committee for Clinical Laboratory Standards Method
Authors: Revankar Sanjay G. , Kirkpatrick William R. , McAtee Robert K. , Fothergill Annette W. , Redding Spencer W. , Rinaldi Michael G. , Patterson Thomas F. 
Published: December 2019

ABSTRACT
Trailing endpoints remain a problem in antifungal susceptibility testing using the National Committee for Clinical Laboratory Standards (NCCLS) method. For isolates for which trailing endpoints are found, MICs of ≤1 μg/ml at 24 h and of >64 μg/ml at 48 h are usually observed. In a study of human immunodeficiency virus (HIV)-infected patients with oropharyngeal candidiasis, we identified three patients with multiple serial isolates for which trailing endpoints were observed with fluconazole. At 24 h, MICs were generally ≤1 μg/ml by both broth macro- and microdilution methods. However, at 48 h, MICs were >64 μg/ml, while the organism remained susceptible by agar dilution testing with fluconazole. Most episodes of oropharyngeal candidiasis with trailing-endpoint isolates responded to doses of fluconazole as low as 100 mg/day. Two patients had both susceptible and trailing-endpoint isolates by NCCLS broth macro- and microdilution testing; these isolates were found to be the same strain by pulsed-field gel electrophoresis using restriction fragment length polymorphisms. Another patient had two different strains, one for which trailing endpoints were observed and one which was susceptible at 48 h. Trailing endpoints may be seen with selected isolates of a strain or may be a characteristic finding for most or all isolates of a strain. In addition, with isolates for which trailing endpoints are observed, reading the endpoint for the NCCLS method at 24 h may be more appropriate.
Detection of Hepatitis G Virus RNA in Persons with and without Known Risk Factors for Blood-Borne Viral Infections in Sweden and Honduras
Authors: Lara Claudia , Halasz Robert , Sönnerborg Anders , Sällberg Matti 
Published: December 2019

ABSTRACT
We analyzed 224 and 163 serum samples from individuals in Sweden and Honduras, respectively, for the presence of the hepatitis G virus (HGV or GB virus-C) RNA. HGV infection in both Sweden and Honduras was related to common risk factors for blood-borne infections, despite a surprisingly high frequency in groups without known risk factors.
Long-Term Predictive Value of a Single Cytomegalovirus (CMV) DNA PCR Assay for CMV Disease in Human Immunodeficiency Virus-Infected Patients
Authors: Walmsley Sharon , Mazzulli Tony , Krajden Mel 
Published: December 2019

ABSTRACT
Universal prophylaxis with oral ganciclovir is not cost-effective for the prevention of cytomegalovirus (CMV) disease in human immunodeficiency virus infection. For a preemptive strategy to be considered, patients at highest risk for CMV disease need to be easily and accurately identified. In this study, the sensitivity, specificity, positive predictive value, and negative predictive value of a single CMV DNA PCR assay for the subsequent development of CMV disease were 0.75, 0.89, 0.75, and 0.89, respectively.
Survey of Human Group C Rotaviruses in Japan during the Winter of 1992 to 1993
Authors: Kuzuya Mitsutaka , Fujii Ritsushi , Hamano Masako , Yamada Masao , Shinozaki Kuniko , Sasagawa Akira , Hasegawa Sumiyo , Kawamoto Hiroyoshi , Matsumoto Kazuo , Kawamoto Ayumi , Itagaki Asao , Funatsumaru Sadayuki , Urasawa Syozo 
Published: December 2019

ABSTRACT
Fecal specimens from patients with acute diarrhea were collected from 10 prefectures in Japan over a 6-month period (November 1992 to April 1993), and the specimens that were negative for human group A rotaviruses were screened for the presence of human group C rotaviruses (CHRVs) by the reverse passive hemagglutination test. Of 784 specimens examined, 53 samples (6.8%) that were collected in 7 of 10 prefectures were positive for CHRV, indicating that CHRVs are widely distributed across Japan. Most of the CHRV isolates were detected in March and April, and CHRVs mainly prevailed in children ages 3 to 8 years. The genome electropherotypes of eight strains isolated in five individual prefectures were surprisingly similar to each other and were different from those of CHRV strains isolated to date. The outer capsid glycoprotein (VP7) gene homologies of the isolates retrieved in 1993 were subsequently analyzed by the dot blot hybridization method. As a result, the VP7 genes of the isolates revealed very high levels of homology not only with each other but also with the VP7 gene of the OK118 strain isolated in 1988. These results suggest that a large-scale outbreak of CHRV occurred during the winter of 1992 and 1993 in Japan.
Clinical Evaluation of a New PCR Assay for Detection of
Coxiella burnetii
in Human Serum Samples
Authors: Zhang G. Q. , Nguyen Sa V. , To H. , Ogawa M. , Hotta A. , Yamaguchi T. , Kim H. J. , Fukushi H. , Hirai K. 
Published: December 2019

ABSTRACT

A nested PCR method was developed for the detection of
Coxiella burnetii
in human serum samples. Two pairs of oligonucleotide primers were designed to amplify a 438-bp fragment of the
com1
gene encoding a 27-kDa outer membrane protein of
C. burnetii
. The primers amplified the predicted fragments of 21 various strains of
C. burnetii
but did not react with DNA samples from other microorganisms. The 438-bp amplification products could be digested with restriction enzymes
Ssp
I and
Sal
I. The utility of the nested PCR was evaluated by testing human serum samples. The
com1
gene fragment was amplified from 135 (87%) of 155 indirect immunofluorescence test (IF)-positive serum samples and from 11 (11%) of 100 IF-negative serum samples. The nested PCR with primers targeted to the
com1
gene appeared to be a sensitive, specific, and useful method for the detection of
C. burnetii
in serum samples.
Comparison of Performance and Cost-Effectiveness of Direct Fluorescent-Antibody, Ligase Chain Reaction, and PCR Assays for Verification of Chlamydial Enzyme Immunoassay Results for Populations with a Low to Moderate Prevalence of
Chlamydia trachomatis
Infection
Authors: Dean Deborah , Ferrero Dennis , McCarthy Michael 
Published: December 2019

ABSTRACT

Many laboratories use a commercial enzyme immunoassay (EIA) with verification testing to diagnose
Chlamydia trachomatis
infections in an effort to contain costs. This study was designed to compare the performance and cost-effectiveness of direct fluorescent-antibody assay (DFA), commercial PCR, and ligase chain reaction (LCR) for the verification of EIA results. Cervical specimens were screened by EIA. DFA, PCR, and LCR were compared as verification tests for EIA-reactive specimens and negative greyzone (NGZ) specimens at 50% below the cutoff value. These samples were also tested by in-house PCR, which was used in the analysis of verification results. A total of 477 (7%) of 6,571 samples were reactive or within the NGZ. EIA results with verification by DFA testing (EIA/DFA results) agreed with 93% of the true results compared with 97% for EIA/PCR results for one set of 242 samples; there was 97% agreement with true results for EIA/DFA results versus 95% for EIA/LCR results for another set of 235 samples. Ten samples were false positive by LCR. Time and costs were equivalent for EIA with the DFA, PCR, or LCR as the verification test but were two- to threefold greater for PCR or LCR alone than for EIA with verification. Since it is important to balance cost containment with public health objectives, DFA, PCR, and LCR as EIA verification tests for cervical samples offer acceptable sensitivities and specificities at reasonable cost for low- to moderate-risk populations and therefore can be extended to a broader spectrum of at-risk populations.
Restriction Fragment Length Polymorphism Analysis of Some Flagellin Genes of
Salmonella enterica
Authors: Dauga Catherine , Zabrovskaia Anna , Grimont Patrick A. D. 
Published: December 2019

ABSTRACT

Salmonellae often have the ability to express two different flagellar antigen specificities (phase 1 and phase 2). At the cell level, only one flagellar phase is expressed at a time. Two genes,
fliC
, encoding phase-1 flagellin, and
fljB
, encoding phase-2 flagellin, are alternatively expressed. Flagellin genes from 264 serovars of
Salmonella enterica
were amplified by two phase-specific PCR systems. Amplification products were subjected to restriction fragment length polymorphism (RFLP) analysis by using endonucleases
Hha
I and
Hph
I. RFLP with
Hha
I and
Hph
I yielded 64 and 42 different restriction profiles, respectively, among 329 flagellin genes coding for 26 antigens. The phase-1 gene showed 46 patterns with
Hha
I and 30 patterns with
Hph
I. The phase-2 gene showed 23 patterns with
Hha
I and 17 patterns with
Hph
I. When the data from both enzymes were combined, 116 patterns were obtained: 74 for
fliC
, 47 for
fljB
, and 5 shared by both genes. Of these combined patterns, 80% were specifically associated with one flagellar antigen and 20% were associated with more than one antigen. Each flagellar antigen was divided into 2 to 18 different combined patterns. In the sample of strains used, determination of the phase-1 and phase-2 flagellin gene RFLP, added to the knowledge of the O antigen, allowed identification of all diphasic serovars. Overall, the diversity uncovered by flagellin gene RFLP did not precisely match that evidenced by flagellar agglutination.
Massilia timonae
gen. nov., sp. nov., Isolated from Blood of an Immunocompromised Patient with Cerebellar Lesions
Authors: La Scola Bernard , Birtles Richard J. , Mallet Marie-Noëlle , Raoult Didier 
Published: December 2019

ABSTRACT

A fastidious, slowly growing, strictly aerobic, gram-negative bacterium was isolated from a culture of blood from a 25-year-old man with common variable immunodeficiency. The man had been admitted to hospital with febrile progressive cerebellar ataxia. The use of standard phenotypic schemes did not lead to identification, but sequence analysis demonstrated that the 16S rRNA gene of the isolate was most similar to those of the environmental bacteria
Duganella zoogloeoides
(formerly
Zoogloea ramigera
115) and
Telluria mixta
. Further characterization of the bacterium by biochemical analysis, electron microscopy, G+C content estimation, and fatty acid analysis demonstrated significant differences between the bacterium and
D. zoogloeoides
and
Telluria
species; thus, we propose it as a new taxon with the name
Massilia timonae
gen. nov., sp. nov.
Evaluation of the ESP Culture System II for Testing Susceptibilities of
Mycobacterium tuberculosis
Isolates to Four Primary Antituberculous Drugs
Authors: Bergmann John S. , Woods Gail L. 
Published: December 2019

ABSTRACT

The reliability of the ESP Culture System II (herein referred to as ESP II) for testing susceptibilities of
Mycobacterium tuberculosis
isolates to isoniazid, rifampin, ethambutol, and streptomycin was evaluated by comparing results to those of the method of proportion (MOP), which was considered the reference method, for 20 clinical isolates and 30 challenge strains provided by the Centers for Disease Control and Prevention (CDC). Clinical isolates also were tested with the BACTEC TB 460 system; these results agreed with those obtained by the MOP for all isolates and all drugs, except the high concentration of isoniazid, for which agreement was 95%. After resolution of discrepancies, levels of agreement between ESP II and MOP for the clinical isolates were 95 and 100%, respectively, for the low and high concentrations of isoniazid, 100% for rifampin and ethambutol, and 95% for streptomycin. For the 30 challenge isolates, ESP II results for both concentrations of isoniazid agreed with the expected results in all cases, whereas agreement was 93% for both rifampin and streptomycin and 90% for ethambutol. All discrepancies with the CDC isolates were due to failure of ESP II to correctly classify resistant strains. By testing isolates yielding discrepant ethambutol and streptomycin results with a lower concentration of both drugs in the ESP II system, agreement increased to 93% for ethambutol and 100% for streptomycin. For the clinical isolates, the times to an ESP II result of susceptible (means ± standard errors of the means) were 8.47 ± 0.12 days (range, 7 to 10 days) and 8.73 ± 0.29 days (range, 5 to 11 days) when the inoculum was prepared from a McFarland equivalent and from a seed bottle, respectively. The time to an ESP II result of resistant varied by drug and method of inoculum preparation, ranging from 5.50 ± 0.22 days for ethambutol with the inoculum prepared from a McFarland standard to 8.0 days for ethambutol with the inoculum prepared from a seed bottle. These data suggest that the ESP II system is a rapid and reliable method for testing susceptibilities of
M. tuberculosis
isolates to isoniazid and rifampin. Performance, however, may be suboptimal for ethambutol and streptomycin. Testing additional ethambutol-resistant and streptomycin-resistant strains with two concentrations of both drugs is necessary.
Detection of Specific Antibodies to an Antigenic Mannoprotein for Diagnosis of
Penicillium marneffei
Penicilliosis
Authors: Cao Liang , Chen Da-Liang , Lee Cindy , Chan Che-Man , Chan King-Man , Vanittanakom Nongnuch , Tsang Dominic N. C. , Yuen Kwok-Yung 
Published: December 2019

ABSTRACT

The disseminated and progressive fungal disease
Penicillium marneffei
penicilliosis is one of the most common infectious diseases in AIDS patients in Southeast Asia. To diagnose systemic penicilliosis, we developed an enzyme-linked immunosorbent assay (ELISA)-based antibody test with Mp1p, a purified recombinant antigenic mannoprotein of
P. marneffei
. Evaluation of the test with guinea pig sera against
P. marneffei
and other pathogenic fungi indicated that this assay was specific for
P. marneffei
. Clinical evaluation revealed that high levels of specific antibody were detected in two immunocompetent penicilliosis patients. Furthermore, approximately 80% (14 of 17) of the documented penicilliosis patients with human immunodeficiency virus tested positive for the specific antibody. No false-positive results were found for serum samples from 90 healthy blood donors, 20 patients with typhoid fever, and 55 patients with tuberculosis, indicating a high specificity of the test. Thus, this ELISA-based test for the detection of anti-Mp1p antibody can be of significant value as a diagnostic for penicilliosis.
Seropositivity for and Intestinal Colonization with
Entamoeba histolytica
and
Entamoeba dispar
in Individuals in Northeastern Brazil
Authors: Braga Lucia L. , Mendonca Yacy , Paiva Clece A. , Sales Andrea , Cavalcante Andre L. M. , Mann Barbara J. 
Published: December 2019

ABSTRACT

In a slum community in northeastern Brazil 20% of a sample population was colonized with
Entamoeba histolytica
or
Entamoeba dispar
and 10.6% was colonized with
E. histolytica
alone. No correlation between seropositivity for anti-GalNAc lectin antibody and colonization was found. These results suggest that colonization does not necessarily produce immunity to reinfection.
Rapid Diagnosis of Pulmonary Tuberculosis with the LCx
Mycobacterium tuberculosis
Assay and Comparison with Conventional Diagnostic Techniques
Authors: Rohner Peter , Jahn Esther I. M. , Ninet Beatrice , Ionati Concetta , Weber Rainer , Auckenthaler Raymond , Pfyffer Gaby E. 
Published: December 2019

ABSTRACT

The LCx MTB amplification assay is a nucleic acid amplification test intended for the direct detection of
Mycobacterium tuberculosis
complex in respiratory specimens. We evaluated its performance on 2,001 consecutive respiratory specimens; 78 were culture positive for
M. tuberculosis
. Sensitivity, specificity, and positive and negative predictive values of this assay for all specimens compared to culture results were 88.5, 97.7, 60.5, and 99.5%, respectively. When referred to resolved clinical diagnosis of active tuberculosis, these values improved to 90.2, 98.4, 72.8, and 99.5%, respectively.
Urine Specimens from Pregnant and Nonpregnant Women Inhibitory to Amplification of
Chlamydia trachomatis
Nucleic Acid by PCR, Ligase Chain Reaction, and Transcription-Mediated Amplification: Identification of Urinary Substances Associated with Inhibition and Removal of Inhibitory Activity
Authors: Mahony J. , Chong S. , Jang D. , Luinstra K. , Faught M. , Dalby D. , Sellors J. , Chernesky M. 
Published: December 2019

ABSTRACT

The presence of endogenous amplification inhibitors in urine may produce false-negative results for the detection of
Chlamydia trachomatis
nucleic acids by tests such as PCR, ligase chain reaction (LCR), and transcription-mediated amplification (TMA). Consecutive urine specimens from 101 pregnant women and 287 nonpregnant women submitted for urinalysis were processed for
C. trachomatis
detection. Aliquots were spiked with the equivalent of one
C. trachomatis
elementary body and were tested by three commercial assays: AMPLICOR CT/NG, Chlamydia LCX, and Chlamydia TMA. The prevalence of inhibitors resulting in complete inhibition of amplification was 4.9% for PCR, 2.6% for LCR, and 7.5% for TMA. In addition, all three assays were partially inhibited by additional urine specimens. Only PCR was more often inhibited by urine from pregnant women than by urine from nonpregnant women (9.9 versus 3.1%;
P
= 0.011). A complete urinalysis including dipstick and a microscopic examination was performed. Logistic regression analysis revealed that the following substances were associated with amplification inhibition: beta-human chorionic gonadotropin (odds ratio [OR], 3.3) and crystals (OR, 3.3) for PCR, nitrites for LCR (OR, 14.4), and hemoglobin (OR, 3.3), nitrites (OR, 3.3), and crystals (OR, 3.3) for TMA. Aliquots of each inhibitory urine specimen were stored at 4 and −70°C overnight or were extracted with phenol-chloroform and then retested at dilutions of 1:1, 1:4, and 1:10. Most inhibition was removed by storage overnight at 4 or −70°C and a dilution of 1:10 (84% for PCR, 100% for LCR, and 92% for TMA). Five urine specimens (three for PCR and two for TMA) required phenol-chloroform extraction to remove inhibitors. The results indicate that the prevalence of nucleic acid amplification inhibitors in female urine is different for each technology, that this prevalence may be predicted by the presence of urinary factors, and that storage and dilution remove most of the inhibitors.
Genospecies Identification and Characterization of Lyme Disease Spirochetes of Genospecies
Borrelia burgdorferi
Sensu Lato Isolated from Rodents in Taiwan
Authors: Shih Chien-Ming , Chang Han-Ming , Chen Show-Li , Chao Li-Lian 
Published: December 2019

ABSTRACT

Lyme disease spirochetes of the genospecies
Borrelia burgdorferi
sensu lato were identified and characterized for the first time in Taiwan. Seven isolates, designated TWKM1 to TWKM7, were purified from the ear tissues of three species of rodents captured from seven localities of Taiwan. The immunological characteristics of these Taiwan isolates were compared with those of other genospecies of Lyme disease spirochetes by analyzing the protein profiles and reactivities with
B. burgdorferi
-specific monoclonal antibodies (MAbs). The genospecies of these Taiwan isolates were also identified by the similarities in their plasmid profiles and differential reactivities with genospecies-specific PCR primers. Although two distinct protein profiles were observed among the seven Taiwan isolates, the MAb reactivities against the outer surface proteins of
B. burgdorferi
of all of these isolates were consistent with those of
B. burgdorferi
sensu lato. The similarities of the plasmid profiles also confirmed the identities of these Taiwan isolates. PCR analysis indicated that all of these Taiwan isolates were genetically related to the genospecies
B. burgdorferi
sensu stricto. These results demonstrate the first identification of Lyme disease spirochetes in Taiwan and also highlight the increasing demand for defining the reservoirs and vector ticks of
B. burgdorferi
. A serosurvey for Lyme disease infection in the human population of Taiwan may also be required.
Sequencing of
Escherichia coli
O111 O-Antigen Gene Cluster and Identification of O111-Specific Genes
Authors: Wang Lei , Curd Heather , Qu Wenjia , Reeves Peter R. 
Published: December 2019

ABSTRACT

Shiga toxin (Stx)-producing
Escherichia coli
strains of serogroup O111 are the most frequently isolated non-O157 strains causing outbreaks of gastroenteritis with hemolytic-uremic syndrome. The O111 O-antigen gene cluster had been cloned and about half of it has been sequenced; we have now sequenced the remainder of the gene cluster, which is 12.5 kb in length and which comprises 11 genes. On the basis of sequence similarity, we have identified all the O-antigen genes expected, including five sugar biosynthetic pathway genes, three transferase genes, the O-unit flippase gene, and the O-antigen polymerase gene. By PCR testing with
E. coli
strains representing all 166 O-antigen forms, some randomly selected gram-negative bacteria, and
Salmonella enterica
serovar Adelaide, we showed that four O-antigen genes are highly specific to O111. This work provides the basis for a sensitive test for the rapid detection of
E. coli
O111. This is important both for decisions related to patient care, because early treatment may reduce the risk of life-threatening complications, and for the detection of sources of contamination.
Extraintestinal Salmonellosis in a General Hospital (1991 to 1996): Relationships between
Salmonella
Genomic Groups and Clinical Presentations
Authors: Rodríguez Mercedes , de Diego Isabel , Mendoza M. Carmen 
Published: December 2019

ABSTRACT

Episodes of extraintestinal salmonellosis treated at a general hospital (1,522 beds) over a 6-year period (1991 to 1996) were characterized by the analysis of phenotypic and genotypic traits of
Salmonella
organisms and clinical data from medical reports. Extraintestinal salmonellosis accounted for 8% of all salmonellosis episodes. Fifty-two medical reports, dealing with 6 cases of typhoid fever, 32 cases of bacteremia, and 14 focal infections, were reviewed. All cases of typhoid fever except 1, 7 cases of bacteremia, and 5 focal infections were not related to any underlying disease or predisposing factors, while 25 cases of bacteremia and 9 focal infections were associated with some of these risk factors. All typhoid isolates and 65.4% of the nontyphoid isolates were susceptible to antimicrobials. Fifty-one nontyphoid strains were analyzed and assigned to 21 genomic groups, which were defined by serotype, combined ribotype, and combined randomly amplified polymorphic DNA type (each genomic group could include organisms differing in some phenotypic traits). The relationships between genomic groups and clinical presentations were traced. Organisms causing 22 episodes (17 episodes of bacteremia, 2 of pneumonia, 1 of peritonitis, 1 of pyelonephritis, and 1 of cystitis) belonged to a prevalent
Salmonella enterica
serotype Enteritidis genomic group, which included organisms assigned to four phage types, five biotypes, and four resistance patterns, causing infections in patients with and without risk factors. Seven other genomic groups, 4 Enteritidis groups (associated with both bacteremia and focal infections), 2 Typhimurium groups (one associated with bacteremia and the other with focal infections) and 1 Brandenburg group (associated with bacteremia) included two or more strains, and the remaining 13 genomic groups consisted of only one strain each.